Index

_

__init__() (galaxy.app.ExecutionTimerFactory method) (galaxy.app.GalaxyManagerApplication method) (galaxy.app.HaltableContainer method) (galaxy.app.MinimalGalaxyApplication method) (galaxy.app.StatsdStructuredExecutionTimer method) (galaxy.app.UniverseApplication method) (galaxy.app_unittest_utils.galaxy_mock.MockApp method) (galaxy.app_unittest_utils.galaxy_mock.MockAppConfig method) (galaxy.app_unittest_utils.galaxy_mock.MockDir method) (galaxy.app_unittest_utils.galaxy_mock.MockTrans method) (galaxy.app_unittest_utils.galaxy_mock.MockWebapp method) (galaxy.auth.AuthManager method) (galaxy.auth.providers.ldap_ad.LDAP method) (galaxy.auth.providers.ldap_ad.LDAP3 method) (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration method) (galaxy.authnz.custos_authnz.OIDCAuthnzBase method) (galaxy.authnz.custos_authnz.OIDCAuthnzBaseCiLogon method) (galaxy.authnz.custos_authnz.OIDCAuthnzBaseCustos method) (galaxy.authnz.custos_authnz.OIDCAuthnzBaseKeycloak method) (galaxy.authnz.IdentityProvider method) (galaxy.authnz.managers.AuthnzManager method) (galaxy.authnz.psa_authnz.PSAAuthnz method) (galaxy.authnz.psa_authnz.Strategy method) (galaxy.celery.GalaxyCelery method) (galaxy.config.BaseAppConfiguration method) (galaxy.config.GalaxyAppConfiguration method) (galaxy.config.schema.AppSchema method) (galaxy.config.schema.Schema method) (galaxy.config_watchers.ConfigWatchers method) (galaxy.datatypes.anvio.AnvioContigsDB method) (galaxy.datatypes.anvio.AnvioDB method) (galaxy.datatypes.anvio.AnvioProfileDB method) (galaxy.datatypes.assembly.Velvet method) (galaxy.datatypes.binary.BigBed method) (galaxy.datatypes.binary.BigWig method) (galaxy.datatypes.binary.Bref3 method) (galaxy.datatypes.binary.DAA method) (galaxy.datatypes.binary.Dcd method) (galaxy.datatypes.binary.DMND method) (galaxy.datatypes.binary.FITS method) (galaxy.datatypes.binary.Grib method) (galaxy.datatypes.binary.H5 method) (galaxy.datatypes.binary.HexrdEtaOmeNpz method) (galaxy.datatypes.binary.HexrdImagesNpz method) (galaxy.datatypes.binary.JP2 method) (galaxy.datatypes.binary.LudwigModel method) (galaxy.datatypes.binary.Npz method) (galaxy.datatypes.binary.Parquet method) (galaxy.datatypes.binary.RMA6 method) (galaxy.datatypes.binary.Vel method) (galaxy.datatypes.blast.BlastDomainDb method) (galaxy.datatypes.blast.BlastDomainDb5 method) (galaxy.datatypes.blast.BlastNucDb method) (galaxy.datatypes.blast.BlastNucDb5 method) (galaxy.datatypes.blast.BlastProtDb method) (galaxy.datatypes.blast.BlastProtDb5 method) (galaxy.datatypes.blast.LastDb method) (galaxy.datatypes.constructive_solid_geometry.GmshMsh method) (galaxy.datatypes.constructive_solid_geometry.NeperPoints method) (galaxy.datatypes.constructive_solid_geometry.NeperPointsTabular method) (galaxy.datatypes.constructive_solid_geometry.NeperTesr method) (galaxy.datatypes.constructive_solid_geometry.NeperTess method) (galaxy.datatypes.constructive_solid_geometry.Ply method) (galaxy.datatypes.constructive_solid_geometry.PlyAscii method) (galaxy.datatypes.constructive_solid_geometry.PlyBinary method) (galaxy.datatypes.constructive_solid_geometry.Vtk method) (galaxy.datatypes.constructive_solid_geometry.VtkAscii method) (galaxy.datatypes.constructive_solid_geometry.VtkBinary method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.data.DataMeta method) (galaxy.datatypes.data.DatatypeValidation method) (galaxy.datatypes.dataproviders.base.DataProvider method) (galaxy.datatypes.dataproviders.base.FilteredDataProvider method) (galaxy.datatypes.dataproviders.base.LimitedOffsetDataProvider method) (galaxy.datatypes.dataproviders.base.MultiSourceDataProvider method) (galaxy.datatypes.dataproviders.chunk.ChunkDataProvider method) (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) (galaxy.datatypes.dataproviders.column.DictDataProvider method) (galaxy.datatypes.dataproviders.dataset.BigWigDataProvider method) (galaxy.datatypes.dataproviders.dataset.ConvertedDatasetDataProvider method) (galaxy.datatypes.dataproviders.dataset.DatasetColumnarDataProvider method) (galaxy.datatypes.dataproviders.dataset.DatasetDataProvider method) (galaxy.datatypes.dataproviders.dataset.DatasetDictDataProvider method) (galaxy.datatypes.dataproviders.dataset.DatasetSubprocessDataProvider method) (galaxy.datatypes.dataproviders.dataset.FastaDataProvider method) (galaxy.datatypes.dataproviders.dataset.GenomicRegionDataProvider method) (galaxy.datatypes.dataproviders.dataset.IntervalDataProvider method) (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider method) (galaxy.datatypes.dataproviders.dataset.SQliteDataDictProvider method) (galaxy.datatypes.dataproviders.dataset.SQliteDataProvider method) (galaxy.datatypes.dataproviders.dataset.SQliteDataTableProvider method) (galaxy.datatypes.dataproviders.dataset.TwoBitFastaDataProvider method) (galaxy.datatypes.dataproviders.dataset.WiggleDataProvider method) (galaxy.datatypes.dataproviders.exceptions.InvalidDataProviderSource method) (galaxy.datatypes.dataproviders.exceptions.NoProviderAvailable method) (galaxy.datatypes.dataproviders.external.GzipDataProvider method) (galaxy.datatypes.dataproviders.external.RegexSubprocessDataProvider method) (galaxy.datatypes.dataproviders.external.SubprocessDataProvider method) (galaxy.datatypes.dataproviders.external.TempfileDataProvider method) (galaxy.datatypes.dataproviders.external.URLDataProvider method) (galaxy.datatypes.dataproviders.hierarchy.HierarchalDataProvider method) (galaxy.datatypes.dataproviders.hierarchy.XMLDataProvider method) (galaxy.datatypes.dataproviders.line.BlockDataProvider method) (galaxy.datatypes.dataproviders.line.FilteredLineDataProvider method) (galaxy.datatypes.dataproviders.line.RegexLineDataProvider method) (galaxy.datatypes.display_applications.application.DisplayApplication method) (galaxy.datatypes.display_applications.application.DisplayApplicationLink method) (galaxy.datatypes.display_applications.application.DynamicDisplayApplicationBuilder method) (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) (galaxy.datatypes.display_applications.parameters.DatasetLikeObject method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationTemplateParameter method) (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper method) (galaxy.datatypes.genetics.Affybatch method) (galaxy.datatypes.genetics.DataIn method) (galaxy.datatypes.genetics.Eigenstratgeno method) (galaxy.datatypes.genetics.Eigenstratpca method) (galaxy.datatypes.genetics.Eset method) (galaxy.datatypes.genetics.Fped method) (galaxy.datatypes.genetics.Fphe method) (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.genetics.GenotypeMatrix method) (galaxy.datatypes.genetics.IdeasPre method) (galaxy.datatypes.genetics.ldIndep method) (galaxy.datatypes.genetics.LinkageStudies method) (galaxy.datatypes.genetics.Lped method) (galaxy.datatypes.genetics.MAlist method) (galaxy.datatypes.genetics.Pbed method) (galaxy.datatypes.genetics.Phe method) (galaxy.datatypes.genetics.Pphe method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.genetics.rgFeatureList method) (galaxy.datatypes.genetics.rgSampleList method) (galaxy.datatypes.genetics.rgTabList method) (galaxy.datatypes.gis.Shapefile method) (galaxy.datatypes.goldenpath.AGPError method) (galaxy.datatypes.goldenpath.AGPFile method) (galaxy.datatypes.goldenpath.AGPGapLine method) (galaxy.datatypes.goldenpath.AGPLine method) (galaxy.datatypes.goldenpath.AGPObject method) (galaxy.datatypes.goldenpath.AGPSeqLine method) (galaxy.datatypes.hdf5.HDF5SummarizedExperiment method) (galaxy.datatypes.images.Analyze75 method) (galaxy.datatypes.images.Image method) (galaxy.datatypes.images.Jpg method) (galaxy.datatypes.interval.BedStrict method) (galaxy.datatypes.interval.CustomTrack method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Gff3 method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.ScIdx method) (galaxy.datatypes.interval.Wiggle method) (galaxy.datatypes.isa.IsaJson method) (galaxy.datatypes.isa.IsaTab method) (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.datatypes.metadata.MetadataElementSpec method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.datatypes.metadata.MetadataSpecCollection method) (galaxy.datatypes.metadata.MetadataTempFile method) (galaxy.datatypes.metadata.RangeParameter method) (galaxy.datatypes.metadata.SelectParameter method) (galaxy.datatypes.metadata.Statement method) (galaxy.datatypes.molecules.OBFS method) (galaxy.datatypes.mothur.AccNos method) (galaxy.datatypes.mothur.AlignCheck method) (galaxy.datatypes.mothur.AlignReport method) (galaxy.datatypes.mothur.Axes method) (galaxy.datatypes.mothur.ConsensusTaxonomy method) (galaxy.datatypes.mothur.CountTable method) (galaxy.datatypes.mothur.Frequency method) (galaxy.datatypes.mothur.Group method) (galaxy.datatypes.mothur.GroupAbund method) (galaxy.datatypes.mothur.LowerTriangleDistanceMatrix method) (galaxy.datatypes.mothur.Names method) (galaxy.datatypes.mothur.Otu method) (galaxy.datatypes.mothur.PairwiseDistanceMatrix method) (galaxy.datatypes.mothur.Quantile method) (galaxy.datatypes.mothur.RefTaxonomy method) (galaxy.datatypes.mothur.Sabund method) (galaxy.datatypes.mothur.SecondaryStructureMap method) (galaxy.datatypes.mothur.SffFlow method) (galaxy.datatypes.mothur.SquareDistanceMatrix method) (galaxy.datatypes.mothur.Summary method) (galaxy.datatypes.mothur.TaxonomySummary method) (galaxy.datatypes.msa.HmmerPress method) (galaxy.datatypes.neo4j.Neo4jDB method) (galaxy.datatypes.neo4j.Neo4jDBzip method) (galaxy.datatypes.proteomics.ImzML method) (galaxy.datatypes.proteomics.Kroenik method) (galaxy.datatypes.proteomics.MzTab method) (galaxy.datatypes.proteomics.MzTab2 method) (galaxy.datatypes.proteomics.PepList method) (galaxy.datatypes.proteomics.PepXmlReport method) (galaxy.datatypes.proteomics.ProtXmlReport method) (galaxy.datatypes.proteomics.PSMS method) (galaxy.datatypes.proteomics.SPLib method) (galaxy.datatypes.proteomics.Wiff method) (galaxy.datatypes.proteomics.Wiff2 method) (galaxy.datatypes.registry.Registry method) (galaxy.datatypes.sniff.ConvertFunction method) (galaxy.datatypes.sniff.FilePrefix method) (galaxy.datatypes.spaln.SpalnNuclDb method) (galaxy.datatypes.spaln.SpalnProtDb method) (galaxy.datatypes.tabular.ConnectivityTable method) (galaxy.datatypes.tabular.Eland method) (galaxy.datatypes.tabular.MatrixMarket method) (galaxy.datatypes.tabular.Psl method) (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.Taxonomy method) (galaxy.datatypes.text.SnpEffDb method) (galaxy.datatypes.text.SnpSiftDbNSFP method) (galaxy.datatypes.util.gff_util.GFFFeature method) (galaxy.datatypes.util.gff_util.GFFInterval method) (galaxy.datatypes.util.gff_util.GFFReaderWrapper method) (galaxy.datatypes.util.maf_utilities.GenomicRegionAlignment method) (galaxy.datatypes.util.maf_utilities.RegionAlignment method) (galaxy.datatypes.util.maf_utilities.SplicedAlignment method) (galaxy.datatypes.util.maf_utilities.TempFileHandler method) (galaxy.datatypes.xml.Dzi method) (galaxy.dependencies.ConditionalDependencies method) (galaxy.exceptions.AcceptedRetryLater method) (galaxy.exceptions.ActionInputError method) (galaxy.exceptions.error_codes.ErrorCode method) (galaxy.exceptions.HandlerAssignmentError method) (galaxy.exceptions.MessageException method) (galaxy.exceptions.ToolExecutionError method) (galaxy.exceptions.ToolInputsNotOKException method) (galaxy.exceptions.ToolMissingException method) (galaxy.files.ConfiguredFileSources method) (galaxy.files.ConfiguredFileSourcesConfig method) (galaxy.files.DictFileSourcesUserContext method) (galaxy.files.NullConfiguredFileSources method) (galaxy.files.ProvidesUserFileSourcesUserContext method) (galaxy.files.sources.FilesSourceOptions method) (galaxy.files.sources.galaxy.LibraryImportFilesSource method) (galaxy.files.sources.galaxy.UserFtpFilesSource method) (galaxy.files.sources.galaxy.UserLibraryImportFilesSource method) (galaxy.files.sources.posix.PosixFilesSource method) (galaxy.files.sources.s3fs.S3FsFilesSource method) (galaxy.files.unittest_utils.TestConfiguredFileSources method) (galaxy.files.unittest_utils.TestPosixConfiguredFileSources method) (galaxy.forms.forms.FormDefinitionFactory method) (galaxy.job_execution.compute_environment.SharedComputeEnvironment method) (galaxy.job_execution.datasets.DatasetPath method) (galaxy.job_execution.datasets.OutputsToWorkingDirectoryPathRewriter method) (galaxy.job_execution.datasets.TaskPathRewriter method) (galaxy.job_execution.output_collect.DatasetCollector method) (galaxy.job_execution.output_collect.JobContext method) (galaxy.job_execution.output_collect.MetadataSourceProvider method) (galaxy.job_execution.output_collect.PermissionProvider method) (galaxy.job_execution.output_collect.SessionlessJobContext method) (galaxy.job_execution.output_collect.ToolMetadataDatasetCollector method) (galaxy.job_execution.ports.JobPortsView method) (galaxy.job_execution.ports.view.JobPortsView method) (galaxy.job_execution.setup.JobIO method) (galaxy.job_execution.setup.JobOutputs method) (galaxy.job_metrics.instrumenters.cgroup.CgroupPlugin method) (galaxy.job_metrics.instrumenters.core.CorePlugin method) (galaxy.job_metrics.instrumenters.cpuinfo.CpuInfoPlugin method) (galaxy.job_metrics.instrumenters.env.EnvPlugin method) (galaxy.job_metrics.instrumenters.hostname.HostnamePlugin method) (galaxy.job_metrics.instrumenters.meminfo.MemInfoPlugin method) (galaxy.job_metrics.instrumenters.uname.UnamePlugin method) (galaxy.job_metrics.JobInstrumenter method) (galaxy.jobs.handler.BaseJobHandlerQueue method) (galaxy.jobs.handler.DefaultJobDispatcher method) (galaxy.jobs.handler.ItemGrabber method) (galaxy.jobs.handler.JobHandler method) (galaxy.jobs.handler.JobHandlerQueue method) (galaxy.jobs.handler.JobHandlerStopQueue method) (galaxy.jobs.JobConfiguration method) (galaxy.jobs.JobDestination method) (galaxy.jobs.JobToolConfiguration method) (galaxy.jobs.JobWrapper method) (galaxy.jobs.manager.JobManager method) (galaxy.jobs.manager.NoopHandler method) (galaxy.jobs.manager.NoopManager method) (galaxy.jobs.mapper.JobMappingException method) (galaxy.jobs.mapper.JobNotReadyException method) (galaxy.jobs.mapper.JobRunnerMapper method) (galaxy.jobs.rule_helper.RuleHelper method) (galaxy.jobs.runners.AsynchronousJobRunner method) (galaxy.jobs.runners.AsynchronousJobState method) (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.chronos.ChronosJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) (galaxy.jobs.runners.godocker.GodockerJobRunner method) (galaxy.jobs.runners.JobState method) (galaxy.jobs.runners.kubernetes.KubernetesJobRunner method) (galaxy.jobs.runners.local.LocalJobRunner method) (galaxy.jobs.runners.pbs.PBSJobRunner method) (galaxy.jobs.runners.tasks.TaskedJobRunner method) (galaxy.jobs.runners.util.cli.CliInterface method) (galaxy.jobs.runners.util.cli.job.BaseJobExec method) (galaxy.jobs.runners.util.cli.shell.BaseShellExec method) (galaxy.jobs.runners.util.cli.shell.local.LocalShell method) (galaxy.jobs.runners.util.cli.shell.rsh.GlobusSecureShell method) (galaxy.jobs.runners.util.cli.shell.rsh.ParamikoShell method) (galaxy.jobs.runners.util.cli.shell.rsh.RemoteShell method) (galaxy.jobs.runners.util.cli.shell.rsh.SecureShell method) (galaxy.jobs.TaskWrapper method) (galaxy.main.GalaxyConfigBuilder method) (galaxy.main_config.WebappConfigResolver method) (galaxy.managers.api_keys.ApiKeyManager method) (galaxy.managers.api_keys.IsUserModel method) (galaxy.managers.base.Deserializer method) (galaxy.managers.base.HasAModelManager method) (galaxy.managers.base.ModelDeserializer method) (galaxy.managers.base.ModelFilterParser method) (galaxy.managers.base.ModelManager method) (galaxy.managers.base.ModelSerializer method) (galaxy.managers.base.Serializer method) (galaxy.managers.base.StorageCleanerManager method) (galaxy.managers.citations.BibtexCitation method) (galaxy.managers.citations.CitationCollection method) (galaxy.managers.citations.CitationsManager method) (galaxy.managers.citations.DoiCache method) (galaxy.managers.citations.DoiCitation method) (galaxy.managers.cloudauthzs.CloudAuthzsSerializer method) (galaxy.managers.collections.DatasetCollectionManager method) (galaxy.managers.configuration.ConfigSerializer method) (galaxy.managers.configuration.ConfigurationManager method) (galaxy.managers.datasets.DatasetAssociationManager method) (galaxy.managers.datasets.DatasetManager method) (galaxy.managers.datasets.DatasetRBACPermissions method) (galaxy.managers.datasets.DatasetSerializer method) (galaxy.managers.display_applications.DisplayApplicationsManager method) (galaxy.managers.folders.SecurityParams method) (galaxy.managers.genomes.GenomesManager method) (galaxy.managers.group_roles.GroupRolesManager method) (galaxy.managers.group_users.GroupUsersManager method) (galaxy.managers.groups.GroupsManager method) (galaxy.managers.hdas.HDADeserializer method) (galaxy.managers.hdas.HDAManager method) (galaxy.managers.hdas.HDASerializer method) (galaxy.managers.hdas.HDAStorageCleanerManager method) (galaxy.managers.hdcas.DCASerializer method) (galaxy.managers.hdcas.DCESerializer method) (galaxy.managers.hdcas.DCSerializer method) (galaxy.managers.hdcas.HDCAManager method) (galaxy.managers.hdcas.HDCASerializer method) (galaxy.managers.histories.HistoryDeserializer method) (galaxy.managers.histories.HistoryExportManager method) (galaxy.managers.histories.HistoryManager method) (galaxy.managers.histories.HistorySerializer method) (galaxy.managers.histories.HistoryStorageCleanerManager method) (galaxy.managers.history_contents.HistoryContentsManager method) (galaxy.managers.history_contents.HistoryContentsSerializer method) (galaxy.managers.interactivetool.InteractiveToolManager method) (galaxy.managers.interactivetool.InteractiveToolSqlite method) (galaxy.managers.jobs.JobManager method) (galaxy.managers.jobs.JobSearch method) (galaxy.managers.lddas.LDDAManager method) (galaxy.managers.library_datasets.LibraryDatasetsManager method) (galaxy.managers.licenses.LicensesManager method) (galaxy.managers.metrics.MetricsManager method) (galaxy.managers.model_stores.ModelStoreManager method) (galaxy.managers.model_stores.ModelStoreUserContext method) (galaxy.managers.pages.PageContentProcessor method) (galaxy.managers.pages.PageDeserializer method) (galaxy.managers.pages.PageManager method) (galaxy.managers.pages.PageSerializer method) (galaxy.managers.quotas.QuotaManager method) (galaxy.managers.rbac_secured.RBACPermission method) (galaxy.managers.remote_files.RemoteFilesManager method) (galaxy.managers.session.GalaxySessionManager method) (galaxy.managers.sharable.SharableModelDeserializer method) (galaxy.managers.sharable.SharableModelManager method) (galaxy.managers.sharable.SharableModelSerializer method) (galaxy.managers.tool_data.ToolDataImportManager method) (galaxy.managers.tool_data.ToolDataManager method) (galaxy.managers.users.UserManager method) (galaxy.managers.users.UserSerializer method) (galaxy.managers.visualizations.VisualizationDeserializer method) (galaxy.managers.visualizations.VisualizationSerializer method) (galaxy.managers.workflows.MissingToolsException method) (galaxy.managers.workflows.RawWorkflowDescription method) (galaxy.managers.workflows.WorkflowContentsManager method) (galaxy.managers.workflows.WorkflowSerializer method) (galaxy.managers.workflows.WorkflowsManager method) (galaxy.metadata.ExtendedDirectoryMetadataGenerator method) (galaxy.metadata.PortableDirectoryMetadataGenerator method) (galaxy.model.APIKeys method) (galaxy.model.Base method) (galaxy.model.base.ModelMapping method) (galaxy.model.BaseJobMetric method) (galaxy.model.CeleryUserRateLimit method) (galaxy.model.CleanupEvent method) (galaxy.model.CleanupEventDatasetAssociation method) (galaxy.model.CleanupEventHistoryAssociation method) (galaxy.model.CleanupEventHistoryDatasetAssociationAssociation method) (galaxy.model.CleanupEventImplicitlyConvertedDatasetAssociationAssociation method) (galaxy.model.CleanupEventLibraryAssociation method) (galaxy.model.CleanupEventLibraryDatasetAssociation method) (galaxy.model.CleanupEventLibraryDatasetDatasetAssociationAssociation method) (galaxy.model.CleanupEventLibraryFolderAssociation method) (galaxy.model.CleanupEventMetadataFileAssociation method) (galaxy.model.CloudAuthz method) (galaxy.model.ConverterDependencyException method) (galaxy.model.CustosAuthnzToken method) (galaxy.model.database_heartbeat.DatabaseHeartbeat method) (galaxy.model.database_utils.DatabaseManager method) (galaxy.model.DataManagerHistoryAssociation method) (galaxy.model.DataManagerJobAssociation method) (galaxy.model.Dataset method) (galaxy.model.dataset_collections.builder.BoundCollectionBuilder method) (galaxy.model.dataset_collections.builder.CollectionBuilder method) (galaxy.model.dataset_collections.matching.CollectionsToMatch method) (galaxy.model.dataset_collections.matching.MatchingCollections method) (galaxy.model.dataset_collections.registry.DatasetCollectionTypesRegistry method) (galaxy.model.dataset_collections.structure.BaseTree method) (galaxy.model.dataset_collections.structure.Tree method) (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) (galaxy.model.dataset_collections.type_description.CollectionTypeDescriptionFactory method) (galaxy.model.dataset_collections.types.list.ListDatasetCollectionType method) (galaxy.model.dataset_collections.types.paired.PairedDatasetCollectionType method) (galaxy.model.DatasetCollection method) (galaxy.model.DatasetCollectionElement method) (galaxy.model.DatasetHash method) (galaxy.model.DatasetInstance method) (galaxy.model.DatasetPermissions method) (galaxy.model.DatasetSource method) (galaxy.model.DatasetSourceHash method) (galaxy.model.DefaultHistoryPermissions method) (galaxy.model.DefaultQuotaAssociation method) (galaxy.model.DefaultUserPermissions method) (galaxy.model.deferred.DatasetInstanceMaterializer method) (galaxy.model.deferred.SimpleTransientPathMapper method) (galaxy.model.DynamicTool method) (galaxy.model.Event method) (galaxy.model.ExtendedMetadata method) (galaxy.model.ExtendedMetadataIndex method) (galaxy.model.FakeDatasetAssociation method) (galaxy.model.FormDefinition method) (galaxy.model.FormDefinitionCurrent method) (galaxy.model.FormValues method) (galaxy.model.GalaxySession method) (galaxy.model.GalaxySessionToHistoryAssociation method) (galaxy.model.GenomeIndexToolData method) (galaxy.model.Group method) (galaxy.model.GroupQuotaAssociation method) (galaxy.model.GroupRoleAssociation method) (galaxy.model.History method) (galaxy.model.HistoryAnnotationAssociation method) (galaxy.model.HistoryAudit method) (galaxy.model.HistoryDatasetAssociation method) (galaxy.model.HistoryDatasetAssociationAnnotationAssociation method) (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization method) (galaxy.model.HistoryDatasetAssociationHistory method) (galaxy.model.HistoryDatasetAssociationRatingAssociation method) (galaxy.model.HistoryDatasetAssociationSubset method) (galaxy.model.HistoryDatasetAssociationTagAssociation method) (galaxy.model.HistoryDatasetCollectionAssociation method) (galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation method) (galaxy.model.HistoryDatasetCollectionRatingAssociation method) (galaxy.model.HistoryDatasetCollectionTagAssociation method) (galaxy.model.HistoryRatingAssociation method) (galaxy.model.HistoryTagAssociation method) (galaxy.model.HistoryUserShareAssociation method) (galaxy.model.ImplicitCollectionJobs method) (galaxy.model.ImplicitCollectionJobsJobAssociation method) (galaxy.model.ImplicitlyConvertedDatasetAssociation method) (galaxy.model.ImplicitlyCreatedDatasetCollectionInput method) (galaxy.model.InteractiveToolEntryPoint method) (galaxy.model.ItemRatingAssociation method) (galaxy.model.Job method) (galaxy.model.JobContainerAssociation method) (galaxy.model.JobExportHistoryArchive method) (galaxy.model.JobExternalOutputMetadata method) (galaxy.model.JobImportHistoryArchive method) (galaxy.model.JobMetricNumeric method) (galaxy.model.JobMetricText method) (galaxy.model.JobParameter method) (galaxy.model.JobStateHistory method) (galaxy.model.JobToImplicitOutputDatasetCollectionAssociation method) (galaxy.model.JobToInputDatasetAssociation method) (galaxy.model.JobToInputDatasetCollectionAssociation method) (galaxy.model.JobToInputDatasetCollectionElementAssociation method) (galaxy.model.JobToInputLibraryDatasetAssociation method) (galaxy.model.JobToOutputDatasetAssociation method) (galaxy.model.JobToOutputDatasetCollectionAssociation method) (galaxy.model.JobToOutputLibraryDatasetAssociation method) (galaxy.model.Library method) (galaxy.model.LibraryDataset method) (galaxy.model.LibraryDatasetCollectionAnnotationAssociation method) (galaxy.model.LibraryDatasetCollectionAssociation method) (galaxy.model.LibraryDatasetCollectionRatingAssociation method) (galaxy.model.LibraryDatasetCollectionTagAssociation method) (galaxy.model.LibraryDatasetDatasetAssociation method) (galaxy.model.LibraryDatasetDatasetAssociationPermissions method) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation method) (galaxy.model.LibraryDatasetDatasetInfoAssociation method) (galaxy.model.LibraryDatasetPermissions method) (galaxy.model.LibraryFolder method) (galaxy.model.LibraryFolderInfoAssociation method) (galaxy.model.LibraryFolderPermissions method) (galaxy.model.LibraryInfoAssociation method) (galaxy.model.LibraryPermissions method) (galaxy.model.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataElementSpec method) (galaxy.model.metadata.MetadataParameter method) (galaxy.model.metadata.MetadataSpecCollection method) (galaxy.model.metadata.MetadataTempFile method) (galaxy.model.metadata.RangeParameter method) (galaxy.model.metadata.SelectParameter method) (galaxy.model.metadata.Statement method) (galaxy.model.MetadataFile method) (galaxy.model.migrations.DatabaseStateVerifier method) (galaxy.model.migrations.InvalidModelIdError method) (galaxy.model.migrations.scripts.LegacyManageDb method) (galaxy.model.migrations.util.AddColumn method) (galaxy.model.migrations.util.AlterColumn method) (galaxy.model.migrations.util.CreateForeignKey method) (galaxy.model.migrations.util.CreateIndex method) (galaxy.model.migrations.util.CreateTable method) (galaxy.model.migrations.util.CreateUniqueConstraint method) (galaxy.model.migrations.util.DDLAlterOperation method) (galaxy.model.migrations.util.DropColumn method) (galaxy.model.migrations.util.DropConstraint method) (galaxy.model.migrations.util.DropIndex method) (galaxy.model.migrations.util.DropTable method) (galaxy.model.NoConverterException method) (galaxy.model.none_like.NoneDataset method) (galaxy.model.Notification method) (galaxy.model.Page method) (galaxy.model.PageAnnotationAssociation method) (galaxy.model.PageRatingAssociation method) (galaxy.model.PageRevision method) (galaxy.model.PageTagAssociation method) (galaxy.model.PageUserShareAssociation method) (galaxy.model.PasswordResetToken method) (galaxy.model.PostJobAction method) (galaxy.model.PostJobActionAssociation method) (galaxy.model.PSAAssociation method) (galaxy.model.PSACode method) (galaxy.model.PSANonce method) (galaxy.model.PSAPartial method) (galaxy.model.Quota method) (galaxy.model.Role method) (galaxy.model.security.GalaxyRBACAgent method) (galaxy.model.security.HostAgent method) (galaxy.model.SerializationOptions method) (galaxy.model.SerializeFilesHandler method) (galaxy.model.store.BagArchiveImportModelStore method) (galaxy.model.store.BagArchiveModelExportStore method) (galaxy.model.store.BagDirectoryModelExportStore method) (galaxy.model.store.BcoExportOptions method) (galaxy.model.store.BcoModelExportStore method) (galaxy.model.store.DictImportModelStore method) (galaxy.model.store.DirectoryImportModelStore1901 method) (galaxy.model.store.DirectoryImportModelStoreLatest method) (galaxy.model.store.DirectoryModelExportStore method) (galaxy.model.store.discover.JsonCollectedDatasetMatch method) (galaxy.model.store.discover.RegexCollectedDatasetMatch method) (galaxy.model.store.discover.SessionlessModelPersistenceContext method) (galaxy.model.store.FileTracebackException method) (galaxy.model.store.ImportOptions method) (galaxy.model.store.ModelImportStore method) (galaxy.model.store.ObjectImportTracker method) (galaxy.model.store.ROCrateArchiveModelExportStore method) (galaxy.model.store.ROCrateModelExportStore method) (galaxy.model.store.SessionlessContext method) (galaxy.model.store.StoreAppProtocol method) (galaxy.model.store.TarModelExportStore method) (galaxy.model.StoredWorkflow method) (galaxy.model.StoredWorkflowAnnotationAssociation method) (galaxy.model.StoredWorkflowMenuEntry method) (galaxy.model.StoredWorkflowRatingAssociation method) (galaxy.model.StoredWorkflowTagAssociation method) (galaxy.model.StoredWorkflowUserShareAssociation method) (galaxy.model.StoreExportAssociation method) (galaxy.model.Tag method) (galaxy.model.tags.CommunityTagHandler method) (galaxy.model.tags.GalaxyTagHandler method) (galaxy.model.tags.GalaxyTagHandlerSession method) (galaxy.model.tags.ItemTagAssocInfo method) (galaxy.model.tags.TagHandler method) (galaxy.model.Task method) (galaxy.model.TaskMetricNumeric method) (galaxy.model.TaskMetricText method) (galaxy.model.tool_shed_install.Base method) (galaxy.model.tool_shed_install.RepositoryDependency method) (galaxy.model.tool_shed_install.RepositoryRepositoryDependencyAssociation method) (galaxy.model.tool_shed_install.ToolDependency method) (galaxy.model.tool_shed_install.ToolShedRepository method) (galaxy.model.tool_shed_install.ToolVersion method) (galaxy.model.tool_shed_install.ToolVersionAssociation method) (galaxy.model.ToolTagAssociation method) (galaxy.model.UCI method) (galaxy.model.unittest_utils.data_app.GalaxyDataTestApp method) (galaxy.model.unittest_utils.data_app.GalaxyDataTestConfig method) (galaxy.model.unittest_utils.GalaxyDataTestApp method) (galaxy.model.unittest_utils.GalaxyDataTestConfig method) (galaxy.model.User method) (galaxy.model.UserAction method) (galaxy.model.UserAddress method) (galaxy.model.UserAuthnzToken method) (galaxy.model.UserGroupAssociation method) (galaxy.model.UserNotificationAssociation method) (galaxy.model.UserPreference method) (galaxy.model.UserQuotaAssociation method) (galaxy.model.UserQuotaSourceUsage method) (galaxy.model.UserRoleAssociation method) (galaxy.model.Vault method) (galaxy.model.Visualization method) (galaxy.model.VisualizationAnnotationAssociation method) (galaxy.model.VisualizationRatingAssociation method) (galaxy.model.VisualizationRevision method) (galaxy.model.VisualizationTagAssociation method) (galaxy.model.VisualizationUserShareAssociation method) (galaxy.model.WorkerProcess method) (galaxy.model.Workflow method) (galaxy.model.WorkflowComment method) (galaxy.model.WorkflowInvocation method) (galaxy.model.WorkflowInvocationMessage method) (galaxy.model.WorkflowInvocationOutputDatasetAssociation method) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation method) (galaxy.model.WorkflowInvocationOutputValue method) (galaxy.model.WorkflowInvocationStep method) (galaxy.model.WorkflowInvocationStepOutputDatasetAssociation method) (galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation method) (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation method) (galaxy.model.WorkflowOutput method) (galaxy.model.WorkflowRequestInputParameter method) (galaxy.model.WorkflowRequestInputStepParameter method) (galaxy.model.WorkflowRequestStepState method) (galaxy.model.WorkflowRequestToInputDatasetAssociation method) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation method) (galaxy.model.WorkflowStep method) (galaxy.model.WorkflowStepAnnotationAssociation method) (galaxy.model.WorkflowStepConnection method) (galaxy.model.WorkflowStepInput method) (galaxy.model.WorkflowStepTagAssociation method) (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.cloud.Cloud method) (galaxy.objectstore.ConcreteObjectStore method) (galaxy.objectstore.DeviceSourceMap method) (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.DistributedObjectStore method) (galaxy.objectstore.HierarchicalObjectStore method) (galaxy.objectstore.irods.IRODSObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStorePopulator method) (galaxy.objectstore.pithos.PithosObjectStore method) (galaxy.objectstore.pulsar.PulsarObjectStore method) (galaxy.objectstore.QuotaSourceMap method) (galaxy.objectstore.s3.S3ObjectStore method) (galaxy.objectstore.unittest_utils.Config method) (galaxy.objectstore.unittest_utils.MockConfig method) (galaxy.queue_worker.ControlTask method) (galaxy.queue_worker.GalaxyQueueWorker method) (galaxy.quota.NoQuotaAgent method) (galaxy.security.Action method) (galaxy.security.idencoding.IdAsLowercaseAlphanumEncodingHelper method) (galaxy.security.idencoding.IdEncodingHelper method) (galaxy.security.object_wrapper.SafeStringWrapper method) (galaxy.security.vault.CustosVault method) (galaxy.security.vault.DatabaseVault method) (galaxy.security.vault.HashicorpVault method) (galaxy.security.vault.UserVaultWrapper method) (galaxy.security.vault.VaultKeyPrefixWrapper method) (galaxy.security.vault.VaultKeyValidationWrapper method) (galaxy.selenium.cli.DriverWrapper method) (galaxy.selenium.context.GalaxySeleniumContextImpl method) (galaxy.selenium.driver_factory.ConfiguredDriver method) (galaxy.selenium.navigates_galaxy.ClientBuildException method) (galaxy.selenium.navigates_galaxy.NotLoggedInException method) (galaxy.selenium.scripts.dump_tour.DumpTourCallback method) (galaxy.selenium.smart_components.SmartComponent method) (galaxy.selenium.smart_components.SmartTarget method) (galaxy.structured_app.MinimalToolApp method) (galaxy.tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) (galaxy.tool_shed.galaxy_install.install_manager.RepositoriesInstalledException method) (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) (galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) (galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) (galaxy.tool_shed.galaxy_install.tools.data_manager.DataManagerHandler method) (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) (galaxy.tool_shed.galaxy_install.update_repository_manager.UpdateRepositoryManager method) (galaxy.tool_shed.metadata.metadata_generator.GalaxyMetadataGenerator method) (galaxy.tool_shed.metadata.metadata_generator.RepositoryProtocol method) (galaxy.tool_shed.tools.data_table_manager.ShedToolDataTableManager method) (galaxy.tool_shed.tools.tool_validator.ToolValidator method) (galaxy.tool_util.biotools.source.ApiBiotoolsMetadataSource method) (galaxy.tool_util.biotools.source.CascadingBiotoolsMetadataSource method) (galaxy.tool_util.biotools.source.GitContentBiotoolsMetadataSource method) (galaxy.tool_util.client.staging.InteractorStaging method) (galaxy.tool_util.cwl.cwltool_deps.CommentedMap method) (galaxy.tool_util.cwl.cwltool_deps.LoadingContext method) (galaxy.tool_util.cwl.cwltool_deps.RuntimeContext method) (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method) (galaxy.tool_util.cwl.runnable.CwlWorkflowOutput method) (galaxy.tool_util.cwl.runnable.ToolOutput method) (galaxy.tool_util.cwl.schema.SchemaLoader method) (galaxy.tool_util.cwl.util.DirectoryUploadTarget method) (galaxy.tool_util.cwl.util.FileLiteralTarget method) (galaxy.tool_util.cwl.util.FileUploadTarget method) (galaxy.tool_util.cwl.util.ObjectUploadTarget method) (galaxy.tool_util.deps.brew_exts.BrewContext method) (galaxy.tool_util.deps.brew_exts.CommandLineException method) (galaxy.tool_util.deps.brew_exts.EnvAction method) (galaxy.tool_util.deps.brew_exts.RecipeContext method) (galaxy.tool_util.deps.brew_util.HomebrewRecipe method) (galaxy.tool_util.deps.CachedDependencyManager method) (galaxy.tool_util.deps.conda_util.CondaContext method) (galaxy.tool_util.deps.conda_util.CondaTarget method) (galaxy.tool_util.deps.container_classes.Container method) (galaxy.tool_util.deps.container_classes.ContainerProtocol method) (galaxy.tool_util.deps.container_classes.Volume method) (galaxy.tool_util.deps.container_resolvers.ContainerResolver method) (galaxy.tool_util.deps.container_resolvers.explicit.CachedExplicitSingularityContainerResolver method) (galaxy.tool_util.deps.container_resolvers.explicit.FallbackContainerResolver method) (galaxy.tool_util.deps.container_resolvers.explicit.MappingContainerResolver method) (galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledDockerContainerResolver method) (galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledSingularityContainerResolver method) (galaxy.tool_util.deps.container_resolvers.mulled.CachedMulledDockerContainerResolver method) (galaxy.tool_util.deps.container_resolvers.mulled.MulledDockerContainerResolver method) (galaxy.tool_util.deps.container_resolvers.mulled.MulledSingularityContainerResolver method) (galaxy.tool_util.deps.container_volumes.ContainerVolume method) (galaxy.tool_util.deps.containers.ContainerFinder method) (galaxy.tool_util.deps.containers.ContainerRegistry method) (galaxy.tool_util.deps.dependencies.AppInfo method) (galaxy.tool_util.deps.dependencies.DependenciesDescription method) (galaxy.tool_util.deps.dependencies.JobInfo method) (galaxy.tool_util.deps.dependencies.ToolInfo method) (galaxy.tool_util.deps.DependencyManager method) (galaxy.tool_util.deps.NullDependencyManager method) (galaxy.tool_util.deps.requirements.ContainerDescription method) (galaxy.tool_util.deps.requirements.RequirementSpecification method) (galaxy.tool_util.deps.requirements.ResourceRequirement method) (galaxy.tool_util.deps.requirements.ToolRequirement method) (galaxy.tool_util.deps.requirements.ToolRequirements method) (galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages.HomebrewToolShedDependencyResolver method) (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method) (galaxy.tool_util.deps.resolvers.ContainerDependency method) (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependency method) (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependencyResolver method) (galaxy.tool_util.deps.resolvers.homebrew.HomebrewDependencyResolver method) (galaxy.tool_util.deps.resolvers.lmod.LmodDependencyResolver method) (galaxy.tool_util.deps.resolvers.modules.ModuleDependencyResolver method) (galaxy.tool_util.deps.resolvers.NullDependency method) (galaxy.tool_util.deps.resolvers.RequirementMapping method) (galaxy.tool_util.deps.resolvers.resolver_mixins.HomebrewDependency method) (galaxy.tool_util.deps.resolvers.tool_shed_packages.ToolShedPackageDependencyResolver method) (galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages.UnlinkedToolShedPackageDependencyResolver method) (galaxy.tool_util.deps.views.ContainerResolutionView method) (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.tool_util.fetcher.ToolLocationFetcher method) (galaxy.tool_util.lint.LintContext method) (galaxy.tool_util.lint.LintMessage method) (galaxy.tool_util.lint.XMLLintMessageLine method) (galaxy.tool_util.lint.XMLLintMessageXPath method) (galaxy.tool_util.locations.http.HttpToolResolver method) (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.PagesSource method) (galaxy.tool_util.parser.interface.RequiredFiles method) (galaxy.tool_util.parser.interface.TestCollectionDef method) (galaxy.tool_util.parser.interface.TestCollectionOutputDef method) (galaxy.tool_util.parser.output_actions.BooleanFilter method) (galaxy.tool_util.parser.output_actions.ColumnReplaceFilter method) (galaxy.tool_util.parser.output_actions.ColumnStripFilter method) (galaxy.tool_util.parser.output_actions.DatatypeIsInstanceToolOutputActionConditionalWhen method) (galaxy.tool_util.parser.output_actions.FormatToolOutputAction method) (galaxy.tool_util.parser.output_actions.FromDataTableOutputActionOption method) (galaxy.tool_util.parser.output_actions.FromFileToolOutputActionOption method) (galaxy.tool_util.parser.output_actions.FromParamToolOutputActionOption method) (galaxy.tool_util.parser.output_actions.InsertColumnToolOutputActionOptionFilter method) (galaxy.tool_util.parser.output_actions.MetadataToolOutputAction method) (galaxy.tool_util.parser.output_actions.MetadataValueFilter method) (galaxy.tool_util.parser.output_actions.MultipleSplitterFilter method) (galaxy.tool_util.parser.output_actions.ParamValueToolOutputActionOptionFilter method) (galaxy.tool_util.parser.output_actions.StringFunctionFilter method) (galaxy.tool_util.parser.output_actions.ToolOutputAction method) (galaxy.tool_util.parser.output_actions.ToolOutputActionConditional method) (galaxy.tool_util.parser.output_actions.ToolOutputActionConditionalWhen method) (galaxy.tool_util.parser.output_actions.ToolOutputActionGroup method) (galaxy.tool_util.parser.output_actions.ToolOutputActionOption method) (galaxy.tool_util.parser.output_actions.ToolOutputActionOptionFilter method) (galaxy.tool_util.parser.output_collection_def.DatasetCollectionDescription method) (galaxy.tool_util.parser.output_collection_def.FilePatternDatasetCollectionDescription method) (galaxy.tool_util.parser.output_objects.ToolExpressionOutput method) (galaxy.tool_util.parser.output_objects.ToolOutput method) (galaxy.tool_util.parser.output_objects.ToolOutputBase method) (galaxy.tool_util.parser.output_objects.ToolOutputCollection method) (galaxy.tool_util.parser.output_objects.ToolOutputCollectionPart method) (galaxy.tool_util.parser.output_objects.ToolOutputCollectionStructure method) (galaxy.tool_util.parser.RequiredFiles method) (galaxy.tool_util.parser.stdio.ToolStdioExitCode method) (galaxy.tool_util.parser.stdio.ToolStdioRegex method) (galaxy.tool_util.parser.ToolOutputCollectionPart method) (galaxy.tool_util.parser.xml.ParallelismInfo method) (galaxy.tool_util.parser.xml.StdioParser method) (galaxy.tool_util.parser.xml.XmlInputSource method) (galaxy.tool_util.parser.xml.XmlPageSource method) (galaxy.tool_util.parser.xml.XmlPagesSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlInputSource method) (galaxy.tool_util.parser.yaml.YamlPageSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) (galaxy.tool_util.provided_metadata.LegacyToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.ToolProvidedMetadata method) (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) (galaxy.tool_util.toolbox.base.ToolBoxRegistryImpl method) (galaxy.tool_util.toolbox.filters.FilterFactory method) (galaxy.tool_util.toolbox.lineages.factory.LineageMap method) (galaxy.tool_util.toolbox.lineages.interface.ToolLineage method) (galaxy.tool_util.toolbox.lineages.interface.ToolLineageVersion method) (galaxy.tool_util.toolbox.lineages.LineageMap method) (galaxy.tool_util.toolbox.lineages.ToolLineage method) (galaxy.tool_util.toolbox.panel.ToolSection method) (galaxy.tool_util.toolbox.panel.ToolSectionLabel method) (galaxy.tool_util.toolbox.ToolSection method) (galaxy.tool_util.toolbox.ToolSectionLabel method) (galaxy.tool_util.toolbox.views.edam.EdamToolPanelView method) (galaxy.tool_util.toolbox.views.sources.StaticToolBoxViewSources method) (galaxy.tool_util.toolbox.views.static.StaticToolPanelView method) (galaxy.tool_util.toolbox.watcher.ToolConfWatcher method) (galaxy.tool_util.toolbox.watcher.ToolFileEventHandler method) (galaxy.tool_util.toolbox.watcher.ToolWatcher method) (galaxy.tool_util.verify.interactor.DictClientTestConfig method) (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) (galaxy.tool_util.verify.interactor.JobOutputsError method) (galaxy.tool_util.verify.interactor.RunToolException method) (galaxy.tool_util.verify.interactor.TestConfig method) (galaxy.tool_util.verify.interactor.ToolTestDescription method) (galaxy.tool_util.verify.script.Results method) (galaxy.tool_util.verify.test_data.FileDataResolver method) (galaxy.tool_util.verify.test_data.GitDataResolver method) (galaxy.tool_util.verify.test_data.TestDataResolver method) (galaxy.tool_util.verify.wait.TimeoutAssertionError method) (galaxy.tools.actions.OutputCollections method) (galaxy.tools.actions.ToolExecutionCache method) (galaxy.tools.actions.upload_common.LibraryParams method) (galaxy.tools.BadValue method) (galaxy.tools.cache.ToolCache method) (galaxy.tools.cache.ToolDocumentCache method) (galaxy.tools.cache.ToolHash method) (galaxy.tools.data.RefgenieToolDataTable method) (galaxy.tools.data.TabularToolDataField method) (galaxy.tools.data.TabularToolDataTable method) (galaxy.tools.data.ToolDataTable method) (galaxy.tools.data_fetch.UploadConfig method) (galaxy.tools.data_manager.manager.DataManager method) (galaxy.tools.data_manager.manager.DataManagers method) (galaxy.tools.data_manager.manager.Tool method) (galaxy.tools.DataManagerTool method) (galaxy.tools.DefaultToolState method) (galaxy.tools.error_reports.ErrorPlugin method) (galaxy.tools.error_reports.ErrorReports method) (galaxy.tools.error_reports.plugins.email.EmailPlugin method) (galaxy.tools.error_reports.plugins.github.GithubPlugin method) (galaxy.tools.error_reports.plugins.gitlab.GitLabPlugin method) (galaxy.tools.error_reports.plugins.influxdb.InfluxDBPlugin method) (galaxy.tools.error_reports.plugins.json.JsonPlugin method) (galaxy.tools.error_reports.plugins.sentry.SentryPlugin method) (galaxy.tools.errors.ErrorReporter method) (galaxy.tools.evaluation.ToolErrorLog method) (galaxy.tools.evaluation.ToolEvaluator method) (galaxy.tools.exception_handling.UCSCOutWrapper method) (galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper method) (galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper method) (galaxy.tools.InteractiveTool method) (galaxy.tools.parameters.basic.BaseDataToolParameter method) (galaxy.tools.parameters.basic.BaseURLToolParameter method) (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.ColorToolParameter method) (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.DirectoryUriToolParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.FileToolParameter method) (galaxy.tools.parameters.basic.FloatToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.GenomeBuildParameter method) (galaxy.tools.parameters.basic.HiddenDataToolParameter method) (galaxy.tools.parameters.basic.HiddenToolParameter method) (galaxy.tools.parameters.basic.IntegerToolParameter method) (galaxy.tools.parameters.basic.ParameterValueError method) (galaxy.tools.parameters.basic.RulesListToolParameter method) (galaxy.tools.parameters.basic.SelectTagParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.SimpleTextToolParameter method) (galaxy.tools.parameters.basic.TextToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.DataCollectionToolParameter method) (galaxy.tools.parameters.DataToolParameter method) (galaxy.tools.parameters.dynamic_options.AdditionalValueFilter method) (galaxy.tools.parameters.dynamic_options.AttributeValueSplitterFilter method) (galaxy.tools.parameters.dynamic_options.DataMetaFilter method) (galaxy.tools.parameters.dynamic_options.DynamicOptions method) (galaxy.tools.parameters.dynamic_options.Filter method) (galaxy.tools.parameters.dynamic_options.FromUrlOptions method) (galaxy.tools.parameters.dynamic_options.MultipleSplitterFilter method) (galaxy.tools.parameters.dynamic_options.ParamValueFilter method) (galaxy.tools.parameters.dynamic_options.RegexpFilter method) (galaxy.tools.parameters.dynamic_options.RemoveValueFilter method) (galaxy.tools.parameters.dynamic_options.SortByColumnFilter method) (galaxy.tools.parameters.dynamic_options.StaticValueFilter method) (galaxy.tools.parameters.dynamic_options.UniqueValueFilter method) (galaxy.tools.parameters.grouping.Conditional method) (galaxy.tools.parameters.grouping.ConditionalWhen method) (galaxy.tools.parameters.grouping.Group method) (galaxy.tools.parameters.grouping.Repeat method) (galaxy.tools.parameters.grouping.Section method) (galaxy.tools.parameters.grouping.UploadDataset method) (galaxy.tools.parameters.history_query.HistoryQuery method) (galaxy.tools.parameters.input_translation.ToolInputTranslator method) (galaxy.tools.parameters.meta.InputKey method) (galaxy.tools.parameters.meta.ParamKey method) (galaxy.tools.parameters.sanitize.ToolParameterSanitizer method) (galaxy.tools.parameters.SelectToolParameter method) (galaxy.tools.parameters.validation.ExpressionValidator method) (galaxy.tools.parameters.validation.InRangeValidator method) (galaxy.tools.parameters.validation.LengthValidator method) (galaxy.tools.parameters.validation.MetadataEqualValidator method) (galaxy.tools.parameters.validation.MetadataInDataTableColumnValidator method) (galaxy.tools.parameters.validation.MetadataInFileColumnValidator method) (galaxy.tools.parameters.validation.MetadataInRangeValidator method) (galaxy.tools.parameters.validation.MetadataNotInDataTableColumnValidator method) (galaxy.tools.parameters.validation.MetadataValidator method) (galaxy.tools.parameters.validation.RegexValidator method) (galaxy.tools.parameters.validation.Validator method) (galaxy.tools.parameters.validation.ValueInDataTableColumnValidator method) (galaxy.tools.parameters.validation.ValueNotInDataTableColumnValidator method) (galaxy.tools.parameters.wrapped.LegacyUnprefixedDict method) (galaxy.tools.parameters.wrapped.WrappedParameters method) (galaxy.tools.PersistentToolTagManager method) (galaxy.tools.recommendations.ToolRecommendations method) (galaxy.tools.remote_tool_eval.ToolApp method) (galaxy.tools.repositories.ValidationContext method) (galaxy.tools.search.ToolBoxSearch method) (galaxy.tools.search.ToolPanelViewSearch method) (galaxy.tools.SetParamAction method) (galaxy.tools.test.ParamContext method) (galaxy.tools.test.RootParamContext method) (galaxy.tools.Tool method) (galaxy.tools.ToolBox method) (galaxy.tools.TracksterConfig method) (galaxy.tools.util.maf_utilities.GenomicRegionAlignment method) (galaxy.tools.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.SplicedAlignment method) (galaxy.tools.util.maf_utilities.TempFileHandler method) (galaxy.tools.wrappers.DatasetCollectionWrapper method) (galaxy.tools.wrappers.DatasetFilenameWrapper method) (galaxy.tools.wrappers.DatasetFilenameWrapper.MetadataWrapper method) (galaxy.tools.wrappers.DatasetListWrapper method) (galaxy.tools.wrappers.ElementIdentifierMapper method) (galaxy.tools.wrappers.InputValueWrapper method) (galaxy.tools.wrappers.RawObjectWrapper method) (galaxy.tools.wrappers.SelectToolParameterWrapper method) (galaxy.tools.wrappers.SelectToolParameterWrapper.SelectToolParameterFieldWrapper method) (galaxy.util.aliaspickler.AliasPickleModule method) (galaxy.util.aliaspickler.AliasUnpickler method) (galaxy.util.bool_expressions.BoolBinaryOperation method) (galaxy.util.bool_expressions.BooleanExpressionEvaluator method) (galaxy.util.bool_expressions.BoolNot method) (galaxy.util.bool_expressions.BoolOperand method) (galaxy.util.bool_expressions.TokenContainedEvaluator method) (galaxy.util.bunch.Bunch method) (galaxy.util.bytesize.ByteSize method) (galaxy.util.classproperty method) (galaxy.util.commands.CommandLineException method) (galaxy.util.compression_utils.CompressedFile method) (galaxy.util.custom_logging.fluent_log.FluentTraceLogger method) (galaxy.util.ExecutionTimer method) (galaxy.util.expressions.ExpressionContext method) (galaxy.util.facts.Facts method) (galaxy.util.filelock.FileLock method) (galaxy.util.form_builder.AddressField method) (galaxy.util.form_builder.BaseField method) (galaxy.util.form_builder.HistoryField method) (galaxy.util.form_builder.SelectField method) (galaxy.util.form_builder.WorkflowField method) (galaxy.util.form_builder.WorkflowMappingField method) (galaxy.util.heartbeat.Heartbeat method) (galaxy.util.jstree.JSTree method) (galaxy.util.jstree.Node method) (galaxy.util.lazy_process.LazyProcess method) (galaxy.util.odict.odict method) (galaxy.util.oset.OrderedSet method) (galaxy.util.Params method) (galaxy.util.ParamsWithSpecs method) (galaxy.util.properties.NicerConfigParser method) (galaxy.util.renamed_temporary_file.RenamedTemporaryFile method) (galaxy.util.resources.Traversable method) (galaxy.util.rules_dsl.RuleSet method) (galaxy.util.simplegraph.SimpleGraph method) (galaxy.util.simplegraph.SimpleGraphEdge method) (galaxy.util.simplegraph.SimpleGraphNode method) (galaxy.util.sleeper.Sleeper method) (galaxy.util.StructuredExecutionTimer method) (galaxy.util.task.IntervalTask method) (galaxy.util.topsort.CycleError method) (galaxy.util.ucsc.UCSCOutWrapper method) (galaxy.util.watcher.BaseWatcher method) (galaxy.util.watcher.EventHandler method) (galaxy.util.watcher.Watcher method) (galaxy.util.yaml_util.OrderedLoader method) (galaxy.util.zipstream.ZipstreamWrapper method) (galaxy.visualization.data_providers.basic.BaseDataProvider method) (galaxy.visualization.data_providers.basic.ColumnDataProvider method) (galaxy.visualization.data_providers.genome.FeatureLocationIndexDataProvider method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) (galaxy.visualization.data_providers.genome.SamDataProvider method) (galaxy.visualization.data_providers.phyloviz.baseparser.Base_Parser method) (galaxy.visualization.data_providers.phyloviz.baseparser.Node method) (galaxy.visualization.data_providers.phyloviz.baseparser.PhyloTree method) (galaxy.visualization.data_providers.phyloviz.newickparser.Newick_Parser method) (galaxy.visualization.data_providers.phyloviz.nexusparser.Nexus_Parser method) (galaxy.visualization.data_providers.phyloviz.PhylovizDataProvider method) (galaxy.visualization.data_providers.phyloviz.phyloxmlparser.Phyloxml_Parser method) (galaxy.visualization.data_providers.registry.DataProviderRegistry method) (galaxy.visualization.genomes.Genome method) (galaxy.visualization.genomes.GenomeRegion method) (galaxy.visualization.genomes.Genomes method) (galaxy.visualization.plugins.config_parser.DictParser method) (galaxy.visualization.plugins.config_parser.ListParser method) (galaxy.visualization.plugins.config_parser.VisualizationsConfigParser method) (galaxy.visualization.plugins.plugin.VisualizationPlugin method) (galaxy.visualization.plugins.registry.VisualizationsRegistry method) (galaxy.visualization.plugins.resource_parser.ResourceParser method) (galaxy.web.form_builder.AddressField method) (galaxy.web.form_builder.BaseField method) (galaxy.web.form_builder.HistoryField method) (galaxy.web.form_builder.SelectField method) (galaxy.web.form_builder.WorkflowField method) (galaxy.web.form_builder.WorkflowMappingField method) (galaxy.web.framework.base.DefaultWebTransaction method) (galaxy.web.framework.base.WebApplication method) (galaxy.web.framework.helpers.grids.GridColumn method) (galaxy.web.framework.helpers.grids.GridData method) (galaxy.web.framework.middleware.error.ErrorMiddleware method) (galaxy.web.framework.middleware.profile.ProfileMiddleware method) (galaxy.web.framework.middleware.remoteuser.RemoteUser method) (galaxy.web.framework.middleware.request_id.RequestIDMiddleware method) (galaxy.web.framework.middleware.sqldebug.SQLDebugMiddleware method) (galaxy.web.framework.middleware.static.CacheableStaticURLParser method) (galaxy.web.framework.middleware.statsd.StatsdMiddleware method) (galaxy.web.framework.middleware.translogger.TransLogger method) (galaxy.web.framework.middleware.xforwardedhost.XForwardedHostMiddleware method) (galaxy.web.legacy_framework.grids.CommunityTagsColumn method) (galaxy.web.legacy_framework.grids.Grid method) (galaxy.web.legacy_framework.grids.GridAction method) (galaxy.web.legacy_framework.grids.GridColumn method) (galaxy.web.legacy_framework.grids.GridColumnFilter method) (galaxy.web.legacy_framework.grids.GridOperation method) (galaxy.web.legacy_framework.grids.MulticolFilterColumn method) (galaxy.web.legacy_framework.grids.OwnerAnnotationColumn method) (galaxy.web.proxy.AuthenticationToken method) (galaxy.web.proxy.JsonFileProxyIpc method) (galaxy.web.proxy.ProxyManager method) (galaxy.web.proxy.ProxyRequests method) (galaxy.web.proxy.RestGolangProxyIpc method) (galaxy.web.proxy.SqliteProxyIpc method) (galaxy.web_stack.ApplicationStack method) (galaxy.web_stack.message.ApplicationStackMessage method) (galaxy.web_stack.message.ApplicationStackMessageDispatcher method) (galaxy.web_stack.message.ParamMessage method) (galaxy.web_stack.transport.ApplicationStackTransport method) (galaxy.web_stack.WeblessApplicationStack method) (galaxy.webapps.base.api.GalaxyFileResponse method) (galaxy.webapps.base.webapp.GalaxyWebTransaction method) (galaxy.webapps.base.webapp.WebApplication method) (galaxy.webapps.galaxy.api.authenticate.FastAPIAuthenticate method) (galaxy.webapps.galaxy.api.BaseGalaxyAPIController method) (galaxy.webapps.galaxy.api.cloudauthz.CloudAuthzController method) (galaxy.webapps.galaxy.api.configuration.FastAPIConfiguration method) (galaxy.webapps.galaxy.api.container_resolution.ContainerResolutionAPIController method) (galaxy.webapps.galaxy.api.datatypes.FastAPIDatatypes method) (galaxy.webapps.galaxy.api.display_applications.FastAPIDisplay method) (galaxy.webapps.galaxy.api.folder_contents.FastAPILibraryFoldersContents method) (galaxy.webapps.galaxy.api.folders.FastAPILibraryFolders method) (galaxy.webapps.galaxy.api.forms.FastAPIForms method) (galaxy.webapps.galaxy.api.GalaxyASGIRequest method) (galaxy.webapps.galaxy.api.GalaxyASGIResponse method) (galaxy.webapps.galaxy.api.GalaxyTypeDepends method) (galaxy.webapps.galaxy.api.genomes.FastAPIGenomes method) (galaxy.webapps.galaxy.api.group_roles.FastAPIGroupRoles method) (galaxy.webapps.galaxy.api.group_users.FastAPIGroupUsers method) (galaxy.webapps.galaxy.api.groups.FastAPIGroups method) (galaxy.webapps.galaxy.api.job_ports.JobPortsAPIController method) (galaxy.webapps.galaxy.api.libraries.FastAPILibraries method) (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method) (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method) (galaxy.webapps.galaxy.api.licenses.FastAPILicenses method) (galaxy.webapps.galaxy.api.metrics.FastAPIMetrics method) (galaxy.webapps.galaxy.api.pages.FastAPIPages method) (galaxy.webapps.galaxy.api.quotas.FastAPIQuota method) (galaxy.webapps.galaxy.api.remote_files.FastAPIRemoteFiles method) (galaxy.webapps.galaxy.api.roles.FastAPIRoles method) (galaxy.webapps.galaxy.api.short_term_storage.FastAPIShortTermStorage method) (galaxy.webapps.galaxy.api.tags.FastAPITags method) (galaxy.webapps.galaxy.api.tasks.FastAPITasks method) (galaxy.webapps.galaxy.api.tool_data.FastAPIToolData method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) (galaxy.webapps.galaxy.api.tool_entry_points.ToolEntryPointsAPIController method) (galaxy.webapps.galaxy.api.tool_shed_repositories.FastAPIToolShedRepositories method) (galaxy.webapps.galaxy.api.tools.FetchTools method) (galaxy.webapps.galaxy.api.tours.FastAPITours method) (galaxy.webapps.galaxy.api.UrlBuilder method) (galaxy.webapps.galaxy.api.users.FastAPIUsers method) (galaxy.webapps.galaxy.api.visualizations.FastAPIVisualizations method) (galaxy.webapps.galaxy.buildapp.GalaxyWebApplication method) (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.root.RootController method) (galaxy.webapps.galaxy.controllers.user.User method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) (galaxy.webapps.galaxy.controllers.workflow.SingleTagContentsParser method) (galaxy.webapps.galaxy.services.authenticate.AuthenticationService method) (galaxy.webapps.galaxy.services.base.ServiceBase method) (galaxy.webapps.galaxy.services.histories.HistoriesService method) (galaxy.webapps.galaxy.services.libraries.LibrariesService method) (galaxy.webapps.galaxy.services.library_folder_contents.LibraryFolderContentsService method) (galaxy.webapps.galaxy.services.library_folder_contents.UserFolderPermissions method) (galaxy.webapps.galaxy.services.library_folders.LibraryFoldersService method) (galaxy.webapps.galaxy.services.pages.PagesService method) (galaxy.webapps.galaxy.services.quotas.QuotasService method) (galaxy.webapps.galaxy.services.sharable.ShareableService method) (galaxy.webapps.galaxy.services.tools.ToolsService method) (galaxy.webapps.galaxy.services.users.UsersService method) (galaxy.webapps.galaxy.services.visualizations.VisualizationsService method) (galaxy.webapps.reports.app.UniverseApplication method) (galaxy.webapps.reports.config.Configuration method) (galaxy.webapps.reports.controllers.jobs.Timer method) (galaxy.webhooks.Webhook method) (galaxy.webhooks.WebhooksRegistry method) (galaxy.work.context.SessionRequestContext method) (galaxy.work.context.WorkRequestContext method) (galaxy.workflow.modules.CancelWorkflowEvaluation method) (galaxy.workflow.modules.DelayedWorkflowEvaluation method) (galaxy.workflow.modules.FailWorkflowEvaluation method) (galaxy.workflow.modules.InputProxy method) (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) (galaxy.workflow.modules.WorkflowModuleFactory method) (galaxy.workflow.modules.WorkflowModuleInjector method) (galaxy.workflow.refactor.execute.WorkflowRefactorExecutor method) (galaxy.workflow.render.WorkflowCanvas method) (galaxy.workflow.run.WorkflowRunConfig method) (galaxy.workflow.run_request.WorkflowRunConfig method) (galaxy.workflow.schedulers.core.CoreWorkflowSchedulingPlugin method) (galaxy.workflow.scheduling_manager.WorkflowRequestMonitor method) (galaxy.workflow.scheduling_manager.WorkflowSchedulingManager method) (galaxy.workflow.trs_proxy.TrsProxy method) (galaxy.workflow.trs_proxy.TrsServer method) (galaxy_test.base.api.AnonymousGalaxyInteractor method) (galaxy_test.base.api.ApiTestInteractor method) (galaxy_test.base.api.HasAnonymousGalaxyInteractor method) (galaxy_test.base.interactor.TestCaseGalaxyInteractor method) (galaxy_test.base.populators.CwlPopulator method) (galaxy_test.base.populators.CwlRun method) (galaxy_test.base.populators.CwlToolRun method) (galaxy_test.base.populators.CwlWorkflowRun method) (galaxy_test.base.populators.DatasetCollectionPopulator method) (galaxy_test.base.populators.DatasetPopulator method) (galaxy_test.base.populators.GiDatasetCollectionPopulator method) (galaxy_test.base.populators.GiDatasetPopulator method) (galaxy_test.base.populators.GiWorkflowPopulator method) (galaxy_test.base.populators.LibraryPopulator method) (galaxy_test.base.populators.WorkflowPopulator method) (galaxy_test.driver.driver_util.TestDriver method) (galaxy_test.selenium.jupyter_context.JupyterTestContextImpl method) (galaxy_test.selenium.test_stock_tours.TourCallback method) (tool_shed.dependencies.attribute_handlers.RepositoryDependencyAttributeHandler method) (tool_shed.dependencies.attribute_handlers.ToolDependencyAttributeHandler method) (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) (tool_shed.grids.repository_grids.RepositoriesWithInvalidToolsGrid.InvalidToolConfigColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.HeadsColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.LatestInstallableRevisionColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.MetadataRevisionColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.TipRevisionColumn method) (tool_shed.grids.repository_grids.ValidRepositoryGrid.InstallableRevisionColumn method) (tool_shed.managers.groups.GroupManager method) (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) (tool_shed.metadata.repository_metadata_manager.ToolShedMetadataGenerator method) (tool_shed.repository_registry.Registry method) (tool_shed.repository_types.metadata.Metadata method) (tool_shed.repository_types.metadata.TipOnly method) (tool_shed.repository_types.registry.Registry method) (tool_shed.repository_types.repository_suite_definition.RepositorySuiteDefinition method) (tool_shed.repository_types.tool_dependency_definition.ToolDependencyDefinition method) (tool_shed.repository_types.unrestricted.Unrestricted method) (tool_shed.test.base.twilltestcase.GalaxyInteractorToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.StandaloneToolShedInstallationClient method) (tool_shed.tools.data_table_manager.ShedToolDataTableManager method) (tool_shed.tools.tool_version_manager.ToolVersionManager method) (tool_shed.util.hgweb_config.HgWebConfigManager method) (tool_shed.utility_containers.FailedTest method) (tool_shed.utility_containers.InvalidRepositoryDependency method) (tool_shed.utility_containers.InvalidToolDependency method) (tool_shed.utility_containers.MissingTestComponent method) (tool_shed.utility_containers.NotTested method) (tool_shed.utility_containers.PassedTest method) (tool_shed.utility_containers.RepositoryInstallationError method) (tool_shed.utility_containers.RepositorySuccessfulInstallation method) (tool_shed.utility_containers.ToolDependencyInstallationError method) (tool_shed.utility_containers.ToolDependencySuccessfulInstallation method) (tool_shed.utility_containers.ToolShedUtilityContainerManager method) (tool_shed.webapp.api.BaseShedAPIController method) (tool_shed.webapp.api.groups.GroupsController method) (tool_shed.webapp.app.UniverseApplication method) (tool_shed.webapp.config.ToolShedAppConfiguration method) (tool_shed.webapp.controllers.hg.PortAsStringMiddleware method) (tool_shed.webapp.framework.middleware.remoteuser.RemoteUser method) (tool_shed.webapp.model.APIKeys method) (tool_shed.webapp.model.Base method) (tool_shed.webapp.model.Category method) (tool_shed.webapp.model.GalaxySession method) (tool_shed.webapp.model.Group method) (tool_shed.webapp.model.GroupRoleAssociation method) (tool_shed.webapp.model.ItemRatingAssociation method) (tool_shed.webapp.model.PasswordResetToken method) (tool_shed.webapp.model.Repository method) (tool_shed.webapp.model.RepositoryCategoryAssociation method) (tool_shed.webapp.model.RepositoryMetadata method) (tool_shed.webapp.model.RepositoryRatingAssociation method) (tool_shed.webapp.model.RepositoryRoleAssociation method) (tool_shed.webapp.model.Role method) (tool_shed.webapp.model.Tag method) (tool_shed.webapp.model.User method) (tool_shed.webapp.model.UserGroupAssociation method) (tool_shed.webapp.model.UserRoleAssociation method) (tool_shed.webapp.security.Action method) (tool_shed.webapp.security.CommunityRBACAgent method) (tool_shed.webapp.util.shed_statistics.ShedCounter method)

A

a_galaxy_workflow (galaxy.schema.schema.WorkflowToExport attribute) Ab1 (class in galaxy.datatypes.binary) abort_when_job_stops() (in module galaxy.celery.tasks) abs_path() (in module galaxy.tool_util.cwl.util) abs_path_or_uri() (in module galaxy.tool_util.cwl.util) absolute_config_path() (in module galaxy.main_config) AbstractToolBox (class in galaxy.tool_util.toolbox) (class in galaxy.tool_util.toolbox.base) AbstractToolTagManager (class in galaxy.tool_util.toolbox) (class in galaxy.tool_util.toolbox.base) accept_alert() (galaxy.selenium.has_driver.HasDriver method) accept_matches() (galaxy.webapps.galaxy.api.APIContentTypeRoute method) accepted_audiences (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute) AcceptedRetryLater access (galaxy.schema.schema.DatasetPermissions attribute) (galaxy.webapps.galaxy.services.library_folder_contents.UserFolderPermissions attribute) access_dataset_roles (galaxy.schema.schema.DatasetAssociationRoles attribute) access_entry_point() (galaxy.webapps.galaxy.api.tool_entry_points.ToolEntryPointsAPIController method) access_entry_point_target() (galaxy.managers.interactivetool.InteractiveToolManager method) access_ids (galaxy.schema.schema.LibraryPermissionsPayload attribute) (galaxy.schema.schema.UpdateDatasetPermissionsPayload attribute) access_library_role_list (galaxy.schema.schema.LibraryCurrentPermissions attribute) access_token (galaxy.model.CustosAuthnzToken attribute) AccessDatasetRBACPermission (class in galaxy.managers.rbac_secured) accessible (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) (galaxy.schema.schema.HDAInaccessible attribute) (galaxy.schema.schema.HDAObject attribute) accessible_count (galaxy.schema.schema.ShareHistoryExtra attribute) AccessibleManagerMixin (class in galaxy.managers.secured) AccessLoggingMiddleware (class in galaxy.webapps.base.api) AccNos (class in galaxy.datatypes.mothur) accumulate_tool_dependencies() (in module galaxy.util.tool_shed.common_util) (in module tool_shed.util.common_util) acquire() (galaxy.util.filelock.FileLock method) Action (class in galaxy.security) (class in galaxy.workflow.refactor.schema) (class in tool_shed.webapp.security) action (galaxy.job_execution.actions.post.RemoveTagDatasetAction attribute) (galaxy.job_execution.actions.post.TagDatasetAction attribute) (galaxy.model.DatasetPermissions attribute) (galaxy.model.DefaultHistoryPermissions attribute) (galaxy.model.DefaultUserPermissions attribute) (galaxy.model.LibraryDatasetDatasetAssociationPermissions attribute) (galaxy.model.LibraryDatasetPermissions attribute) (galaxy.model.LibraryFolderPermissions attribute) (galaxy.model.LibraryPermissions attribute) (galaxy.model.UserAction attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.schema.schema.LibraryFolderPermissionsPayload attribute) (galaxy.schema.schema.LibraryPermissionsPayload attribute) (galaxy.schema.schema.UpdateDatasetPermissionsPayload attribute) (galaxy.security.Action attribute) (galaxy.tools.ApplyRulesTool attribute) (galaxy.tools.AsyncDataSourceTool attribute) (galaxy.tools.BuildListCollectionTool attribute) (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.DataDestinationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.DuplicateFileToCollectionTool attribute) (galaxy.tools.ExportHistoryTool attribute) (galaxy.tools.ExpressionTool attribute) (galaxy.tools.ExtractDatasetCollectionTool attribute) (galaxy.tools.FilterDatasetsTool attribute) (galaxy.tools.FilterEmptyDatasetsTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) (galaxy.tools.FilterFromFileTool attribute) (galaxy.tools.FlattenTool attribute) (galaxy.tools.HarmonizeTool attribute) (galaxy.tools.ImportHistoryTool attribute) (galaxy.tools.InteractiveTool attribute) (galaxy.tools.KeepSuccessDatasetsTool attribute) (galaxy.tools.MergeCollectionTool attribute) (galaxy.tools.OutputParameterJSONTool attribute) (galaxy.tools.RelabelFromFileTool attribute) (galaxy.tools.SortTool attribute) (galaxy.tools.TagFromFileTool attribute) (galaxy.tools.UnzipCollectionTool attribute) (galaxy.tools.ZipCollectionTool attribute) (galaxy.workflow.refactor.schema.RefactorActionExecution attribute) action_arguments (galaxy.model.PostJobAction attribute) (galaxy.schema.schema.PostJobAction attribute) action_chains() (galaxy.selenium.has_driver.HasDriver method) action_class (in module galaxy.workflow.refactor.schema) action_executions (galaxy.managers.workflows.RefactorResponse attribute) ACTION_NAME (galaxy.datatypes.display_applications.parameters.DisplayDataValueWrapper attribute) action_name (galaxy.datatypes.display_applications.parameters.DisplayDataValueWrapper property) ACTION_NAME (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper attribute) action_name (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper property) (galaxy.managers.rbac_secured.AccessDatasetRBACPermission attribute) (galaxy.managers.rbac_secured.DatasetRBACPermission attribute) (galaxy.managers.rbac_secured.ManageDatasetRBACPermission attribute) action_type (galaxy.model.PostJobAction attribute) (galaxy.schema.schema.PostJobAction attribute) (galaxy.workflow.refactor.schema.Action attribute) (galaxy.workflow.refactor.schema.AddInputAction attribute) (galaxy.workflow.refactor.schema.AddStepAction attribute) (galaxy.workflow.refactor.schema.ConnectAction attribute) (galaxy.workflow.refactor.schema.DisconnectAction attribute) (galaxy.workflow.refactor.schema.ExtractInputAction attribute) (galaxy.workflow.refactor.schema.ExtractUntypedParameter attribute) (galaxy.workflow.refactor.schema.FileDefaultsAction attribute) (galaxy.workflow.refactor.schema.FillStepDefaultsAction attribute) (galaxy.workflow.refactor.schema.RemoveUnlabeledWorkflowOutputs attribute) (galaxy.workflow.refactor.schema.UpdateAnnotationAction attribute) (galaxy.workflow.refactor.schema.UpdateCreatorAction attribute) (galaxy.workflow.refactor.schema.UpdateLicenseAction attribute) (galaxy.workflow.refactor.schema.UpdateNameAction attribute) (galaxy.workflow.refactor.schema.UpdateOutputLabelAction attribute) (galaxy.workflow.refactor.schema.UpdateReportAction attribute) (galaxy.workflow.refactor.schema.UpdateStepLabelAction attribute) (galaxy.workflow.refactor.schema.UpdateStepPositionAction attribute) (galaxy.workflow.refactor.schema.UpgradeAllStepsAction attribute) (galaxy.workflow.refactor.schema.UpgradeSubworkflowAction attribute) (galaxy.workflow.refactor.schema.UpgradeToolAction attribute) (in module galaxy.tool_util.parser.output_actions) ActionBox (class in galaxy.job_execution.actions.post) ActionInputError actions (galaxy.job_execution.actions.post.ActionBox attribute) (galaxy.model.Dataset attribute) (galaxy.model.Library attribute) (galaxy.model.LibraryDataset attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryFolder attribute) (galaxy.workflow.refactor.schema.RefactorActions attribute) activatable_datasets (galaxy.model.History property) activatable_library_datasets (galaxy.model.LibraryFolder property) activate (galaxy.tool_util.deps.conda_util.CondaContext property) activate() (galaxy.managers.users.UserManager method) (galaxy.webapps.galaxy.controllers.user.User method) activate_repository() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) activation_token (galaxy.model.User attribute) active (galaxy.managers.jobs.JobLock attribute) (galaxy.model.DynamicTool attribute) (galaxy.model.InteractiveToolEntryPoint property) (galaxy.model.User attribute) (galaxy.model.WorkflowInvocation property) (galaxy.schema.schema.HistoryActiveContentCounts attribute) (galaxy.schema.schema.UserModel attribute) active_authenticators() (galaxy.auth.AuthManager method) active_contents (galaxy.model.History property) active_counts() (galaxy.managers.history_contents.HistoryContentsManager method) active_dataset_collections (galaxy.model.History attribute) active_datasets (galaxy.model.History attribute) (galaxy.model.LibraryFolder attribute) active_datasets_and_roles (galaxy.model.History property) active_folders (galaxy.model.LibraryFolder attribute) active_folders() (in module galaxy.tools.actions.upload_common) active_histories (galaxy.model.User attribute) active_history_associations (galaxy.model.Dataset attribute) active_history_jobs() (galaxy_test.base.populators.BaseDatasetPopulator method) active_library_associations (galaxy.model.Dataset attribute) active_repositories (tool_shed.webapp.model.User attribute) active_visible_dataset_collections (galaxy.model.History property) active_visible_datasets_and_roles (galaxy.model.History property) ActiveDirectory (class in galaxy.auth.providers.ldap_ad) ActiveWorkflowSchedulingPlugin (class in galaxy.workflow.schedulers) activity (galaxy.tool_util.toolbox.views.definitions.StaticToolBoxViewTypeEnum attribute) (galaxy.tool_util.toolbox.views.interface.ToolPanelViewModelType attribute) add (galaxy.webapps.galaxy.services.library_folder_contents.UserFolderPermissions attribute) add() (galaxy.managers.citations.CitationCollection method) (galaxy.model.dataset_collections.matching.CollectionsToMatch method) (galaxy.model.store.SessionlessContext method) (galaxy.util.oset.OrderedSet method) add_api_controller() (galaxy.web.framework.base.WebApplication method) add_api_controllers() (galaxy.webapps.base.webapp.WebApplication method) add_boxes() (galaxy.workflow.render.WorkflowCanvas method) add_category_entry() (tool_shed.repository_registry.Registry method) add_change_callback() (galaxy.model.database_heartbeat.DatabaseHeartbeat method) add_changeset() (in module tool_shed.util.hg_util) add_client_route() (galaxy.web.framework.base.WebApplication method) add_column() (in module galaxy.model.migrations.util) add_composite_file() (galaxy.datatypes.data.Data method) add_connection() (galaxy.model.WorkflowStep method) (galaxy.workflow.render.WorkflowCanvas method) add_custom_build() (galaxy_test.selenium.test_custom_builds.TestCustomBuilds method) add_custom_builds() (galaxy.webapps.galaxy.api.users.FastAPIUsers method) add_data_table_watch() (galaxy.datatypes.display_applications.application.DisplayApplication method) add_dataset() (galaxy.model.dataset_collections.builder.CollectionBuilder method) (galaxy.model.History method) (galaxy.model.store.DirectoryModelExportStore method) (galaxy.model.store.ModelExportStore method) add_dataset_collection() (galaxy.job_execution.output_collect.BaseJobContext method) (galaxy.job_execution.output_collect.SessionlessJobContext method) (galaxy.model.History method) (galaxy.model.store.DirectoryModelExportStore method) (galaxy.model.store.ModelExportStore method) add_datasets() (galaxy.model.History method) add_datasets_to_history() (galaxy.job_execution.output_collect.JobContext method) (galaxy.model.store.discover.ModelPersistenceContext method) (galaxy.model.store.discover.SessionlessModelPersistenceContext method) add_db_urls_to_command_arguments() (in module galaxy.model.migrations.scripts) add_deserializers() (galaxy.managers.annotatable.AnnotatableDeserializerMixin method) (galaxy.managers.base.ModelDeserializer method) (galaxy.managers.cloudauthzs.CloudAuthzsDeserializer method) (galaxy.managers.datasets.DatasetAssociationDeserializer method) (galaxy.managers.deletable.DeletableDeserializerMixin method) (galaxy.managers.deletable.PurgableDeserializerMixin method) (galaxy.managers.hdas.HDADeserializer method) (galaxy.managers.histories.HistoryDeserializer method) (galaxy.managers.pages.PageDeserializer method) (galaxy.managers.ratable.RatableDeserializerMixin method) (galaxy.managers.sharable.SharableModelDeserializer method) (galaxy.managers.taggable.TaggableDeserializerMixin method) (galaxy.managers.users.UserDeserializer method) (galaxy.managers.visualizations.VisualizationDeserializer method) add_display_app() (galaxy.datatypes.data.Data method) add_display_application() (galaxy.datatypes.data.Data method) add_dummy_datasets() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) add_edge() (galaxy.util.simplegraph.SimpleGraph method) add_entries() (galaxy.tools.data.ToolDataTable method) add_entry() (galaxy.tools.data.ToolDataTable method) (tool_shed.repository_registry.Registry method) (tool_shed.util.hgweb_config.HgWebConfigManager method) add_entry_to_installed_repository_dependencies_of_installed_repositories() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) add_entry_to_repository_dependencies_of_installed_repositories() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) add_error() (galaxy.tools.evaluation.ToolErrorLog method) add_exception_handler() (in module galaxy.webapps.base.api) add_file_to_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) add_folder() (galaxy.model.LibraryFolder method) add_galaxy_middleware() (in module galaxy.webapps.galaxy.fast_app) add_galaxy_session() (galaxy.model.History method) add_handler() (galaxy.web_stack.handlers.ConfiguresHandlers method) add_history() (galaxy.model.GalaxySession method) add_ids (galaxy.schema.schema.LibraryPermissionsPayloadBase attribute) add_implicit_conversion_dataset() (galaxy.model.store.DirectoryModelExportStore method) add_implicit_input_collection() (galaxy.model.HistoryDatasetCollectionAssociation method) add_implicit_output_dataset_collection() (galaxy.model.Job method) add_input() (galaxy.model.WorkflowInvocation method) add_input_dataset() (galaxy.model.Job method) add_input_dataset_collection() (galaxy.model.Job method) add_input_dataset_collection_element() (galaxy.model.Job method) add_input_library_dataset() (galaxy.model.Job method) add_item_annotation() (galaxy.model.item_attrs.UsesAnnotations method) add_job_output_dataset_associations() (galaxy.model.store.DirectoryModelExportStore method) add_library_dataset() (galaxy.model.LibraryFolder method) add_library_dataset_to_folder() (galaxy.job_execution.output_collect.JobContext method) (galaxy.model.store.discover.ModelPersistenceContext method) (galaxy.model.store.discover.SessionlessModelPersistenceContext method) add_library_item_role_list (galaxy.schema.schema.LibraryCurrentPermissions attribute) (galaxy.schema.schema.LibraryFolderCurrentPermissions attribute) add_line() (galaxy.datatypes.goldenpath.AGPObject method) add_line_to_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method) add_manager() (galaxy.tools.data_manager.manager.DataManagers method) add_message() (galaxy.model.WorkflowInvocation method) add_metric() (galaxy.model.JobLike method) add_node() (galaxy.util.simplegraph.SimpleGraph method) add_object_to_object_session() (in module galaxy.model.orm.util) add_object_to_session() (in module galaxy.model.orm.util) add_option() (galaxy.util.form_builder.SelectField method) (galaxy.web.form_builder.SelectField method) add_output() (galaxy.model.WorkflowInvocation method) (galaxy.model.WorkflowInvocationStep method) add_output_dataset() (galaxy.model.Job method) add_output_dataset_association() (galaxy.job_execution.output_collect.JobContext method) (galaxy.job_execution.output_collect.SessionlessJobContext method) (galaxy.model.store.discover.ModelPersistenceContext method) (galaxy.model.store.discover.SessionlessModelPersistenceContext method) add_output_dataset_collection() (galaxy.model.Job method) add_output_library_dataset() (galaxy.model.Job method) add_parameter() (galaxy.model.Job method) add_path() (galaxy.util.zipstream.ZipstreamWrapper method) add_pending_items() (galaxy.model.History method) add_post_job_action() (galaxy.model.Job method) add_raw_context_middlewares() (in module galaxy.webapps.base.api) add_referent() (galaxy.tool_util.cwl.cwltool_deps.CommentedMap method) add_repository_registry_entry() (tool_shed.webapp.api.repositories.RepositoriesController method) add_request_id_middleware() (in module galaxy.webapps.base.api) (in module tool_shed.webapp.fast_app) add_route() (galaxy.web.framework.base.WebApplication method) add_sample_file_to_defaults (galaxy.config.BaseAppConfiguration attribute) (galaxy.config.GalaxyAppConfiguration attribute) (tool_shed.webapp.config.ToolShedAppConfiguration attribute) add_selenium_arguments() (in module galaxy.selenium.cli) add_sentry_middleware() (in module galaxy.webapps.base.api) add_serializers() (galaxy.managers.annotatable.AnnotatableSerializerMixin method) (galaxy.managers.base.ModelSerializer method) (galaxy.managers.cloudauthzs.CloudAuthzsSerializer method) (galaxy.managers.configuration.AdminConfigSerializer method) (galaxy.managers.configuration.ConfigSerializer method) (galaxy.managers.datasets.DatasetAssociationSerializer method) (galaxy.managers.datasets.DatasetSerializer method) (galaxy.managers.deletable.DeletableSerializerMixin method) (galaxy.managers.deletable.PurgableSerializerMixin method) (galaxy.managers.hdas.HDASerializer method) (galaxy.managers.hdcas.DCASerializer method) (galaxy.managers.hdcas.DCESerializer method) (galaxy.managers.hdcas.DCSerializer method) (galaxy.managers.hdcas.HDCASerializer method) (galaxy.managers.histories.HistorySerializer method) (galaxy.managers.history_contents.HistoryContentsSerializer method) (galaxy.managers.pages.PageSerializer method) (galaxy.managers.ratable.RatableSerializerMixin method) (galaxy.managers.sharable.SharableModelSerializer method) (galaxy.managers.taggable.TaggableSerializerMixin method) (galaxy.managers.users.UserSerializer method) (galaxy.managers.visualizations.VisualizationSerializer method) (galaxy.managers.workflows.WorkflowSerializer method) add_species() (galaxy.datatypes.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.RegionAlignment method) add_steps() (galaxy.workflow.render.WorkflowCanvas method) add_tag() (galaxy_test.selenium.test_histories_list.TestSavedHistories method) add_tag_async() (galaxy.webapps.galaxy.controllers.tag.TagsController method) add_tags (galaxy.schema.schema.HistoryContentItemOperation attribute) add_tags_from_list() (galaxy.model.tags.TagHandler method) add_tags_to_datasets() (galaxy.model.store.discover.ModelPersistenceContext method) (galaxy.model.store.discover.SessionlessModelPersistenceContext method) add_tar_to_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) add_text() (galaxy.workflow.render.WorkflowCanvas method) add_to_shed_tool_config() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) add_to_tool_panel() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) add_tool_to_cache() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) add_tool_to_tool_panel_view() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) (galaxy.tool_util.toolbox.base.ToolBoxRegistryImpl method) (galaxy.tool_util.toolbox.views.interface.ToolBoxRegistry method) add_ui_controller() (galaxy.web.framework.base.WebApplication method) add_ui_controllers() (galaxy.webapps.base.webapp.WebApplication method) (in module galaxy.webapps.reports.buildapp) (in module tool_shed.webapp.buildapp) add_validation_error() (galaxy.model.DatasetInstance method) add_view() (galaxy.managers.base.ModelSerializer method) add_yaml_merge() (galaxy.tool_util.cwl.cwltool_deps.CommentedMap method) addAttributesToRoot() (galaxy.visualization.data_providers.phyloviz.baseparser.PhyloTree method) addChildNode() (galaxy.visualization.data_providers.phyloviz.baseparser.Node method) addChildrenToJson() (galaxy.visualization.data_providers.phyloviz.baseparser.Node method) AddColumn (class in galaxy.model.migrations.util) AddColumnBasenameRuleDefinition (class in galaxy.util.rules_dsl) AddColumnConcatenateRuleDefinition (class in galaxy.util.rules_dsl) AddColumnGroupTagValueRuleDefinition (class in galaxy.util.rules_dsl) AddColumnMetadataRuleDefinition (class in galaxy.util.rules_dsl) AddColumnRegexRuleDefinition (class in galaxy.util.rules_dsl) AddColumnRownumRuleDefinition (class in galaxy.util.rules_dsl) AddColumnSubstrRuleDefinition (class in galaxy.util.rules_dsl) AddColumnValueRuleDefinition (class in galaxy.util.rules_dsl) AddFilterCompareRuleDefinition (class in galaxy.util.rules_dsl) AddFilterCountRuleDefinition (class in galaxy.util.rules_dsl) AddFilterEmptyRuleDefinition (class in galaxy.util.rules_dsl) AddFilterMatchesRuleDefinition (class in galaxy.util.rules_dsl) AddFilterRegexRuleDefinition (class in galaxy.util.rules_dsl) AddInputAction (class in galaxy.workflow.refactor.schema) AdditionalValueFilter (class in galaxy.tools.parameters.dynamic_options) addMiscToJson() (galaxy.visualization.data_providers.phyloviz.baseparser.Node method) address (galaxy.model.UserAddress attribute) (galaxy.schema.schema.Creator attribute) addresses (galaxy.model.User attribute) AddressField (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) addRoot() (galaxy.visualization.data_providers.phyloviz.baseparser.PhyloTree method) AddStepAction (class in galaxy.workflow.refactor.schema) adjust_total_disk_usage() (galaxy.model.User method) Admin (class in tool_shed.util.admin_util) ADMIN (galaxy.model.Role.types attribute) admin_job_lock() (in module galaxy.queue_worker) admin_only (galaxy.webapps.galaxy.api.IndexQueryTag attribute) admin_open() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) admin_role (tool_shed.webapp.model.Repository property) admin_user_dependency (galaxy.webapps.galaxy.api.FrameworkRouter attribute) (galaxy.webapps.galaxy.api.Router attribute) admin_users (galaxy.config.CommonConfigurationMixin property) (galaxy.tools.remote_tool_eval.ToolAppConfig attribute) AdminConfigSerializer (class in galaxy.managers.configuration) AdminController (class in tool_shed.webapp.controllers.admin) AdminGalaxy (class in galaxy.webapps.galaxy.controllers.admin) AdminRepositoryGrid (class in tool_shed.grids.admin_grids) AdminRepositoryGrid.DeletedColumn (class in tool_shed.grids.admin_grids) AdminRequiredException admins() (galaxy.managers.users.UserManager method) AdminToolshed (class in galaxy.webapps.galaxy.controllers.admin_toolshed) AdminUserFilterParser (class in galaxy.managers.users) Affybatch (class in galaxy.datatypes.genetics) after_setting_metadata() (galaxy.datatypes.data.Data method) aggressive_error_checks() (in module galaxy.tool_util.parser.stdio) agp_version (galaxy.datatypes.goldenpath.AGPFile property) AGPError AGPFile (class in galaxy.datatypes.goldenpath) AGPGapLine (class in galaxy.datatypes.goldenpath) AGPLine (class in galaxy.datatypes.goldenpath) AGPObject (class in galaxy.datatypes.goldenpath) AGPSeqLine (class in galaxy.datatypes.goldenpath) alembic_manager (galaxy.model.migrations.DatabaseStateVerifier property) AlembicManager (class in galaxy.model.migrations) alias (galaxy.webapps.galaxy.api.IndexQueryTag attribute) AliasPickleModule (class in galaxy.util.aliaspickler) AliasUnpickler (class in galaxy.util.aliaspickler) AlignCheck (class in galaxy.datatypes.mothur) Alignment (class in galaxy.datatypes.sequence) AlignReport (class in galaxy.datatypes.mothur) ALL (galaxy.tool_util.lint.LintLevel attribute) all() (galaxy.selenium.smart_components.SmartTarget method) all_control_queues_for_declare() (in module galaxy.queues) all_datasets (galaxy.schema.schema.CreateHistoryPayload attribute) all_entry_points_configured (galaxy.model.Job property) all_jobs (galaxy.model.JobStateSummary attribute) (galaxy.schema.schema.HDCJobStateSummary attribute) all_metadata_files (galaxy.tools.wrappers.DatasetCollectionWrapper property) (galaxy.tools.wrappers.DatasetFilenameWrapper property) all_notifications (galaxy.model.User attribute) all_paths (galaxy.tools.wrappers.DatasetCollectionWrapper property) all_requirements (galaxy.tools.ToolBox property) all_requirements() (galaxy.webapps.galaxy.api.tools.ToolsController method) all_roles() (galaxy.model.User method) (galaxy.schema.BootstrapAdminUser method) (tool_shed.webapp.model.User method) all_roles_exploiting_cache() (galaxy.model.User method) all_webhooks() (galaxy.webapps.galaxy.api.webhooks.WebhooksController method) AllegroLOD (class in galaxy.datatypes.genetics) ALLOW (galaxy.model.store.ImportDiscardedDataType attribute) allow_action() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.model.security.HostAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) allow_action_on_libitems() (galaxy.model.security.GalaxyRBACAgent method) allow_cors (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink property) allow_dataset_object_edit (galaxy.model.store.ImportOptions attribute) allow_datatype_change (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.hdf5.HDF5SummarizedExperiment attribute) (galaxy.datatypes.interval.BedStrict attribute) allow_edit (galaxy.model.store.ImportOptions attribute) allow_errored_inputs (galaxy.tools.DatabaseOperationTool property) allow_fetching_all_results (galaxy.web.legacy_framework.grids.Grid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) allow_library_creation (galaxy.model.store.ImportOptions attribute) allow_missing_tools (galaxy.managers.workflows.WorkflowUpdateOptions attribute) allow_path_paste (galaxy_test.api.test_workflows_cwl.BaseCwlWorkflowsApiTestCase attribute) allow_push() (tool_shed.webapp.model.Repository method) allow_user_access() (galaxy.tools.DataManagerTool method) (galaxy.tools.Tool method) allowed() (galaxy.web.legacy_framework.grids.GridOperation method) allowed_comp_types (galaxy.datatypes.goldenpath.AGPGapLine attribute) (galaxy.datatypes.goldenpath.AGPLine attribute) (galaxy.datatypes.goldenpath.AGPSeqLine attribute) ALLOWED_DATA_SOURCE_ATTRIBUTES (galaxy.visualization.plugins.config_parser.DataSourceParser attribute) ALLOWED_ENTRY_POINT_TYPES (galaxy.visualization.plugins.config_parser.VisualizationsConfigParser attribute) allowed_evidence_types (galaxy.datatypes.goldenpath.AGPGapLine attribute) allowed_gap_types (galaxy.datatypes.goldenpath.AGPGapLine attribute) allowed_linkage_types (galaxy.datatypes.goldenpath.AGPGapLine attribute) allowed_middleware() (galaxy.web_stack.ApplicationStack method) ALLOWED_MODEL_CLASSES (galaxy.visualization.plugins.config_parser.DataSourceParser attribute) allowed_orientations (galaxy.datatypes.goldenpath.AGPSeqLine attribute) allowed_origin_hostnames (galaxy.config.GalaxyAppConfiguration attribute) allowed_to_disconnect() (in module galaxy.authnz.psa_authnz) already_executed() (galaxy.tool_util.verify.script.Results method) already_successful() (galaxy.tool_util.verify.script.Results method) alter_column() (in module galaxy.model.migrations.util) AlterColumn (class in galaxy.model.migrations.util) alternate_name (galaxy.schema.schema.Creator attribute) AlwaysReject (class in galaxy.auth.providers.alwaysreject) Amos (class in galaxy.datatypes.assembly) amount (galaxy.model.Quota property) amqp_internal_connection_obj (galaxy.structured_app.StructuredApp attribute) amqp_type (galaxy.app_unittest_utils.galaxy_mock.MockApp attribute) Analyze75 (class in galaxy.datatypes.images) Anndata (class in galaxy.datatypes.binary) AnnotatableDeserializerMixin (class in galaxy.managers.annotatable) AnnotatableFilterMixin (class in galaxy.managers.annotatable) AnnotatableManagerMixin (class in galaxy.managers.annotatable) AnnotatableSerializerMixin (class in galaxy.managers.annotatable)

annotate() (galaxy.managers.annotatable.AnnotatableManagerMixin method) annotate_async() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) annotation (galaxy.model.HistoryAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation attribute) (galaxy.model.LibraryDatasetCollectionAnnotationAssociation attribute) (galaxy.model.PageAnnotationAssociation attribute) (galaxy.model.StoredWorkflowAnnotationAssociation attribute) (galaxy.model.Visualization property) (galaxy.model.VisualizationAnnotationAssociation attribute) (galaxy.model.WorkflowStepAnnotationAssociation attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.ArchivedHistorySummary attribute) (galaxy.schema.schema.CreatePagePayload attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) (galaxy.schema.schema.HistorySummary attribute) (galaxy.schema.schema.UpdateHistoryContentsPayload attribute) (galaxy.schema.schema.WorkflowStepBase attribute) (galaxy.schema.schema.WorkflowStepToExportBase attribute) (galaxy.schema.schema.WorkflowToExport attribute) (galaxy.workflow.refactor.schema.UpdateAnnotationAction attribute) annotation() (galaxy.managers.annotatable.AnnotatableManagerMixin method) (galaxy.managers.hdas.HDAManager method) annotation_assoc (galaxy.managers.annotatable.AnnotatableManagerMixin attribute) (galaxy.managers.hdas.HDAManager attribute) (galaxy.managers.hdcas.HDCAManager attribute) (galaxy.managers.histories.HistoryManager attribute) (galaxy.managers.pages.PageManager attribute) (galaxy.managers.visualizations.VisualizationManager attribute) (galaxy.managers.workflows.WorkflowsManager attribute) annotations (galaxy.model.History attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetCollectionAssociation attribute) (galaxy.model.Page attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.Visualization attribute) (galaxy.model.WorkflowStep attribute) (galaxy.schema.schema.StoredWorkflowSummary attribute) AnonUserModel (class in galaxy.schema.schema) anonymous (galaxy.managers.context.ProvidesUserContext property) anonymous_galaxy_interactor (galaxy_test.base.api.HasAnonymousGalaxyInteractor property) (galaxy_test.base.api.UsesApiTestCaseMixin property) AnonymousGalaxyInteractor (class in galaxy_test.base.api) AnVILFilesSource (class in galaxy.files.sources.anvil) AnvioComposite (class in galaxy.datatypes.anvio) AnvioContigsDB (class in galaxy.datatypes.anvio) AnvioDB (class in galaxy.datatypes.anvio) AnvioGenomesDB (class in galaxy.datatypes.anvio) AnvioPanDB (class in galaxy.datatypes.anvio) AnvioProfileDB (class in galaxy.datatypes.anvio) AnvioSamplesDB (class in galaxy.datatypes.anvio) AnvioStructureDB (class in galaxy.datatypes.anvio) any_output_dataset_collection_instances_deleted (galaxy.model.Job attribute) any_output_dataset_deleted (galaxy.model.Job attribute) apache_xsendfile (galaxy.webapps.base.api.GalaxyFileResponse attribute) api_delete() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) api_get() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) api_key (galaxy.tool_util.verify.interactor.GalaxyInteractorApi attribute) (galaxy.webapps.galaxy.services.authenticate.APIKeyResponse attribute) (galaxy_test.base.api.AnonymousGalaxyInteractor attribute) (galaxy_test.base.api.ApiTestInteractor attribute) (galaxy_test.base.interactor.TestCaseGalaxyInteractor attribute) api_key_header() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) api_keys (galaxy.model.User attribute) (tool_shed.webapp.model.User attribute) api_keys() (tool_shed.webapp.controllers.user.User method) api_keys_manager (galaxy.structured_app.StructuredApp attribute) api_name (galaxy_test.api.sharable.SharingApiTests attribute) (galaxy_test.api.test_histories.TestSharingHistory attribute) (galaxy_test.api.test_pages.TestPagesApi attribute) (galaxy_test.api.test_visualizations.TestVisualizationsApi attribute) (galaxy_test.api.test_workflows.TestWorkflowSharingApi attribute) api_payload_to_create_params() (in module galaxy.managers.collections_util) api_post() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) api_type (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) ApiBiotoolsMetadataSource (class in galaxy.tool_util.biotools.source) APIContentTypeRoute (class in galaxy.webapps.galaxy.api) ApiKeyManager (class in galaxy.managers.api_keys) APIKeyModel (class in galaxy.schema) APIKeyResponse (class in galaxy.webapps.galaxy.services.authenticate) APIKeys (class in galaxy.model) (class in tool_shed.webapp.model) (galaxy.model.base.SharedModelMapping attribute) ApiTestInteractor (class in galaxy_test.base.api) App (class in galaxy.config.config_manage) app (galaxy.managers.base.HasAModelManager attribute) (galaxy.managers.base.ModelDeserializer attribute) (galaxy.managers.base.ModelManager attribute) (galaxy.managers.cloudauthzs.CloudAuthzsDeserializer attribute) (galaxy.managers.cloudauthzs.CloudAuthzsSerializer attribute) (galaxy.managers.configuration.AdminConfigSerializer attribute) (galaxy.managers.configuration.ConfigSerializer attribute) (galaxy.managers.context.ProvidesAppContext property) (galaxy.managers.datasets.DatasetAssociationDeserializer attribute) (galaxy.managers.datasets.DatasetAssociationFilterParser attribute) (galaxy.managers.datasets.DatasetAssociationManager attribute) (galaxy.managers.datasets.DatasetAssociationSerializer attribute) (galaxy.managers.datasets.DatasetManager attribute) (galaxy.managers.datasets.DatasetSerializer attribute) (galaxy.managers.hdas.HDADeserializer attribute) (galaxy.managers.hdas.HDAFilterParser attribute) (galaxy.managers.hdas.HDAManager attribute) (galaxy.managers.hdas.HDASerializer attribute) (galaxy.managers.hdcas.DCASerializer attribute) (galaxy.managers.hdcas.DCESerializer attribute) (galaxy.managers.hdcas.DCSerializer attribute) (galaxy.managers.hdcas.HDCAManager attribute) (galaxy.managers.hdcas.HDCASerializer attribute) (galaxy.managers.histories.HistoryDeserializer attribute) (galaxy.managers.histories.HistoryFilters attribute) (galaxy.managers.history_contents.HistoryContentsFilters attribute) (galaxy.managers.history_contents.HistoryContentsSerializer attribute) (galaxy.managers.lddas.LDDAManager attribute) (galaxy.managers.library_datasets.LibraryDatasetsManager attribute) (galaxy.managers.model_stores.ModelStoreUserContext property) (galaxy.managers.pages.PageDeserializer attribute) (galaxy.managers.roles.RoleManager attribute) (galaxy.managers.sharable.SharableModelDeserializer attribute) (galaxy.managers.sharable.SharableModelFilters attribute) (galaxy.managers.tools.DynamicToolManager attribute) (galaxy.managers.users.AdminUserFilterParser attribute) (galaxy.managers.users.CurrentUserSerializer attribute) (galaxy.managers.users.UserDeserializer attribute) (galaxy.managers.users.UserManager attribute) (galaxy.managers.users.UserSerializer attribute) (galaxy.managers.visualizations.VisualizationDeserializer attribute) (galaxy.managers.visualizations.VisualizationManager attribute) (galaxy.managers.visualizations.VisualizationSerializer attribute) (galaxy.managers.workflows.WorkflowSerializer attribute) (galaxy.managers.workflows.WorkflowsManager attribute) (galaxy.model.store.BagArchiveImportModelStore attribute) (galaxy.model.store.BagDirectoryModelExportStore attribute) (galaxy.model.store.BaseDirectoryImportModelStore attribute) (galaxy.model.store.BcoModelExportStore attribute) (galaxy.model.store.DictImportModelStore attribute) (galaxy.model.store.DirectoryImportModelStore1901 attribute) (galaxy.model.store.DirectoryImportModelStoreLatest attribute) (galaxy.model.store.DirectoryModelExportStore attribute) (galaxy.model.store.ModelImportStore attribute) (galaxy.model.store.ROCrateModelExportStore attribute) (galaxy.model.store.WorkflowInvocationOnlyExportStore attribute) (galaxy.tool_shed.galaxy_install.install_manager.InstallRepositoryManager attribute) (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager attribute) (galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager attribute) (galaxy.tool_shed.galaxy_install.tools.data_manager.DataManagerHandler attribute) (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager attribute) (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator attribute) (galaxy.tool_shed.metadata.metadata_generator.GalaxyMetadataGenerator attribute) (galaxy.tool_shed.tools.data_table_manager.ShedToolDataTableManager attribute) (galaxy.tools.evaluation.PartialToolEvaluator attribute) (galaxy.tools.evaluation.RemoteToolEvaluator attribute) (galaxy.tools.evaluation.ToolEvaluator attribute) (galaxy.webapps.base.webapp.GalaxyWebTransaction property) (galaxy.work.context.WorkRequestContext property) (tool_shed.dependencies.attribute_handlers.RepositoryDependencyAttributeHandler attribute) (tool_shed.dependencies.attribute_handlers.ToolDependencyAttributeHandler attribute) (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager attribute) (tool_shed.metadata.repository_metadata_manager.ToolShedMetadataGenerator attribute) (tool_shed.tools.data_table_manager.ShedToolDataTableManager attribute) (tool_shed.webapp.api.authenticate.ToolShedAuthenticationController attribute) (tool_shed.webapp.api.BaseShedAPIController attribute) (tool_shed.webapp.api.configuration.ConfigurationController attribute) (tool_shed.webapp.api.groups.GroupsController attribute) (tool_shed.webapp.api.repositories.RepositoriesController attribute) (tool_shed.webapp.api.repository_revisions.RepositoryRevisionsController attribute) (tool_shed.webapp.api.tools.ToolsController attribute) (tool_shed.webapp.api.users.UsersController attribute) app_factory() (in module galaxy.webapps.galaxy.buildapp) (in module galaxy.webapps.reports.buildapp) (in module tool_shed.webapp.buildapp) app_info (galaxy.tool_util.deps.container_classes.ContainerProtocol property) app_kwds() (galaxy.main.GalaxyConfigBuilder method) app_loop() (in module galaxy.main) app_name (galaxy.config.config_manage.App property) (galaxy.main_config.WebappSetupProps attribute) app_pair() (in module galaxy.webapps.galaxy.buildapp) (in module tool_shed.webapp.buildapp) app_properties_from_args() (in module galaxy.util.script) app_vault (galaxy.files.DictFileSourcesUserContext property) (galaxy.files.ProvidesUserFileSourcesUserContext property) append() (galaxy.datatypes.metadata.MetadataSpecCollection method) (galaxy.model.custom_types.MutationList method) (galaxy.model.metadata.MetadataSpecCollection method) (galaxy.tool_util.deps.requirements.ToolRequirements method) append_section() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) append_tool() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) append_user_filter() (in module galaxy.model.index_filter_util) AppInfo (class in galaxy.tool_util.deps.dependencies) application (galaxy.web.framework.middleware.sqldebug.SQLDebugMiddleware attribute) application_stack (galaxy.app.SentryClientMixin attribute) (galaxy.structured_app.BasicSharedApp attribute) (galaxy.webapps.reports.app.UniverseApplication attribute) application_stack_class() (in module galaxy.web_stack) application_stack_instance() (in module galaxy.web_stack) application_stack_log_filter() (in module galaxy.web_stack) application_stack_log_formatter() (in module galaxy.web_stack) ApplicationStack (class in galaxy.web_stack) ApplicationStackLogFilter (class in galaxy.web_stack) ApplicationStackMessage (class in galaxy.web_stack.message) ApplicationStackMessageDispatcher (class in galaxy.web_stack.message) ApplicationStackTransport (class in galaxy.web_stack.transport) apply() (galaxy.tool_util.deps.resolvers.RequirementMapping method) (galaxy.util.rules_dsl.AddColumnBasenameRuleDefinition method) (galaxy.util.rules_dsl.AddColumnConcatenateRuleDefinition method) (galaxy.util.rules_dsl.AddColumnGroupTagValueRuleDefinition method) (galaxy.util.rules_dsl.AddColumnMetadataRuleDefinition method) (galaxy.util.rules_dsl.AddColumnRegexRuleDefinition method) (galaxy.util.rules_dsl.AddColumnRownumRuleDefinition method) (galaxy.util.rules_dsl.AddColumnSubstrRuleDefinition method) (galaxy.util.rules_dsl.AddColumnValueRuleDefinition method) (galaxy.util.rules_dsl.AddFilterCompareRuleDefinition method) (galaxy.util.rules_dsl.AddFilterCountRuleDefinition method) (galaxy.util.rules_dsl.AddFilterEmptyRuleDefinition method) (galaxy.util.rules_dsl.AddFilterMatchesRuleDefinition method) (galaxy.util.rules_dsl.AddFilterRegexRuleDefinition method) (galaxy.util.rules_dsl.BaseRuleDefinition method) (galaxy.util.rules_dsl.RemoveColumnsRuleDefinition method) (galaxy.util.rules_dsl.RuleSet method) (galaxy.util.rules_dsl.SortRuleDefinition method) (galaxy.util.rules_dsl.SplitColumnsRuleDefinition method) (galaxy.util.rules_dsl.SwapColumnsRuleDefinition method) apply_action() (galaxy.tool_util.parser.output_actions.FormatToolOutputAction method) (galaxy.tool_util.parser.output_actions.MetadataToolOutputAction method) (galaxy.tool_util.parser.output_actions.ToolOutputAction method) (galaxy.tool_util.parser.output_actions.ToolOutputActionConditional method) (galaxy.tool_util.parser.output_actions.ToolOutputActionConditionalWhen method) (galaxy.tool_util.parser.output_actions.ToolOutputActionGroup method) apply_filter() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) apply_item_tag() (galaxy.model.tags.TagHandler method) apply_item_tags() (galaxy.model.tags.TagHandler method) apply_query_filter() (galaxy.web.legacy_framework.grids.Grid method) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid method) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid method) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid method) (galaxy.webapps.galaxy.controllers.forms.FormsGrid method) (tool_shed.grids.admin_grids.RoleGrid method) apply_regex() (in module galaxy.util.rules_dsl) apply_rules() (galaxy.managers.collections.DatasetCollectionManager method) apply_view() (galaxy.tool_util.toolbox.views.edam.EdamToolPanelView method) (galaxy.tool_util.toolbox.views.interface.ToolPanelView method) (galaxy.tool_util.toolbox.views.static.StaticToolPanelView method) ApplyRulesTool (class in galaxy.tools) AppSchema (class in galaxy.config.schema) archive (galaxy.schema.fetch_data.ElementsFromType attribute) (galaxy.util.compression_utils.CompressedFile attribute) archive_dir (galaxy.model.JobImportHistoryArchive attribute) (galaxy.model.store.BagArchiveImportModelStore attribute) (galaxy.model.store.BaseDirectoryImportModelStore attribute) (galaxy.model.store.DictImportModelStore attribute) (galaxy.model.store.DirectoryImportModelStore1901 attribute) (galaxy.model.store.DirectoryImportModelStoreLatest attribute) (galaxy.model.store.ModelImportStore attribute) archive_export() (galaxy.webapps.galaxy.services.histories.HistoriesService method) archive_export_id (galaxy.model.History attribute) (galaxy.schema.schema.ArchiveHistoryRequestPayload attribute) archive_file (galaxy.schema.schema.CreateHistoryPayload attribute) archive_history() (galaxy.managers.histories.HistoryManager method) (galaxy.webapps.galaxy.services.histories.HistoriesService method) (galaxy_test.base.populators.BaseDatasetPopulator method) archive_repository_revision() (in module tool_shed.util.hg_util) archive_source (galaxy.managers.workflows.WorkflowCreateOptions attribute) (galaxy.schema.schema.CreateHistoryPayload attribute) archive_type (galaxy.schema.schema.CreateHistoryPayload attribute) archived (galaxy.model.History attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.ArchivedHistorySummary attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.HistorySummary attribute) ArchivedHistoryDetailed (class in galaxy.schema.schema) ArchivedHistorySummary (class in galaxy.schema.schema) ArchiveHistoryRequestPayload (class in galaxy.schema.schema) Arff (class in galaxy.datatypes.text) arg_parser() (in module galaxy.tool_util.verify.script) args (galaxy.managers.metrics.Metric attribute) argv_to_str() (in module galaxy.util.commands) artifact_class() (in module galaxy.managers.executables) as_dict() (galaxy.model.tool_shed_install.ToolShedRepository method) (galaxy.util.simplegraph.SimpleGraph method) as_display_type() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) as_file() (in module galaxy.util.resources) as_form() (in module galaxy.webapps.galaxy.api) as_gbrowse_display_file() (galaxy.datatypes.tabular.Tabular method) as_markdown() (galaxy.webapps.galaxy.api.IndexQueryTag method) as_ucsc_display_file() (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.interval.Bed method) (galaxy.datatypes.interval.BedGraph method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.tabular.Tabular method) asbool() (in module galaxy.util) ase_format (galaxy.datatypes.molecules.AtomicStructFile attribute) (galaxy.datatypes.molecules.Cell attribute) (galaxy.datatypes.molecules.CIF attribute) (galaxy.datatypes.molecules.Magres attribute) (galaxy.datatypes.molecules.XYZ attribute) assemble_current_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method) assert_absent() (galaxy.selenium.has_driver.HasDriver method) (galaxy.selenium.smart_components.SmartTarget method) assert_absent_or_hidden() (galaxy.selenium.has_driver.HasDriver method) (galaxy.selenium.smart_components.SmartTarget method) assert_absent_or_hidden_after_transitions() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) (galaxy.selenium.smart_components.SmartTarget method) assert_attribute_is() (in module galaxy.tool_util.verify.asserts.xml) assert_attribute_matches() (in module galaxy.tool_util.verify.asserts.xml) assert_connected() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) assert_connection_invalid() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) assert_custom_builds_in_grid() (galaxy_test.selenium.test_custom_builds.TestCustomBuilds method) assert_data_value() (galaxy.selenium.smart_components.SmartTarget method) assert_disabled() (galaxy.selenium.has_driver.HasDriver method) (galaxy.selenium.smart_components.SmartTarget method) assert_download_request_ok() (galaxy_test.base.populators.BaseDatasetPopulator method) assert_element_text() (in module galaxy.tool_util.verify.asserts.xml) assert_element_text_is() (in module galaxy.tool_util.verify.asserts.xml) assert_element_text_matches() (in module galaxy.tool_util.verify.asserts.xml) assert_error_code_is() (in module galaxy_test.base.api_asserts) assert_error_message() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) assert_error_message_contains() (in module galaxy_test.base.api_asserts) assert_grid_histories_are() (galaxy_test.selenium.test_histories_list.TestSavedHistories method) assert_has_archive_member() (in module galaxy.tool_util.verify.asserts.archive) assert_has_element_with_path() (in module galaxy.tool_util.verify.asserts.xml) assert_has_h5_attribute() (in module galaxy.tool_util.verify.asserts.hdf5) assert_has_h5_keys() (in module galaxy.tool_util.verify.asserts.hdf5) assert_has_key() (in module galaxy_test.base.api_asserts) assert_has_keys() (in module galaxy_test.base.api_asserts) assert_has_line() (in module galaxy.tool_util.verify.asserts.text) assert_has_line_matching() (in module galaxy.tool_util.verify.asserts.text) assert_has_n_columns() (in module galaxy.tool_util.verify.asserts.tabular) assert_has_n_elements_with_path() (in module galaxy.tool_util.verify.asserts.xml) assert_has_n_lines() (in module galaxy.tool_util.verify.asserts.text) assert_has_size() (in module galaxy.tool_util.verify.asserts.size) assert_has_text() (in module galaxy.tool_util.verify.asserts.text) assert_has_text_matching() (in module galaxy.tool_util.verify.asserts.text) assert_hash_value() (galaxy_test.api.test_datasets.TestDatasetsApi method) assert_hashes_initialized() (galaxy.tools.cache.ToolCache method) assert_histories_in_grid() (galaxy_test.selenium.test_histories_list.TestSavedHistories method) assert_histories_present() (galaxy_test.selenium.test_histories_list.TestSavedHistories method) assert_input_mapped() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) assert_input_not_mapped() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) assert_is_valid_xml() (in module galaxy.tool_util.verify.asserts.xml) assert_message() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) assert_modal_has_text() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) assert_name_changed() (galaxy_test.selenium.test_history_panel.TestHistoryPanel method) assert_no_axe_violations_with_impact_of_at_least() (galaxy.selenium.smart_components.SmartTarget method) assert_no_error_message() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) assert_node_output_is() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) assert_not_connected() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) assert_not_has_keys() (in module galaxy_test.base.api_asserts) assert_not_has_text() (in module galaxy.tool_util.verify.asserts.text) assert_object_id_error() (in module galaxy_test.base.api_asserts) assert_selector() (galaxy.selenium.has_driver.HasDriver method) assert_selector_absent() (galaxy.selenium.has_driver.HasDriver method) assert_selector_absent_or_hidden() (galaxy.selenium.has_driver.HasDriver method) assert_selector_absent_or_hidden_after_transitions() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) assert_status_code_is() (in module galaxy_test.base.api_asserts) assert_status_code_is_ok() (in module galaxy_test.base.api_asserts) assert_success_message() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) assert_throws_param_value_error() (in module galaxy.tools.parameters.basic) assert_tooltip_text() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) assert_tooltip_text_contains() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) assert_warning_message() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) assert_wf_annotation_is() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) assert_wf_name_is() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) assert_xml_element() (in module galaxy.tool_util.verify.asserts.xml) assert_xpath() (galaxy.selenium.has_driver.HasDriver method) AssertionDict (class in galaxy.tool_util.parser.interface) assign_admin_role() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) assign_handler() (galaxy.web_stack.handlers.ConfiguresHandlers method) assoc_type (galaxy.model.PSAAssociation attribute) (galaxy.model.UserAuthnzToken attribute) associate() (galaxy.managers.base.ModelManager method) associate_action_dataset_role() (galaxy.model.security.GalaxyRBACAgent method) associate_components() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) (tool_shed.webapp.security.RBACAgent method) associate_group_role() (galaxy.model.security.GalaxyRBACAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) associate_repository_category() (tool_shed.webapp.security.CommunityRBACAgent method) associate_user_group() (galaxy.model.security.GalaxyRBACAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) associate_user_role() (galaxy.model.security.GalaxyRBACAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) (tool_shed.webapp.security.RBACAgent method) association (galaxy.authnz.psa_authnz.Storage attribute) ASync (class in galaxy.webapps.galaxy.controllers.async) async_request_user (galaxy.managers.context.ProvidesUserContext property) async_task_summary() (in module galaxy.webapps.galaxy.services.base) async_template (galaxy.web.legacy_framework.grids.Grid attribute) AsyncDataSourceTool (class in galaxy.tools) AsyncFile (class in galaxy.schema.schema) AsynchronousJobRunner (class in galaxy.jobs.runners) AsynchronousJobState (class in galaxy.jobs.runners) AsyncTaskResultSummary (class in galaxy.schema.schema) AtomicStructFile (class in galaxy.datatypes.molecules) attach_identifier() (galaxy.model.SerializationOptions method) attach_implicitly_converted_dataset() (galaxy.model.DatasetInstance method) attach_ordered_steps() (in module galaxy.workflow.steps) attach_stored_workflow() (galaxy.managers.workflows.WorkflowsManager method) attach_subworkflow_invocation_for_step() (galaxy.model.WorkflowInvocation method) attempt_create_private_role() (galaxy.model.User method) attempt_unlink() (in module galaxy.tool_util.deps.brew_exts) attempt_unlink_all() (in module galaxy.tool_util.deps.brew_exts) ATTRIBUTE_SPLIT_CHAR (galaxy.visualization.plugins.config_parser.DataSourceParser attribute) attributes (galaxy.tool_util.parser.interface.AssertionDict attribute) AttributeValueSplitterFilter (class in galaxy.tools.parameters.dynamic_options) ATTRS_FILENAME_HISTORY (galaxy.model.JobExportHistoryArchive attribute) Audio (class in galaxy.datatypes.media) augment_tool_state_for_input_connections() (galaxy.workflow.modules.ToolModule method) Augustus (class in galaxy.datatypes.annotation) auth_manager (galaxy.structured_app.BasicSharedApp attribute) (galaxy.webapps.reports.app.UniverseApplication attribute) authenticate() (galaxy.auth.providers.alwaysreject.AlwaysReject method) (galaxy.auth.providers.AuthProvider method) (galaxy.auth.providers.ldap_ad.LDAP method) (galaxy.auth.providers.localdb.LocalDB method) (galaxy.auth.providers.pam_auth.PAM method) (galaxy.authnz.custos_authnz.OIDCAuthnzBase method) (galaxy.authnz.IdentityProvider method) (galaxy.authnz.managers.AuthnzManager method) (galaxy.authnz.psa_authnz.PSAAuthnz method) authenticate_user() (galaxy.auth.providers.alwaysreject.AlwaysReject method) (galaxy.auth.providers.AuthProvider method) (galaxy.auth.providers.ldap_ad.LDAP method) (galaxy.auth.providers.localdb.LocalDB method) (galaxy.auth.providers.pam_auth.PAM method) authentication_service (galaxy.webapps.galaxy.api.authenticate.AuthenticationController attribute) (galaxy.webapps.galaxy.api.authenticate.FastAPIAuthenticate attribute) (tool_shed.webapp.api.authenticate.ToolShedAuthenticationController attribute) AuthenticationController (class in galaxy.webapps.galaxy.api.authenticate) AuthenticationFailed AuthenticationRequired AuthenticationService (class in galaxy.webapps.galaxy.services.authenticate) AuthenticationToken (class in galaxy.web.proxy) Authenticator (class in galaxy.auth.util) AuthManager (class in galaxy.auth) authn (galaxy.model.CloudAuthz attribute) authn_id (galaxy.model.CloudAuthz attribute) AuthnzManager (class in galaxy.authnz.managers) authorization_endpoint (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute) AuthProvider (class in galaxy.auth.providers) auto_decompress (galaxy.schema.fetch_data.BaseDataElement attribute) (galaxy.schema.fetch_data.BaseFetchDataTarget attribute) (galaxy.tools.parameters.grouping.Dataset attribute) auto_propagated_tags (galaxy.model.HasTags property) available (galaxy.schema.schema.LibraryPermissionScope attribute) available_roles() (galaxy.managers.datasets.DatasetRBACPermissions method) average_rating (galaxy.model.History attribute) (galaxy.model.Page attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.Visualization attribute) axe_eval() (galaxy.selenium.has_driver.HasDriver method) (galaxy.selenium.smart_components.SmartTarget method) axe_script_url (galaxy.selenium.has_driver.HasDriver attribute) axe_skip (galaxy.selenium.has_driver.HasDriver attribute) Axes (class in galaxy.datatypes.mothur) Axt (class in galaxy.datatypes.sequence) AzureBlobObjectStore (class in galaxy.objectstore.azure_blob)

B

backend (galaxy.model.PSAPartial attribute) (galaxy.tool_util.biotools.source.InMemoryCache attribute) badges (galaxy.objectstore.ConcreteObjectStore attribute) (galaxy.objectstore.ConcreteObjectStoreModel attribute) (galaxy.objectstore.DiskObjectStore attribute) (galaxy.objectstore.irods.IRODSObjectStore attribute) (galaxy.objectstore.pithos.PithosObjectStore attribute) (galaxy.objectstore.s3.GenericS3ObjectStore attribute) BadValue (class in galaxy.tools) BafTar (class in galaxy.datatypes.binary) BAG_DOT_TAR (galaxy.schema.schema.ModelStoreFormat attribute) BAG_DOT_TGZ (galaxy.schema.schema.ModelStoreFormat attribute) BAG_DOT_ZIP (galaxy.schema.schema.ModelStoreFormat attribute) BagArchiveImportModelStore (class in galaxy.model.store) BagArchiveModelExportStore (class in galaxy.model.store) BagDirectoryModelExportStore (class in galaxy.model.store) bagit (galaxy.schema.fetch_data.ElementsFromType attribute) bagit_archive (galaxy.schema.fetch_data.ElementsFromType attribute) Bam (class in galaxy.datatypes.binary) BamDataProvider (class in galaxy.visualization.data_providers.genome) BamInputSorted (class in galaxy.datatypes.binary) BamNative (class in galaxy.datatypes.binary) BamQuerynameSorted (class in galaxy.datatypes.binary) bare_ampersand (galaxy.managers.pages.PageContentProcessor attribute) Base (class in galaxy.model) (class in galaxy.model.tool_shed_install) (class in tool_shed.webapp.model) base (galaxy.webapps.galaxy.api.GalaxyASGIRequest property) (galaxy.work.context.GalaxyAbstractRequest property) Base64ChunkDataProvider (class in galaxy.datatypes.dataproviders.chunk) base_dataprovider() (galaxy.datatypes.data.Data method) Base_Parser (class in galaxy.visualization.data_providers.phyloviz.baseparser) BASE_URL (galaxy.visualization.plugins.registry.VisualizationsRegistry attribute) BaseAction (class in galaxy.workflow.refactor.schema) BaseAnnotationsController (class in galaxy.webapps.galaxy.api.annotations) BaseAppConfiguration (class in galaxy.config) baseauth_headers() (in module galaxy_test.base.api_util) BaseBcf (class in galaxy.datatypes.binary) BaseCitation (class in galaxy.managers.citations) BaseCollectionTarget (class in galaxy.schema.fetch_data) BaseCSV (class in galaxy.datatypes.tabular) BaseCwlWorkflowsApiTestCase (class in galaxy_test.api.test_workflows_cwl) BaseDataElement (class in galaxy.schema.fetch_data) BaseDataPayload (class in galaxy.schema.fetch_data) BaseDataProvider (class in galaxy.visualization.data_providers.basic) BaseDatasetCollectionPopulator (class in galaxy_test.base.populators) BaseDatasetCollectionType (class in galaxy.model.dataset_collections.types) BaseDatasetPopulator (class in galaxy_test.base.populators) BaseDataTarget (class in galaxy.schema.fetch_data) BaseDataToolParameter (class in galaxy.tools.parameters.basic) BaseDirectoryImportModelStore (class in galaxy.model.store) BaseExtendedMetadataController (class in galaxy.webapps.galaxy.api.extended_metadata) BaseFastq (class in galaxy.datatypes.sequence) BaseFetchDataTarget (class in galaxy.schema.fetch_data) BaseField (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) BaseFilesSource (class in galaxy.files.sources) BaseGalaxyAPIController (class in galaxy.webapps.galaxy.api) BaseGitPlugin (class in galaxy.tools.error_reports.plugins.base_git) BaseHistories (class in galaxy_test.api.test_histories) BaseJobContext (class in galaxy.job_execution.output_collect) BaseJobExec (class in galaxy.jobs.runners.util.cli.job) BaseJobHandlerQueue (class in galaxy.jobs.handler) BaseJobMetric (class in galaxy.model) BaseJobRunner (class in galaxy.jobs.runners) BaseJsonToolParameter (class in galaxy.tools.parameters.basic) BaseMetadataGenerator (class in galaxy.tool_shed.metadata.metadata_generator) basename (galaxy.tool_util.cwl.util.OutputPropertiesType attribute) BaseObjectStore (class in galaxy.objectstore) BasePagesApiTestCase (class in galaxy_test.api.test_pages) BasePopulator (class in galaxy_test.base.populators) BaseProvenanceController (class in galaxy.webapps.galaxy.api.provenance) BaseRuleDefinition (class in galaxy.util.rules_dsl) bases_regexp (galaxy.datatypes.sequence.BaseFastq attribute) (galaxy.datatypes.sequence.FastqCSSanger attribute) (galaxy.datatypes.sequence.FastqSanger attribute) BaseShedAPIController (class in tool_shed.webapp.api) BaseShellExec (class in galaxy.jobs.runners.util.cli.shell) BaseSpaceFilesSource (class in galaxy.files.sources.basespace) basestring() (galaxy.managers.base.ModelValidator static method) basestring_list() (galaxy.managers.base.ModelValidator static method) BaseToolProvidedMetadata (class in galaxy.tool_util.provided_metadata) BaseTree (class in galaxy.model.dataset_collections.structure) BaseUploadToolAction (class in galaxy.tools.actions.upload) BaseURLToolParameter (class in galaxy.tools.parameters.basic) BaseUserModel (class in galaxy.schema.schema) BaseVcf (class in galaxy.datatypes.tabular) BaseWatcher (class in galaxy.util.watcher) BaseWorkflowPopulator (class in galaxy_test.base.populators) BaseWorkflowsApiTestCase (class in galaxy_test.api.test_workflows) basic_markdown (galaxy.schema.tasks.GeneratePdfDownload attribute) BasicRoleModel (class in galaxy.schema.schema) BasicSharedApp (class in galaxy.structured_app) batch_execute() (galaxy.model.migrations.util.AlterColumn method) (galaxy.model.migrations.util.CreateForeignKey method) (galaxy.model.migrations.util.CreateUniqueConstraint method) (galaxy.model.migrations.util.DDLAlterOperation method) (galaxy.model.migrations.util.DropColumn method) (galaxy.model.migrations.util.DropConstraint method) BBIDataProvider (class in galaxy.visualization.data_providers.genome) Bcf (class in galaxy.datatypes.binary) BcfUncompressed (class in galaxy.datatypes.binary) BCO_JSON (galaxy.schema.schema.ModelStoreFormat attribute) bco_merge_history_metadata (galaxy.schema.schema.BcoGenerationParametersMixin attribute) bco_override_algorithmic_error (galaxy.schema.schema.BcoGenerationParametersMixin attribute) bco_override_empirical_error (galaxy.schema.schema.BcoGenerationParametersMixin attribute) bco_override_environment_variables (galaxy.schema.schema.BcoGenerationParametersMixin attribute) bco_override_xref (galaxy.schema.schema.BcoGenerationParametersMixin attribute) BcoExportOptions (class in galaxy.model.store) BcoGenerationParametersMixin (class in galaxy.schema.schema) BcoGenerationTaskParametersMixin (class in galaxy.schema.tasks) BcoModelExportStore (class in galaxy.model.store) BCSLmodel (class in galaxy.datatypes.text) BCSLts (class in galaxy.datatypes.text) Bed (class in galaxy.datatypes.interval) Bed12 (class in galaxy.datatypes.interval) Bed6 (class in galaxy.datatypes.interval) BedDataProvider (class in galaxy.visualization.data_providers.genome) BedGraph (class in galaxy.datatypes.interval) BedStrict (class in galaxy.datatypes.interval) BedTabix (class in galaxy.datatypes.interval) BedTabixDataProvider (class in galaxy.visualization.data_providers.genome) before_setting_metadata() (galaxy.datatypes.data.Data method) before_start() (galaxy.celery.GalaxyTask method) BIBTEX_UNSET (galaxy.managers.citations.DoiCitation attribute) BibtexCitation (class in galaxy.managers.citations) big_peek_size (galaxy.datatypes.tabular.BaseCSV attribute) BigBed (class in galaxy.datatypes.binary) BigBedDataProvider (class in galaxy.visualization.data_providers.genome) BigWig (class in galaxy.datatypes.binary) BigWigDataProvider (class in galaxy.datatypes.dataproviders.dataset) (class in galaxy.visualization.data_providers.genome) Binary (class in galaxy.datatypes.binary) binary (galaxy.datatypes.sniff.FilePrefix property) bind_and_start() (galaxy.queue_worker.GalaxyQueueWorker method) bind_default_handler() (galaxy.web_stack.message.ApplicationStackMessage method) Biom1 (class in galaxy.datatypes.text) Biom2 (class in galaxy.datatypes.binary) biomart() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) biotools_reference (galaxy.tools.Tool property) biotools_reference() (in module galaxy.tool_util.ontologies.ontology_data) BiotoolsEntry (class in galaxy.tool_util.biotools.interface) biotoolsID (galaxy.tool_util.biotools.interface.BiotoolsEntry attribute) (galaxy.tool_util.biotools.interface.ParsedBiotoolsEntry attribute) (galaxy.tool_util.biotools.ParsedBiotoolsEntry attribute) BiotoolsMetadataSource (class in galaxy.tool_util.biotools) (class in galaxy.tool_util.biotools.source) BiotoolsMetadataSourceConfig (class in galaxy.tool_util.biotools) (class in galaxy.tool_util.biotools.source) BlastDomainDb (class in galaxy.datatypes.blast) BlastDomainDb5 (class in galaxy.datatypes.blast) BlastNucDb (class in galaxy.datatypes.blast) BlastNucDb5 (class in galaxy.datatypes.blast) BlastProtDb (class in galaxy.datatypes.blast) BlastProtDb5 (class in galaxy.datatypes.blast) BlastXml (class in galaxy.datatypes.blast) BlibSQlite (class in galaxy.datatypes.binary) BlockDataProvider (class in galaxy.datatypes.dataproviders.line) blurb (galaxy.datatypes.media.Wav attribute) (galaxy.datatypes.proteomics.ConsensusXML attribute) (galaxy.datatypes.proteomics.FeatureXML attribute) (galaxy.datatypes.proteomics.IdXML attribute) (galaxy.datatypes.proteomics.MascotXML attribute) (galaxy.datatypes.proteomics.MzData attribute) (galaxy.datatypes.proteomics.MzIdentML attribute) (galaxy.datatypes.proteomics.MzML attribute) (galaxy.datatypes.proteomics.MzQuantML attribute) (galaxy.datatypes.proteomics.MzXML attribute) (galaxy.datatypes.proteomics.NmrML attribute) (galaxy.datatypes.proteomics.ParamXml attribute) (galaxy.datatypes.proteomics.PepXml attribute) (galaxy.datatypes.proteomics.ProtXML attribute) (galaxy.datatypes.proteomics.QCML attribute) (galaxy.datatypes.proteomics.TandemXML attribute) (galaxy.datatypes.proteomics.TrafoXML attribute) (galaxy.datatypes.proteomics.TraML attribute) (galaxy.datatypes.proteomics.UniProtXML attribute) (galaxy.datatypes.proteomics.XquestSpecXML attribute) (galaxy.datatypes.proteomics.XquestXML attribute) (galaxy.datatypes.speech.TextGrid attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) Bmp (class in galaxy.datatypes.images) bool() (galaxy.managers.base.ModelValidator static method) BoolAnd (class in galaxy.util.bool_expressions) BoolBinaryOperation (class in galaxy.util.bool_expressions) BOOLEAN (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute) BooleanColumn (class in galaxy.web.legacy_framework.grids) BooleanExpressionEvaluator (class in galaxy.util.bool_expressions) BooleanFilter (class in galaxy.tool_util.parser.output_actions) BooleanToolParameter (class in galaxy.tools.parameters.basic) BoolNot (class in galaxy.util.bool_expressions) BoolOperand (class in galaxy.util.bool_expressions) BoolOr (class in galaxy.util.bool_expressions) bootstrap_admin_user (galaxy.model.User attribute) (galaxy.schema.BootstrapAdminUser attribute) (tool_shed.webapp.model.User attribute) BootstrapAdminUser (class in galaxy.schema) bottom (galaxy.schema.schema.WorkflowStepLayoutPosition attribute) BoundCollectionBuilder (class in galaxy.model.dataset_collections.builder) BowtieBaseIndex (class in galaxy.datatypes.ngsindex)

BowtieColorIndex (class in galaxy.datatypes.ngsindex) BowtieIndex (class in galaxy.datatypes.ngsindex) BPF (class in galaxy.datatypes.speech) Bref3 (class in galaxy.datatypes.binary) brew_deps() (in module galaxy.tool_util.deps.brew_exts) brew_execute() (in module galaxy.tool_util.deps.brew_exts) brew_head_at_commit() (in module galaxy.tool_util.deps.brew_exts) brew_head_at_version() (in module galaxy.tool_util.deps.brew_exts) brew_info() (in module galaxy.tool_util.deps.brew_exts) brew_versions_info() (in module galaxy.tool_util.deps.brew_exts) BrewContext (class in galaxy.tool_util.deps.brew_exts) browsable (galaxy.files.sources.FilesSourceProperties attribute) (galaxy.schema.remote_files.BrowsableFilesSourcePlugin attribute) (galaxy.schema.remote_files.FilesSourcePlugin attribute) BrowsableFilesSourcePlugin (class in galaxy.schema.remote_files) browse_categories() (tool_shed.webapp.controllers.repository.RepositoryController method) browse_category() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) browse_datatypes() (tool_shed.webapp.controllers.repository.RepositoryController method) browse_deprecated_repositories_i_own() (tool_shed.webapp.controllers.repository.RepositoryController method) browse_my_writable_repositories() (tool_shed.webapp.controllers.repository.RepositoryController method) browse_my_writable_repositories_missing_tool_test_components() (tool_shed.webapp.controllers.repository.RepositoryController method) browse_my_writable_repositories_with_invalid_tools() (tool_shed.webapp.controllers.repository.RepositoryController method) browse_repositories() (tool_shed.webapp.controllers.admin.AdminController method) (tool_shed.webapp.controllers.repository.RepositoryController method) browse_repositories_by_user() (tool_shed.webapp.controllers.repository.RepositoryController method) browse_repositories_i_can_administer() (tool_shed.webapp.controllers.repository.RepositoryController method) browse_repositories_i_own() (tool_shed.webapp.controllers.repository.RepositoryController method) browse_repositories_in_category() (tool_shed.webapp.controllers.repository.RepositoryController method) browse_repositories_missing_tool_test_components() (tool_shed.webapp.controllers.repository.RepositoryController method) browse_repositories_with_invalid_tools() (tool_shed.webapp.controllers.repository.RepositoryController method) browse_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) (tool_shed.webapp.controllers.repository.RepositoryController method) browse_repository_dependencies() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) (tool_shed.webapp.controllers.repository.RepositoryController method) browse_repository_metadata() (tool_shed.webapp.controllers.admin.AdminController method) browse_tool_dependencies() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) (tool_shed.webapp.controllers.repository.RepositoryController method) browse_tool_shed() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) browse_tools() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) (tool_shed.webapp.controllers.repository.RepositoryController method) browse_valid_categories() (tool_shed.webapp.controllers.repository.RepositoryController method) browse_valid_repositories() (tool_shed.webapp.controllers.repository.RepositoryController method) build() (galaxy.model.dataset_collections.builder.CollectionBuilder method) (galaxy.tools.evaluation.PartialToolEvaluator method) (galaxy.tools.evaluation.RemoteToolEvaluator method) (galaxy.tools.evaluation.ToolEvaluator method) (galaxy.tools.parameters.basic.ToolParameter class method) (galaxy.webapps.galaxy.api.tools.ToolsController method) build_absolute_uri() (galaxy.authnz.psa_authnz.Strategy method) build_apispec() (galaxy.webapps.base.webapp.WebApplication method) build_app() (in module galaxy.celery) build_cache() (galaxy.tool_util.deps.CachedDependencyManager method) build_case_references() (in module galaxy.tool_util.verify.script) build_changeset_revision_select_field() (in module tool_shed.grids.util) build_cli_interface() (in module galaxy.jobs.runners.util.cli.factory) build_collection() (in module galaxy.model.dataset_collections.builder) build_collection_and_assert() (galaxy_test.selenium.test_library_to_collections.TestLibraryToCollections method) build_command() (in module galaxy.jobs.command_factory) (in module galaxy.tool_util.deps.docker_util) build_command_line() (galaxy.jobs.runners.BaseJobRunner method) build_command_list() (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider method) build_dependency_cache() (galaxy.tools.Tool method) (galaxy.webapps.galaxy.api.tools.ToolsController method) build_dependency_manager() (in module galaxy.tool_util.deps) build_dependency_shell_commands() (galaxy.tools.Tool method) build_docker_cache_command() (in module galaxy.tool_util.deps.docker_util) build_docker_images_command() (in module galaxy.tool_util.deps.docker_util) build_docker_load_command() (in module galaxy.tool_util.deps.docker_util) build_docker_run_command() (in module galaxy.tool_util.deps.docker_util) build_docker_simple_command() (in module galaxy.tool_util.deps.docker_util) build_drop_trigger() (in module galaxy.model.triggers.history_update_time_field) build_ds_map() (galaxy_test.base.populators.BaseWorkflowPopulator method) build_elements() (galaxy.model.dataset_collections.builder.CollectionBuilder method) build_engine() (in module galaxy.model.orm.engine_factory) build_env() (galaxy.tool_util.deps.brew_exts.EnvAction static method) build_env_actions() (in module galaxy.tool_util.deps.brew_exts) build_env_statements() (in module galaxy.tool_util.deps.brew_exts) build_env_statements_from_recipe_context() (in module galaxy.tool_util.deps.brew_exts) build_filter() (in module galaxy.tool_util.toolbox.views.static) build_filter_function() (galaxy.tool_util.toolbox.filters.FilterFactory method) build_filter_params() (galaxy.managers.base.ModelFilterParser method) build_filters() (galaxy.tool_util.toolbox.filters.FilterFactory method) build_folder_path() (galaxy.managers.folders.FolderManager method) build_from_current_history() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) build_index() (galaxy.tools.search.ToolBoxSearch method) (galaxy.tools.search.ToolPanelViewSearch method) (in module tool_shed.util.shed_index) build_initial_query() (galaxy.web.legacy_framework.grids.Grid method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid method) (tool_shed.grids.admin_grids.AdminRepositoryGrid method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid method) (tool_shed.grids.repository_grids.DatatypesGrid method) (tool_shed.grids.repository_grids.DeprecatedRepositoriesIOwnGrid method) (tool_shed.grids.repository_grids.MatchedRepositoryGrid method) (tool_shed.grids.repository_grids.MyWritableRepositoriesGrid method) (tool_shed.grids.repository_grids.MyWritableRepositoriesMissingToolTestComponentsGrid method) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithInvalidToolsGrid method) (tool_shed.grids.repository_grids.RepositoriesByUserGrid method) (tool_shed.grids.repository_grids.RepositoriesICanAdministerGrid method) (tool_shed.grids.repository_grids.RepositoriesInCategoryGrid method) (tool_shed.grids.repository_grids.RepositoriesIOwnGrid method) (tool_shed.grids.repository_grids.RepositoriesMissingToolTestComponentsGrid method) (tool_shed.grids.repository_grids.RepositoriesWithInvalidToolsGrid method) (tool_shed.grids.repository_grids.RepositoryDependenciesGrid method) (tool_shed.grids.repository_grids.RepositoryGrid method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid method) (tool_shed.grids.repository_grids.ToolDependenciesGrid method) (tool_shed.grids.repository_grids.ToolsGrid method) (tool_shed.grids.repository_grids.ValidRepositoryGrid method) build_invalid_repository_dependencies_root_folder() (tool_shed.utility_containers.ToolShedUtilityContainerManager method) build_invalid_tool_dependencies_root_folder() (tool_shed.utility_containers.ToolShedUtilityContainerManager method) build_invocations_query() (galaxy.managers.workflows.WorkflowsManager method) build_key1 (galaxy_test.selenium.test_custom_builds.TestCustomBuilds attribute) build_key2 (galaxy_test.selenium.test_custom_builds.TestCustomBuilds attribute) build_logger() (in module galaxy_test.driver.driver_util) build_maf_index() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) build_maf_index_species_chromosomes() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) build_mulled_singularity_pull_command() (galaxy.tool_util.deps.container_classes.SingularityContainer method) build_name1 (galaxy_test.selenium.test_custom_builds.TestCustomBuilds attribute) build_name2 (galaxy_test.selenium.test_custom_builds.TestCustomBuilds attribute) build_notification_request() (galaxy.webapps.galaxy.services.sharable.SharedItemNotificationFactory static method) build_object_store_from_config() (in module galaxy.objectstore) build_order_by() (galaxy.webapps.galaxy.services.base.ServiceBase method) build_param_dict() (galaxy.tools.evaluation.ToolEvaluator method) build_parameter_dict() (galaxy.datatypes.display_applications.application.DisplayApplicationLink method) build_pg_timestamp_fn() (in module galaxy.model.triggers.history_update_time_field) build_pg_trigger() (in module galaxy.model.triggers.history_update_time_field) build_pull_command() (galaxy.tool_util.deps.container_classes.DockerContainer method) (in module galaxy.tool_util.deps.docker_util) build_readme_files_dict() (in module tool_shed.util.readme_util) build_redirect_url_params() (galaxy.tools.Tool method) build_repository_containers() (tool_shed.utility_containers.ToolShedUtilityContainerManager method) build_repository_dependency_relationships() (galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) build_repository_ids_select_field() (galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) build_repository_type_select_field() (in module tool_shed.repository_types.util) build_resolver() (in module galaxy.tool_util.verify.test_data) build_save_image_command() (in module galaxy.tool_util.deps.docker_util) build_search_index() (tool_shed.webapp.api.tools.ToolsController method) build_select_input() (in module galaxy.webapps.galaxy.controllers.admin) build_shed_tool_conf_select_field() (in module galaxy.tool_shed.util.tool_util) build_singularity_pull_command() (galaxy.tool_util.deps.container_classes.SingularityContainer method) build_singularity_run_command() (in module galaxy.tool_util.deps.singularity_util) build_sniff_from_prefix() (in module galaxy.datatypes.sniff) build_state_handlers() (in module galaxy.jobs.runners.state_handler_factory) build_submit_description() (in module galaxy.jobs.runners.util.condor) build_target() (in module galaxy.tool_util.deps.mulled.mulled_build) (in module galaxy.tool_util.deps.mulled.util) build_template_error_formatters() (in module galaxy.webapps.util) build_timestamp_trigger() (in module galaxy.model.triggers.history_update_time_field) build_tool_panel_section_select_field() (in module galaxy.tool_shed.util.tool_util) build_tool_state() (galaxy_test.base.populators.BaseDatasetPopulator method) build_tours_registry() (in module galaxy.tours) build_url() (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter method) (galaxy.selenium.cli.DriverWrapper method) (galaxy.selenium.context.GalaxySeleniumContext method) (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) (in module galaxy.util) build_url_map() (in module galaxy.webapps.base.webapp) build_workflow_from_raw_description() (galaxy.managers.workflows.WorkflowContentsManager method) build_workflow_run_configs() (in module galaxy.workflow.run_request) BuildListCollectionTool (class in galaxy.tools) buildMockEnviron() (in module galaxy.app_unittest_utils.galaxy_mock) BuildMulledDockerContainerResolver (class in galaxy.tool_util.deps.container_resolvers.mulled) BuildMulledSingularityContainerResolver (class in galaxy.tool_util.deps.container_resolvers.mulled) builds_file_path (galaxy.config.GalaxyAppConfiguration attribute) (galaxy.tools.remote_tool_eval.ToolAppConfig attribute) (galaxy.tools.repositories.ValidationContextConfig attribute) builds_on_resolution (galaxy.tool_util.deps.container_resolvers.ContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledDockerContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledSingularityContainerResolver attribute) BUILT_IN_VISUALIZATIONS (galaxy.app_unittest_utils.galaxy_mock.MockVisualizationsRegistry attribute) (galaxy.visualization.plugins.registry.VisualizationsRegistry attribute) BulkOperationItemError (class in galaxy.schema.schema) BulkOperationParams (class in galaxy.schema.schema) Bunch (class in galaxy.util.bunch) burst() (in module galaxy.jobs.stock_rules) bwa_repository_long_description (in module tool_shed.test.functional.test_0460_upload_to_repository) bwa_tool_dependency_repository_long_description (in module tool_shed.test.functional.test_0440_deleting_dependency_definitions) by (galaxy.selenium.has_driver.HasDriver attribute) by_api_key() (galaxy.managers.users.UserManager method) by_dataset() (galaxy.managers.rbac_secured.DatasetRBACPermission method) by_email() (galaxy.managers.users.UserManager method) by_id() (galaxy.managers.base.ModelManager method) (galaxy.managers.secured.AccessibleManagerMixin method) (galaxy.managers.secured.OwnableManagerMixin method) (galaxy.managers.users.UserManager method) by_ids() (galaxy.managers.base.ModelManager method) by_oidc_access_token() (galaxy.managers.users.UserManager method) by_role() (galaxy.managers.rbac_secured.DatasetRBACPermission method) by_roles() (galaxy.managers.rbac_secured.DatasetRBACPermission method) by_tool_input() (galaxy.managers.jobs.JobSearch method) by_user() (galaxy.managers.datasets.DatasetAssociationManager method) (galaxy.managers.histories.HistoryManager method) (galaxy.managers.sharable.SharableModelManager method) bytes (galaxy.model.Quota attribute) bytes_to_str() (in module galaxy.jobs.dynamic_tool_destination) ByteSize (class in galaxy.util.bytesize) Bz2DynamicCompressedArchive (class in galaxy.datatypes.binary)

C

ca_bundle (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute) cache (galaxy.tool_util.biotools.BiotoolsMetadataSourceConfig attribute) (galaxy.tool_util.biotools.source.BiotoolsMetadataSourceConfig attribute) cache_file_is_writeable (galaxy.tools.cache.ToolDocumentCache property) cache_job_destination() (galaxy.jobs.mapper.JobRunnerMapper method) cache_monitor (galaxy.objectstore.azure_blob.AzureBlobObjectStore attribute) (galaxy.objectstore.cloud.Cloud attribute) (galaxy.objectstore.s3.S3ObjectStore attribute) cache_ok (galaxy.model.custom_types.DoubleEncodedJsonType attribute) (galaxy.model.custom_types.JSONType attribute) (galaxy.model.custom_types.MetadataType attribute) (galaxy.model.custom_types.TrimmedString attribute) (galaxy.model.custom_types.UUIDType attribute) cache_target (galaxy.objectstore.azure_blob.AzureBlobObjectStore property) (galaxy.objectstore.cloud.Cloud property) (galaxy.objectstore.ConcreteObjectStore property) (galaxy.objectstore.s3.S3ObjectStore property) cache_targets() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ConcreteObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) cache_tool() (galaxy.tools.cache.ToolCache method) cacheable (galaxy.tool_util.deps.resolvers.Dependency attribute) CacheableStaticURLParser (class in galaxy.web.framework.middleware.static) cached (galaxy.tool_util.deps.CachedDependencyManager attribute) (galaxy.tool_util.deps.DependencyManager attribute) (galaxy.tool_util.deps.NullDependencyManager attribute) cached_container_description() (galaxy.tool_util.deps.container_resolvers.mulled.MulledDockerContainerResolver method) (galaxy.tool_util.deps.container_resolvers.mulled.MulledSingularityContainerResolver method) cached_create_tool_from_representation() (in module galaxy.celery.tasks) cached_id() (in module galaxy.model) CachedDependencyManager (class in galaxy.tool_util.deps) CachedExplicitSingularityContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit) CachedMulledDockerContainerResolver (class in galaxy.tool_util.deps.container_resolvers.mulled) CachedMulledSingularityContainerResolver (class in galaxy.tool_util.deps.container_resolvers.mulled) calculate_and_set_disk_usage() (galaxy.model.User method) calculate_disk_usage_default_source() (galaxy.model.User method) calculate_user_disk_usage_statements() (in module galaxy.model) call_hook() (galaxy.tools.Tool method) CallableSafeStringWrapper (class in galaxy.security.object_wrapper) callback() (galaxy.authnz.custos_authnz.OIDCAuthnzBase method) (galaxy.authnz.IdentityProvider method) (galaxy.authnz.managers.AuthnzManager method) (galaxy.authnz.psa_authnz.PSAAuthnz method) (galaxy.webapps.galaxy.controllers.authnz.OIDC method) can_access_collection() (galaxy.model.security.GalaxyRBACAgent method) can_access_dataset() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_access_datasets() (galaxy.model.security.GalaxyRBACAgent method) can_access_entry_point() (galaxy.managers.interactivetool.InteractiveToolManager method) can_access_entry_points() (galaxy.managers.interactivetool.InteractiveToolManager method) can_access_job() (galaxy.managers.interactivetool.InteractiveToolManager method) can_access_library() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_access_library_item() (galaxy.model.security.GalaxyRBACAgent method) can_add_item() (galaxy.managers.folders.FolderManager method) can_add_library_item (galaxy.schema.schema.LibraryFolderMetadata attribute) can_add_library_item() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_add_to_key_rd_dicts() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) can_change (galaxy.schema.schema.ShareHistoryExtra attribute) can_change_object_store_id() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_change_type() (tool_shed.webapp.model.Repository method) can_change_type_to() (tool_shed.webapp.model.Repository method) can_convert_to() (galaxy.model.DatasetInstance method) can_deactivate (galaxy.model.tool_shed_install.ToolShedRepository property) can_decompress() (galaxy.util.compression_utils.CompressedFile static method) can_eliminate_repository_dependency() (in module galaxy.tool_shed.util.shed_util_common) can_install (galaxy.model.tool_shed_install.ToolDependency property) (galaxy.model.tool_shed_install.ToolShedRepository property) can_install() (galaxy.tool_util.deps.conda_util.CondaContext method) (galaxy.tool_util.deps.installable.InstallableContext method) can_install_conda() (galaxy.tool_util.deps.conda_util.CondaContext method) can_list_containers (galaxy.tool_util.deps.container_resolvers.mulled.MulledDockerContainerResolver property) (galaxy.tool_util.deps.container_resolvers.mulled.MulledSingularityContainerResolver property) can_load_config_file() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) (galaxy.tools.ToolBox method) can_manage (galaxy.schema.schema.LibraryFolderItemBase attribute) can_manage_dataset() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_manage_library_item() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_manage_repo() (in module tool_shed.managers.repositories) can_map_over() (galaxy.tools.parameters.history_query.HistoryQuery method) can_match() (galaxy.model.dataset_collections.structure.Tree method) can_match_type() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) can_modify (galaxy.schema.schema.FolderLibraryFolderItem attribute) can_modify_folder (galaxy.schema.schema.LibraryFolderMetadata attribute) can_modify_library_item() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_push() (tool_shed.webapp.security.CommunityRBACAgent method) can_reinstall_or_activate (galaxy.model.tool_shed_install.ToolShedRepository property) can_reset_metadata (galaxy.model.tool_shed_install.ToolShedRepository property) can_share (galaxy.managers.sharable.ShareWithExtra attribute) (galaxy.schema.schema.ShareWithExtra attribute) can_split() (galaxy.jobs.TaskWrapper method) can_uninstall (galaxy.model.tool_shed_install.ToolDependency property) (galaxy.model.tool_shed_install.ToolShedRepository property) can_uninstall_dependencies (galaxy.tool_util.deps.container_resolvers.ContainerResolver attribute) (galaxy.tool_util.deps.resolvers.DependencyResolver property) can_update (galaxy.model.tool_shed_install.ToolDependency property) can_update_repo() (in module tool_shed.managers.repositories) can_use_tool_config_disk_file() (tool_shed.tools.tool_validator.ToolValidator method) can_user_add (galaxy.schema.schema.LibrarySummary attribute) can_user_assume_authn() (galaxy.authnz.managers.AuthnzManager static method) can_user_manage (galaxy.schema.schema.LibrarySummary attribute) can_user_modify (galaxy.schema.schema.LibrarySummary attribute) cancel() (galaxy.model.WorkflowInvocation method) cancel_history_jobs() (galaxy_test.base.populators.BaseDatasetPopulator method) cancel_invocation() (galaxy_test.base.populators.BaseWorkflowPopulator method) cancel_invocation_steps() (galaxy.model.WorkflowInvocation method) cancel_job() (galaxy_test.base.populators.BaseDatasetPopulator method) CancelWorkflowEvaluation cannot_change (galaxy.schema.schema.ShareHistoryExtra attribute) capitalized_install_environment (galaxy.tool_util.deps.conda_util.CondaTarget property) carbon_intensity (galaxy.config.GalaxyAppConfiguration attribute) CascadingBiotoolsMetadataSource (class in galaxy.tool_util.biotools.source) case_insensitive (galaxy.managers.base.ParsedFilter attribute) Castep (class in galaxy.datatypes.text) categories (tool_shed.webapp.model.Repository attribute) CategoriesController (class in tool_shed.webapp.api.categories) Category (class in tool_shed.webapp.model) category (galaxy.model.Notification attribute) (tool_shed.webapp.model.RepositoryCategoryAssociation attribute) category_0060_name (in module tool_shed.test.functional.test_1300_reset_all_metadata) category_description (in module tool_shed.test.functional.test_0140_tool_help_images) (in module tool_shed.test.functional.test_0150_prior_installation_required) (in module tool_shed.test.functional.test_0160_circular_prior_installation_required) (in module tool_shed.test.functional.test_0170_complex_prior_installation_required) (in module tool_shed.test.functional.test_0310_hg_api_features) (in module tool_shed.test.functional.test_0530_repository_admin_feature) (in module tool_shed.test.functional.test_0550_metadata_updated_dependencies) (in module tool_shed.test.functional.test_1170_prior_installation_required) (in module tool_shed.test.functional.test_1180_circular_prior_installation_required) (in module tool_shed.test.functional.test_1190_complex_prior_installation_required) (in module tool_shed.test.functional.test_1410_update_manager) (in module tool_shed.test.functional.test_1470_updating_installed_repositories) category_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) category_id (tool_shed.webapp.model.RepositoryCategoryAssociation attribute) category_manager (tool_shed.webapp.api.categories.CategoriesController attribute) CategoryGrid (class in tool_shed.grids.repository_grids) CategoryGrid.DescriptionColumn (class in tool_shed.grids.repository_grids) CategoryGrid.NameColumn (class in tool_shed.grids.repository_grids) CategoryGrid.RepositoriesColumn (class in tool_shed.grids.repository_grids) cbv (galaxy.webapps.galaxy.api.FrameworkRouter property) Cel (class in galaxy.datatypes.binary) celery_config() (in module galaxy_test.base.api) celery_includes() (in module galaxy_test.conftest) celery_parameters() (galaxy_test.base.api.UsesCeleryTasks method) celery_worker_parameters() (galaxy_test.base.api.UsesCeleryTasks method) CeleryUserRateLimit (class in galaxy.model) Cell (class in galaxy.datatypes.molecules) cellar_path (galaxy.tool_util.deps.brew_exts.RecipeContext property) center() (tool_shed.util.admin_util.Admin method) CgroupPlugin (class in galaxy.job_metrics.instrumenters.cgroup) change_datatype (galaxy.schema.schema.HistoryContentItemOperation attribute) change_datatype() (galaxy.datatypes.registry.Registry method) (galaxy.model.DatasetInstance method) change_datatype_actions (galaxy.job_execution.output_collect.JobContext property) (galaxy.job_execution.output_collect.SessionlessJobContext property) change_datatype_value_and_click_submit() (galaxy_test.selenium.test_collection_edit.TestCollectionEdit method) change_dbkey (galaxy.schema.schema.HistoryContentItemOperation attribute) change_dbkey_value_and_click_submit() (galaxy_test.selenium.test_collection_edit.TestCollectionEdit method) change_entry() (tool_shed.util.hgweb_config.HgWebConfigManager method) change_password() (galaxy.managers.users.UserManager method) (galaxy.webapps.galaxy.controllers.user.User method) (tool_shed.webapp.controllers.user.User method) change_repository_name_in_hgrc_file() (in module tool_shed.util.repository_util) change_state() (galaxy.config_watchers.ConfigWatchers method) (galaxy.jobs.TaskWrapper method) changed() (galaxy.model.UserAuthnzToken class method) ChangeDatatypeAction (class in galaxy.job_execution.actions.post) ChangeDatatypeOperationParams (class in galaxy.schema.schema) ChangeDatatypeTests (class in galaxy_test.api.test_workflows) ChangeDbkeyOperationParams (class in galaxy.schema.schema) ChangeFormatModel (class in galaxy.tool_util.parser.output_objects) changeset2rev() (in module tool_shed.util.hg_util) changeset_revision (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.schema.schema.InstalledToolShedRepository attribute) (galaxy.schema.schema.ToolShedRepositoryChangeset attribute) (galaxy.schema.schema.ToolShedRepositorySummary attribute) (galaxy.tool_shed.galaxy_install.update_repository_manager.UpdateToChangeset attribute) (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator attribute) (tool_shed.managers.repositories.UpdatesRequest attribute) (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) ChartVisualizationPlugin (class in galaxy.visualization.plugins.plugin) check() (galaxy.config.GalaxyAppConfiguration method) (galaxy.dependencies.ConditionalDependencies method) (galaxy.tool_util.toolbox.watcher.ToolConfWatcher method) (galaxy.webapps.reports.config.Configuration method) (tool_shed.webapp.config.ToolShedAppConfiguration method) check_accessible() (galaxy.managers.folders.FolderManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.managers.library_datasets.LibraryDatasetsManager method) check_advanced_search_filter() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) check_all_jobs() (galaxy.jobs.runners.pbs.PBSJobRunner method) check_and_reload() (galaxy.visualization.genomes.Genomes method) check_and_update_param_values() (galaxy.tools.Tool method) check_and_update_state() (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) check_archive() (in module galaxy.tools.imp_exp.unpack_tar_gz_archive) (in module tool_shed.util.commit_util) check_attribute (galaxy.tool_util.parser.output_objects.ChangeFormatModel attribute) check_auto_registration() (galaxy.auth.AuthManager method) check_azure_storage() (galaxy.dependencies.ConditionalDependencies method) check_binary() (in module galaxy.datatypes.checkers) (in module galaxy.util.checkers) check_block() (galaxy.datatypes.sequence.BaseFastq class method) check_bootstrap_admin_api_key() (galaxy.managers.users.UserManager method) check_boto3_python() (galaxy.dependencies.ConditionalDependencies method) check_bz2() (in module galaxy.datatypes.checkers) (in module galaxy.util.checkers) check_change_password() (galaxy.auth.AuthManager method) check_chronos_python() (galaxy.dependencies.ConditionalDependencies method) check_config() (galaxy.auth.providers.ldap_ad.LDAP method) check_count_of_metadata_revisions_associated_with_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) check_csrf_token() (galaxy.app_unittest_utils.galaxy_mock.MockTrans method) (galaxy.webapps.base.webapp.GalaxyWebTransaction method) check_current_data_value() (galaxy_test.selenium.test_collection_edit.TestCollectionEdit method) check_custos_sdk() (galaxy.dependencies.ConditionalDependencies method) check_database_connection() (in module galaxy.model.base) check_drmaa() (galaxy.dependencies.ConditionalDependencies method) check_example_1() (in module galaxy_test.base.rules_test_data) check_example_2() (in module galaxy_test.base.rules_test_data) check_example_3() (in module galaxy_test.base.rules_test_data) check_example_4() (in module galaxy_test.base.rules_test_data) check_example_5() (in module galaxy_test.base.rules_test_data) check_example_6() (in module galaxy_test.base.rules_test_data) check_file_content_for_html_and_images() (in module tool_shed.util.commit_util) check_file_contents_for_email_alerts() (in module tool_shed.util.commit_util) check_first_block() (galaxy.datatypes.sequence.BaseFastq class method) check_fluent_logger() (galaxy.dependencies.ConditionalDependencies method) check_folder_contents() (galaxy.model.security.GalaxyRBACAgent method) check_for_strings() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) check_for_updates() (galaxy.webapps.galaxy.api.tool_shed_repositories.FastAPIToolShedRepositories method) (in module galaxy.tool_shed.util.repository_util) check_for_valid_tools() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) check_fs_anvilfs() (galaxy.dependencies.ConditionalDependencies method) check_fs_basespace() (galaxy.dependencies.ConditionalDependencies method) check_fs_dropboxfs() (galaxy.dependencies.ConditionalDependencies method) check_fs_gcsfs() (galaxy.dependencies.ConditionalDependencies method) check_fs_googledrivefs() (galaxy.dependencies.ConditionalDependencies method) check_fs_onedatarestfs() (galaxy.dependencies.ConditionalDependencies method) check_fs_sshfs() (galaxy.dependencies.ConditionalDependencies method) check_fs_webdavfs() (galaxy.dependencies.ConditionalDependencies method) check_galaxy_repository_db_status() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) check_galaxy_repository_tool_panel_section() (tool_shed.test.base.twilltestcase.GalaxyInteractorToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) (tool_shed.test.base.twilltestcase.StandaloneToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ToolShedInstallationClient method) check_galaxy_root (galaxy.main_config.WebappSetupProps attribute) check_galaxycloudrunner() (galaxy.dependencies.ConditionalDependencies method) check_github_api_response_rate_limit() (in module galaxy.util) check_google_cloud_storage() (galaxy.dependencies.ConditionalDependencies method) check_grid_rows() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) check_gzip() (in module galaxy.datatypes.checkers) (in module galaxy.util.checkers) check_html() (in module galaxy.datatypes.checkers) (in module galaxy.util.checkers) check_hvac() (galaxy.dependencies.ConditionalDependencies method) check_if_output_datasets_deleted() (galaxy.model.Job method) check_image() (in module galaxy.datatypes.checkers) (in module galaxy.util.checkers) check_image_type() (in module galaxy.util.image_util) check_influxdb() (galaxy.dependencies.ConditionalDependencies method) check_inputs_ready() (galaxy.tools.actions.model_operations.ModelOperationToolAction method) (galaxy.tools.DatabaseOperationTool method) check_kamaki() (galaxy.dependencies.ConditionalDependencies method) check_ldap3() (galaxy.dependencies.ConditionalDependencies method) check_limits() (galaxy.jobs.runners.AsynchronousJobState method) check_manageable() (galaxy.managers.folders.FolderManager method) check_modifiable() (galaxy.managers.library_datasets.LibraryDatasetsManager method) check_modifyable() (galaxy.managers.folders.FolderManager method) check_mysqlclient() (galaxy.dependencies.ConditionalDependencies method) check_output() (in module galaxy.tool_util.output_checker) check_output_regex() (in module galaxy.tool_util.output_checker) check_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) check_page_for_string() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) check_password() (galaxy.auth.AuthManager method) (galaxy.model.User method) (in module galaxy.security.passwords) (tool_shed.webapp.model.User method) check_password_PBKDF2() (in module galaxy.security.passwords) check_pbs_python() (galaxy.dependencies.ConditionalDependencies method) check_pg() (in module galaxy.jobs.runners.util.process_groups) check_pkce() (galaxy.dependencies.ConditionalDependencies method) check_psycopg2_binary() (galaxy.dependencies.ConditionalDependencies method) check_pydyf() (galaxy.dependencies.ConditionalDependencies method) check_pygithub() (galaxy.dependencies.ConditionalDependencies method) check_pykube_ng() (galaxy.dependencies.ConditionalDependencies method) check_python_gitlab() (galaxy.dependencies.ConditionalDependencies method) check_python_irodsclient() (galaxy.dependencies.ConditionalDependencies method) check_python_ldap() (galaxy.dependencies.ConditionalDependencies method) check_python_pam() (galaxy.dependencies.ConditionalDependencies method) check_registration_allowed() (galaxy.auth.AuthManager method) check_repository_changelog() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) check_repository_dependency() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) check_repository_invalid_tools_for_changeset_revision() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) check_repository_metadata() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) check_repository_tools_for_changeset_revision() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) check_required_metadata (galaxy.datatypes.interval.Bed attribute) check_role_dict() (galaxy_test.api.test_roles.TestRolesApi static method) check_run() (galaxy_test.base.populators.BaseDatasetPopulator method) check_security() (galaxy.managers.workflows.WorkflowsManager method) check_sentry_sdk() (galaxy.dependencies.ConditionalDependencies method) check_single_job() (galaxy.jobs.runners.pbs.PBSJobRunner method) check_some_ids_passed() (galaxy.schema.schema.RequireOneSetOption method) check_statsd() (galaxy.dependencies.ConditionalDependencies method) check_string_count_in_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) check_string_not_in_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) check_tag_attributes() (tool_shed.dependencies.attribute_handlers.RepositoryDependencyAttributeHandler method) check_tensorflow() (galaxy.dependencies.ConditionalDependencies method) check_tool_input_params() (galaxy.tool_shed.tools.tool_validator.ToolValidator method) check_tool_tag_set() (in module galaxy.util.tool_shed.common_util) (in module tool_shed.util.common_util) check_total_perspective_vortex() (galaxy.dependencies.ConditionalDependencies method) check_updates() (in module tool_shed.managers.repositories) check_user_activation() (galaxy.managers.context.ProvidesUserContext method) check_user_is_authenticated() (galaxy.webapps.galaxy.services.base.ServiceBase method) check_user_library_import_dir() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) check_watchdog() (galaxy.dependencies.ConditionalDependencies method) check_watched_item() (galaxy.jobs.runners.AsynchronousJobRunner method) (galaxy.jobs.runners.chronos.ChronosJobRunner method) (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) (galaxy.jobs.runners.godocker.GodockerJobRunner method) (galaxy.jobs.runners.kubernetes.KubernetesJobRunner method) (galaxy.jobs.runners.univa.UnivaJobRunner method) check_watched_items() (galaxy.jobs.runners.AsynchronousJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.condor.CondorJobRunner method) (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) (galaxy.jobs.runners.pbs.PBSJobRunner method) check_weasyprint() (galaxy.dependencies.ConditionalDependencies method) check_workflow_compatible() (galaxy.tools.Tool method) check_zip() (in module galaxy.datatypes.checkers) (in module galaxy.util.checkers) CheckboxField (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) checkComments() (galaxy.visualization.data_providers.phyloviz.nexusparser.Nexus_Parser method) CheckForUpdatesResponse (class in galaxy.schema.schema) checksum (galaxy.tool_util.cwl.util.OutputPropertiesType attribute) child_collection (galaxy.model.DatasetCollectionElement attribute) child_collection_id (galaxy.model.DatasetCollectionElement attribute) child_collection_type() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) child_collection_type_description() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) child_comments (galaxy.model.WorkflowComment attribute) child_steps (galaxy.model.WorkflowComment attribute) child_tool_association (galaxy.model.tool_shed_install.ToolVersion attribute) children (galaxy.model.ExtendedMetadata attribute) (galaxy.model.Tag attribute) (galaxy.model.Vault attribute) (galaxy.tool_util.parser.interface.AssertionDict attribute) (tool_shed.webapp.model.Tag attribute) children_known (galaxy.model.dataset_collections.structure.Leaf attribute) (galaxy.model.dataset_collections.structure.Tree attribute) (galaxy.model.dataset_collections.structure.UninitializedTree attribute) ChiraSQLite (class in galaxy.datatypes.binary) choose_one() (galaxy.jobs.rule_helper.RuleHelper method) (in module galaxy.jobs.stock_rules) chop_block_by_region() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) ChromatinInteractions (class in galaxy.datatypes.interval) ChromatinInteractionsDataProvider (class in galaxy.visualization.data_providers.genome) ChromatinInteractionsTabixDataProvider (class in galaxy.visualization.data_providers.genome) ChromInfo (class in galaxy.datatypes.chrominfo) chroms() (galaxy.visualization.genomes.Genomes method) ChronosJobRunner (class in galaxy.jobs.runners.chronos) chunk64_dataprovider() (galaxy.datatypes.data.Data method) chunk_dataprovider() (galaxy.datatypes.data.Data method) chunk_iterable() (in module galaxy.util) CHUNKABLE (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.tabular.TabularData attribute) ChunkDataProvider (class in galaxy.datatypes.dataproviders.chunk) CIF (class in galaxy.datatypes.molecules) CisML (class in galaxy.datatypes.xml) CitationCollection (class in galaxy.managers.citations) citations() (galaxy.webapps.galaxy.api.tools.ToolsController method) (galaxy.webapps.galaxy.services.histories.HistoriesService method) citations_for_tool() (galaxy.managers.citations.CitationsManager method) citations_for_tool_ids() (galaxy.managers.citations.CitationsManager method) CitationsFound (class in galaxy.tool_util.linters.citations) CitationsManager (class in galaxy.managers.citations) CitationsMissing (class in galaxy.tool_util.linters.citations) CitationsNoText (class in galaxy.tool_util.linters.citations) CitationsNoValid (class in galaxy.tool_util.linters.citations) city (galaxy.model.UserAddress attribute) class (galaxy.files.sources.RemoteDirectory attribute) (galaxy.files.sources.RemoteFile attribute) (galaxy.files.sources.TDirectoryClass attribute) (galaxy.files.sources.TFileClass attribute) (galaxy.tool_util.cwl.util.OutputPropertiesType attribute) class_ (galaxy.schema.remote_files.RemoteDirectory attribute) (galaxy.schema.remote_files.RemoteFile attribute) (galaxy.schema.schema.Creator attribute) (galaxy.schema.schema.Organization attribute) (galaxy.schema.schema.Person attribute) class_id (galaxy.model.InteractiveToolEntryPoint property) class_to_classes (galaxy.managers.datatypes.DatatypesMap attribute) classproperty (class in galaxy.util) clean() (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method) (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) clean_base_dir() (galaxy.tools.data.TabularToolDataField method) clean_dependency_relationships() (in module galaxy.tool_shed.util.shed_util_common) clean_multiline_string() (in module galaxy.util) cleanNewickString() (galaxy.visualization.data_providers.phyloviz.newickparser.Newick_Parser method) cleanTag() (galaxy.visualization.data_providers.phyloviz.phyloxmlparser.Phyloxml_Parser method) cleanup() (galaxy.jobs.runners.JobState method) (galaxy.jobs.TaskWrapper method) (galaxy.tools.cache.ToolCache method) cleanup_after_job() (galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper method) cleanup_event_id (galaxy.model.CleanupEventDatasetAssociation attribute) (galaxy.model.CleanupEventHistoryAssociation attribute) (galaxy.model.CleanupEventHistoryDatasetAssociationAssociation attribute) (galaxy.model.CleanupEventImplicitlyConvertedDatasetAssociationAssociation attribute) (galaxy.model.CleanupEventLibraryAssociation attribute) (galaxy.model.CleanupEventLibraryDatasetAssociation attribute) (galaxy.model.CleanupEventLibraryDatasetDatasetAssociationAssociation attribute) (galaxy.model.CleanupEventLibraryFolderAssociation attribute) (galaxy.model.CleanupEventMetadataFileAssociation attribute) cleanup_from_JSON_dict_filename() (galaxy.datatypes.metadata.MetadataTempFile class method) (galaxy.model.metadata.MetadataTempFile class method) cleanup_items() (galaxy.managers.base.StorageCleanerManager method) (galaxy.managers.hdas.HDAStorageCleanerManager method) (galaxy.managers.histories.HistoryStorageCleanerManager method) CleanupEvent (class in galaxy.model) CleanupEventDatasetAssociation (class in galaxy.model) CleanupEventHistoryAssociation (class in galaxy.model) CleanupEventHistoryDatasetAssociationAssociation (class in galaxy.model) CleanupEventImplicitlyConvertedDatasetAssociationAssociation (class in galaxy.model) CleanupEventLibraryAssociation (class in galaxy.model) CleanupEventLibraryDatasetAssociation (class in galaxy.model) CleanupEventLibraryDatasetDatasetAssociationAssociation (class in galaxy.model) CleanupEventLibraryFolderAssociation (class in galaxy.model) CleanupEventMetadataFileAssociation (class in galaxy.model) clear() (galaxy.managers.rbac_secured.DatasetRBACPermission method) (galaxy.model.ImplicitlyConvertedDatasetAssociation method) (galaxy.util.odict.odict method) clear_associated_files() (galaxy.model.DatasetInstance method) (galaxy.model.HistoryDatasetAssociation method) (galaxy.model.LibraryDatasetDatasetAssociation method) clear_display_apps() (galaxy.datatypes.data.Data method) clear_input_field_and_write() (galaxy_test.selenium.test_personal_information.TestManageInformation method) clear_module_extras() (galaxy.model.WorkflowStep method) clear_tags() (galaxy_test.selenium.test_history_panel.TestHistoryPanel method) clear_tooltips() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) cli (galaxy.tool_util.deps.container_resolvers.explicit.CachedExplicitSingularityContainerResolver attribute) click() (galaxy.selenium.has_driver.HasDriver method) click_button_new_workflow() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) click_center() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) click_history_option() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) click_history_option_export_to_file() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) click_history_option_sharing() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) click_history_options() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) click_label() (galaxy.selenium.has_driver.HasDriver method) click_masthead_data() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) click_masthead_user() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) click_masthead_workflow() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) click_menu_item() (galaxy_test.selenium.test_tool_form.TestToolForm static method) click_selector() (galaxy.selenium.has_driver.HasDriver method) click_submit() (galaxy.selenium.has_driver.HasDriver method) click_xpath() (galaxy.selenium.has_driver.HasDriver method) client_id (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute) client_message (galaxy.objectstore.ObjectCreationProblemSharingDisabled attribute) (galaxy.objectstore.ObjectCreationProblemStoreFull attribute) client_secret (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute) ClientBuildException CliInterface (class in galaxy.jobs.runners.util.cli) clone() (galaxy.model.dataset_collections.structure.Leaf method) (galaxy.model.dataset_collections.structure.Tree method) (galaxy.model.dataset_collections.structure.UninitializedTree method) clone_repository() (in module galaxy.tool_shed.util.hg_util) (in module tool_shed.util.hg_util) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) cloned_repo() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) CLONING (galaxy.model.tool_shed_install.ToolShedRepository.installation_status attribute) close() (galaxy.datatypes.util.maf_utilities.TempFileHandler method) (galaxy.tools.cache.ToolDocumentCache method) (galaxy.tools.util.maf_utilities.TempFileHandler method) close_history_editor() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) close_logs() (galaxy.util.heartbeat.Heartbeat method) closest_section() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) Cloud (class in galaxy.objectstore.cloud) CloudAuthz (class in galaxy.model) cloudauthz (galaxy.model.User attribute) CloudAuthzController (class in galaxy.webapps.galaxy.api.cloudauthz) CloudAuthzManager (class in galaxy.managers.cloudauthzs) CloudAuthzsDeserializer (class in galaxy.managers.cloudauthzs) CloudAuthzsSerializer (class in galaxy.managers.cloudauthzs) CloudConfigMixin (class in galaxy.objectstore.cloud) (class in galaxy.objectstore.irods) (class in galaxy.objectstore.s3) CloudManager (class in galaxy.managers.cloud) CMAP (class in galaxy.datatypes.tabular) CML (class in galaxy.datatypes.molecules) cmp() (in module galaxy.security.object_wrapper) code (galaxy.authnz.psa_authnz.Storage attribute) (galaxy.model.PSACode attribute) coerce() (galaxy.model.custom_types.MutationDict class method) (galaxy.model.custom_types.MutationList class method) (galaxy.model.custom_types.MutationObj class method) (in module galaxy.security.object_wrapper) col_name_data_attr_mapping (galaxy.visualization.data_providers.genome.GenomeDataProvider attribute) (galaxy.visualization.data_providers.genome.IntervalIndexDataProvider attribute) (galaxy.visualization.data_providers.genome.TabixDataProvider attribute) (galaxy.visualization.data_providers.genome.VcfDataProvider attribute) collect_dynamic_outputs() (in module galaxy.job_execution.output_collect) collect_extra_files() (in module galaxy.job_execution.output_collect) collect_input_dataset_collections() (galaxy.tools.actions.DefaultToolAction method) collect_inputs() (galaxy.tool_util.parser.interface.TestCollectionDef method) collect_primary_datasets() (in module galaxy.job_execution.output_collect) collect_properties() (galaxy.job_metrics.JobInstrumenter method) collect_shrinked_content_from_path() (in module galaxy.job_execution.output_collect) collection (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetCollectionAssociation attribute) (galaxy.tools.wrappers.DatasetCollectionWrapper attribute) collection_builder_clear_filters() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) collection_builder_click_paired_item() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) collection_builder_create() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) collection_builder_for() (galaxy.managers.collections.DatasetCollectionManager method) collection_builder_hide_originals() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) collection_builder_set_name() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) collection_datasets (galaxy.model.store.BagDirectoryModelExportStore attribute) (galaxy.model.store.BcoModelExportStore attribute) (galaxy.model.store.ROCrateModelExportStore attribute) (galaxy.model.store.WorkflowInvocationOnlyExportStore attribute) collection_export() (galaxy_test.selenium.test_library_to_collections.TestLibraryToCollections method) collection_id (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetCollectionAssociation attribute) (galaxy.schema.schema.HDCASummary attribute) collection_prototype() (galaxy.tool_util.parser.output_objects.ToolOutputCollectionStructure method) collection_type (galaxy.model.dataset_collections.type_description.CollectionTypeDescription attribute) (galaxy.model.dataset_collections.types.list.ListDatasetCollectionType attribute) (galaxy.model.dataset_collections.types.paired.PairedDatasetCollectionType attribute) (galaxy.model.DatasetCollection attribute) (galaxy.schema.fetch_data.BaseCollectionTarget attribute) (galaxy.schema.fetch_data.BaseDataElement attribute) (galaxy.schema.fetch_data.FtpImportElement attribute) (galaxy.schema.schema.CollectionElementIdentifier attribute) (galaxy.schema.schema.CreateNewCollectionPayload attribute) (galaxy.schema.schema.DCObject attribute) (galaxy.schema.schema.DCSummary attribute) (galaxy.schema.schema.HDCASummary attribute) (galaxy.tool_util.cwl.representation.TypeRepresentation attribute) (galaxy.util.rules_dsl.RuleSet property) (galaxy.workflow.modules.InputDataCollectionModule attribute) (galaxy.workflow.refactor.schema.AddInputAction attribute) collection_types (galaxy.tools.parameters.basic.DataCollectionToolParameter property) (galaxy.tools.parameters.DataCollectionToolParameter property) collection_wrapper_to_array() (in module galaxy.tool_util.cwl.representation) collection_wrapper_to_record() (in module galaxy.tool_util.cwl.representation) CollectionBuilder (class in galaxy.model.dataset_collections.builder) CollectionElementIdentifier (class in galaxy.schema.schema) collections_attrs (galaxy.model.store.BagDirectoryModelExportStore attribute) (galaxy.model.store.BcoModelExportStore attribute) (galaxy.model.store.ROCrateModelExportStore attribute) (galaxy.model.store.WorkflowInvocationOnlyExportStore attribute) collections_properties() (galaxy.model.store.BaseDirectoryImportModelStore method) (galaxy.model.store.DictImportModelStore method) (galaxy.model.store.ModelImportStore method) CollectionsToMatch (class in galaxy.model.dataset_collections.matching) CollectionTypeDescription (class in galaxy.model.dataset_collections.type_description) CollectionTypeDescriptionFactory (class in galaxy.model.dataset_collections.type_description) collector (galaxy.model.store.discover.DiscoveredDeferredFile attribute) (galaxy.model.store.discover.DiscoveredFile attribute) (galaxy.model.store.discover.DiscoveredFileError attribute) ColletionSourceType (class in galaxy.schema.schema) color (galaxy.model.WorkflowComment attribute) ColorToolParameter (class in galaxy.tools.parameters.basic) column (galaxy.model.InnerCollectionFilter attribute) column_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.TabularData method) column_exists() (in module galaxy.model.migrations.util) COLUMN_NAMES (galaxy.datatypes.dataproviders.dataset.BigWigDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.GenomicRegionDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.IntervalDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.WiggleDataProvider attribute) column_names (galaxy.datatypes.interval.Bed attribute) (galaxy.datatypes.interval.ChromatinInteractions attribute) (galaxy.datatypes.interval.ENCODEPeak attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Gff3 attribute) (galaxy.datatypes.interval.Gtf attribute) (galaxy.datatypes.interval.ProBed attribute) (galaxy.datatypes.molecules.InChI attribute) (galaxy.datatypes.molecules.SMILES attribute) (galaxy.datatypes.tabular.BaseVcf attribute) column_repository_long_description (in module tool_shed.test.functional.test_1430_repair_installed_repository) column_spec_to_index() (galaxy.tools.parameters.dynamic_options.DynamicOptions method) ColumnarDataProvider (class in galaxy.datatypes.dataproviders.column) ColumnDataProvider (class in galaxy.visualization.data_providers.basic) ColumnListParameter (class in galaxy.tools.parameters.basic) ColumnParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) ColumnReplaceFilter (class in galaxy.tool_util.parser.output_actions) columns (galaxy.web.framework.helpers.grids.GridData attribute) (galaxy.web.legacy_framework.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.grids.admin_grids.AdminRepositoryGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.ManageCategoryGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.DatatypesGrid attribute) (tool_shed.grids.repository_grids.DeprecatedRepositoriesIOwnGrid attribute) (tool_shed.grids.repository_grids.DockerImageGrid attribute) (tool_shed.grids.repository_grids.EmailAlertsRepositoryGrid attribute) (tool_shed.grids.repository_grids.InstallMatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithInvalidToolsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesByUserGrid attribute) (tool_shed.grids.repository_grids.RepositoriesICanAdministerGrid attribute) (tool_shed.grids.repository_grids.RepositoriesInCategoryGrid attribute) (tool_shed.grids.repository_grids.RepositoriesIOwnGrid attribute) (tool_shed.grids.repository_grids.RepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithInvalidToolsGrid attribute) (tool_shed.grids.repository_grids.RepositoryDependenciesGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ToolDependenciesGrid attribute) (tool_shed.grids.repository_grids.ToolsGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_grids.ValidRepositoryGrid attribute) ColumnSetAction (class in galaxy.job_execution.actions.post) ColumnStripFilter (class in galaxy.tool_util.parser.output_actions) ColumnTypesParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) combine_lists() (in module galaxy.managers.base) commaify() (in module galaxy.util) command (galaxy.tool_util.parser.interface.ToolSourceTest attribute) command_line (galaxy.model.Job attribute) (galaxy.model.Task attribute) (galaxy.schema.schema.JobSummary attribute) (galaxy.tool_util.verify.interactor.ToolTestDescription attribute) (galaxy.tool_util.verify.interactor.ToolTestDescriptionDict attribute) (galaxy.tool_util.verify.interactor.ValidToolTestDict attribute) (galaxy.tools.evaluation.PartialToolEvaluator attribute) (galaxy.tools.evaluation.RemoteToolEvaluator attribute) command_list() (in module galaxy.tool_util.deps.docker_util) command_shell() (in module galaxy.tool_util.deps.docker_util) command_version (galaxy.model.Job property) (galaxy.schema.schema.JobDetails attribute) (galaxy.tool_util.parser.interface.ToolSourceTest attribute) (galaxy.tool_util.verify.interactor.ToolTestDescription attribute) (galaxy.tool_util.verify.interactor.ToolTestDescriptionDict attribute) (galaxy.tool_util.verify.interactor.ValidToolTestDict attribute) CommandEmpty (class in galaxy.tool_util.linters.command) CommandInfo (class in galaxy.tool_util.linters.command) CommandInterpreterDeprecated (class in galaxy.tool_util.linters.command) CommandLineException, [1] CommandMissing (class in galaxy.tool_util.linters.command) CommandTODO (class in galaxy.tool_util.linters.command) comment (tool_shed.webapp.model.RepositoryRatingAssociation attribute) comment_lines (galaxy.datatypes.proteomics.Dta attribute) (galaxy.datatypes.proteomics.Dta2d attribute) (galaxy.datatypes.proteomics.Edta attribute) (galaxy.datatypes.proteomics.ProtXmlReport attribute) CommentedMap (class in galaxy.tool_util.cwl.cwltool_deps) comments (galaxy.model.Workflow attribute) commit() (galaxy.model.store.SessionlessContext method) commit_and_push() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) commit_changeset() (in module tool_shed.util.hg_util) commit_for_version() (in module galaxy.tool_util.deps.brew_exts) commit_tar_to_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) common_columns (galaxy.managers.history_contents.HistoryContentsManager attribute) common_prefix_dir (galaxy.util.compression_utils.CompressedFile property) CommonConfigurationMixin (class in galaxy.config) CommunityRatingColumn (class in galaxy.web.legacy_framework.grids) CommunityRBACAgent (class in tool_shed.webapp.security) CommunityTagHandler (class in galaxy.model.tags) CommunityTagsColumn (class in galaxy.web.legacy_framework.grids) CommunityWebApplication (class in tool_shed.webapp.buildapp) compare_changeset_revisions() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) compare_data_manager() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) compare_endswith() (in module galaxy.tool_util.parser.output_actions) compare_eq() (in module galaxy.tool_util.parser.output_actions) compare_gt() (in module galaxy.tool_util.parser.output_actions) compare_gte() (in module galaxy.tool_util.parser.output_actions) compare_in() (in module galaxy.tool_util.parser.output_actions) compare_lt() (in module galaxy.tool_util.parser.output_actions) compare_lte() (in module galaxy.tool_util.parser.output_actions) compare_neq() (in module galaxy.tool_util.parser.output_actions) compare_re_search() (in module galaxy.tool_util.parser.output_actions) compare_repository_dependencies() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) compare_startswith() (in module galaxy.tool_util.parser.output_actions) compare_tool_dependencies() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) compare_urls() (in module galaxy.util) compare_values() (galaxy.model.custom_types.JSONType method) complete() (galaxy.authnz.psa_authnz.Strategy method) component_overlaps_region() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) components (galaxy.selenium.navigates_galaxy.NavigatesGalaxy property) components_are_associated() (galaxy.security.RBACAgent method) composite (galaxy.schema.fetch_data.CompositeDataElement attribute) (galaxy.schema.fetch_data.Src attribute) composite_files (galaxy.datatypes.data.Data attribute) (galaxy.managers.datatypes.DatatypeDetails attribute) (galaxy.tools.parameters.grouping.Dataset attribute) composite_type (galaxy.datatypes.anvio.AnvioComposite attribute) (galaxy.datatypes.assembly.Velvet attribute) (galaxy.datatypes.binary.LudwigModel attribute) (galaxy.datatypes.blast.BlastDomainDb attribute) (galaxy.datatypes.blast.BlastDomainDb5 attribute) (galaxy.datatypes.blast.BlastNucDb attribute) (galaxy.datatypes.blast.BlastNucDb5 attribute) (galaxy.datatypes.blast.BlastProtDb attribute) (galaxy.datatypes.blast.BlastProtDb5 attribute) (galaxy.datatypes.blast.LastDb attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.genetics.IdeasPre attribute) (galaxy.datatypes.genetics.RexpBase attribute) (galaxy.datatypes.genetics.Rgenetics attribute) (galaxy.datatypes.gis.Shapefile attribute) (galaxy.datatypes.hdf5.HDF5SummarizedExperiment attribute) (galaxy.datatypes.images.Analyze75 attribute) (galaxy.datatypes.molecules.OBFS attribute) (galaxy.datatypes.msa.HmmerPress attribute) (galaxy.datatypes.neo4j.Neo4jDB attribute) (galaxy.datatypes.neo4j.Neo4jDBzip attribute) (galaxy.datatypes.ngsindex.BowtieIndex attribute) (galaxy.datatypes.proteomics.ImzML attribute) (galaxy.datatypes.proteomics.SPLib attribute) (galaxy.datatypes.proteomics.Wiff attribute) (galaxy.datatypes.proteomics.Wiff2 attribute) (galaxy.datatypes.text.SnpSiftDbNSFP attribute) (galaxy.datatypes.tracks.UCSCTrackHub attribute) CompositeDataElement (class in galaxy.schema.fetch_data) CompositeItems (class in galaxy.schema.fetch_data) compressed (galaxy.datatypes.annotation.Augustus attribute) (galaxy.datatypes.binary.BcfUncompressed attribute) (galaxy.datatypes.binary.CompressedArchive attribute) (galaxy.datatypes.binary.Xlsx attribute) (galaxy.datatypes.interval.IntervalTabix attribute) (galaxy.datatypes.tabular.Eland attribute) (galaxy.datatypes.tabular.VcfGz attribute) (galaxy.model.JobExportHistoryArchive attribute) compressed_format (galaxy.datatypes.binary.Bz2DynamicCompressedArchive attribute) (galaxy.datatypes.binary.DynamicCompressedArchive attribute) (galaxy.datatypes.binary.GzDynamicCompressedArchive attribute) (galaxy.datatypes.interval.IntervalTabix attribute) (galaxy.datatypes.tabular.Eland attribute) (galaxy.datatypes.tabular.VcfGz attribute) compressed_type (galaxy.datatypes.sniff.HandleCompressedFileResponse attribute) (galaxy.datatypes.sniff.HandleUploadedDatasetFileInternalResponse attribute) CompressedArchive (class in galaxy.datatypes.binary) CompressedFile (class in galaxy.util.compression_utils)

CompressedZipArchive (class in galaxy.datatypes.binary) compute_collection_info() (galaxy.workflow.modules.WorkflowModule method) compute_fasta_length() (in module galaxy.datatypes.converters.fasta_to_len) compute_hash() (galaxy.managers.datasets.DatasetManager method) (galaxy_test.base.populators.BaseDatasetPopulator method) compute_outputs() (galaxy.job_execution.setup.JobIO method) compute_runtime_state() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) (galaxy.workflow.modules.WorkflowModuleInjector method) ComputeDatasetHashTaskRequest (class in galaxy.schema.tasks) ComputeEnvironment (class in galaxy.job_execution.compute_environment) concat_messages() (tool_shed.tools.tool_validator.ToolValidator method) ConcreteObjectStore (class in galaxy.objectstore) ConcreteObjectStoreModel (class in galaxy.objectstore) cond_plural() (galaxy.util.inflection.Inflector method) conda_build_available (galaxy.tool_util.deps.conda_util.CondaContext property) conda_build_target_str() (in module galaxy.tool_util.deps.mulled.util) conda_info() (galaxy.tool_util.deps.conda_util.CondaContext method) conda_version (galaxy.tool_util.deps.conda_util.CondaContext property) CondaContext (class in galaxy.tool_util.deps.conda_util) CondaDependencyResolver (class in galaxy.tool_util.deps.resolvers.conda) CondaTarget (class in galaxy.tool_util.deps.conda_util) Conditional (class in galaxy.tools.parameters.grouping) CONDITIONAL (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute) ConditionalDependencies (class in galaxy.dependencies) ConditionalOptionMissing (class in galaxy.tool_util.linters.inputs) ConditionalOptionMissingBoolean (class in galaxy.tool_util.linters.inputs) ConditionalParamIncompatibleAttributes (class in galaxy.tool_util.linters.inputs) ConditionalParamType (class in galaxy.tool_util.linters.inputs) ConditionalParamTypeBool (class in galaxy.tool_util.linters.inputs) ConditionalStepWhen (class in galaxy.workflow.modules) ConditionalWhen (class in galaxy.tools.parameters.grouping) ConditionalWhenMissing (class in galaxy.tool_util.linters.inputs) condor_stop() (in module galaxy.jobs.runners.util.condor) condor_submit() (in module galaxy.jobs.runners.util.condor) CondorJobRunner (class in galaxy.jobs.runners.condor) Config (class in galaxy.objectstore.unittest_utils) config (galaxy.app.MinimalGalaxyApplication attribute) (galaxy.app.SentryClientMixin attribute) (galaxy.app_unittest_utils.galaxy_mock.MockApp attribute) CONFIG (galaxy.datatypes.binary.H5MLM attribute) config (galaxy.model.CloudAuthz attribute) (galaxy.model.VisualizationRevision attribute) (galaxy.model.WorkflowStep attribute) (galaxy.structured_app.BasicSharedApp attribute) (galaxy.structured_app.MinimalToolApp attribute) (galaxy.tools.remote_tool_eval.ToolApp attribute) (galaxy.tools.repositories.ValidationContext attribute) (galaxy.webapps.reports.app.UniverseApplication attribute) config_allows_origin() (in module galaxy.webapps.base.webapp) config_celery_app() (in module galaxy.celery) config_dict (galaxy.app_unittest_utils.galaxy_mock.MockAppConfig property) (galaxy.config.CommonConfigurationMixin attribute) config_directories_from_setting() (in module galaxy.util) config_directory() (galaxy.job_execution.compute_environment.ComputeEnvironment method) (galaxy.job_execution.compute_environment.SimpleComputeEnvironment method) config_elems_to_xml_file() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) config_file_from_args() (in module galaxy.util.script) config_is_ini (galaxy.main.GalaxyConfigBuilder property) config_is_ini() (in module galaxy.main_config) config_options (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.DependencyResolver attribute) config_paths (galaxy.config.config_manage.App attribute) config_to_dict() (in module galaxy.objectstore) config_value_for_host() (galaxy.config.GalaxyAppConfiguration method) ConfigDoesNotAllowException ConfigSerializer (class in galaxy.managers.configuration) Configuration (class in galaxy.webapps.reports.config) (in module galaxy.config) (in module tool_shed.webapp.config) configuration_manager (galaxy.webapps.galaxy.api.configuration.FastAPIConfiguration attribute) ConfigurationController (class in tool_shed.webapp.api.configuration) ConfigurationError, [1], [2] ConfigurationManager (class in galaxy.managers.configuration) configure_and_load() (galaxy.tools.data.RefgenieToolDataTable method) (galaxy.tools.data.TabularToolDataTable method) configure_entry_point() (galaxy.managers.interactivetool.InteractiveToolManager method) configure_entry_points() (galaxy.managers.interactivetool.InteractiveToolManager method) configure_fluent_log() (galaxy.app.MinimalGalaxyApplication method) configure_logging() (in module galaxy.config) configure_model_mapping() (in module galaxy.model.mapping) (in module galaxy.model.tool_shed_install.mapping) configure_provider() (galaxy.managers.cloud.CloudManager static method) configure_sentry_client() (galaxy.app.SentryClientMixin method) configured (galaxy.model.InteractiveToolEntryPoint attribute) configured_driver (galaxy.selenium.context.GalaxySeleniumContext attribute) (galaxy.selenium.context.GalaxySeleniumContextImpl attribute) (galaxy.selenium.jupyter_context.JupyterContextImpl attribute) (galaxy_test.selenium.jupyter_context.JupyterTestContextImpl attribute) configured_pools (galaxy.web_stack.ApplicationStack property) (galaxy.web_stack.WeblessApplicationStack property) ConfiguredDriver (class in galaxy.selenium.driver_factory) ConfiguredFileSources (class in galaxy.files) ConfiguredFileSourcesConfig (class in galaxy.files) ConfiguresDatabaseVault (class in galaxy_test.driver.integration_util) ConfiguresHandlers (class in galaxy.web_stack.handlers) ConfiguresObjectStores (class in galaxy_test.driver.integration_util) ConfigWatchers (class in galaxy.config_watchers) Conflict conformance_tests_gen() (in module galaxy_test.base.populators) connect() (galaxy.jobs.runners.util.cli.shell.rsh.ParamikoShell method) (in module galaxy.util.sqlite) ConnectAction (class in galaxy.workflow.refactor.schema) connection (galaxy.queue_worker.ControlTask property) connection_configuration (galaxy.tool_util.deps.container_classes.DockerContainer property) (galaxy.tool_util.deps.container_classes.SingularityContainer property) connection_drop_forced (galaxy.workflow.refactor.schema.RefactorActionExecutionMessageTypeEnum attribute) connection_from_config() (in module galaxy.queues) connections (galaxy.model.WorkflowStepInput attribute) ConnectivityTable (class in galaxy.datatypes.tabular) ConsensusTaxonomy (class in galaxy.datatypes.mothur) ConsensusXML (class in galaxy.datatypes.proteomics) construct_aliases() (galaxy.webapps.galaxy.api.FrameworkRouter static method) construct_path() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) ConsumesModelStores (class in galaxy.webapps.galaxy.services.base) contained_class (galaxy.managers.history_contents.HistoryContentsManager attribute) contained_class_manager_class (galaxy.managers.history_contents.HistoryContentsManager attribute) contained_class_type_name (galaxy.managers.history_contents.HistoryContentsManager attribute) Container (class in galaxy.di) (class in galaxy.tool_util.deps.container_classes) container (galaxy.model.Job attribute) container_description (galaxy.tool_util.deps.containers.ResolvedContainerDescription attribute) container_finder (galaxy.app.MinimalGalaxyApplication attribute) (galaxy.structured_app.StructuredApp attribute) container_from_element() (in module galaxy.tool_util.deps.requirements) container_ids (galaxy.web.proxy.ProxyMapping attribute) container_info (galaxy.model.JobContainerAssociation attribute) (galaxy.tool_util.deps.container_classes.DockerContainer attribute) (galaxy.tool_util.deps.container_classes.SingularityContainer attribute) container_interface (galaxy.web.proxy.ProxyMapping attribute) container_name (galaxy.model.JobContainerAssociation attribute) container_resolver (galaxy.tool_util.deps.containers.ResolvedContainerDescription attribute) container_resolvers_config_file (galaxy.config.GalaxyAppConfiguration attribute) container_testing() (in module galaxy.tool_util.deps.mulled.mulled_update_singularity_containers) container_type (galaxy.model.JobContainerAssociation attribute) (galaxy.tool_util.deps.container_classes.Container attribute) (galaxy.tool_util.deps.container_classes.DockerContainer attribute) (galaxy.tool_util.deps.container_classes.SingularityContainer attribute) (galaxy.tool_util.deps.container_resolvers.explicit.CachedExplicitSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.ExplicitSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.FallbackContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.FallbackNoRequirementsSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.FallbackSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.RequiresGalaxyEnvironmentSingularityContainerResolver attribute) ContainerDependency (class in galaxy.tool_util.deps.resolvers) ContainerDescription (class in galaxy.tool_util.deps.requirements) ContainerFinder (class in galaxy.tool_util.deps.containers) containerize_command() (galaxy.tool_util.deps.container_classes.Container method) (galaxy.tool_util.deps.container_classes.DockerContainer method) (galaxy.tool_util.deps.container_classes.SingularityContainer method) ContainerProtocol (class in galaxy.tool_util.deps.container_classes) ContainerRegistry (class in galaxy.tool_util.deps.containers) ContainerResolutionAPIController (class in galaxy.webapps.galaxy.api.container_resolution) ContainerResolutionView (class in galaxy.tool_util.deps.views) ContainerResolver (class in galaxy.tool_util.deps.container_resolvers) ContainerVolume (class in galaxy.tool_util.deps.container_volumes) contains_collection() (galaxy.model.HistoryDatasetCollectionAssociation method) contains_non_orm_filter() (galaxy.managers.base.ModelFilterParser method) contains_required_data() (in module galaxy.authnz.psa_authnz) contains_workflow_parameter() (in module galaxy.tools.parameters.basic) content (galaxy.model.FormValues attribute) (galaxy.model.Notification attribute) (galaxy.model.PageRevision attribute) (galaxy.schema.schema.CreatePagePayload attribute) (galaxy.schema.schema.MaterializeDatasetInstanceAPIRequest attribute) (galaxy.schema.schema.PageDetails attribute) (galaxy.schema.tasks.MaterializeDatasetInstanceTaskRequest attribute) (galaxy.tours.TourStep attribute) content_directory (galaxy.tool_util.biotools.BiotoolsMetadataSourceConfig attribute) (galaxy.tool_util.biotools.source.BiotoolsMetadataSourceConfig attribute) content_format (galaxy.model.PageRevision attribute) (galaxy.schema.schema.CreatePagePayload attribute) (galaxy.schema.schema.PageDetails attribute) content_id (galaxy.model.WorkflowStep property) (galaxy.schema.schema.WorkflowStepToExport attribute) (galaxy.schema.tasks.GenerateHistoryContentDownload attribute) (galaxy.schema.tasks.WriteHistoryContentTo attribute) (galaxy.workflow.refactor.schema.UpgradeSubworkflowAction attribute) content_item_by_attributes() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) content_type (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.schema.tasks.GenerateHistoryContentDownload attribute) (galaxy.schema.tasks.WriteHistoryContentTo attribute) (galaxy.tool_util.toolbox.views.definitions.ItemsFrom attribute) (galaxy.tool_util.toolbox.views.definitions.Label attribute) (galaxy.tool_util.toolbox.views.definitions.LabelShortcut attribute) (galaxy.tool_util.toolbox.views.definitions.Section attribute) (galaxy.tool_util.toolbox.views.definitions.SectionAlias attribute) (galaxy.tool_util.toolbox.views.definitions.SectionAliases attribute) (galaxy.tool_util.toolbox.views.definitions.Tool attribute) (galaxy.tool_util.toolbox.views.definitions.Workflow attribute) contents (galaxy.schema.schema.HistoryContentsWithStatsResult attribute) contents() (galaxy.managers.history_contents.HistoryContentsManager method) contents_active (galaxy.schema.schema.CustomHistoryView attribute) contents_count() (galaxy.managers.history_contents.HistoryContentsManager method) contents_iter() (galaxy.model.History method) contents_query() (galaxy.managers.history_contents.HistoryContentsManager method) contents_states (galaxy.schema.schema.CustomHistoryView attribute) contents_url (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.DCObject attribute) (galaxy.schema.schema.HDCASummary attribute) (galaxy.schema.schema.HistoryDetailed attribute) context (galaxy.model.base.ModelMapping property) (galaxy.model.UserAction attribute) context_remove() (galaxy.util.custom_logging.fluent_log.FluentTraceLogger method) context_set() (galaxy.util.custom_logging.fluent_log.FluentTraceLogger method) continue_pipeline() (galaxy.authnz.psa_authnz.Strategy method) control_queues (galaxy.queue_worker.ControlTask property) control_queues_from_config() (in module galaxy.queues) controller_name (galaxy.webapps.galaxy.api.annotations.HistoryAnnotationsController attribute) (galaxy.webapps.galaxy.api.annotations.HistoryContentAnnotationsController attribute) (galaxy.webapps.galaxy.api.annotations.WorkflowAnnotationsController attribute) (galaxy.webapps.galaxy.api.extended_metadata.HistoryDatasetExtendMetadataController attribute) (galaxy.webapps.galaxy.api.extended_metadata.LibraryDatasetExtendMetadataController attribute) (galaxy.webapps.galaxy.api.provenance.HDAProvenanceController attribute) (galaxy.webapps.galaxy.api.provenance.LDDAProvenanceController attribute) ControlTask (class in galaxy.queue_worker) conversion() (galaxy.webapps.galaxy.api.tools.ToolsController method) convert_bed_coords_to_gff() (in module galaxy.datatypes.util.gff_util) convert_dataset() (galaxy.datatypes.data.Data method) (galaxy.datatypes.dataproviders.dataset.ConvertedDatasetDataProvider method) (galaxy.model.DatasetInstance method) convert_function() (in module galaxy.datatypes.sniff) convert_gff_coords_to_bed() (in module galaxy.datatypes.util.gff_util) convert_legacy_destinations() (galaxy.jobs.JobConfiguration method) convert_newlines() (in module galaxy.datatypes.sniff) convert_newlines_sep2tabs() (in module galaxy.datatypes.sniff) convert_permitted_action_strings() (galaxy.security.RBACAgent method) (tool_shed.webapp.security.RBACAgent method) convert_sep2tabs() (in module galaxy.datatypes.sniff) convert_statjob_to_bunches() (galaxy.jobs.runners.pbs.PBSJobRunner method) convert_to_csv() (in module galaxy.datatypes.converters.tabular_csv) convert_to_tsv() (in module galaxy.datatypes.converters.tabular_csv) converted_newlines (galaxy.datatypes.sniff.ConvertResult attribute) (galaxy.datatypes.sniff.HandleUploadedDatasetFileInternalResponse attribute) (galaxy.datatypes.upload_util.HandleUploadResponse attribute) converted_path (galaxy.datatypes.sniff.ConvertResult attribute) (galaxy.datatypes.sniff.HandleUploadedDatasetFileInternalResponse attribute) (galaxy.datatypes.upload_util.HandleUploadResponse attribute) converted_regex (galaxy.datatypes.sniff.ConvertResult attribute) converted_spaces (galaxy.datatypes.sniff.HandleUploadedDatasetFileInternalResponse attribute) (galaxy.datatypes.upload_util.HandleUploadResponse attribute) ConvertedDatasetDataProvider (class in galaxy.datatypes.dataproviders.dataset) converter_safe() (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.DataToolParameter method) ConverterDependencyException converters() (galaxy.webapps.galaxy.api.datatypes.FastAPIDatatypes method) ConvertFunction (class in galaxy.datatypes.sniff) ConvertResult (class in galaxy.datatypes.sniff) cookie_path (galaxy.webapps.base.webapp.GalaxyWebTransaction property) cookies (galaxy.tool_util.verify.interactor.GalaxyInteractorApi attribute) (galaxy_test.base.api.AnonymousGalaxyInteractor attribute) (galaxy_test.base.api.ApiTestInteractor attribute) (galaxy_test.base.interactor.TestCaseGalaxyInteractor attribute) Cool (class in galaxy.datatypes.binary) copied_from_history_dataset_association (galaxy.model.DatasetInstance attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) copied_from_history_dataset_association_id (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) copied_from_history_dataset_collection_association (galaxy.model.HistoryDatasetCollectionAssociation attribute) copied_from_history_dataset_collection_association_id (galaxy.model.HistoryDatasetCollectionAssociation attribute) copied_from_job_id (galaxy.model.Job attribute) copied_from_ldda_id (galaxy.schema.schema.HDACommon attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDAObject attribute) copied_from_library_dataset_dataset_association (galaxy.model.DatasetInstance attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) copied_from_library_dataset_dataset_association_id (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) copied_to_history_dataset_associations (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) copied_to_history_dataset_collection_association (galaxy.model.HistoryDatasetCollectionAssociation attribute) copied_to_library_dataset_dataset_associations (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) copy() (galaxy.datatypes.util.gff_util.GFFFeature method) (galaxy.datatypes.util.gff_util.GFFInterval method) (galaxy.managers.base.ModelManager method) (galaxy.managers.collections.DatasetCollectionManager method) (galaxy.managers.datasets.DatasetManager method) (galaxy.managers.hdas.HDAManager method) (galaxy.managers.histories.HistoryManager method) (galaxy.model.DatasetCollection method) (galaxy.model.DatasetHash method) (galaxy.model.DatasetSource method) (galaxy.model.DatasetSourceHash method) (galaxy.model.History method) (galaxy.model.HistoryDatasetAssociation method) (galaxy.model.HistoryDatasetCollectionAssociation method) (galaxy.model.ItemTagAssociation method) (galaxy.model.JobParameter method) (galaxy.model.LibraryDatasetDatasetAssociation method) (galaxy.model.Visualization method) (galaxy.model.VisualizationRevision method) (galaxy.model.Workflow method) (galaxy.model.WorkflowComment method) (galaxy.model.WorkflowOutput method) (galaxy.model.WorkflowStepConnection method) (galaxy.model.WorkflowStepInput method) (galaxy.tool_util.cwl.cwltool_deps.CommentedMap method) (galaxy.tool_util.cwl.cwltool_deps.LoadingContext method) (galaxy.tool_util.cwl.cwltool_deps.RuntimeContext method) (galaxy.tool_util.deps.requirements.ToolRequirement method) (galaxy.tool_util.toolbox.panel.ToolPanelElements method) (galaxy.tool_util.toolbox.panel.ToolSection method) (galaxy.tool_util.toolbox.ToolSection method) (galaxy.tools.DefaultToolState method) (galaxy.util.odict.odict method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) copy_attributes() (galaxy.model.DatasetInstance method) (galaxy.model.HistoryDatasetAssociation method) copy_database_template() (in module galaxy_test.driver.driver_util) copy_dataset_instance_metadata_attributes() (in module galaxy.model.store) copy_dataset_permissions() (galaxy.job_execution.output_collect.PermissionProvider method) (galaxy.model.security.GalaxyRBACAgent method) (galaxy.model.store.discover.PermissionProvider method) (galaxy.model.store.discover.UnusedPermissionProvider method) copy_disk_sample_files_to_dir() (tool_shed.tools.tool_validator.ToolValidator method) copy_elements (galaxy.schema.schema.CreateNewCollectionPayload attribute) copy_file_from_manifest() (in module galaxy.tool_shed.util.hg_util) (in module tool_shed.util.hg_util) copy_from() (galaxy.model.HistoryDatasetAssociation method) copy_hid_for (galaxy.model.store.ObjectImportTracker attribute) copy_history() (galaxy_test.base.populators.BaseDatasetPopulator method) copy_item_annotation() (galaxy.model.item_attrs.UsesAnnotations method) copy_library_permissions() (galaxy.model.security.GalaxyRBACAgent method) copy_list() (in module galaxy.model) copy_sample_file() (in module galaxy.tool_shed.util.tool_util) (in module tool_shed.util.tool_util) copy_sample_files() (in module galaxy.tool_shed.util.tool_util) (in module tool_shed.util.tool_util) copy_tags_from() (galaxy.model.HasTags method) (galaxy.model.StoredWorkflow method) copy_tags_to() (galaxy.model.HistoryDatasetAssociation method) copy_to() (galaxy.model.WorkflowStep method) copy_to_collection() (galaxy.model.DatasetCollectionElement method) copy_value() (galaxy.model.custom_types.JSONType method) CorePlugin (class in galaxy.job_metrics.instrumenters.core) CoreWorkflowSchedulingPlugin (class in galaxy.workflow.schedulers.core) count (galaxy.model.History property) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.ArchivedHistorySummary attribute) (galaxy.schema.schema.CreatedCustomBuild attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.HistorySummary attribute) count() (galaxy.managers.base.ModelManager method) (galaxy.webapps.galaxy.services.histories.HistoriesService method) count_data_lines() (galaxy.datatypes.data.Text method) count_lines() (in module galaxy.datatypes.molecules) count_repositories_in_category() (in module tool_shed.util.shed_util_common) count_special_lines() (in module galaxy.datatypes.util.generic_util) count_stored_workflow_user_assocs() (galaxy.model.User method) country (galaxy.model.UserAddress attribute) CountTable (class in galaxy.datatypes.mothur) Cpt (class in galaxy.datatypes.binary) CpuInfoPlugin (class in galaxy.job_metrics.instrumenters.cpuinfo) CRAM (class in galaxy.datatypes.binary) create() (galaxy.managers.base.ModelManager method) (galaxy.managers.collections.DatasetCollectionManager method) (galaxy.managers.datasets.DatasetManager method) (galaxy.managers.folders.FolderManager method) (galaxy.managers.groups.GroupsManager method) (galaxy.managers.hdas.HDAManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.managers.metrics.MetricsManager method) (galaxy.managers.users.UserManager method) (galaxy.model.database_utils.MySQLDatabaseManager method) (galaxy.model.database_utils.PosgresDatabaseManager method) (galaxy.model.database_utils.SqliteDatabaseManager method) (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController method) (galaxy.webapps.galaxy.api.cloudauthz.CloudAuthzController method) (galaxy.webapps.galaxy.api.dynamic_tools.DynamicToolsController method) (galaxy.webapps.galaxy.api.extended_metadata.BaseExtendedMetadataController method) (galaxy.webapps.galaxy.api.folder_contents.FastAPILibraryFoldersContents method) (galaxy.webapps.galaxy.api.folders.FastAPILibraryFolders method) (galaxy.webapps.galaxy.api.forms.FormDefinitionAPIController method) (galaxy.webapps.galaxy.api.groups.FastAPIGroups method) (galaxy.webapps.galaxy.api.job_files.JobFilesAPIController method) (galaxy.webapps.galaxy.api.job_ports.JobPortsAPIController method) (galaxy.webapps.galaxy.api.libraries.FastAPILibraries method) (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method) (galaxy.webapps.galaxy.api.metrics.FastAPIMetrics method) (galaxy.webapps.galaxy.api.page_revisions.PageRevisionsController method) (galaxy.webapps.galaxy.api.pages.FastAPIPages method) (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method) (galaxy.webapps.galaxy.api.quotas.FastAPIQuota method) (galaxy.webapps.galaxy.api.roles.FastAPIRoles method) (galaxy.webapps.galaxy.api.sanitize_allow.SanitizeAllowController method) (galaxy.webapps.galaxy.api.tool_data.FastAPIToolData method) (galaxy.webapps.galaxy.api.tools.ToolsController method) (galaxy.webapps.galaxy.api.users.FastAPIUsers method) (galaxy.webapps.galaxy.api.visualizations.VisualizationsController method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.user.User method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) (galaxy.webapps.galaxy.services.histories.HistoriesService method) (galaxy.webapps.galaxy.services.libraries.LibrariesService method) (galaxy.webapps.galaxy.services.library_folder_contents.LibraryFolderContentsService method) (galaxy.webapps.galaxy.services.library_folders.LibraryFoldersService method) (galaxy.webapps.galaxy.services.pages.PagesService method) (galaxy.webapps.galaxy.services.quotas.QuotasService method) (galaxy_test.api.sharable.SharingApiTests method) (galaxy_test.api.test_histories.TestSharingHistory method) (galaxy_test.api.test_pages.TestPagesApi method) (galaxy_test.api.test_visualizations.TestVisualizationsApi method) (galaxy_test.api.test_workflows.TestWorkflowSharingApi method) (tool_shed.managers.groups.GroupManager method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) (tool_shed.webapp.api.categories.CategoriesController method) (tool_shed.webapp.api.groups.GroupsController method) (tool_shed.webapp.api.repositories.RepositoriesController method) (tool_shed.webapp.api.users.UsersController method) (tool_shed.webapp.controllers.user.User method) create_additional_database_objects() (in module galaxy.model.mapping) create_and_write_tmp_file() (in module galaxy.util.tool_shed.xml_util) (in module tool_shed.util.xml_util) create_api_key() (galaxy.managers.api_keys.ApiKeyManager method) (galaxy.webapps.galaxy.api.users.FastAPIUsers method) (galaxy.webapps.galaxy.services.users.UsersService method) create_archive() (in module galaxy.tools.imp_exp.export_history) create_category() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) (tool_shed.webapp.controllers.admin.AdminController method) create_changeset_revision() (tool_shed.webapp.api.repositories.RepositoriesController method) create_collection() (galaxy.tools.actions.OutputCollections method) create_compiler_class() (in module galaxy.util.template) create_contents_from_store() (galaxy_test.base.populators.BaseDatasetPopulator method) create_contents_from_store_raw() (galaxy_test.base.populators.BaseDatasetPopulator method) create_database() (in module galaxy.model.database_utils) create_database_objects() (in module galaxy.model.tool_shed_install.mapping) create_dataset() (galaxy.model.store.discover.ModelPersistenceContext method) create_dataset_collection() (galaxy.managers.collections.DatasetCollectionManager method) create_dataset_request() (galaxy_test.base.populators.LibraryPopulator method) create_deferred_hda() (galaxy_test.base.populators.BaseDatasetPopulator method) create_dynamic_tool() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) (galaxy.tools.ToolBox method) create_entry() (galaxy.files.sources.BaseFilesSource method) (galaxy.managers.remote_files.RemoteFilesManager method) (galaxy.webapps.galaxy.api.remote_files.FastAPIRemoteFiles method) create_entry_points() (galaxy.managers.interactivetool.InteractiveToolManager method) create_export_association() (galaxy.managers.histories.HistoryExportManager method) create_extended_metadata() (galaxy.webapps.base.controller.UsesExtendedMetadataMixin method) create_extra_files_path() (galaxy.model.Dataset method) create_fetch() (galaxy.webapps.galaxy.services.tools.ToolsService method) create_file() (galaxy.app_unittest_utils.galaxy_mock.MockDir method) (galaxy.datatypes.dataproviders.external.TempfileDataProvider method) create_file_source_config_file_on() (in module galaxy_test.driver.integration_setup) create_for_history() (galaxy.model.JobExportHistoryArchive static method) create_foreign_key() (in module galaxy.model.migrations.util) create_form() (galaxy.webapps.galaxy.controllers.forms.Forms method) create_from_store() (galaxy.webapps.galaxy.api.libraries.FastAPILibraries method) (galaxy.webapps.galaxy.services.histories.HistoriesService method) (galaxy.webapps.galaxy.services.libraries.LibrariesService method) (galaxy_test.base.populators.BaseDatasetPopulator method) (galaxy_test.base.populators.LibraryPopulator method) create_from_store_async() (galaxy.webapps.galaxy.services.histories.HistoriesService method) (galaxy_test.base.populators.BaseDatasetPopulator method) create_from_store_raw() (galaxy_test.base.populators.BaseDatasetPopulator method) (galaxy_test.base.populators.LibraryPopulator method) create_from_store_raw_async() (galaxy_test.base.populators.BaseDatasetPopulator method) create_galaxy_docker_image() (tool_shed.webapp.controllers.repository.RepositoryController method) create_genome_filter() (galaxy.managers.genomes.GenomeFilterMixin method) create_group() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (tool_shed.util.admin_util.Admin method) create_hdca() (galaxy.job_execution.output_collect.JobContext method) (galaxy.model.store.discover.SessionlessModelPersistenceContext method) create_hgrc_file() (in module tool_shed.util.hg_util) create_history() (galaxy_test.selenium.test_histories_list.TestSavedHistories method) create_index() (in module galaxy.model.migrations.util) create_interactivetool() (galaxy.managers.interactivetool.InteractiveToolManager method) create_invocation_from_store() (galaxy_test.base.populators.BaseWorkflowPopulator method) create_invocation_from_store_raw() (galaxy_test.base.populators.BaseWorkflowPopulator method) create_item_slug() (galaxy.managers.sharable.SlugBuilder method) create_job() (in module galaxy.tools.actions.upload_common) create_library_folder() (galaxy.job_execution.output_collect.JobContext method) (galaxy.model.store.discover.ModelPersistenceContext method) (galaxy.model.store.discover.SessionlessModelPersistenceContext method) create_list_filter() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) create_list_from_pairs() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method) create_list_in_history() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method) create_list_of_list_in_history() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method) create_list_of_pairs_in_history() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method) create_list_payload() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method) create_log_file() (galaxy.jobs.runners.godocker.GodockerJobRunner method) create_mako_template_lookup() (galaxy.webapps.base.webapp.WebApplication method) create_nested_collection() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method) create_new_current() (galaxy.webapps.galaxy.controllers.history.HistoryController method) create_new_library() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) create_new_session() (in module galaxy.webapps.base.webapp) create_new_user() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (tool_shed.util.admin_util.Admin method) create_numeric_filter() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) create_objects_from_store() (galaxy.webapps.galaxy.services.base.ConsumesModelStores method) (in module galaxy.managers.model_stores) create_or_update_repository_metadata() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) create_or_update_tool_shed_repository() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) create_or_update_workflow_output() (galaxy.model.WorkflowStep method) create_outdir() (galaxy.tool_util.cwl.cwltool_deps.RuntimeContext method) create_page() (galaxy.managers.pages.PageManager method) (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) create_page_and_edit() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) create_pair_in_history() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method) create_pair_payload() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method) create_panel_section() (in module galaxy.queue_worker) create_paramfile() (in module galaxy.tools.actions.upload_common) create_private_user_role() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) (tool_shed.webapp.security.RBACAgent method) create_quota() (galaxy.managers.quotas.QuotaManager method) (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (galaxy_test.base.populators.BaseDatasetPopulator method) create_repo_info_dict() (in module tool_shed.util.repository_util) create_report() (galaxy.tools.errors.ErrorReporter method) create_repository() (in module tool_shed.managers.repositories) (in module tool_shed.util.repository_util) (tool_shed.webapp.controllers.repository.RepositoryController method) create_repository_admin_role() (in module tool_shed.util.repository_util) create_repository_dependency() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) create_repository_dependency_objects() (galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) create_role() (galaxy.managers.roles.RoleManager method) (galaxy.model.security.GalaxyRBACAgent method) (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (galaxy_test.base.populators.BaseDatasetPopulator method) (tool_shed.util.admin_util.Admin method) create_root() (galaxy.app_unittest_utils.galaxy_mock.MockDir method) create_section() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) create_social_auth() (galaxy.model.UserAuthnzToken class method) create_string_filter() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) create_structure() (galaxy.app_unittest_utils.galaxy_mock.MockDir method) create_subworkflow_invocation_for_step() (galaxy.model.WorkflowInvocation method) create_table() (in module galaxy.model.migrations.util) create_tables (tool_shed.webapp.model.mapping.ToolShedModelMapping attribute) create_tag_filter() (galaxy.managers.taggable.TaggableFilterMixin method) create_tag_handler_session() (galaxy.model.tags.TagHandler method) create_time (galaxy.model.APIKeys attribute) (galaxy.model.CleanupEvent attribute) (galaxy.model.CleanupEventDatasetAssociation attribute) (galaxy.model.CleanupEventHistoryAssociation attribute) (galaxy.model.CleanupEventHistoryDatasetAssociationAssociation attribute) (galaxy.model.CleanupEventImplicitlyConvertedDatasetAssociationAssociation attribute) (galaxy.model.CleanupEventLibraryAssociation attribute) (galaxy.model.CleanupEventLibraryDatasetAssociation attribute) (galaxy.model.CleanupEventLibraryDatasetDatasetAssociationAssociation attribute) (galaxy.model.CleanupEventLibraryFolderAssociation attribute) (galaxy.model.CleanupEventMetadataFileAssociation attribute) (galaxy.model.CloudAuthz attribute) (galaxy.model.DataManagerHistoryAssociation attribute) (galaxy.model.DataManagerJobAssociation attribute) (galaxy.model.Dataset attribute) (galaxy.model.DatasetCollection attribute) (galaxy.model.DatasetPermissions attribute) (galaxy.model.DefaultQuotaAssociation attribute) (galaxy.model.DynamicTool attribute) (galaxy.model.Event attribute) (galaxy.model.FormDefinition attribute) (galaxy.model.FormDefinitionCurrent attribute) (galaxy.model.FormValues attribute) (galaxy.model.GalaxySession attribute) (galaxy.model.GalaxySessionToHistoryAssociation attribute) (galaxy.model.Group attribute) (galaxy.model.GroupQuotaAssociation attribute) (galaxy.model.GroupRoleAssociation attribute) (galaxy.model.History attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) (galaxy.model.Job attribute) (galaxy.model.JobStateHistory attribute) (galaxy.model.Library attribute) (galaxy.model.LibraryDataset attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationPermissions attribute) (galaxy.model.LibraryDatasetPermissions attribute) (galaxy.model.LibraryFolder attribute) (galaxy.model.LibraryFolderPermissions attribute) (galaxy.model.LibraryPermissions attribute) (galaxy.model.MetadataFile attribute) (galaxy.model.Notification attribute) (galaxy.model.Page attribute) (galaxy.model.PageRevision attribute) (galaxy.model.Quota attribute) (galaxy.model.Role attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.StoreExportAssociation attribute) (galaxy.model.Task attribute) (galaxy.model.tool_shed_install.RepositoryDependency attribute) (galaxy.model.tool_shed_install.RepositoryRepositoryDependencyAssociation attribute) (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.model.tool_shed_install.ToolVersion attribute) (galaxy.model.User attribute) (galaxy.model.UserAction attribute) (galaxy.model.UserAddress attribute) (galaxy.model.UserGroupAssociation attribute) (galaxy.model.UserQuotaAssociation attribute) (galaxy.model.UserRoleAssociation attribute) (galaxy.model.Vault attribute) (galaxy.model.Visualization attribute) (galaxy.model.VisualizationRevision attribute) (galaxy.model.Workflow attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowStep attribute) (galaxy.schema.APIKeyModel attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.DatasetSummary attribute) (galaxy.schema.schema.DCSummary attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HistoryDetailed attribute) (galaxy.schema.schema.HistoryItemCommon attribute) (galaxy.schema.schema.InvocationSortByEnum attribute) (galaxy.schema.schema.JobBaseModel attribute) (galaxy.schema.schema.JobIndexSortByEnum attribute) (galaxy.schema.schema.LibraryFolderItemBase attribute) (galaxy.schema.schema.LibraryLegacySummary attribute) (galaxy.schema.schema.ObjectExportTaskResponse attribute) (galaxy.schema.schema.PageSummary attribute) (galaxy.schema.schema.StoredWorkflowSummary attribute) (tool_shed.webapp.model.APIKeys attribute) (tool_shed.webapp.model.Category attribute) (tool_shed.webapp.model.GalaxySession attribute) (tool_shed.webapp.model.Group attribute) (tool_shed.webapp.model.GroupRoleAssociation attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) (tool_shed.webapp.model.RepositoryRatingAssociation attribute) (tool_shed.webapp.model.RepositoryRoleAssociation attribute) (tool_shed.webapp.model.Role attribute) (tool_shed.webapp.model.User attribute) (tool_shed.webapp.model.UserGroupAssociation attribute) (tool_shed.webapp.model.UserRoleAssociation attribute) create_time_pretty (galaxy.schema.schema.LibrarySummary attribute) create_tmpdir() (galaxy.tool_util.cwl.cwltool_deps.RuntimeContext method) create_tool() (galaxy.managers.tools.DynamicToolManager method) (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) (galaxy.tools.ToolBox method) (galaxy_test.base.populators.BaseDatasetPopulator method) create_tool_filter() (galaxy.managers.tools.ToolFilterMixin method) create_tool_from_path() (galaxy_test.base.populators.BaseDatasetPopulator method) create_tool_from_representation() (in module galaxy.tools) create_tool_from_source() (in module galaxy.tools) create_transformer_model() (galaxy.tools.recommendations.ToolRecommendations method) create_unique_constraint() (in module galaxy.model.migrations.util) create_unique_slug() (galaxy.managers.sharable.SharableModelManager method) create_user() (galaxy.authnz.custos_authnz.OIDCAuthnzBase method) (galaxy.authnz.managers.AuthnzManager method) (galaxy.model.UserAuthnzToken class method) (galaxy.webapps.galaxy.controllers.authnz.OIDC method) create_user_role() (galaxy.model.security.GalaxyRBACAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) (tool_shed.webapp.security.RBACAgent method) create_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method) create_workflow_response() (galaxy_test.base.populators.BaseWorkflowPopulator method) create_working_directory_for_job() (in module galaxy.job_execution.setup) created_from_basename (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance property) (galaxy.model.store.DatasetAttributeImportModel attribute) (galaxy.model.store.discover.JsonCollectedDatasetMatch property) (galaxy.schema.fetch_data.BaseDataElement attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) created_time (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.JobContainerAssociation attribute) CreatedCustomBuild (class in galaxy.schema.schema) CreatedEntryResponse (class in galaxy.schema.remote_files) CreatedUserModel (class in galaxy.schema.schema) CreatedWorkflow (class in galaxy.managers.workflows) CreateEntryPayload (class in galaxy.schema.remote_files) CreateForeignKey (class in galaxy.model.migrations.util) CreateHistoryFromStore (class in galaxy.schema.schema) CreateHistoryPayload (class in galaxy.schema.schema) CreateIndex (class in galaxy.model.migrations.util) CreateLibrariesFromStore (class in galaxy.schema.schema) CreateLibraryFilePayload (class in galaxy.schema.schema) CreateLibraryFolderPayload (class in galaxy.schema.schema) CreateLibraryPayload (class in galaxy.schema.schema) CreateMetricsPayload (class in galaxy.managers.metrics) CreateNewCollectionPayload (class in galaxy.schema.schema) CreatePagePayload (class in galaxy.schema.schema) CreateTable (class in galaxy.model.migrations.util) CreateUniqueConstraint (class in galaxy.model.migrations.util) creating_job (galaxy.model.DatasetInstance property) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) creating_job() (galaxy.managers.datasets.DatasetAssociationManager method) creating_job_associations (galaxy.model.DatasetInstance attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) Creator (class in galaxy.schema.schema) creator (galaxy.schema.schema.WorkflowToExport attribute) (galaxy.workflow.refactor.schema.UpdateCreatorAction attribute) creator_metadata (galaxy.model.Workflow attribute) credential_url (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute) csFasta (class in galaxy.datatypes.sequence) css() (galaxy.app_unittest_utils.galaxy_mock.MockTemplateHelpers method) (in module galaxy.web.framework.helpers) CSV (class in galaxy.datatypes.tabular) ctime (galaxy.files.sources.RemoteFile attribute) (galaxy.schema.remote_files.RemoteFile attribute) CTLresult (class in galaxy.datatypes.text) ctx_rev (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.schema.schema.InstalledToolShedRepository attribute) (galaxy.tool_shed.galaxy_install.update_repository_manager.UpdateToChangeset attribute) CuffDiffSQlite (class in galaxy.datatypes.binary) cur_filter_pref_name (galaxy.web.legacy_framework.grids.Grid attribute) cur_sort_key_pref_name (galaxy.web.legacy_framework.grids.Grid attribute) current (galaxy.schema.schema.LibraryPermissionScope attribute) current_galaxy_session (galaxy.model.User attribute) (tool_shed.webapp.model.User property) current_history (galaxy.model.GalaxySession attribute) current_history() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) current_history_id (galaxy.model.GalaxySession attribute) current_history_id() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) current_history_json() (galaxy.webapps.galaxy.controllers.history.HistoryController method) current_history_publish() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) current_user() (galaxy.managers.users.UserManager method) current_version (galaxy.tools.safe_update attribute) CurrentUserSerializer (class in galaxy.managers.users) CustomBuildBaseModel (class in galaxy.schema.schema) CustomBuildCreationPayload (class in galaxy.schema.schema) CustomBuildLenType (class in galaxy.schema.schema) CustomBuildModel (class in galaxy.schema.schema) CustomBuildsCollection (class in galaxy.schema.schema) CustomBuildsMetadataResponse (class in galaxy.schema.schema) CustomHistoryView (class in galaxy.schema.schema) CustomTrack (class in galaxy.datatypes.interval) custos_auth (galaxy.model.User attribute) CustosAuthFactory (class in galaxy.authnz.custos_authnz) CustosAuthnzConfiguration (class in galaxy.authnz.custos_authnz) CustosAuthnzToken (class in galaxy.model) CustosVault (class in galaxy.security.vault) cut_and_decode() (galaxy.managers.folders.FolderManager method) cut_the_prefix() (galaxy.managers.folders.FolderManager method) CWLDescriptionMissing (class in galaxy.tool_util.linters.cwl) CWLDockerGood (class in galaxy.tool_util.linters.cwl) CWLDockerMissing (class in galaxy.tool_util.linters.cwl) CWLHelpTODO (class in galaxy.tool_util.linters.cwl) CWLInValid (class in galaxy.tool_util.linters.cwl) CwlPopulator (class in galaxy_test.base.populators) CwlRun (class in galaxy_test.base.populators) CwlToolRun (class in galaxy_test.base.populators) CwlToolSource (class in galaxy.tool_util.parser.cwl) CWLValid (class in galaxy.tool_util.linters.cwl) CWLVersionGood (class in galaxy.tool_util.linters.cwl) CWLVersionMissing (class in galaxy.tool_util.linters.cwl) CWLVersionUnknown (class in galaxy.tool_util.linters.cwl) CwlWorkflowOutput (class in galaxy.tool_util.cwl.runnable) CwlWorkflowRun (class in galaxy_test.base.populators) CycleError

D

DAA (class in galaxy.datatypes.binary) Data (class in galaxy.datatypes.data) DATA (galaxy.model.Dataset.conversion_messages attribute) (galaxy.model.DatasetInstance.conversion_messages attribute) data (galaxy.model.ExtendedMetadata attribute) (galaxy.model.PSAPartial attribute) (galaxy.model.WorkflowComment attribute) DATA (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute) data (galaxy.tools.data.RefgenieToolDataTable attribute) (galaxy.tools.data.TabularToolDataTable attribute) (galaxy.tools.data.ToolDataTable attribute) (galaxy.webapps.galaxy.controllers.admin.DatatypesEntryT attribute) DATA_COLLECTION (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute) data_conversion_status() (galaxy.managers.hdas.HDAManager method) data_dir (galaxy.app_unittest_utils.galaxy_mock.MockAppConfig attribute) (galaxy.model.unittest_utils.data_app.GalaxyDataTestConfig attribute) (galaxy.model.unittest_utils.GalaxyDataTestConfig attribute) data_line_offset (galaxy.datatypes.tabular.SraManifest attribute) (galaxy.datatypes.tabular.TabularData attribute) data_manager_association (galaxy.model.Job attribute) data_manager_configs (galaxy.config_watchers.ConfigWatchers property) data_manager_histories (galaxy.model.User attribute) data_manager_id (galaxy.model.DataManagerJobAssociation attribute) data_manager_tar_file (in module tool_shed.test.functional.test_1460_data_managers) data_managers (galaxy.tools.data_manager.manager.DataManagers attribute) data_managers_list() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) data_managers_path (galaxy.tool_shed.galaxy_install.tools.data_manager.DataManagerHandler property) data_provider_registry (galaxy.structured_app.StructuredApp attribute) data_source_redirect() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) data_sources (galaxy.datatypes.binary.Bam attribute) (galaxy.datatypes.binary.BigBed attribute) (galaxy.datatypes.binary.BigWig attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.interval.Bed attribute) (galaxy.datatypes.interval.BedGraph attribute) (galaxy.datatypes.interval.ChromatinInteractions attribute) (galaxy.datatypes.interval.ENCODEPeak attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.interval.Wiggle attribute) (galaxy.datatypes.tabular.BaseVcf attribute) (galaxy.datatypes.tabular.Pileup attribute) (galaxy.datatypes.tabular.Psl attribute) (galaxy.datatypes.tabular.Sam attribute) data_table_names (galaxy.tools.data_manager.manager.DataManager property) data_tables (galaxy.managers.tool_data.ToolDataManager property) (galaxy.tools.data.ToolDataTableManager attribute) data_tables_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) data_type (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) data_types_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) data_value() (galaxy.selenium.smart_components.SmartTarget method) database_conf() (in module galaxy_test.driver.driver_util) database_connection (galaxy.app_unittest_utils.galaxy_mock.MockAppConfig attribute) (galaxy.config.GalaxyAppConfiguration attribute) (galaxy.managers.genomes.GenomeFilterMixin attribute) (galaxy.model.unittest_utils.data_app.GalaxyDataTestConfig attribute) (galaxy.model.unittest_utils.GalaxyDataTestConfig attribute) database_exists() (in module galaxy.model.database_utils) DATABASE_OPERATION (galaxy.selenium.navigates_galaxy.WAIT_TYPES attribute) DatabaseConfig (class in galaxy.model.migrations) DatabaseHeartbeat (class in galaxy.model.database_heartbeat) DatabaseManager (class in galaxy.model.database_utils) DatabaseOperationTool (class in galaxy.tools) DatabaseStateVerifier (class in galaxy.model.migrations) DatabaseVault (class in galaxy.security.vault) DataCollectionToolParameter (class in galaxy.tools.parameters) (class in galaxy.tools.parameters.basic) DataDestinationTool (class in galaxy.tools) DataElementsFromTarget (class in galaxy.schema.fetch_data) DataElementsTarget (class in galaxy.schema.fetch_data) DataIn (class in galaxy.datatypes.genetics) DataItemSourceType (class in galaxy.schema.schema) DataManager (class in galaxy.tools.data_manager.manager) (class in galaxy.webapps.galaxy.controllers.data_manager) DataManagerHandler (class in galaxy.tool_shed.galaxy_install.tools.data_manager) DataManagerHistoryAssociation (class in galaxy.model) DataManagerJobAssociation (class in galaxy.model) DataManagerJson (class in galaxy.datatypes.text) DataManagers (class in galaxy.tools.data_manager.manager) DataManagerTool (class in galaxy.tools) DataManagerToolAction (class in galaxy.tools.actions.data_manager) DataMeta (class in galaxy.datatypes.data) DataMetaFilter (class in galaxy.tools.parameters.dynamic_options) DataProvider (class in galaxy.datatypes.dataproviders.base) dataprovider() (galaxy.datatypes.data.Data method) dataprovider_factory() (in module galaxy.datatypes.dataproviders.decorators) DataProviderRegistry (class in galaxy.visualization.data_providers.registry) dataproviders (galaxy.datatypes.binary.Bam attribute) (galaxy.datatypes.binary.SQlite attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.data.Text attribute) (galaxy.datatypes.graph.Sif attribute) (galaxy.datatypes.graph.Xgmml attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.interval.Wiggle attribute) (galaxy.datatypes.tabular.BaseCSV attribute) (galaxy.datatypes.tabular.BaseVcf attribute) (galaxy.datatypes.tabular.CSV attribute) (galaxy.datatypes.tabular.Pileup attribute) (galaxy.datatypes.tabular.Sam attribute) (galaxy.datatypes.tabular.Tabular attribute) (galaxy.datatypes.tabular.TabularData attribute) (galaxy.datatypes.tabular.TSV attribute) (galaxy.datatypes.xml.GenericXml attribute) Dataset (class in galaxy.model) (class in galaxy.tools.parameters.grouping) dataset (galaxy.job_execution.setup.JobOutput attribute) (galaxy.model.DatasetCollectionElement property) (galaxy.model.DatasetHash attribute) (galaxy.model.DatasetPermissions attribute) (galaxy.model.DatasetSource attribute) (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) (galaxy.model.JobExportHistoryArchive attribute) (galaxy.model.JobExternalOutputMetadata property) (galaxy.model.JobToInputDatasetAssociation attribute) (galaxy.model.JobToInputLibraryDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetAssociation attribute) (galaxy.model.JobToOutputLibraryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.MetadataFile property) (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.schema.schema.HistoryContentType attribute) Dataset.conversion_messages (class in galaxy.model) dataset_access_mapping() (galaxy.model.security.GalaxyRBACAgent method) dataset_action_tuples (galaxy.model.DatasetCollection property) dataset_actions (galaxy.model.Role attribute) dataset_collection (galaxy.model.HistoryDatasetCollectionRatingAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.JobToImplicitOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetCollectionAnnotationAssociation attribute) (galaxy.model.LibraryDatasetCollectionRatingAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) (galaxy.schema.schema.DCEType attribute) (galaxy.schema.schema.HistoryContentType attribute) dataset_collection_description() (in module galaxy.tool_util.parser.output_collection_def) dataset_collection_element (galaxy.model.JobToInputDatasetCollectionElementAssociation attribute) dataset_collection_element_id (galaxy.model.JobToInputDatasetCollectionElementAssociation attribute) dataset_collection_id (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.ImplicitlyCreatedDatasetCollectionInput attribute) (galaxy.model.JobToImplicitOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetCollectionAssociation attribute) (galaxy.model.JobToOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) dataset_collection_instance (galaxy.model.JobToOutputDatasetCollectionAssociation attribute) dataset_collection_manager (galaxy.app_unittest_utils.galaxy_mock.MockApp attribute) (galaxy.structured_app.MinimalManagerApp attribute) dataset_collection_populator (galaxy_test.api.test_tools.TestsTools attribute) (galaxy_test.base.populators.BaseWorkflowPopulator attribute) dataset_collections (galaxy.model.History attribute) dataset_collector() (in module galaxy.job_execution.output_collect) dataset_collector_descriptions (galaxy.tool_util.parser.output_objects.ToolOutputCollection property) dataset_collector_descriptions_from_elem() (in module galaxy.tool_util.parser.output_collection_def) dataset_collector_descriptions_from_list() (in module galaxy.tool_util.parser.output_collection_def) dataset_collector_descriptions_from_output_dict() (in module galaxy.tool_util.parser.output_collection_def) dataset_column_dataprovider() (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.TabularData method) dataset_content_needs_grooming() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.binary.BamInputSorted method) (galaxy.datatypes.binary.BamQuerynameSorted method) (galaxy.datatypes.data.Data method) dataset_dbkeys_and_extensions_summary (galaxy.model.HistoryDatasetCollectionAssociation property) dataset_dict_dataprovider() (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.TabularData method) dataset_elements (galaxy.model.DatasetCollection property) dataset_elements_and_identifiers() (galaxy.model.DatasetCollection method) dataset_id (galaxy.model.CleanupEventDatasetAssociation attribute) (galaxy.model.DatasetHash attribute) (galaxy.model.DatasetPermissions attribute) (galaxy.model.DatasetSource attribute) (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.JobExportHistoryArchive attribute) (galaxy.model.JobToInputDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDASummary attribute) (galaxy.schema.tasks.ComputeDatasetHashTaskRequest attribute) dataset_id_to_path (galaxy.model.store.BagDirectoryModelExportStore attribute) (galaxy.model.store.BcoModelExportStore attribute) (galaxy.model.store.ROCrateModelExportStore attribute) (galaxy.model.store.WorkflowInvocationOnlyExportStore attribute) (galaxy.model.store.WriteCrates attribute) dataset_ids (galaxy.schema.tasks.PurgeDatasetsTaskRequest attribute) dataset_implicit_conversions (galaxy.model.store.BagDirectoryModelExportStore attribute) (galaxy.model.store.BcoModelExportStore attribute) (galaxy.model.store.ROCrateModelExportStore attribute) (galaxy.model.store.WorkflowInvocationOnlyExportStore attribute) (galaxy.model.store.WriteCrates attribute) dataset_info() (galaxy.webapps.reports.controllers.system.System method) dataset_instance (galaxy.model.DatasetCollectionElement property) dataset_instances (galaxy.model.DatasetCollection property) (galaxy.model.DatasetCollectionElement property) (galaxy.model.DatasetCollectionInstance property) dataset_is_private_to_a_user() (galaxy.model.security.GalaxyRBACAgent method) dataset_is_private_to_user() (galaxy.model.security.GalaxyRBACAgent method) dataset_is_public() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) dataset_is_unrestricted() (galaxy.model.security.GalaxyRBACAgent method) dataset_ldda (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) dataset_path (galaxy.job_execution.setup.JobOutput attribute) dataset_path_rewriter (galaxy.job_execution.setup.JobIO property) dataset_path_rewrites() (in module galaxy.job_execution.datasets) dataset_path_to_extra_path() (in module galaxy.job_execution.compute_environment) dataset_permission_map_for_access() (galaxy.model.security.GalaxyRBACAgent method) dataset_populator (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi attribute) (galaxy_test.api.test_datasets.TestDatasetsApi attribute) (galaxy_test.api.test_folder_contents.TestFolderContentsApi attribute) (galaxy_test.api.test_folders.TestFoldersApi attribute) (galaxy_test.api.test_group_roles.TestGroupRolesApi attribute) (galaxy_test.api.test_group_users.TestGroupUsersApi attribute) (galaxy_test.api.test_groups.TestGroupsApi attribute) (galaxy_test.api.test_history_contents.TestHistoryContentsApi attribute) (galaxy_test.api.test_history_contents_provenance.TestProvenance attribute) (galaxy_test.api.test_jobs.TestJobsApi attribute) (galaxy_test.api.test_libraries.TestLibrariesApi attribute) (galaxy_test.api.test_page_revisions.TestPageRevisionsApi attribute) (galaxy_test.api.test_pages.BasePagesApiTestCase attribute) (galaxy_test.api.test_pages.TestPagesApi attribute) (galaxy_test.api.test_roles.TestRolesApi attribute) (galaxy_test.api.test_tools.TestsTools attribute) (galaxy_test.api.test_tools.TestToolsApi attribute) (galaxy_test.api.test_tools_upload.TestToolsUpload attribute) (galaxy_test.api.test_workflow_extraction.TestWorkflowExtractionApi attribute) (galaxy_test.api.test_workflows.BaseWorkflowsApiTestCase attribute) (galaxy_test.api.test_workflows.ChangeDatatypeTests attribute) (galaxy_test.api.test_workflows.TestAdminWorkflowsApi attribute) (galaxy_test.api.test_workflows.TestWorkflowsApi attribute) (galaxy_test.api.test_workflows_cwl.BaseCwlWorkflowsApiTestCase attribute) (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi attribute) (galaxy_test.base.populators.BaseDatasetCollectionPopulator attribute) (galaxy_test.base.populators.BaseWorkflowPopulator attribute) (galaxy_test.base.populators.DatasetCollectionPopulator attribute) (galaxy_test.driver.integration_util.IntegrationInstance attribute) (galaxy_test.driver.integration_util.IntegrationTestCase attribute) dataset_source_id (galaxy.model.DatasetSourceHash attribute) dataset_states_and_extensions_summary (galaxy.model.DatasetCollection property) dataset_storage_info() (galaxy_test.base.populators.BaseDatasetPopulator method) dataset_storage_info_raw() (galaxy_test.base.populators.BaseDatasetPopulator method) dataset_to_param() (in module galaxy_test.api.test_tools) dataset_type (galaxy.visualization.data_providers.genome.BamDataProvider attribute) (galaxy.visualization.data_providers.genome.BBIDataProvider attribute) (galaxy.visualization.data_providers.genome.BedDataProvider attribute) (galaxy.visualization.data_providers.genome.ChromatinInteractionsDataProvider attribute) (galaxy.visualization.data_providers.genome.ENCODEPeakDataProvider attribute) (galaxy.visualization.data_providers.genome.GenomeDataProvider attribute) (galaxy.visualization.data_providers.genome.IntervalDataProvider attribute) (galaxy.visualization.data_providers.genome.IntervalIndexDataProvider attribute) (galaxy.visualization.data_providers.genome.RawGFFDataProvider attribute) (galaxy.visualization.data_providers.genome.SamDataProvider attribute) (galaxy.visualization.data_providers.genome.TabixDataProvider attribute) (galaxy.visualization.data_providers.genome.VcfDataProvider attribute) (galaxy.visualization.data_providers.genome.VcfTabixDataProvider attribute) (galaxy.visualization.data_providers.phyloviz.PhylovizDataProvider attribute) dataset_version (galaxy.model.JobToInputDatasetAssociation attribute) dataset_wrapper_to_directory_json() (in module galaxy.tool_util.cwl.representation) dataset_wrapper_to_file_json() (in module galaxy.tool_util.cwl.representation) DatasetAccessPermissionFailedException DatasetAssociationDeserializer (class in galaxy.managers.datasets) DatasetAssociationFilterParser (class in galaxy.managers.datasets) DatasetAssociationManager (class in galaxy.managers.datasets) DatasetAssociationRoles (class in galaxy.schema.schema) DatasetAssociationSerializer (class in galaxy.managers.datasets) DatasetAttributeImportModel (class in galaxy.model.store) DatasetCollection (class in galaxy.model) DatasetCollectionDescription (class in galaxy.tool_util.parser.output_collection_def) DatasetCollectionElement (class in galaxy.model) DatasetCollectionInstance (class in galaxy.model) DatasetCollectionManager (class in galaxy.managers.collections) DatasetCollectionPopulatedState (class in galaxy.schema.schema) DatasetCollectionPopulator (class in galaxy_test.base.populators) DatasetCollectionType (class in galaxy.model.dataset_collections.types) DatasetCollectionTypesRegistry (class in galaxy.model.dataset_collections.registry) DatasetCollectionWrapper (class in galaxy.tools.wrappers) DatasetCollector (class in galaxy.job_execution.output_collect) DatasetColumnarDataProvider (class in galaxy.datatypes.dataproviders.dataset) DatasetDataProvider (class in galaxy.datatypes.dataproviders.dataset) DatasetDictDataProvider (class in galaxy.datatypes.dataproviders.dataset) DatasetEmptyValidator (class in galaxy.tools.parameters.validation) DatasetExtraFilesPathEmptyValidator (class in galaxy.tools.parameters.validation) DatasetFilenameWrapper (class in galaxy.tools.wrappers) DatasetFilenameWrapper.MetadataWrapper (class in galaxy.tools.wrappers) DatasetHash (class in galaxy.model) (class in galaxy.schema.schema) DatasetInstance (class in galaxy.model) DatasetInstance.conversion_messages (class in galaxy.model) DatasetInstanceMaterializer (class in galaxy.model.deferred) DatasetJobInfo (class in galaxy.schema.schema) DatasetLikeObject (class in galaxy.datatypes.display_applications.parameters) DatasetListWrapper (class in galaxy.tools.wrappers) DatasetManagePermissionFailedException DatasetManager (class in galaxy.managers.datasets) DatasetOkValidator (class in galaxy.tools.parameters.validation) DatasetPath (class in galaxy.job_execution.datasets) DatasetPathRewriter (class in galaxy.job_execution.datasets) DatasetPermissionAction (class in galaxy.schema.schema) DatasetPermissions (class in galaxy.model) (class in galaxy.schema.schema) DatasetPopulator (class in galaxy_test.base.populators) DatasetRBACPermission (class in galaxy.managers.rbac_secured) DatasetRBACPermissions (class in galaxy.managers.datasets) datasets (galaxy.model.History attribute) (galaxy.model.LibraryFolder attribute) datasets_are_public() (galaxy.model.security.GalaxyRBACAgent method) datasets_properties() (galaxy.model.store.BaseDirectoryImportModelStore method) (galaxy.model.store.DictImportModelStore method) (galaxy.model.store.ModelImportStore method) DatasetSerializer (class in galaxy.managers.datasets) DatasetSource (class in galaxy.model) (class in galaxy.schema.schema) DatasetSourceHash (class in galaxy.model) DatasetSourceId (class in galaxy.schema.schema) DatasetSourceIdBase (class in galaxy.schema.schema) DatasetSourceType (class in galaxy.schema.schema) DatasetState (class in galaxy.schema.schema) DatasetSubprocessDataProvider (class in galaxy.datatypes.dataproviders.dataset) DatasetSummary (class in galaxy.schema.schema) DatasetValidatedState (class in galaxy.schema.schema) datasource_tool_open() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) DataSourceParser (class in galaxy.visualization.plugins.config_parser) DataSourceTool (class in galaxy.tools) DataSourceToolAction (class in galaxy.tools.actions.data_source) DataToolParameter (class in galaxy.tools.parameters) (class in galaxy.tools.parameters.basic) datatype (galaxy.datatypes.display_applications.parameters.DatasetLikeObject attribute) (galaxy.datatypes.upload_util.HandleUploadResponse attribute) (galaxy.model.DatasetInstance property) (galaxy.schema.schema.ChangeDatatypeOperationParams attribute) (galaxy.tools.parameters.grouping.Dataset attribute) datatype_for_extension() (in module galaxy.model) DatatypeConverterList (class in galaxy.managers.datatypes) DatatypeConverterNotFoundException DatatypeDetails (class in galaxy.managers.datatypes) DatatypeIsInstanceToolOutputActionConditionalWhen (class in galaxy.tool_util.parser.output_actions) datatypes (galaxy.managers.datatypes.DatatypesCombinedMap attribute) datatypes_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) datatypes_mapping (galaxy.managers.datatypes.DatatypesCombinedMap attribute) datatypes_registry (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter property) (galaxy.managers.display_applications.DisplayApplicationsManager property) (galaxy.model.store.StoreAppProtocol attribute) (galaxy.structured_app.BasicSharedApp attribute) (galaxy.structured_app.MinimalToolApp attribute) (galaxy.tools.remote_tool_eval.ToolApp attribute) (galaxy.webapps.galaxy.api.datatypes.FastAPIDatatypes attribute) (galaxy.webapps.reports.app.UniverseApplication attribute) DatatypesCombinedMap (class in galaxy.managers.datatypes) DatatypesEDAMDetailsDict (class in galaxy.managers.datatypes) DatatypesEntryT (class in galaxy.webapps.galaxy.controllers.admin) DatatypesGrid (class in tool_shed.grids.repository_grids) DatatypesGrid.DatatypesColumn (class in tool_shed.grids.repository_grids) DatatypesMap (class in galaxy.managers.datatypes) DatatypeValidation (class in galaxy.datatypes.data) date_range_max (galaxy.schema.schema.JobIndexQueryPayload attribute) date_range_min (galaxy.schema.schema.JobIndexQueryPayload attribute) date_string_re (galaxy.managers.base.ModelFilterParser attribute) date_uploaded (galaxy.schema.schema.FileLibraryFolderItem attribute) DateTimeColumn (class in galaxy.web.legacy_framework.grids) db_builds (galaxy.managers.context.ProvidesHistoryContext property) db_dataset_for() (galaxy.managers.context.ProvidesHistoryContext method) DB_PREASSIGN (galaxy.web_stack.handlers.HANDLER_ASSIGNMENT_METHODS attribute) DB_SELF (galaxy.web_stack.handlers.HANDLER_ASSIGNMENT_METHODS attribute) DB_SKIP_LOCKED (galaxy.web_stack.handlers.HANDLER_ASSIGNMENT_METHODS attribute) db_state (galaxy.model.migrations.DatabaseStateVerifier property) DB_TRANSACTION_ISOLATION (galaxy.web_stack.handlers.HANDLER_ASSIGNMENT_METHODS attribute) dbkey (galaxy.datatypes.display_applications.parameters.DatasetLikeObject attribute) (galaxy.model.DatasetInstance property) (galaxy.model.store.discover.JsonCollectedDatasetMatch property) (galaxy.model.Visualization attribute) (galaxy.model.VisualizationRevision attribute) (galaxy.schema.fetch_data.BaseDataElement attribute) (galaxy.schema.schema.ChangeDbkeyOperationParams attribute) (galaxy.tools.parameters.grouping.Dataset attribute) DBKeyParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) dc (galaxy.schema.schema.DataItemSourceType attribute) DCASerializer (class in galaxy.managers.hdcas) Dcd (class in galaxy.datatypes.binary) DCDetailed (class in galaxy.schema.schema) dce (galaxy.schema.schema.DataItemSourceType attribute) dces_by_id (galaxy.model.store.ObjectImportTracker attribute) dces_by_key (galaxy.model.store.ObjectImportTracker attribute) DCESerializer (class in galaxy.managers.hdcas) DCESummary (class in galaxy.schema.schema) DCEType (class in galaxy.schema.schema) DCObject (class in galaxy.schema.schema) DCSerializer (class in galaxy.managers.hdcas) DCSummary (class in galaxy.schema.schema) DDLAlterOperation (class in galaxy.model.migrations.util) DDLOperation (class in galaxy.model.migrations.util) deactivate (galaxy.tool_util.deps.conda_util.CondaContext property) deactivate() (galaxy.managers.tools.DynamicToolManager method) deactivate_dynamic_tool() (galaxy_test.base.populators.BaseDatasetPopulator method) deactivate_repository() (tool_shed.test.base.twilltestcase.GalaxyInteractorToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) (tool_shed.test.base.twilltestcase.StandaloneToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ToolShedInstallationClient method) DEACTIVATED (galaxy.model.tool_shed_install.ToolShedRepository.installation_status attribute) debug_handler() (in module tool_shed.util.shed_index) debugging (galaxy.managers.metrics.MetricsManager attribute) declare_queues (galaxy.queue_worker.ControlTask property) (galaxy.queue_worker.GalaxyQueueWorker property) decode() (galaxy.tools.DefaultToolState method) (in module galaxy.web_stack.message) decode_dataset_user() (in module galaxy.datatypes.display_applications.util) decode_dbkey() (in module galaxy.visualization.genomes) decode_folder_id() (galaxy.managers.folders.FolderManager method) decode_guid() (galaxy.security.idencoding.IdEncodingHelper method) decode_id() (galaxy.managers.configuration.ConfigurationManager method) (galaxy.security.idencoding.IdAsLowercaseAlphanumEncodingHelper method) (galaxy.security.idencoding.IdEncodingHelper method) (galaxy.webapps.galaxy.api.configuration.FastAPIConfiguration method) (galaxy.webapps.galaxy.services.base.ServiceBase method) (in module galaxy.managers.base) decode_ids() (galaxy.webapps.galaxy.services.base.ServiceBase method) decode_runtime_state() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) decode_type_id() (galaxy.managers.history_contents.HistoryContentsFilters method) decode_user_access_token() (galaxy.authnz.custos_authnz.OIDCAuthnzBase method) (galaxy.authnz.IdentityProvider method) decode_with_security() (in module galaxy.managers.base) decoder() (in module galaxy.tools.cache) decompress_bytes_to_directory() (in module galaxy.util.compression_utils) decompress_path_to_directory() (in module galaxy.util.compression_utils) deep_test_search() (in module galaxy.tool_util.deps.mulled.get_tests) default (galaxy.model.Quota attribute) (galaxy.workflow.refactor.schema.AddInputAction attribute) default() (galaxy.model.custom_types.SafeJsonEncoder method) (galaxy.webapps.galaxy.controllers.async.ASync method) (galaxy.webapps.galaxy.controllers.root.RootController method) (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) default_app_name (galaxy.web_stack.ApplicationStack attribute) DEFAULT_BASE_HANDLER_POOLS (galaxy.jobs.JobConfiguration attribute) (galaxy.web_stack.handlers.ConfiguresHandlers attribute) (galaxy.workflow.scheduling_manager.WorkflowSchedulingManager attribute) default_build_pulsar_app (galaxy.jobs.runners.pulsar.PulsarEmbeddedJobRunner attribute) (galaxy.jobs.runners.pulsar.PulsarEmbeddedMQJobRunner attribute) DEFAULT_CHUNK_SIZE (galaxy.datatypes.dataproviders.chunk.ChunkDataProvider attribute) default_collection_type (galaxy.workflow.modules.InputDataCollectionModule attribute) DEFAULT_COMMENT_CHAR (galaxy.datatypes.dataproviders.line.FilteredLineDataProvider attribute) default_config_file_name (galaxy.config.GalaxyAppConfiguration attribute) (tool_shed.webapp.config.ToolShedAppConfiguration attribute) DEFAULT_CONTENT_FORMAT (galaxy.model.PageRevision attribute) default_default_value (galaxy.workflow.modules.InputParameterModule attribute) default_deserializer() (galaxy.managers.base.ModelDeserializer method) default_exit_code_file() (in module galaxy.job_execution.output_collect) default_filter (galaxy.web.legacy_framework.grids.Grid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.grids.repository_grids.RepositoriesByUserGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) default_handler (galaxy.web_stack.message.ApplicationStackMessage attribute) default_handler() (galaxy.web_stack.message.TaskMessage static method) DEFAULT_HANDLER_READY_WINDOW_SIZE (galaxy.jobs.JobConfiguration attribute) DEFAULT_HANDLER_TAG (galaxy.web_stack.handlers.ConfiguresHandlers attribute) DEFAULT_INVALID_CHAR (galaxy.tools.parameters.sanitize.ToolParameterSanitizer attribute) default_job_file() (galaxy.jobs.runners.JobState static method) default_job_tool_configuration (galaxy.jobs.JobConfiguration property) default_length (galaxy.selenium.navigates_galaxy.WaitType attribute) default_limit (galaxy.web.framework.helpers.grids.GridData attribute) default_loader() (in module galaxy.tool_util.cwl.cwltool_deps) DEFAULT_MAX_OPEN_FILES (galaxy.datatypes.util.maf_utilities.TempFileHandler attribute) (galaxy.tools.util.maf_utilities.TempFileHandler attribute) default_name (galaxy.model.History attribute) DEFAULT_NWORKERS (galaxy.jobs.JobConfiguration attribute) default_optional (galaxy.tool_util.parser.interface.InputSource attribute) (galaxy.workflow.modules.InputModule attribute) (galaxy.workflow.modules.InputParameterModule attribute) default_order_by (galaxy.managers.history_contents.HistoryContentsManager attribute) DEFAULT_PARAM_TYPE (galaxy.visualization.plugins.config_parser.ParamParser attribute) default_parameter_type (galaxy.workflow.modules.InputParameterModule attribute) default_password (galaxy.selenium.navigates_galaxy.NavigatesGalaxy attribute) default_pbs_server (galaxy.jobs.runners.pbs.PBSJobRunner property) default_permissions (galaxy.model.History attribute) (galaxy.model.User attribute) default_permissions() (galaxy.managers.users.UserManager method) default_port (galaxy.config.config_manage.App attribute) DEFAULT_POSITION (galaxy.model.WorkflowStep attribute) default_printer() (in module galaxy.tools.util.galaxyops) default_quota (galaxy.quota.NoQuotaAgent property) default_relative_config_paths_for() (in module galaxy.main_config) default_safety (galaxy.job_metrics.instrumenters.core.CorePlugin attribute) (galaxy.job_metrics.instrumenters.env.EnvPlugin attribute) (galaxy.job_metrics.instrumenters.InstrumentPlugin attribute) (galaxy.job_metrics.instrumenters.meminfo.MemInfoPlugin attribute) default_section_name (galaxy.main_config.WebappSetupProps attribute) default_serializer() (galaxy.managers.base.ModelSerializer method) (galaxy.managers.configuration.ConfigSerializer method) default_shed_tool_conf_dict() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) default_sort_key (galaxy.web.legacy_framework.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.DatatypesGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryDependenciesGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ToolDependenciesGrid attribute) (tool_shed.grids.repository_grids.ToolsGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) DEFAULT_SPECS (galaxy.jobs.runners.BaseJobRunner attribute) DEFAULT_TEMPLATE_COLLECTION_SIZE (galaxy.visualization.plugins.plugin.ServesTemplatesPluginMixin attribute) default_timeout (galaxy.selenium.cli.DriverWrapper property) default_tool_action (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.Tool attribute) default_type (galaxy.tool_util.toolbox.views.interface.ToolPanelViewModelType attribute) default_url_path() (in module galaxy.webapps.base.webapp) default_usage_excluded_ids() (galaxy.objectstore.QuotaSourceMap method) default_value (galaxy.model.WorkflowStepInput attribute) (galaxy.workflow.modules.InputParameterModule attribute) default_value_set (galaxy.model.WorkflowStepInput attribute) DEFAULT_VERSION (galaxy.tools.data_manager.manager.DataManager attribute) default_view (galaxy.managers.base.ModelSerializer attribute) (galaxy.managers.cloudauthzs.CloudAuthzsSerializer attribute) (galaxy.managers.configuration.AdminConfigSerializer attribute) (galaxy.managers.configuration.ConfigSerializer attribute) (galaxy.managers.datasets.DatasetAssociationSerializer attribute) (galaxy.managers.datasets.DatasetSerializer attribute) (galaxy.managers.hdcas.DCESerializer attribute) (galaxy.managers.hdcas.DCSerializer attribute) (galaxy.managers.hdcas.HDCASerializer attribute) (galaxy.managers.history_contents.HistoryContentsSerializer attribute) (galaxy.managers.users.CurrentUserSerializer attribute) (galaxy.managers.users.UserSerializer attribute) (galaxy.managers.visualizations.VisualizationSerializer attribute) (galaxy.managers.workflows.WorkflowSerializer attribute) (galaxy.schema.SerializationParams attribute) DefaultHistoryPermissions (class in galaxy.model) DefaultJobAction (class in galaxy.job_execution.actions.post) DefaultJobDispatcher (class in galaxy.jobs.handler) DefaultQuotaAssociation (class in galaxy.model) DefaultQuotaAssociation.types (class in galaxy.model) defaults (galaxy.app_unittest_utils.galaxy_mock.MockAppConfig.MockSchema attribute) (galaxy.config.schema.AppSchema property) defaults() (galaxy.util.properties.NicerConfigParser method) DefaultToolAction (class in galaxy.tools.actions) DefaultToolState (class in galaxy.tools) DefaultUserPermissions (class in galaxy.model) DefaultWebTransaction (class in galaxy.web.framework.base) deferred (galaxy.schema.fetch_data.BaseDataElement attribute) DEFERRED (galaxy.schema.schema.DatasetState attribute) deferred_hda_model_store_dict() (in module galaxy.model.unittest_utils.store_fixtures) deferred_hda_model_store_dict_bam() (in module galaxy.model.unittest_utils.store_fixtures) defines_new_history() (galaxy.model.store.BaseDirectoryImportModelStore method) (galaxy.model.store.DictImportModelStore method) (galaxy.model.store.ModelImportStore method) DelayedWorkflowEvaluation DeletableDeserializerMixin (class in galaxy.managers.deletable) DeletableFiltersMixin (class in galaxy.managers.deletable) DeletableManagerMixin (class in galaxy.managers.deletable) DeletableSerializerMixin (class in galaxy.managers.deletable) delete (galaxy.schema.schema.HistoryContentItemOperation attribute) (galaxy.webapps.galaxy.api.RestVerb attribute) delete() (galaxy.jobs.runners.util.cli.job.BaseJobExec method) (galaxy.jobs.runners.util.cli.job.lsf.LSF method) (galaxy.jobs.runners.util.cli.job.slurm.Slurm method) (galaxy.jobs.runners.util.cli.job.torque.Torque method) (galaxy.managers.collections.DatasetCollectionManager method) (galaxy.managers.datasets.DatasetAssociationManager method) (galaxy.managers.deletable.DeletableManagerMixin method) (galaxy.managers.folders.FolderManager method) (galaxy.managers.group_roles.GroupRolesManager method) (galaxy.managers.group_users.GroupUsersManager method) (galaxy.managers.groups.GroupsManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.managers.roles.RoleManager method) (galaxy.managers.tool_data.ToolDataManager method) (galaxy.managers.users.UserManager method) (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.tools.cache.ToolDocumentCache method) (galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController method) (galaxy.webapps.galaxy.api.cloudauthz.CloudAuthzController method) (galaxy.webapps.galaxy.api.dynamic_tools.DynamicToolsController method) (galaxy.webapps.galaxy.api.folders.FastAPILibraryFolders method) (galaxy.webapps.galaxy.api.forms.FastAPIForms method) (galaxy.webapps.galaxy.api.FrameworkRouter method) (galaxy.webapps.galaxy.api.group_roles.FastAPIGroupRoles method) (galaxy.webapps.galaxy.api.group_users.FastAPIGroupUsers method) (galaxy.webapps.galaxy.api.groups.FastAPIGroups method) (galaxy.webapps.galaxy.api.libraries.FastAPILibraries method) (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method) (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method) (galaxy.webapps.galaxy.api.pages.FastAPIPages method) (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method) (galaxy.webapps.galaxy.api.quotas.FastAPIQuota method) (galaxy.webapps.galaxy.api.roles.FastAPIRoles method) (galaxy.webapps.galaxy.api.sanitize_allow.SanitizeAllowController method) (galaxy.webapps.galaxy.api.tool_data.FastAPIToolData method) (galaxy.webapps.galaxy.api.users.FastAPIUsers method) (galaxy.webapps.galaxy.services.histories.HistoriesService method) (galaxy.webapps.galaxy.services.libraries.LibrariesService method) (galaxy.webapps.galaxy.services.library_folders.LibraryFoldersService method) (galaxy.webapps.galaxy.services.pages.PagesService method) (galaxy.webapps.galaxy.services.quotas.QuotasService method) (galaxy_test.base.api.ApiTestInteractor method) (tool_shed.managers.groups.GroupManager method) delete_api_key() (galaxy.managers.api_keys.ApiKeyManager method) (galaxy.webapps.galaxy.api.users.FastAPIUsers method) (galaxy.webapps.galaxy.services.users.UsersService method) delete_custom_build() (galaxy_test.selenium.test_custom_builds.TestCustomBuilds method) delete_custom_builds() (galaxy.webapps.galaxy.api.users.FastAPIUsers method) delete_dataset() (galaxy_test.base.populators.BaseDatasetPopulator method) delete_extended_metadata() (galaxy.webapps.base.controller.UsesExtendedMetadataMixin method) delete_files_from_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) delete_history() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) (galaxy_test.base.populators.BaseDatasetPopulator method) delete_ingress() (in module galaxy.jobs.runners.util.pykube_util) delete_item_annotation() (galaxy.model.item_attrs.UsesAnnotations method) delete_item_tags() (galaxy.model.tags.TagHandler method) delete_job() (in module galaxy.jobs.runners.util.pykube_util) delete_operation (tool_shed.util.admin_util.Admin attribute) (tool_shed.webapp.controllers.admin.AdminController attribute) delete_quota() (galaxy.managers.quotas.QuotaManager method) delete_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) (tool_shed.webapp.controllers.admin.AdminController method) delete_repository_metadata() (tool_shed.webapp.controllers.admin.AdminController method) delete_service() (in module galaxy.jobs.runners.util.pykube_util) delete_task() (galaxy.jobs.runners.godocker.GodockerJobRunner method) delete_unused_dependency_paths() (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) deleted (galaxy.model.APIKeys attribute) (galaxy.model.Dataset attribute) (galaxy.model.FormDefinitionCurrent attribute) (galaxy.model.Group attribute) (galaxy.model.History attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.JobStateSummary attribute) (galaxy.model.Library attribute) (galaxy.model.LibraryDataset attribute) (galaxy.model.LibraryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) (galaxy.model.LibraryFolder attribute) (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryInfoAssociation attribute) (galaxy.model.MetadataFile attribute) (galaxy.model.Page attribute) (galaxy.model.Quota attribute) (galaxy.model.Role attribute) (galaxy.model.StoredWorkflow attribute) DELETED (galaxy.model.Task.states attribute) deleted (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.model.User attribute) (galaxy.model.UserAddress attribute) (galaxy.model.UserNotificationAssociation attribute) (galaxy.model.Visualization attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.ArchivedHistorySummary attribute) (galaxy.schema.schema.BaseUserModel attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.DatasetSummary attribute) (galaxy.schema.schema.DeleteHistoryContentResult attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDCJobStateSummary attribute) (galaxy.schema.schema.HistoryActiveContentCounts attribute) (galaxy.schema.schema.HistoryItemBase attribute) (galaxy.schema.schema.HistorySummary attribute) (galaxy.schema.schema.InstalledToolShedRepository attribute)

DELETED (galaxy.schema.schema.JobState attribute) deleted (galaxy.schema.schema.LibraryFolderDetails attribute) (galaxy.schema.schema.LibraryFolderItemBase attribute) (galaxy.schema.schema.LibraryLegacySummary attribute) (galaxy.schema.schema.PageIndexQueryPayload attribute) (galaxy.schema.schema.PageSummary attribute) (galaxy.schema.schema.StoredWorkflowSummary attribute) (galaxy.schema.schema.UpdateHistoryContentsPayload attribute) (tool_shed.webapp.model.APIKeys attribute) (tool_shed.webapp.model.Category attribute) (tool_shed.webapp.model.Group attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.Role attribute) (tool_shed.webapp.model.User attribute) deleted_datasets() (galaxy.webapps.reports.controllers.system.System method) deleted_histories() (galaxy.webapps.reports.controllers.system.System method) deleted_new (galaxy.schema.schema.HDCJobStateSummary attribute) DeleteDatasetAction (class in galaxy.job_execution.actions.post) DeletedColumn (class in galaxy.web.legacy_framework.grids) DeletedCustomBuild (class in galaxy.schema.schema) DeleteHistoryContentPayload (class in galaxy.schema.schema) DeleteHistoryContentResult (class in galaxy.schema.schema) DeleteIntermediatesAction (class in galaxy.job_execution.actions.post) DeleteLibraryPayload (class in galaxy.schema.schema) deleting (galaxy.model.JobStateSummary attribute) DELETING (galaxy.schema.schema.JobState attribute) delimiter (galaxy.datatypes.tabular.BaseCSV attribute) dependencies (galaxy.model.Job attribute) (galaxy.tools.ApplyRulesTool attribute) (galaxy.tools.AsyncDataSourceTool attribute) (galaxy.tools.BuildListCollectionTool attribute) (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.DataDestinationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.DuplicateFileToCollectionTool attribute) (galaxy.tools.ExportHistoryTool attribute) (galaxy.tools.ExpressionTool attribute) (galaxy.tools.ExtractDatasetCollectionTool attribute) (galaxy.tools.FilterDatasetsTool attribute) (galaxy.tools.FilterEmptyDatasetsTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) (galaxy.tools.FilterFromFileTool attribute) (galaxy.tools.FlattenTool attribute) (galaxy.tools.HarmonizeTool attribute) (galaxy.tools.ImportHistoryTool attribute) (galaxy.tools.InteractiveTool attribute) (galaxy.tools.KeepSuccessDatasetsTool attribute) (galaxy.tools.MergeCollectionTool attribute) (galaxy.tools.OutputParameterJSONTool attribute) (galaxy.tools.RelabelFromFileTool attribute) (galaxy.tools.SortTool attribute) (galaxy.tools.TagFromFileTool attribute) (galaxy.tools.UnzipCollectionTool attribute) (galaxy.tools.ZipCollectionTool attribute) DependenciesDescription (class in galaxy.tool_util.deps.dependencies) Dependency (class in galaxy.tool_util.deps.resolvers) dependency_resolvers_view (galaxy.structured_app.StructuredApp attribute) dependency_shell_commands() (galaxy.tool_util.deps.CachedDependencyManager method) (galaxy.tool_util.deps.DependencyManager method) (galaxy.tool_util.deps.NullDependencyManager method) dependency_type (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependency attribute) (galaxy.tool_util.deps.resolvers.galaxy_packages.ToolShedDependency attribute) (galaxy.tool_util.deps.resolvers.NullDependency attribute) (galaxy.tool_util.deps.resolvers.tool_shed_packages.ToolShedPackageDependencyResolver attribute) DependencyException DependencyManager (class in galaxy.tool_util.deps) DependencyResolver (class in galaxy.tool_util.deps.resolvers) DependencyResolversView (class in galaxy.tool_util.deps.views) DEPENDENT_CONFIG_DEFAULTS (in module galaxy.config) dependent_jobs (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) dependent_workflow_step (galaxy.model.WorkflowInvocationMessage attribute) dependent_workflow_step_id (galaxy.model.WorkflowInvocationMessage attribute) dependent_workflow_step_index (galaxy.model.WorkflowInvocationMessage property) depends() (in module galaxy.webapps.galaxy.api) deprecate() (tool_shed.webapp.controllers.repository.RepositoryController method) deprecated (tool_shed.webapp.model.Repository attribute) deprecated_dirs (galaxy.config.BaseAppConfiguration attribute) (galaxy.config.GalaxyAppConfiguration attribute) deprecated_options (galaxy.config.GalaxyAppConfiguration attribute) deprecated_repositories_i_own_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) DeprecatedMethod DeprecatedRepositoriesIOwnGrid (class in tool_shed.grids.repository_grids) deregister_func() (galaxy.web_stack.message.ApplicationStackMessageDispatcher method) derive_roles_from_access() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) desc (galaxy.model.FormDefinition attribute) (galaxy.model.UserAddress attribute) desc() (galaxy.tool_util.parser.stdio.StdioErrorLevel static method) description (galaxy.managers.datatypes.DatatypeDetails attribute) (galaxy.model.CloudAuthz attribute) (galaxy.model.Library attribute) (galaxy.model.LibraryFolder attribute) (galaxy.model.Quota attribute) (galaxy.model.Role attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.objectstore.ConcreteObjectStoreModel attribute) (galaxy.schema.fetch_data.BaseDataElement attribute) (galaxy.schema.fetch_data.LibraryDestination attribute) (galaxy.schema.schema.CreateLibraryFolderPayload attribute) (galaxy.schema.schema.CreateLibraryPayload attribute) (galaxy.schema.schema.FolderLibraryFolderItem attribute) (galaxy.schema.schema.Input attribute) (galaxy.schema.schema.LibraryFolderDetails attribute) (galaxy.schema.schema.LibraryLegacySummary attribute) (galaxy.schema.schema.RoleDefinitionModel attribute) (galaxy.schema.schema.RoleModelResponse attribute) (galaxy.schema.schema.UpdateLibraryFolderPayload attribute) (galaxy.schema.schema.UpdateLibraryPayload attribute) (galaxy.security.Action attribute) (galaxy.tool_util.toolbox.views.definitions.StaticToolBoxView attribute) (galaxy.tool_util.toolbox.views.interface.ToolPanelViewModel attribute) (galaxy.tools.data_manager.manager.Tool attribute) (galaxy.tours.TourCore attribute) (galaxy.webapps.galaxy.api.IndexQueryTag attribute) (tool_shed.webapp.model.Category attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.Role attribute) description_from_tool_object() (in module galaxy.tools.test) description_url (galaxy.managers.datatypes.DatatypeDetails attribute) descs (galaxy.tool_util.parser.stdio.StdioErrorLevel attribute) deserializable_keyset (galaxy.managers.cloudauthzs.CloudAuthzsDeserializer attribute) (galaxy.managers.datasets.DatasetAssociationDeserializer attribute) (galaxy.managers.hdas.HDADeserializer attribute) (galaxy.managers.histories.HistoryDeserializer attribute) (galaxy.managers.pages.PageDeserializer attribute) (galaxy.managers.sharable.SharableModelDeserializer attribute) (galaxy.managers.users.UserDeserializer attribute) (galaxy.managers.visualizations.VisualizationDeserializer attribute) deserialize() (galaxy.managers.base.ModelDeserializer method) deserialize_and_validate_authn_id() (galaxy.managers.cloudauthzs.CloudAuthzsDeserializer method) deserialize_annotation() (galaxy.managers.annotatable.AnnotatableDeserializerMixin method) deserialize_basestring() (galaxy.managers.base.ModelDeserializer method) deserialize_bool() (galaxy.managers.base.ModelDeserializer method) deserialize_datatype() (galaxy.managers.datasets.DatasetAssociationDeserializer method) deserialize_deleted() (galaxy.managers.deletable.DeletableDeserializerMixin method) deserialize_genome_build() (galaxy.managers.base.ModelDeserializer method) deserialize_importable() (galaxy.managers.sharable.SharableModelDeserializer method) deserialize_int() (galaxy.managers.base.ModelDeserializer method) deserialize_metadata() (galaxy.managers.datasets.DatasetAssociationDeserializer method) deserialize_metadatum() (galaxy.managers.datasets.DatasetAssociationDeserializer method) deserialize_preferred_object_store_id() (galaxy.managers.histories.HistoryDeserializer method) (galaxy.managers.users.UserDeserializer method) deserialize_published() (galaxy.managers.sharable.SharableModelDeserializer method) deserialize_purged() (galaxy.managers.deletable.PurgableDeserializerMixin method) deserialize_rating() (galaxy.managers.ratable.RatableDeserializerMixin method) deserialize_tags() (galaxy.managers.taggable.TaggableDeserializerMixin method) deserialize_username() (galaxy.managers.users.UserDeserializer method) deserialize_users_shared_with() (galaxy.managers.sharable.SharableModelDeserializer method) Deserializer (class in galaxy.managers.base) deserializers (galaxy.managers.annotatable.AnnotatableDeserializerMixin attribute) (galaxy.managers.cloudauthzs.CloudAuthzsDeserializer attribute) (galaxy.managers.deletable.DeletableDeserializerMixin attribute) (galaxy.managers.deletable.PurgableDeserializerMixin attribute) (galaxy.managers.pages.PageDeserializer attribute) (galaxy.managers.sharable.SharableModelDeserializer attribute) (galaxy.managers.users.UserDeserializer attribute) (galaxy.managers.visualizations.VisualizationDeserializer attribute) designation (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.store.discover.JsonCollectedDatasetMatch property) (galaxy.schema.schema.HDAExtended attribute) destination (galaxy.config.config_manage.App attribute) (galaxy.schema.fetch_data.BaseCollectionTarget attribute) (galaxy.schema.fetch_data.BaseDataTarget attribute) destination_defaults (galaxy.jobs.runners.pulsar.PulsarEmbeddedJobRunner attribute) (galaxy.jobs.runners.pulsar.PulsarLegacyJobRunner attribute) (galaxy.jobs.runners.pulsar.PulsarMQJobRunner attribute) (galaxy.jobs.runners.pulsar.PulsarRESTJobRunner attribute) destination_id (galaxy.model.Job attribute) destination_list (in module galaxy.jobs.dynamic_tool_destination) destination_params (galaxy.model.Job attribute) DESTINATION_PARAMS_SPEC (galaxy.jobs.runners.chronos.ChronosJobRunner attribute) destinations (galaxy.jobs.JobConfiguration attribute) DestinationType (class in galaxy.schema.fetch_data) destroy() (galaxy.model.PSAPartial class method) destroy_tree() (in module galaxy.tool_util.parser.xml) DetailedUserModel (class in galaxy.schema.schema) details (galaxy.model.WorkflowInvocationMessage attribute) detailsUrl (galaxy.managers.licenses.LicenseMetadataModel attribute) detect_datatype() (galaxy.managers.datasets.DatasetAssociationManager method) DETECTED_JOB_STATE (class in galaxy.tool_util.output_checker) determine_output_format() (in module galaxy.tools.actions) deterministic_handler_assignment (galaxy.web_stack.handlers.ConfiguresHandlers property) device (galaxy.objectstore.ConcreteObjectStoreModel attribute) device_id (galaxy.objectstore.ConcreteObjectStore attribute) device_source_info (galaxy.model.Dataset property) device_source_label (galaxy.model.Dataset property) DeviceSourceMap (class in galaxy.objectstore) diagnostics() (galaxy.webapps.galaxy.api.tools.ToolsController method) dialect (galaxy.datatypes.tabular.BaseCSV property) (galaxy.datatypes.tabular.CSV attribute) (galaxy.datatypes.tabular.TSV attribute) dict() (galaxy.util.bunch.Bunch method) dict_collection_visible_keys (galaxy.files.FileSourceDictifiable attribute) (galaxy.job_execution.setup.JobIO attribute) (galaxy.model.DatasetCollection attribute) (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.DatasetHash attribute) (galaxy.model.DatasetSource attribute) (galaxy.model.DynamicTool attribute) (galaxy.model.FormDefinition attribute) (galaxy.model.Group attribute) (galaxy.model.HasTags attribute) (galaxy.model.History attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.ItemTagAssociation attribute) (galaxy.model.Job attribute) (galaxy.model.Library attribute) (galaxy.model.Quota attribute) (galaxy.model.Role attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.model.User attribute) (galaxy.model.Workflow attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationOutputValue attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.model.WorkflowRequestInputStepParameter attribute) (galaxy.model.WorkflowRequestStepState attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) (galaxy.tool_util.deps.container_resolvers.ContainerResolver attribute) (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.ContainerDependency attribute) (galaxy.tool_util.deps.resolvers.Dependency attribute) (galaxy.tool_util.deps.resolvers.DependencyResolver attribute) (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependency attribute) (galaxy.tool_util.deps.resolvers.lmod.LmodDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.modules.ModuleDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages.UnlinkedToolShedPackageDependencyResolver attribute) (galaxy.tool_util.parser.output_objects.ToolExpressionOutput attribute) (galaxy.tool_util.parser.output_objects.ToolOutput attribute) (galaxy.tool_util.parser.output_objects.ToolOutputCollection attribute) (galaxy.tool_util.toolbox.panel.ToolSection attribute) (galaxy.tool_util.toolbox.panel.ToolSectionLabel attribute) (galaxy.tool_util.toolbox.ToolSection attribute) (galaxy.tool_util.toolbox.ToolSectionLabel attribute) (galaxy.tools.data.RefgenieToolDataTable attribute) (galaxy.tools.data.TabularToolDataField attribute) (galaxy.tools.data.TabularToolDataTable attribute) (galaxy.tools.parameters.basic.FloatToolParameter attribute) (galaxy.tools.parameters.basic.IntegerToolParameter attribute) (galaxy.tools.parameters.basic.ToolParameter attribute) (galaxy.tools.parameters.grouping.ConditionalWhen attribute) (galaxy.tools.parameters.grouping.Group attribute) (galaxy.tools.parameters.grouping.Repeat attribute) (galaxy.tools.parameters.grouping.Section attribute) (galaxy.tools.Tool attribute) (tool_shed.webapp.model.Category attribute) (tool_shed.webapp.model.Group attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) (tool_shed.webapp.model.Role attribute) (tool_shed.webapp.model.User attribute) dict_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.TabularData method) dict_dbkeysandextensions_visible_keys (galaxy.model.HistoryDatasetCollectionAssociation attribute) dict_element_visible_keys (galaxy.model.DatasetCollection attribute) (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.DatasetHash attribute) (galaxy.model.DatasetSource attribute) (galaxy.model.DefaultQuotaAssociation attribute) (galaxy.model.DynamicTool attribute) (galaxy.model.FormDefinition attribute) (galaxy.model.Group attribute) (galaxy.model.GroupQuotaAssociation attribute) (galaxy.model.HasTags attribute) (galaxy.model.History attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.ItemTagAssociation attribute) (galaxy.model.Job attribute) (galaxy.model.Library attribute) (galaxy.model.LibraryFolder attribute) (galaxy.model.Page attribute) (galaxy.model.PageRevision attribute) (galaxy.model.Quota attribute) (galaxy.model.Role attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.model.tool_shed_install.ToolVersion attribute) (galaxy.model.User attribute) (galaxy.model.UserQuotaAssociation attribute) (galaxy.model.UserQuotaSourceUsage attribute) (galaxy.model.Visualization attribute) (galaxy.model.Workflow attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute) (galaxy.tools.data.RefgenieToolDataTable attribute) (galaxy.tools.data.TabularToolDataTable attribute) (tool_shed.webapp.model.Category attribute) (tool_shed.webapp.model.Group attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) (tool_shed.webapp.model.Role attribute) (tool_shed.webapp.model.User attribute) dict_export_visible_keys (galaxy.tools.data.RefgenieToolDataTable attribute) (galaxy.tools.data.TabularToolDataTable attribute) dict_for() (in module galaxy.util.dictifiable) dict_map() (in module galaxy.model.dataset_collections.structure) DictClientTestConfig (class in galaxy.tool_util.verify.interactor) DictDataProvider (class in galaxy.datatypes.dataproviders.column) DictFileSourcesUserContext (class in galaxy.files) Dictifiable (class in galaxy.util.dictifiable) dictify_dataset_collection_instance() (in module galaxy.managers.collections_util) dictify_usage() (galaxy.model.User method) dictify_usage_for() (galaxy.model.User method) DictImportModelStore (class in galaxy.model.store) DictParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) DictParser (class in galaxy.visualization.plugins.config_parser) different_revision_defines_tip_only_repository_dependency() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) dimension (galaxy.model.dataset_collections.type_description.CollectionTypeDescription property) direct_match() (galaxy.tools.parameters.history_query.HistoryQuery method) direction (galaxy.job_execution.actions.post.RemoveTagDatasetAction attribute) (galaxy.job_execution.actions.post.TagDatasetAction attribute) Directory (class in galaxy.datatypes.data) directory (galaxy.schema.fetch_data.ElementsFromType attribute) directory_hash_id() (in module galaxy.util) directory_uri (galaxy.schema.schema.ExportHistoryArchivePayload attribute) DirectoryImportModelStore1901 (class in galaxy.model.store) DirectoryImportModelStoreLatest (class in galaxy.model.store) DirectoryModelExportStore (class in galaxy.model.store) DirectoryUploadTarget (class in galaxy.tool_util.cwl.util) DirectoryUriToolParameter (class in galaxy.tools.parameters.basic) disable_link_access() (galaxy.webapps.galaxy.api.pages.FastAPIPages method) (galaxy.webapps.galaxy.api.visualizations.FastAPIVisualizations method) (galaxy.webapps.galaxy.services.sharable.ShareableService method) disable_parent_class_sniffing() (in module galaxy.datatypes.sniff) disabled (galaxy.tool_util.deps.resolvers.DependencyResolver attribute) discard() (galaxy.util.oset.OrderedSet method) DISCARDED (galaxy.schema.schema.DatasetState attribute) discarded_data (galaxy.model.store.ImportOptions attribute) disconnect() (galaxy.authnz.custos_authnz.OIDCAuthnzBase method) (galaxy.authnz.IdentityProvider method) (galaxy.authnz.managers.AuthnzManager method) (galaxy.authnz.psa_authnz.PSAAuthnz method) (galaxy.webapps.galaxy.controllers.authnz.OIDC method) (in module galaxy.authnz.psa_authnz) DisconnectAction (class in galaxy.workflow.refactor.schema) discover_files() (in module galaxy.job_execution.output_collect) discover_outputs() (galaxy.tools.Tool method) discover_patterns (galaxy.tool_util.parser.output_collection_def.DatasetCollectionDescription property) (galaxy.tool_util.parser.output_collection_def.FilePatternDatasetCollectionDescription property) discover_target_directory() (in module galaxy.model.store.discover) discover_via (galaxy.tool_util.parser.output_collection_def.FilePatternDatasetCollectionDescription attribute) (galaxy.tool_util.parser.output_collection_def.ToolProvidedMetadataDatasetCollection attribute) discovered_file_count (galaxy.job_execution.output_collect.JobContext attribute) (galaxy.job_execution.output_collect.SessionlessJobContext attribute) (galaxy.model.store.discover.ModelPersistenceContext attribute) (galaxy.model.store.discover.SessionlessModelPersistenceContext attribute) discovered_file_for_element() (in module galaxy.model.store.discover) discovered_state() (galaxy.model.store.discover.DiscoveredDeferredFile method) (galaxy.model.store.discover.DiscoveredFile method) (galaxy.model.store.discover.DiscoveredFileError method) DiscoveredDeferredFile (class in galaxy.model.store.discover) DiscoveredFile (class in galaxy.model.store.discover) DiscoveredFileError (class in galaxy.model.store.discover) DiscoveredResultState (class in galaxy.model.store.discover) disk_nice_size (galaxy.model.History property) disk_size (galaxy.model.History attribute) disk_usage (galaxy.model.GalaxySession attribute) (galaxy.model.User attribute) (galaxy.model.UserQuotaSourceUsage attribute) disk_usage() (galaxy.webapps.reports.controllers.system.System method) DiskObjectStore (class in galaxy.objectstore) DiskUsageUserModel (class in galaxy.schema.schema) dispatch() (galaxy.web_stack.message.ApplicationStackMessageDispatcher method) display (galaxy.util.rules_dsl.RuleSet property) display() (galaxy.webapps.galaxy.controllers.page.PageController method) display_amount (galaxy.model.Quota property) display_apps (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) display_as() (galaxy.webapps.galaxy.controllers.root.RootController method) display_as_markdown() (galaxy.datatypes.data.Data method) (galaxy.datatypes.tabular.TabularData method) display_by_page (galaxy.tools.ApplyRulesTool attribute) (galaxy.tools.AsyncDataSourceTool attribute) (galaxy.tools.BuildListCollectionTool attribute) (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.DataDestinationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.DuplicateFileToCollectionTool attribute) (galaxy.tools.ExportHistoryTool attribute) (galaxy.tools.ExpressionTool attribute) (galaxy.tools.ExtractDatasetCollectionTool attribute) (galaxy.tools.FilterDatasetsTool attribute) (galaxy.tools.FilterEmptyDatasetsTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) (galaxy.tools.FilterFromFileTool attribute) (galaxy.tools.FlattenTool attribute) (galaxy.tools.HarmonizeTool attribute) (galaxy.tools.ImportHistoryTool attribute) (galaxy.tools.InteractiveTool attribute) (galaxy.tools.KeepSuccessDatasetsTool attribute) (galaxy.tools.MergeCollectionTool attribute) (galaxy.tools.OutputParameterJSONTool attribute) (galaxy.tools.RelabelFromFileTool attribute) (galaxy.tools.SortTool attribute) (galaxy.tools.TagFromFileTool attribute) (galaxy.tools.UnzipCollectionTool attribute) (galaxy.tools.ZipCollectionTool attribute) display_by_username_and_slug() (galaxy.webapps.base.controller.SharableMixin method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) display_chunk() (galaxy_test.base.populators.BaseDatasetPopulator method) display_data() (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.binary.H5MLM method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.sequence.BaseFastq method) (galaxy.datatypes.tabular.TabularData method) (galaxy.datatypes.text.Ipynb method) display_image_in_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (tool_shed.webapp.controllers.repository.RepositoryController method) display_in_upload (galaxy.managers.datatypes.DatatypeDetails attribute) display_info() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) display_installed_jobs_list_page() (tool_shed.test.base.twilltestcase.GalaxyInteractorToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) (tool_shed.test.base.twilltestcase.StandaloneToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ToolShedInstallationClient method) display_installed_repository_manage_json() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) display_manage_repository_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) display_name() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetCollectionInstance method) (galaxy.model.DatasetInstance method) (galaxy.model.LibraryDataset method) display_peek() (galaxy.datatypes.annotation.Augustus method) (galaxy.datatypes.annotation.SnapHmm method) (galaxy.datatypes.anvio.AnvioComposite method) (galaxy.datatypes.binary.Ab1 method) (galaxy.datatypes.binary.Anndata method) (galaxy.datatypes.binary.BafTar method) (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.binary.BigWig method) (galaxy.datatypes.binary.Biom2 method) (galaxy.datatypes.binary.Bref3 method) (galaxy.datatypes.binary.CompressedArchive method) (galaxy.datatypes.binary.CompressedZipArchive method) (galaxy.datatypes.binary.Cool method) (galaxy.datatypes.binary.CuffDiffSQlite method) (galaxy.datatypes.binary.Dcd method) (galaxy.datatypes.binary.ExcelXls method) (galaxy.datatypes.binary.Fast5Archive method) (galaxy.datatypes.binary.FITS method) (galaxy.datatypes.binary.GeminiSQLite method) (galaxy.datatypes.binary.GmxBinary method) (galaxy.datatypes.binary.Grib method) (galaxy.datatypes.binary.H5 method) (galaxy.datatypes.binary.H5MLM method) (galaxy.datatypes.binary.HexrdEtaOmeNpz method) (galaxy.datatypes.binary.HexrdImagesNpz method) (galaxy.datatypes.binary.IdpDB method) (galaxy.datatypes.binary.JP2 method) (galaxy.datatypes.binary.Loom method) (galaxy.datatypes.binary.MCool method) (galaxy.datatypes.binary.MongoDBArchive method) (galaxy.datatypes.binary.NcbiTaxonomySQlite method) (galaxy.datatypes.binary.NetCDF method) (galaxy.datatypes.binary.Npz method) (galaxy.datatypes.binary.Numpy method) (galaxy.datatypes.binary.PostgresqlArchive method) (galaxy.datatypes.binary.Pretext method) (galaxy.datatypes.binary.Scf method) (galaxy.datatypes.binary.SearchGuiArchive method) (galaxy.datatypes.binary.Sff method) (galaxy.datatypes.binary.SQlite method) (galaxy.datatypes.binary.Sra method) (galaxy.datatypes.binary.TwoBit method) (galaxy.datatypes.binary.Vel method) (galaxy.datatypes.blast.LastDb method) (galaxy.datatypes.constructive_solid_geometry.Ply method) (galaxy.datatypes.constructive_solid_geometry.Vtk method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.flow.FCS method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.genetics.rgTabList method) (galaxy.datatypes.gis.Shapefile method) (galaxy.datatypes.interval.CustomTrack method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.Wiggle method) (galaxy.datatypes.molecules.OBFS method) (galaxy.datatypes.msa.Hmmer method) (galaxy.datatypes.msa.HmmerPress method) (galaxy.datatypes.neo4j.Neo4j method) (galaxy.datatypes.ngsindex.BowtieIndex method) (galaxy.datatypes.plant_tribes.PlantTribesKsComponents method) (galaxy.datatypes.plant_tribes.Smat method) (galaxy.datatypes.proteomics.Kroenik method) (galaxy.datatypes.proteomics.PepList method) (galaxy.datatypes.proteomics.PepXmlReport method) (galaxy.datatypes.proteomics.ProtXmlReport method) (galaxy.datatypes.proteomics.PSMS method) (galaxy.datatypes.proteomics.ThermoRAW method) (galaxy.datatypes.sequence.Maf method) (galaxy.datatypes.tabular.BaseVcf method) (galaxy.datatypes.tabular.Pileup method) (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.TabularData method) (galaxy.datatypes.tabular.Taxonomy method) (galaxy.datatypes.text.Json method) (galaxy.datatypes.tracks.UCSCTrackHub method) (galaxy.model.DatasetInstance method) display_ready() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) display_repository_clone_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) display_repository_file_contents() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) display_tool() (tool_shed.webapp.controllers.repository.RepositoryController method) display_types (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) display_url() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) displayable() (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.tabular.TabularData method) DisplayApp (class in galaxy.schema.schema) DisplayApplication (class in galaxy.datatypes.display_applications.application) (class in galaxy.managers.display_applications) DisplayApplicationDataParameter (class in galaxy.datatypes.display_applications.parameters) DisplayApplicationLink (class in galaxy.datatypes.display_applications.application) DisplayApplicationParameter (class in galaxy.datatypes.display_applications.parameters) DisplayApplicationsManager (class in galaxy.managers.display_applications) DisplayApplicationTemplateParameter (class in galaxy.datatypes.display_applications.parameters) DisplayByUsernameAndSlugGridOperation (class in galaxy.web.legacy_framework.grids) DisplayDataValueWrapper (class in galaxy.datatypes.display_applications.parameters) DisplayParameterValueWrapper (class in galaxy.datatypes.display_applications.parameters) dist_css() (in module galaxy.web.framework.helpers) dist_js() (in module galaxy.web.framework.helpers) dist_to_shed (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.schema.schema.InstalledToolShedRepository attribute) DistanceMatrix (class in galaxy.datatypes.mothur) DistributedObjectStore (class in galaxy.objectstore) DlibSQlite (class in galaxy.datatypes.binary) DMND (class in galaxy.datatypes.binary) DNA_COMPLEMENT (galaxy.datatypes.util.maf_utilities.RegionAlignment attribute) (galaxy.datatypes.util.maf_utilities.SplicedAlignment attribute) (galaxy.tools.util.maf_utilities.RegionAlignment attribute) (galaxy.tools.util.maf_utilities.SplicedAlignment attribute) do_eval() (in module galaxy.tools.expressions) (in module galaxy.tools.expressions.evaluation) do_fast_split() (galaxy.datatypes.sequence.Sequence class method) do_fetch() (in module galaxy.tools.data_fetch) do_invocation_step_action() (galaxy.workflow.modules.PauseModule method) (galaxy.workflow.modules.WorkflowModule method) do_merge() (in module galaxy.jobs.splitters.basic) (in module galaxy.jobs.splitters.multi) do_not_cache() (in module galaxy.web) (in module galaxy.web.framework.decorators) do_post_fork (galaxy.web_stack.GunicornApplicationStack attribute) do_refactor() (galaxy.managers.workflows.WorkflowContentsManager method) do_slow_split() (galaxy.datatypes.sequence.Sequence class method) do_split() (in module galaxy.jobs.splitters.basic) (in module galaxy.jobs.splitters.multi) doc (galaxy.files.sources.FilesSourceProperties attribute) (galaxy.schema.remote_files.FilesSourcePlugin attribute) docker_cache_path() (in module galaxy.tool_util.deps.container_classes) docker_dispatch() (in module galaxy.jobs.stock_rules) docker_host_args() (in module galaxy.tool_util.deps.dockerfiles) docker_host_props (galaxy.tool_util.deps.container_classes.DockerContainer property) docker_image_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) docker_to_singularity() (in module galaxy.tool_util.deps.mulled.mulled_update_singularity_containers) DockerContainer (class in galaxy.tool_util.deps.container_classes) dockerfile_build() (in module galaxy.tool_util.deps.dockerfiles) DockerImageGrid (class in tool_shed.grids.repository_grids) DockerVolume (class in galaxy.tool_util.deps.container_volumes) DockStoreResolver (class in galaxy.tool_util.locations.dockstore) docstring_trim() (in module galaxy.util) document_type (galaxy.schema.tasks.GeneratePdfDownload attribute) doi() (galaxy.managers.citations.DoiCitation method) DoiCache (class in galaxy.managers.citations) DoiCitation (class in galaxy.managers.citations) DotBracket (class in galaxy.datatypes.sequence) DoubleEncodedJsonType (class in galaxy.model.custom_types) download() (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method) (galaxy.webapps.galaxy.api.tools.ToolsController method) (tool_shed.webapp.controllers.repository.RepositoryController method) download_command() (in module galaxy.util.commands) download_contents_to_store() (galaxy_test.base.populators.BaseDatasetPopulator method) download_dataset_from_library() (galaxy_test.selenium.test_library_contents.TestLibraryContents method) download_directory() (in module galaxy.objectstore.s3) download_field_file() (galaxy.webapps.galaxy.api.tool_data.FastAPIToolData method) download_history_to_store() (galaxy_test.base.populators.BaseDatasetPopulator method) download_invocation_to_store() (galaxy_test.base.populators.BaseWorkflowPopulator method) download_invocation_to_uri() (galaxy_test.base.populators.BaseWorkflowPopulator method) download_output() (in module galaxy.tool_util.cwl.util) download_to_file() (in module galaxy.util) download_url (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) (galaxy.schema.schema.JobExportHistoryArchiveModel attribute) (galaxy.schema.schema.MetadataFile attribute) download_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method) downloadable (tool_shed.webapp.model.RepositoryMetadata attribute) downloadable_revisions (tool_shed.webapp.model.Repository attribute) DRF (class in galaxy.datatypes.molecules) DrillDownSelectToolParameter (class in galaxy.tools.parameters.basic) drive_test() (in module galaxy_test.driver.driver_util) DrivenFunctionalTestCase (class in galaxy_test.driver.testcase) driver (galaxy.selenium.cli.DriverWrapper attribute) (galaxy.selenium.context.GalaxySeleniumContext property) (galaxy.selenium.driver_factory.ConfiguredDriver attribute) (galaxy.selenium.has_driver.HasDriver attribute) (galaxy.selenium.navigates_galaxy.NavigatesGalaxy attribute) driver_wrapper (galaxy.selenium.scripts.dump_tour.DumpTourCallback attribute) DriverWrapper (class in galaxy.selenium.cli) drmaa_external_runjob_script (galaxy.config.GalaxyAppConfiguration attribute) DRMAAJobRunner (class in galaxy.jobs.runners.drmaa) drop_column() (in module galaxy.model.migrations.util) drop_constraint() (in module galaxy.model.migrations.util) drop_index() (in module galaxy.model.migrations.util) drop_table() (in module galaxy.model.migrations.util) drop_timestamp_triggers() (in module galaxy.model.triggers.history_update_time_field) DropboxFilesSource (class in galaxy.files.sources.dropbox) DropColumn (class in galaxy.model.migrations.util) DropConstraint (class in galaxy.model.migrations.util) DropIndex (class in galaxy.model.migrations.util) dropout (galaxy.tools.recommendations.ToolRecommendations attribute) DropTable (class in galaxy.model.migrations.util) drs (galaxy.files.sources.PluginKind attribute) drs_id (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) dry_run (galaxy.managers.workflows.RefactorResponse attribute) (galaxy.managers.workflows.WorkflowUpdateOptions attribute) (galaxy.workflow.refactor.schema.RefactorActions attribute) ds_entry() (galaxy_test.base.populators.BaseDatasetPopulator method) Dta (class in galaxy.datatypes.proteomics) Dta2d (class in galaxy.datatypes.proteomics) dump() (galaxy.util.aliaspickler.AliasPickleModule method) (galaxy.util.heartbeat.Heartbeat method) dump_signal_handler() (galaxy.util.heartbeat.Heartbeat method) dump_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method) dumps() (galaxy.util.aliaspickler.AliasPickleModule method) DumpTourCallback (class in galaxy.selenium.scripts.dump_tour) DuplicatedIdentifierException DuplicatedSlugException DuplicateFileToCollectionTool (class in galaxy.tools) duration (galaxy.schema.schema.ShortTermStoreExportPayload attribute) dynamic_conf_filenames() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) dynamic_confs() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) dynamic_structure (galaxy.tool_util.parser.output_objects.ToolOutputCollection property) dynamic_tool (galaxy.model.WorkflowStep attribute) dynamic_tool_confs() (galaxy.managers.configuration.ConfigurationManager method) (galaxy.webapps.galaxy.api.configuration.FastAPIConfiguration method) dynamic_tool_id (galaxy.model.Job attribute) (galaxy.model.WorkflowStep attribute) dynamic_tool_manager (galaxy.structured_app.MinimalManagerApp attribute) DynamicCompressedArchive (class in galaxy.datatypes.binary) DynamicDisplayApplicationBuilder (class in galaxy.datatypes.display_applications.application) DynamicOptions (class in galaxy.tools.parameters.dynamic_options) DynamicTool (class in galaxy.model) DynamicToolManager (class in galaxy.managers.tools) DynamicToolsController (class in galaxy.webapps.galaxy.api.dynamic_tools) Dzi (class in galaxy.datatypes.xml)

E

edam_data (galaxy.datatypes.annotation.Augustus attribute) (galaxy.datatypes.annotation.SnapHmm attribute) (galaxy.datatypes.assembly.Amos attribute) (galaxy.datatypes.assembly.Sequences attribute) (galaxy.datatypes.binary.Ab1 attribute) (galaxy.datatypes.binary.BafTar attribute) (galaxy.datatypes.binary.Bam attribute) (galaxy.datatypes.binary.BamNative attribute) (galaxy.datatypes.binary.BaseBcf attribute) (galaxy.datatypes.binary.BigBed attribute) (galaxy.datatypes.binary.BigWig attribute) (galaxy.datatypes.binary.Cel attribute) (galaxy.datatypes.binary.CRAM attribute) (galaxy.datatypes.binary.Dcd attribute) (galaxy.datatypes.binary.GeminiSQLite attribute) (galaxy.datatypes.binary.GenericAsn1Binary attribute) (galaxy.datatypes.binary.ICM attribute) (galaxy.datatypes.binary.Idat attribute) (galaxy.datatypes.binary.NetCDF attribute) (galaxy.datatypes.binary.ProBam attribute) (galaxy.datatypes.binary.Scf attribute) (galaxy.datatypes.binary.Sff attribute) (galaxy.datatypes.binary.TwoBit attribute) (galaxy.datatypes.blast.BlastXml attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.data.GenericAsn1 attribute) (galaxy.datatypes.data.Newick attribute) (galaxy.datatypes.data.Nexus attribute) (galaxy.datatypes.images.Image attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.microarrays.Gal attribute) (galaxy.datatypes.microarrays.Gpr attribute) (galaxy.datatypes.msa.Hmmer attribute) (galaxy.datatypes.msa.Msf attribute) (galaxy.datatypes.msa.Stockholm_1_0 attribute) (galaxy.datatypes.phylip.Phylip attribute) (galaxy.datatypes.proteomics.MascotDat attribute) (galaxy.datatypes.proteomics.Mgf attribute) (galaxy.datatypes.proteomics.MzTab attribute) (galaxy.datatypes.proteomics.PepXmlReport attribute) (galaxy.datatypes.proteomics.ProteomicsXml attribute) (galaxy.datatypes.proteomics.ProtXmlReport attribute) (galaxy.datatypes.proteomics.ThermoRAW attribute) (galaxy.datatypes.proteomics.Wiff attribute) (galaxy.datatypes.proteomics.Wiff2 attribute) (galaxy.datatypes.qualityscore.QualityScore attribute) (galaxy.datatypes.registry.Registry property) (galaxy.datatypes.sequence.Alignment attribute) (galaxy.datatypes.sequence.Axt attribute) (galaxy.datatypes.sequence.DotBracket attribute) (galaxy.datatypes.sequence.Genbank attribute) (galaxy.datatypes.sequence.Lav attribute) (galaxy.datatypes.sequence.Sequence attribute) (galaxy.datatypes.tabular.Sam attribute) (galaxy.datatypes.text.Obo attribute) (galaxy.datatypes.tracks.GeneTrack attribute) (galaxy.datatypes.triples.Triples attribute) (galaxy.datatypes.xml.Phyloxml attribute) (galaxy.datatypes.xml.Sbml attribute) edam_data() (galaxy.webapps.galaxy.api.datatypes.FastAPIDatatypes method) edam_data_detailed() (galaxy.webapps.galaxy.api.datatypes.FastAPIDatatypes method) edam_format (galaxy.datatypes.assembly.Amos attribute) (galaxy.datatypes.assembly.Roadmaps attribute) (galaxy.datatypes.binary.Ab1 attribute) (galaxy.datatypes.binary.BafTar attribute) (galaxy.datatypes.binary.Bam attribute) (galaxy.datatypes.binary.BamNative attribute) (galaxy.datatypes.binary.BaseBcf attribute) (galaxy.datatypes.binary.BigBed attribute) (galaxy.datatypes.binary.BigWig attribute) (galaxy.datatypes.binary.Binary attribute) (galaxy.datatypes.binary.Biom2 attribute) (galaxy.datatypes.binary.Cel attribute) (galaxy.datatypes.binary.CRAM attribute) (galaxy.datatypes.binary.CuffDiffSQlite attribute) (galaxy.datatypes.binary.ExcelXls attribute) (galaxy.datatypes.binary.GeminiSQLite attribute) (galaxy.datatypes.binary.GenericAsn1Binary attribute) (galaxy.datatypes.binary.Grib attribute) (galaxy.datatypes.binary.H5 attribute) (galaxy.datatypes.binary.HexrdMaterials attribute) (galaxy.datatypes.binary.Idat attribute) (galaxy.datatypes.binary.Loom attribute) (galaxy.datatypes.binary.NetCDF attribute) (galaxy.datatypes.binary.ProBam attribute) (galaxy.datatypes.binary.Scf attribute) (galaxy.datatypes.binary.Sff attribute) (galaxy.datatypes.binary.SQlite attribute) (galaxy.datatypes.binary.TwoBit attribute) (galaxy.datatypes.blast.BlastXml attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.data.GenericAsn1 attribute) (galaxy.datatypes.data.Newick attribute) (galaxy.datatypes.data.Nexus attribute) (galaxy.datatypes.data.Text attribute) (galaxy.datatypes.goldenpath.GoldenPath attribute) (galaxy.datatypes.images.Bmp attribute) (galaxy.datatypes.images.Eps attribute) (galaxy.datatypes.images.Gif attribute) (galaxy.datatypes.images.Gmaj attribute) (galaxy.datatypes.images.Im attribute) (galaxy.datatypes.images.Image attribute) (galaxy.datatypes.images.Jpg attribute) (galaxy.datatypes.images.Pbm attribute) (galaxy.datatypes.images.Pcd attribute) (galaxy.datatypes.images.Pcx attribute) (galaxy.datatypes.images.Pdf attribute) (galaxy.datatypes.images.Pgm attribute) (galaxy.datatypes.images.Png attribute) (galaxy.datatypes.images.Ppm attribute) (galaxy.datatypes.images.Psd attribute) (galaxy.datatypes.images.Rast attribute) (galaxy.datatypes.images.Rgb attribute) (galaxy.datatypes.images.Tiff attribute) (galaxy.datatypes.images.Xbm attribute) (galaxy.datatypes.images.Xpm attribute) (galaxy.datatypes.interval.Bed attribute) (galaxy.datatypes.interval.Bed12 attribute) (galaxy.datatypes.interval.Bed6 attribute) (galaxy.datatypes.interval.BedGraph attribute) (galaxy.datatypes.interval.BedStrict attribute) (galaxy.datatypes.interval.CustomTrack attribute) (galaxy.datatypes.interval.ENCODEPeak attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Gff3 attribute) (galaxy.datatypes.interval.Gtf attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.interval.IntervalTabix attribute) (galaxy.datatypes.interval.ProBed attribute) (galaxy.datatypes.interval.Wiggle attribute) (galaxy.datatypes.microarrays.Gal attribute) (galaxy.datatypes.microarrays.Gpr attribute) (galaxy.datatypes.msa.Hmmer attribute) (galaxy.datatypes.msa.Hmmer2 attribute) (galaxy.datatypes.msa.Hmmer3 attribute) (galaxy.datatypes.msa.Msf attribute) (galaxy.datatypes.msa.Stockholm_1_0 attribute) (galaxy.datatypes.phylip.Phylip attribute) (galaxy.datatypes.proteomics.ImzML attribute) (galaxy.datatypes.proteomics.MascotDat attribute) (galaxy.datatypes.proteomics.Mgf attribute) (galaxy.datatypes.proteomics.MzData attribute) (galaxy.datatypes.proteomics.MzIdentML attribute) (galaxy.datatypes.proteomics.MzML attribute) (galaxy.datatypes.proteomics.MzQuantML attribute) (galaxy.datatypes.proteomics.MzXML attribute) (galaxy.datatypes.proteomics.PepXml attribute) (galaxy.datatypes.proteomics.ProteomicsXml attribute) (galaxy.datatypes.proteomics.TandemXML attribute) (galaxy.datatypes.proteomics.ThermoRAW attribute) (galaxy.datatypes.proteomics.TraML attribute) (galaxy.datatypes.proteomics.Wiff attribute) (galaxy.datatypes.proteomics.Wiff2 attribute) (galaxy.datatypes.qualityscore.QualityScore attribute) (galaxy.datatypes.qualityscore.QualityScore454 attribute) (galaxy.datatypes.qualityscore.QualityScoreIllumina attribute) (galaxy.datatypes.qualityscore.QualityScoreSolexa attribute) (galaxy.datatypes.qualityscore.QualityScoreSOLiD attribute) (galaxy.datatypes.sequence.Axt attribute) (galaxy.datatypes.sequence.BaseFastq attribute) (galaxy.datatypes.sequence.csFasta attribute) (galaxy.datatypes.sequence.DotBracket attribute) (galaxy.datatypes.sequence.Fasta attribute) (galaxy.datatypes.sequence.Fastg attribute) (galaxy.datatypes.sequence.Fastq attribute) (galaxy.datatypes.sequence.FastqIllumina attribute) (galaxy.datatypes.sequence.FastqSanger attribute) (galaxy.datatypes.sequence.FastqSolexa attribute) (galaxy.datatypes.sequence.Genbank attribute) (galaxy.datatypes.sequence.Lav attribute) (galaxy.datatypes.sequence.Maf attribute) (galaxy.datatypes.sequence.RNADotPlotMatrix attribute) (galaxy.datatypes.tabular.BaseVcf attribute) (galaxy.datatypes.tabular.ConnectivityTable attribute) (galaxy.datatypes.tabular.Pileup attribute) (galaxy.datatypes.tabular.Psl attribute) (galaxy.datatypes.tabular.Sam attribute) (galaxy.datatypes.tabular.TabularData attribute) (galaxy.datatypes.text.Arff attribute) (galaxy.datatypes.text.Biom1 attribute) (galaxy.datatypes.text.Html attribute) (galaxy.datatypes.text.Json attribute) (galaxy.datatypes.text.Obo attribute) (galaxy.datatypes.text.SnpEffDb attribute) (galaxy.datatypes.tracks.GeneTrack attribute) (galaxy.datatypes.triples.HDT attribute) (galaxy.datatypes.triples.Jsonld attribute) (galaxy.datatypes.triples.N3 attribute) (galaxy.datatypes.triples.NTriples attribute) (galaxy.datatypes.triples.Rdf attribute) (galaxy.datatypes.triples.Sbol attribute) (galaxy.datatypes.triples.Triples attribute) (galaxy.datatypes.triples.Turtle attribute) (galaxy.datatypes.xml.GenericXml attribute) (galaxy.datatypes.xml.Owl attribute) (galaxy.datatypes.xml.Phyloxml attribute) (galaxy.datatypes.xml.Sbml attribute) edam_formats (galaxy.datatypes.registry.Registry property) edam_formats() (galaxy.webapps.galaxy.api.datatypes.FastAPIDatatypes method) edam_formats_detailed() (galaxy.webapps.galaxy.api.datatypes.FastAPIDatatypes method) edam_info (galaxy.tool_util.biotools.interface.BiotoolsEntry property) edam_operations (galaxy.tool_util.biotools.interface.ParsedBiotoolsEntry attribute) (galaxy.tool_util.biotools.ParsedBiotoolsEntry attribute) (galaxy.tool_util.ontologies.ontology_data.OntologyData attribute) edam_topics (galaxy.tool_util.biotools.interface.ParsedBiotoolsEntry attribute) (galaxy.tool_util.biotools.ParsedBiotoolsEntry attribute) (galaxy.tool_util.ontologies.ontology_data.OntologyData attribute) EdamPanelMode (class in galaxy.tool_util.toolbox.views.edam) EdamToolPanelView (class in galaxy.tool_util.toolbox.views.edam) edgelist_for_workflow_steps() (in module galaxy.workflow.steps) edit() (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) edit_category() (tool_shed.webapp.controllers.admin.AdminController method) edit_category_entry() (tool_shed.repository_registry.Registry method) edit_details() (in module galaxy.selenium.navigates_galaxy) edit_form() (galaxy.webapps.galaxy.controllers.forms.Forms method) edit_info() (tool_shed.webapp.controllers.user.User method) edit_quota() (galaxy.managers.quotas.QuotaManager method) (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) edit_repository_categories() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) edit_repository_information() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) edit_username() (tool_shed.webapp.controllers.user.User method) editable_keys (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetCollectionAssociation attribute) editor() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) Edr (class in galaxy.datatypes.binary) Edta (class in galaxy.datatypes.proteomics) effective_collection_type() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) effective_collection_type_description() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) effective_output_name (galaxy.tool_util.parser.output_objects.ToolOutputCollectionPart property) (galaxy.tool_util.parser.ToolOutputCollectionPart property) effective_state (galaxy.model.store.discover.JsonCollectedDatasetMatch property) EffectiveOutput (class in galaxy.model) Eigenstratgeno (class in galaxy.datatypes.genetics) Eigenstratpca (class in galaxy.datatypes.genetics) Eland (class in galaxy.datatypes.tabular) ElandMulti (class in galaxy.datatypes.tabular) elapsed (galaxy.util.ExecutionTimer property) (galaxy.util.StructuredExecutionTimer property) elem() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) Element (class in galaxy.util) element (galaxy.tours.TourStep attribute) element_absent() (galaxy.selenium.has_driver.HasDriver method) element_as_dict() (galaxy.datatypes.dataproviders.hierarchy.XMLDataProvider method) element_count (galaxy.model.DatasetCollection attribute) (galaxy.schema.schema.DCObject attribute) (galaxy.schema.schema.DCSummary attribute) (galaxy.schema.schema.HDCASummary attribute) element_identifier (galaxy.model.DatasetCollectionElement attribute) (galaxy.schema.schema.DCESummary attribute) (galaxy.tools.wrappers.DatasetCollectionWrapper property) (galaxy.tools.wrappers.DatasetFilenameWrapper property) element_identifiers (galaxy.model.store.discover.JsonCollectedDatasetMatch property) (galaxy.schema.schema.CollectionElementIdentifier attribute) (galaxy.schema.schema.CreateNewCollectionPayload attribute) element_identifiers_extensions_paths_and_metadata_files (galaxy.model.DatasetCollection property) (galaxy.tools.wrappers.DatasetCollectionWrapper property) element_index (galaxy.model.DatasetCollectionElement attribute) (galaxy.schema.schema.DCESummary attribute) element_is_set() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataCollection method) (galaxy.tools.wrappers.DatasetFilenameWrapper.MetadataWrapper method) element_is_valid() (galaxy.tools.FilterDatasetsTool static method) (galaxy.tools.FilterEmptyDatasetsTool static method) (galaxy.tools.FilterFailedDatasetsTool static method) (galaxy.tools.KeepSuccessDatasetsTool static method) element_object (galaxy.model.DatasetCollectionElement property) element_symbols (galaxy.datatypes.molecules.GenericMolFile attribute) element_type (galaxy.model.DatasetCollectionElement property) (galaxy.schema.schema.DCESummary attribute) ElementIdentifierMapper (class in galaxy.tools.wrappers) elements (galaxy.model.DatasetCollection attribute) (galaxy.schema.schema.DCDetailed attribute) (galaxy.schema.schema.DCObject attribute) (galaxy.schema.schema.HDCADetailed attribute) elements_datatypes (galaxy.schema.schema.HDCADetailed attribute) elements_no_end_tag (galaxy.managers.pages.PageContentProcessor attribute) elements_tree_map() (in module galaxy.tools.data_fetch) ELEMENTS_UNINITIALIZED (galaxy.managers.collections.DatasetCollectionManager attribute) ElementsFromType (class in galaxy.schema.fetch_data) ElementTree (class in galaxy.util) ElibSQlite (class in galaxy.datatypes.binary) email (galaxy.files.DictFileSourcesUserContext property) (galaxy.files.ProvidesUserFileSourcesUserContext property) (galaxy.model.PSACode attribute) (galaxy.model.User attribute) (galaxy.schema.BootstrapAdminUser attribute) (galaxy.schema.schema.BaseUserModel attribute) (galaxy.schema.schema.Creator attribute) (galaxy.schema.schema.GroupUserResponse attribute) (galaxy.schema.schema.LimitedUserModel attribute) (galaxy.schema.schema.UserCreationPayload attribute) (galaxy.schema.schema.UserEmail attribute) (tool_shed.webapp.model.User attribute) email_alerts (tool_shed.webapp.model.Repository attribute) email_alerts_repository_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) email_from (galaxy.config.GalaxyAppConfiguration attribute) email_hash (galaxy.model.Page property) (galaxy.schema.schema.PageSummary attribute) (galaxy.schema.schema.SharingStatus attribute) EmailAction (class in galaxy.job_execution.actions.post) EmailAlertsRepositoryGrid (class in tool_shed.grids.repository_grids) EmailErrorReporter (class in galaxy.tools.errors) EmailPlugin (class in galaxy.tools.error_reports.plugins.email) embed_dim (galaxy.tools.recommendations.ToolRecommendations attribute) embedded_driver() (in module galaxy_test.conftest) (in module galaxy_test.selenium.conftest) emboss_repository_long_description (in module tool_shed.test.functional.test_0470_tool_dependency_repository_type) empty (galaxy.model.History property) EMPTY (galaxy.schema.schema.DatasetState attribute) empty() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) empty_field_value (galaxy.tools.data.RefgenieToolDataTable attribute) (galaxy.tools.data.TabularToolDataTable attribute) (galaxy.tools.data.ToolDataTable attribute) empty_field_values (galaxy.tools.data.RefgenieToolDataTable attribute) (galaxy.tools.data.TabularToolDataTable attribute) (galaxy.tools.data.ToolDataTable attribute) EmptyTextfieldValidator (class in galaxy.tools.parameters.validation) enable_email_alerts() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) enable_link_access() (galaxy.webapps.galaxy.api.pages.FastAPIPages method) (galaxy.webapps.galaxy.api.visualizations.FastAPIVisualizations method) (galaxy.webapps.galaxy.services.sharable.ShareableService method) enable_tool_shed_check (galaxy.config.GalaxyAppConfiguration attribute) enabled (galaxy.objectstore.QuotaModel attribute) (galaxy.schema.schema.UserBeaconSetting attribute) enabled_container_types (galaxy.tool_util.deps.DependencyManager property) encode() (galaxy.datatypes.dataproviders.chunk.Base64ChunkDataProvider method) (galaxy.datatypes.dataproviders.chunk.ChunkDataProvider method) (galaxy.tools.DefaultToolState method) (galaxy.web_stack.message.ApplicationStackMessage method) encode_all_ids() (galaxy.security.idencoding.IdEncodingHelper method) (galaxy.webapps.galaxy.services.base.ServiceBase method) encode_dataset_user() (in module galaxy.datatypes.display_applications.util) encode_dict_ids() (galaxy.security.idencoding.IdEncodingHelper method) encode_guid() (galaxy.security.idencoding.IdEncodingHelper method) encode_id() (galaxy.managers.configuration.ConfigurationManager method) (galaxy.security.idencoding.IdAsLowercaseAlphanumEncodingHelper method) (galaxy.security.idencoding.IdEncodingHelper method) (galaxy.webapps.galaxy.api.configuration.FastAPIConfiguration method) (galaxy.webapps.galaxy.services.base.ServiceBase method) encode_runtime_state() (galaxy.workflow.modules.WorkflowModule method) encode_with_security() (in module galaxy.managers.base) EncodedDataItemSourceId (class in galaxy.schema.schema) EncodedDatasetSourceId (class in galaxy.schema.schema) EncodedHistoryContentItem (class in galaxy.schema.schema) EncodedJobParameterHistoryItem (class in galaxy.schema.schema) ENCODEPeak (class in galaxy.datatypes.interval) ENCODEPeakDataProvider (class in galaxy.visualization.data_providers.genome) ENCODEPeakTabixDataProvider (class in galaxy.visualization.data_providers.genome) encoder() (in module galaxy.tools.cache) encoding (galaxy.model.migrations.DatabaseConfig attribute) end (galaxy.datatypes.util.maf_utilities.SplicedAlignment property) (galaxy.tools.util.maf_utilities.SplicedAlignment property) end_session_endpoint (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute) engine (galaxy.model.Dataset attribute) enqueue() (galaxy.jobs.manager.JobManager method) (galaxy.jobs.manager.NoopManager method) enrich_response() (galaxy.webapps.base.api.AccessLoggingMiddleware method) ensure_brew_on_path() (in module galaxy.tool_util.deps.brew_exts) ensure_can_change_datatype() (galaxy.managers.datasets.DatasetAssociationManager method) ensure_can_set_metadata() (galaxy.managers.datasets.DatasetAssociationManager method) ensure_celery_tasks_enabled() (in module galaxy.webapps.galaxy.services.base) ensure_conda_build_installed_if_needed() (galaxy.tool_util.deps.conda_util.CondaContext method) ensure_configs_directory() (in module galaxy.job_execution.setup) ensure_cwltool_available() (in module galaxy.tool_util.cwl.cwltool_deps) ensure_dataset_on_disk() (galaxy.managers.datasets.DatasetAssociationManager method) ensure_history_annotation_area_displayed() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) ensure_in_working_directory() (galaxy.tools.data_fetch.UploadConfig method) ensure_installed() (in module galaxy.tool_util.deps.installable) ensure_materialized() (galaxy.model.deferred.DatasetInstanceMaterializer method) ensure_object_added_to_session() (in module galaxy.model.base) (in module galaxy.model.database_utils) ensure_pykube() (in module galaxy.jobs.runners.util.pykube_util) ensure_raw_description() (galaxy.managers.workflows.WorkflowContentsManager method) ensure_registered (galaxy_test.selenium.test_collection_builders.TestCollectionBuilders attribute) (galaxy_test.selenium.test_collection_edit.TestCollectionEdit attribute) (galaxy_test.selenium.test_data_source_tools.TestDataSource attribute) (galaxy_test.selenium.test_dataset_metadata_download.TestHistoryDatasetState attribute) (galaxy_test.selenium.test_history_copy_elements.TestHistoryCopyElements attribute) (galaxy_test.selenium.test_history_dataset_state.TestHistoryDatasetState attribute) (galaxy_test.selenium.test_history_multi_view.TestHistoryMultiView attribute) (galaxy_test.selenium.test_history_panel.TestHistoryPanel attribute) (galaxy_test.selenium.test_history_panel_collections.TestHistoryPanelCollections attribute) (galaxy_test.selenium.test_history_sharing.TestHistoryRequiresLoginSelenium attribute) (galaxy_test.selenium.test_invocation_grid.TestInvocationGridSelenium attribute) (galaxy_test.selenium.test_pages.TestPages attribute) (galaxy_test.selenium.test_tool_form.TestLoggedInToolForm attribute) (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor attribute) (galaxy_test.selenium.test_workflow_invocation_details.TestWorkflowInvocationDetails attribute) (galaxy_test.selenium.test_workflow_management.TestWorkflowManagement attribute) (galaxy_test.selenium.test_workflow_run.TestWorkflowRun attribute) (galaxy_test.selenium.test_workflow_sharing.TestWorkflowSharingRedirect attribute) ensure_shareable() (galaxy.model.Dataset method) ensure_tempdir() (galaxy.config.GalaxyAppConfiguration method) ensure_tool_conf_item() (in module galaxy.tool_util.toolbox.parser) ensure_tool_run_response_okay() (in module galaxy.tool_util.verify.interactor) ensure_user_with_email() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) ensure_valid_folder_id() (in module galaxy.schema.fields) ensure_valid_id() (in module galaxy.schema.fields) Entry (class in galaxy.files.sources) entry_url (galaxy.model.InteractiveToolEntryPoint attribute) EntryData (class in galaxy.files.sources) enum_values() (in module galaxy.util) env_config_directory() (galaxy.job_execution.compute_environment.ComputeEnvironment method) (galaxy.job_execution.compute_environment.SharedComputeEnvironment method)

env_config_file (galaxy.main_config.WebappSetupProps attribute) env_config_section (galaxy.main_config.WebappSetupProps attribute) env_path() (galaxy.tool_util.deps.conda_util.CondaContext method) env_to_statement() (in module galaxy.jobs.runners.util.env) EnvAction (class in galaxy.tool_util.deps.brew_exts) environ (galaxy.webapps.galaxy.api.GalaxyASGIRequest property) environment_variables (galaxy.tools.evaluation.PartialToolEvaluator attribute) (galaxy.tools.evaluation.RemoteToolEvaluator attribute) EnvPlugin (class in galaxy.job_metrics.instrumenters.env) envs_path (galaxy.tool_util.deps.conda_util.CondaContext property) Eps (class in galaxy.datatypes.images) eq_datatype() (galaxy.managers.datasets.DatasetAssociationFilterParser method) equals() (galaxy.managers.citations.BaseCitation method) (galaxy.model.CloudAuthz method) err_code (galaxy.exceptions.AcceptedRetryLater attribute) (galaxy.exceptions.ActionInputError attribute) (galaxy.exceptions.AdminRequiredException attribute) (galaxy.exceptions.AuthenticationFailed attribute) (galaxy.exceptions.AuthenticationRequired attribute) (galaxy.exceptions.ConfigDoesNotAllowException attribute) (galaxy.exceptions.ConfigurationError attribute) (galaxy.exceptions.Conflict attribute) (galaxy.exceptions.DeprecatedMethod attribute) (galaxy.exceptions.DuplicatedIdentifierException attribute) (galaxy.exceptions.DuplicatedSlugException attribute) (galaxy.exceptions.InconsistentDatabase attribute) (galaxy.exceptions.InsufficientPermissionsException attribute) (galaxy.exceptions.InternalServerError attribute) (galaxy.exceptions.InvalidFileFormatError attribute) (galaxy.exceptions.ItemAccessibilityException attribute) (galaxy.exceptions.ItemImmutableException attribute) (galaxy.exceptions.ItemOwnershipException attribute) (galaxy.exceptions.MalformedContents attribute) (galaxy.exceptions.MalformedId attribute) (galaxy.exceptions.MessageException attribute) (galaxy.exceptions.NoContentException attribute) (galaxy.exceptions.NotImplemented attribute) (galaxy.exceptions.ObjectAttributeInvalidException attribute) (galaxy.exceptions.ObjectAttributeMissingException attribute) (galaxy.exceptions.ObjectNotFound attribute) (galaxy.exceptions.ReferenceDataError attribute) (galaxy.exceptions.RequestParameterInvalidException attribute) (galaxy.exceptions.RequestParameterMissingException attribute) (galaxy.exceptions.ServerNotConfiguredForRequest attribute) (galaxy.exceptions.ToolExecutionError attribute) (galaxy.exceptions.ToolMetaParameterException attribute) (galaxy.exceptions.ToolMissingException attribute) (galaxy.exceptions.UnknownContentsType attribute) (galaxy.exceptions.UserActivationRequiredException attribute) (galaxy.exceptions.UserCannotRunAsException attribute) (galaxy.exceptions.UserInvalidRunAsException attribute) Error (class in galaxy.webapps.galaxy.controllers.error) ERROR (galaxy.model.Dataset.conversion_messages attribute) (galaxy.model.DatasetInstance.conversion_messages attribute) error (galaxy.model.JobStateSummary attribute) ERROR (galaxy.model.Task.states attribute) (galaxy.model.tool_shed_install.ToolDependency.states attribute) (galaxy.model.tool_shed_install.ToolShedRepository.installation_status attribute) (galaxy.model.tool_shed_install.ToolShedRepository.states attribute) error (galaxy.schema.schema.BulkOperationItemError attribute) ERROR (galaxy.schema.schema.DatasetState attribute) error (galaxy.schema.schema.ExportObjectResultMetadata attribute) (galaxy.schema.schema.HDCJobStateSummary attribute) ERROR (galaxy.schema.schema.JobState attribute) (galaxy.tool_util.lint.LintLevel attribute) error (galaxy.tool_util.verify.interactor.InvalidToolTestDict attribute) (galaxy.tool_util.verify.interactor.ToolTestDescriptionDict attribute) (galaxy.tool_util.verify.interactor.ValidToolTestDict attribute) error() (galaxy.tool_util.lint.LintContext method) (galaxy.web.framework.middleware.remoteuser.RemoteUser method) (in module galaxy.web) (in module galaxy.web.framework.decorators) (tool_shed.webapp.framework.middleware.remoteuser.RemoteUser method) error_code (galaxy.exceptions.RealUserRequiredException attribute) (galaxy.exceptions.ToolInputsNotOKException attribute) (galaxy.exceptions.ToolInputsNotReadyException attribute) error_if_anonymous() (galaxy.managers.users.UserManager method) error_if_uploading() (galaxy.managers.hdas.HDAManager method) error_message (galaxy.model.store.discover.DiscoveredFileError attribute) (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.schema.schema.InstalledToolShedRepository attribute) ERROR_MESSAGE_UNRECOGNIZED_ARG (galaxy.jobs.runners.util.cli.job.pbs.OpenPBS attribute) (galaxy.jobs.runners.util.cli.job.torque.Torque attribute) error_messages (galaxy.tool_util.lint.LintContext property) error_on_exit_code() (in module galaxy.tool_util.parser.stdio) error_reports (galaxy.structured_app.MinimalManagerApp attribute) error_stack() (galaxy.webapps.galaxy.api.tools.ToolsController method) error_unless_accessible() (galaxy.managers.secured.AccessibleManagerMixin method) error_unless_admin() (galaxy.managers.users.UserManager method) error_unless_dataset_purge_allowed() (galaxy.managers.datasets.DatasetManager method) error_unless_mutable() (galaxy.managers.secured.OwnableManagerMixin method) error_unless_owner() (galaxy.managers.secured.OwnableManagerMixin method) error_unless_permitted() (galaxy.managers.rbac_secured.RBACPermission method) ErrorCode (class in galaxy.exceptions.error_codes) ErrorMiddleware (class in galaxy.web.framework.middleware.error) ErrorPlugin (class in galaxy.tools.error_reports) (class in galaxy.tools.error_reports.plugins) ErrorReporter (class in galaxy.tools.errors) ErrorReports (class in galaxy.tools.error_reports) errors (galaxy.schema.schema.HistoryContentBulkOperationResult attribute) (galaxy.schema.schema.ShareWithStatus attribute) (galaxy.schema.schema.WorkflowStepToExport attribute) errors_per_tool() (galaxy.webapps.reports.controllers.jobs.Jobs method) escape() (in module tool_shed.util.web_util) escape_html() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) Eset (class in galaxy.datatypes.genetics) estimate_file_lines() (galaxy.datatypes.data.Text method) evalop (galaxy.util.bool_expressions.BoolBinaryOperation attribute) evalop() (galaxy.util.bool_expressions.BoolAnd method) (galaxy.util.bool_expressions.BoolOr method) evaluate() (galaxy.util.bool_expressions.TokenContainedEvaluator method) (galaxy.util.bool_expressions.TokenEvaluator method) (galaxy.util.bool_expressions.ValidationOnlyTokenEvaluator method) (in module galaxy.tools.expressions) (in module galaxy.tools.expressions.evaluation) evaluate_expression() (galaxy.util.bool_expressions.BooleanExpressionEvaluator method) evaluate_value_from_expressions() (in module galaxy.workflow.modules) evaluator (galaxy.util.bool_expressions.BoolOperand attribute) Event (class in galaxy.model) EventHandler (class in galaxy.util.watcher) exact (galaxy.tool_util.deps.resolvers.ContainerDependency property) (galaxy.tool_util.deps.resolvers.Dependency property) (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependency property) (galaxy.tool_util.deps.resolvers.NullDependency attribute) (galaxy.tool_util.deps.resolvers.resolver_mixins.HomebrewDependency property) exact_tools (galaxy.managers.workflows.WorkflowStateResolutionOptions attribute) example_datatype_registry_for_sample() (in module galaxy.datatypes.registry) ExcelXls (class in galaxy.datatypes.binary) exception (galaxy.tool_util.verify.interactor.InvalidToolTestDict attribute) (galaxy.tool_util.verify.interactor.ToolTestDescription attribute) (galaxy.tool_util.verify.interactor.ToolTestDescriptionDict attribute) (galaxy.tool_util.verify.script.TestException attribute) exception_handler() (galaxy.web.framework.middleware.error.ErrorMiddleware method) exception_indicates_click_intercepted() (in module galaxy.selenium.has_driver) exception_indicates_not_clickable() (in module galaxy.selenium.has_driver) exception_indicates_stale_element() (in module galaxy.selenium.has_driver) exception_seems_to_indicate_transition() (in module galaxy.selenium.navigates_galaxy) exchange (galaxy.queue_worker.ControlTask property) excludes (galaxy.tool_util.toolbox.views.definitions.ItemsFrom attribute) (galaxy.tool_util.toolbox.views.definitions.Section attribute) (galaxy.tool_util.toolbox.views.definitions.SectionAlias attribute) (galaxy.tool_util.toolbox.views.definitions.SectionAliases attribute) (galaxy.tool_util.toolbox.views.definitions.StaticToolBoxView attribute) ExcludeTool (class in galaxy.tool_util.toolbox.views.definitions) ExcludeToolRegex (class in galaxy.tool_util.toolbox.views.definitions) ExcludeTypes (class in galaxy.tool_util.toolbox.views.definitions) exec_after_process() (galaxy.tools.DataManagerTool method) (galaxy.tools.ExpressionTool method) (galaxy.tools.ImportHistoryTool method) (galaxy.tools.InteractiveTool method) (galaxy.tools.SetMetadataTool method) (galaxy.tools.Tool method) exec_before_job() (galaxy.tools.DataSourceTool method) (galaxy.tools.ExpressionTool method) (galaxy.tools.OutputParameterJSONTool method) (galaxy.tools.Tool method) exec_clean() (galaxy.tool_util.deps.conda_util.CondaContext method) exec_command() (galaxy.tool_util.deps.conda_util.CondaContext method) exec_create() (galaxy.tool_util.deps.conda_util.CondaContext method) exec_install() (galaxy.tool_util.deps.conda_util.CondaContext method) exec_remove() (galaxy.tool_util.deps.conda_util.CondaContext method) exec_search() (galaxy.tool_util.deps.conda_util.CondaContext method) execute() (galaxy.job_execution.actions.post.ActionBox class method) (galaxy.job_execution.actions.post.ChangeDatatypeAction class method) (galaxy.job_execution.actions.post.ColumnSetAction class method) (galaxy.job_execution.actions.post.DefaultJobAction class method) (galaxy.job_execution.actions.post.DeleteDatasetAction class method) (galaxy.job_execution.actions.post.DeleteIntermediatesAction class method) (galaxy.job_execution.actions.post.EmailAction class method) (galaxy.job_execution.actions.post.HideDatasetAction class method) (galaxy.job_execution.actions.post.RenameDatasetAction class method) (galaxy.job_execution.actions.post.SetMetadataAction class method) (galaxy.job_execution.actions.post.TagDatasetAction class method) (galaxy.job_execution.actions.post.ValidateOutputsAction class method) (galaxy.jobs.runners.util.cli.shell.BaseShellExec method) (galaxy.jobs.runners.util.cli.shell.local.LocalShell method) (galaxy.jobs.runners.util.cli.shell.rsh.ParamikoShell method) (galaxy.jobs.runners.util.cli.shell.rsh.RemoteShell method) (galaxy.model.migrations.util.AddColumn method) (galaxy.model.migrations.util.CreateIndex method) (galaxy.model.migrations.util.CreateTable method) (galaxy.model.migrations.util.DDLAlterOperation method) (galaxy.model.migrations.util.DDLOperation method) (galaxy.model.migrations.util.DropIndex method) (galaxy.model.migrations.util.DropTable method) (galaxy.tool_util.verify.test_data.GitDataResolver method) (galaxy.tools.actions.data_manager.DataManagerToolAction method) (galaxy.tools.actions.DefaultToolAction method) (galaxy.tools.actions.history_imp_exp.ExportHistoryToolAction method) (galaxy.tools.actions.history_imp_exp.ImportHistoryToolAction method) (galaxy.tools.actions.metadata.SetMetadataToolAction method) (galaxy.tools.actions.model_operations.ModelOperationToolAction method) (galaxy.tools.actions.ToolAction method) (galaxy.tools.actions.upload.BaseUploadToolAction method) (galaxy.tools.Tool method) (galaxy.workflow.modules.InputModule method) (galaxy.workflow.modules.InputParameterModule method) (galaxy.workflow.modules.PauseModule method) (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) (in module galaxy.tool_util.deps.brew_exts) (in module galaxy.tools.execute) (in module galaxy.util.commands) execute_on_mapped_over() (galaxy.job_execution.actions.post.ActionBox class method) (galaxy.job_execution.actions.post.DefaultJobAction class method) (galaxy.job_execution.actions.post.DeleteDatasetAction class method) (galaxy.job_execution.actions.post.HideDatasetAction class method) (galaxy.job_execution.actions.post.RenameDatasetAction class method) (galaxy.job_execution.actions.post.TagDatasetAction class method) execute_statements() (in module galaxy.model.triggers.utils) execute_tool_hooks() (galaxy.tools.evaluation.RemoteToolEvaluator method) (galaxy.tools.evaluation.ToolEvaluator method) execute_via_app() (galaxy.tools.actions.metadata.SetMetadataToolAction method) execution_time (galaxy.model.Task attribute) ExecutionTimer (class in galaxy.util) ExecutionTimerFactory (class in galaxy.app) exists() (galaxy.model.database_utils.MySQLDatabaseManager method) (galaxy.model.database_utils.PosgresDatabaseManager method) (galaxy.model.database_utils.SqliteDatabaseManager method) (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method) (galaxy.tool_util.verify.test_data.FileDataResolver method) (galaxy.tool_util.verify.test_data.GitDataResolver method) exit_code (galaxy.model.Job attribute) (galaxy.model.Task attribute) (galaxy.schema.schema.JobBaseModel attribute) exit_code_file (galaxy.jobs.runners.JobState property) exmeta_item_id (galaxy.webapps.galaxy.api.extended_metadata.BaseExtendedMetadataController attribute) (galaxy.webapps.galaxy.api.extended_metadata.HistoryDatasetExtendMetadataController attribute) (galaxy.webapps.galaxy.api.extended_metadata.LibraryDatasetExtendMetadataController attribute) expand_incoming() (galaxy.tools.Tool method) expand_meta_parameters() (in module galaxy.tools.parameters.meta) expand_multi_inputs() (in module galaxy.util.permutations) expand_ontology_data() (in module galaxy.tool_util.ontologies.ontology_data) expand_pretty_datetime_format() (in module galaxy.config) expand_user_properties() (galaxy.model.User static method) expand_workflow_inputs() (in module galaxy.tools.parameters.meta) expect_exit_code (galaxy.tool_util.parser.interface.ToolSourceTest attribute) (galaxy.tool_util.verify.interactor.ToolTestDescription attribute) (galaxy.tool_util.verify.interactor.ToolTestDescriptionDict attribute) (galaxy.tool_util.verify.interactor.ValidToolTestDict attribute) expect_failure (galaxy.tool_util.parser.interface.ToolSourceTest attribute) (galaxy.tool_util.verify.interactor.ToolTestDescription attribute) (galaxy.tool_util.verify.interactor.ToolTestDescriptionDict attribute) (galaxy.tool_util.verify.interactor.ValidToolTestDict attribute) expect_num_outputs (galaxy.tool_util.parser.interface.ToolSourceTest attribute) expect_repo_created_strings() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) expect_test_failure (galaxy.tool_util.parser.interface.ToolSourceTest attribute) (galaxy.tool_util.verify.interactor.ToolTestDescription attribute) (galaxy.tool_util.verify.interactor.ToolTestDescriptionDict attribute) (galaxy.tool_util.verify.interactor.ValidToolTestDict attribute) expected_app_factories (galaxy.config.config_manage.App attribute) expected_value (galaxy.model.InnerCollectionFilter attribute) expiration_time (galaxy.model.CustosAuthnzToken attribute) (galaxy.model.Notification attribute) (galaxy.model.PasswordResetToken attribute) (tool_shed.webapp.model.PasswordResetToken attribute) expire_tool() (galaxy.tools.cache.ToolCache method) expired_datasets (galaxy.model.LibraryDataset attribute) explanation (galaxy.webapps.base.controller.HTTPBadRequest attribute) ExplicitContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit) ExplicitSingularityContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit) export_association_id (galaxy.schema.tasks.GenerateHistoryDownload attribute) (galaxy.schema.tasks.WriteHistoryTo attribute) export_collection() (galaxy.model.store.DirectoryModelExportStore method) export_directory (galaxy.model.store.WriteCrates attribute) export_for_update() (galaxy_test.base.populators.BaseWorkflowPopulator method) export_history() (galaxy.model.store.DirectoryModelExportStore method) (galaxy.model.store.ModelExportStore method) (galaxy.model.store.WorkflowInvocationOnlyExportStore method) export_history_to_uri_async() (galaxy_test.base.populators.BaseDatasetPopulator method) export_job() (galaxy.model.store.DirectoryModelExportStore method) export_jobs() (galaxy.model.store.DirectoryModelExportStore method) export_library() (galaxy.model.store.DirectoryModelExportStore method) (galaxy.model.store.ModelExportStore method) (galaxy.model.store.WorkflowInvocationOnlyExportStore method) export_library_folder() (galaxy.model.store.DirectoryModelExportStore method) (galaxy.model.store.ModelExportStore method) export_library_folder_contents() (galaxy.model.store.DirectoryModelExportStore method) export_list() (galaxy.tool_util.deps.conda_util.CondaContext method) export_metadata (galaxy.model.StoreExportAssociation attribute) (galaxy.schema.schema.ObjectExportTaskResponse attribute) export_name (galaxy.model.JobExportHistoryArchive property) export_object_type (galaxy.managers.histories.HistoryExportManager attribute) export_record_data (galaxy.schema.schema.ExportAssociationData attribute) export_store (galaxy.webapps.galaxy.services.base.ServedExportStore attribute) export_target (galaxy.webapps.galaxy.services.base.ServedExportStore attribute) export_to_file() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) export_url() (galaxy_test.base.populators.BaseDatasetPopulator method) export_via_api() (tool_shed.webapp.controllers.repository.RepositoryController method) export_workflow_invocation() (galaxy.model.store.DirectoryModelExportStore method) (galaxy.model.store.ModelExportStore method) ExportAssociationData (class in galaxy.schema.schema) exported_key() (galaxy.model.store.DirectoryModelExportStore method) ExportHistoryArchivePayload (class in galaxy.schema.schema) ExportHistoryTool (class in galaxy.tools) ExportHistoryToolAction (class in galaxy.tools.actions.history_imp_exp) ExportObjectMetadata (class in galaxy.schema.schema) ExportObjectRequestMetadata (class in galaxy.schema.schema) ExportObjectResultMetadata (class in galaxy.schema.schema) ExportObjectType (class in galaxy.schema.schema) ExportRecordData (class in galaxy.schema.schema) exports (galaxy.model.History attribute) ExportTaskListResponse (class in galaxy.schema.schema) expose() (in module galaxy.web) (in module galaxy.web.framework.decorators) (in module galaxy.webapps.reports) (in module tool_shed.webapp) expose_api() (in module galaxy.web) (in module galaxy.web.framework.decorators) expose_api_anonymous() (in module galaxy.web) (in module galaxy.web.framework.decorators) expose_api_anonymous_and_sessionless() (in module galaxy.web) (in module galaxy.web.framework.decorators) expose_api_raw() (in module galaxy.web) (in module galaxy.web.framework.decorators) expose_api_raw_anonymous() (in module galaxy.web) (in module galaxy.web.framework.decorators) expose_api_raw_anonymous_and_sessionless() (in module galaxy.web) (in module galaxy.web.framework.decorators) EXPRESSION_INPUTS_NAME (galaxy.tools.ExpressionTool attribute) ExpressionContext (class in galaxy.util.expressions) ExpressionJson (class in galaxy.datatypes.text) ExpressionTool (class in galaxy.tools) ExpressionValidator (class in galaxy.tools.parameters.validation) ext (galaxy.datatypes.sniff.HandleCompressedFileResponse attribute) (galaxy.datatypes.sniff.HandleUploadedDatasetFileInternalResponse attribute) (galaxy.datatypes.upload_util.HandleUploadResponse attribute) (galaxy.model.DatasetInstance property) (galaxy.model.store.discover.JsonCollectedDatasetMatch property) (galaxy.schema.fetch_data.BaseDataElement attribute) (galaxy.tools.parameters.grouping.Dataset attribute) ext_to_class_name (galaxy.managers.datatypes.DatatypesMap attribute) extend() (galaxy.model.custom_types.MutationList method) extend_data_with() (galaxy.tools.data.TabularToolDataTable method) extend_validation_errors() (galaxy.model.DatasetInstance method) extended (galaxy.metadata.ExtendedDirectoryMetadataGenerator attribute) (galaxy.metadata.MetadataCollectionStrategy attribute) extended_brew_info() (in module galaxy.tool_util.deps.brew_exts) extended_metadata (galaxy.model.ExtendedMetadataIndex attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) extended_metadata_id (galaxy.model.ExtendedMetadataIndex attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetAssociationHistory attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) ExtendedDirectoryMetadataGenerator (class in galaxy.metadata) ExtendedMetadata (class in galaxy.model) ExtendedMetadataIndex (class in galaxy.model) ExtendedXYZ (class in galaxy.datatypes.molecules) extension (galaxy.datatypes.display_applications.parameters.DatasetLikeObject attribute) (galaxy.managers.datatypes.DatatypeDetails attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetAssociationHistory attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDASummary attribute) external (galaxy.model.User attribute) (tool_shed.webapp.model.User attribute) external_download_latest_url (galaxy.schema.schema.JobExportHistoryArchiveModel attribute) external_download_permanent_url (galaxy.schema.schema.JobExportHistoryArchiveModel attribute) external_extra_files_path (galaxy.model.deferred.TransientDatasetPaths attribute) external_filename (galaxy.model.Dataset attribute) (galaxy.model.deferred.TransientDatasetPaths attribute) (galaxy.model.store.DatasetAttributeImportModel attribute) external_id (galaxy.schema.schema.JobSummary attribute) external_link (galaxy.files.sources.Entry attribute) (galaxy.schema.remote_files.CreatedEntryResponse attribute) external_metadata_set_successfully() (galaxy.metadata.MetadataCollectionStrategy method) (galaxy.metadata.PortableDirectoryMetadataGenerator method) external_output_metadata (galaxy.model.Job attribute) external_runjob() (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) external_user_id (galaxy.model.CustosAuthnzToken attribute) extra (galaxy.schema.schema.ShareHistoryWithStatus attribute) (galaxy.schema.schema.ShareWithStatus attribute) extra_data (galaxy.model.UserAuthnzToken attribute) extra_filenames (galaxy.tools.evaluation.PartialToolEvaluator attribute) (galaxy.tools.evaluation.RemoteToolEvaluator attribute) extra_files (galaxy.model.store.discover.JsonCollectedDatasetMatch property) (galaxy.schema.fetch_data.BaseDataElement attribute) extra_files() (galaxy.managers.datasets.DatasetAssociationManager method) extra_files_path (galaxy.model.Dataset property) (galaxy.model.DatasetHash attribute) (galaxy.model.DatasetInstance property) (galaxy.model.DatasetSource attribute) (galaxy.schema.schema.DatasetHash attribute) (galaxy.schema.schema.DatasetSource attribute) (galaxy.schema.tasks.ComputeDatasetHashTaskRequest attribute) extra_files_path_exists() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) extra_files_path_name (galaxy.model.Dataset property) extra_files_path_name_from() (galaxy.model.Dataset method) extra_params (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute) extra_preferences (galaxy.model.User property) extra_props (galaxy.files.sources.FilesSourceOptions attribute) extract() (galaxy.util.compression_utils.CompressedFile method) extract_components_from_tuple() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) extract_domain() (in module galaxy.security.validate_user_input) extract_options_from_dict() (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider class method) extract_value() (galaxy.tools.test.ParamContext method) extract_workflow() (in module galaxy.workflow.extract) ExtractDatasetCollectionTool (class in galaxy.tools) ExtractInputAction (class in galaxy.workflow.refactor.schema) ExtractUntypedParameter (class in galaxy.workflow.refactor.schema) ExtraFiles (class in galaxy.schema.fetch_data)

F

factory() (in module galaxy.webapps.galaxy.fast_factory) (in module galaxy.webapps.reports.fast_factory) (in module tool_shed.webapp.fast_factory) Facts (class in galaxy.util.facts) facts (galaxy.web_stack.ApplicationStack property) fail() (galaxy.jobs.TaskWrapper method) (galaxy.model.WorkflowInvocation method) (in module galaxy.tools.util.galaxyops) fail_job() (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.kubernetes.KubernetesJobRunner method) failed (galaxy.managers.display_applications.ReloadFeedback attribute) FAILED (galaxy.model.ImplicitCollectionJobs.populated_states attribute) failed (galaxy.model.JobStateSummary attribute) FAILED (galaxy.schema.schema.DatasetCollectionPopulatedState attribute) failed (galaxy.schema.schema.HDCJobStateSummary attribute) FAILED (galaxy.schema.schema.JobState attribute) failed() (galaxy.tool_util.lint.LintContext method) FAILED_METADATA (galaxy.schema.schema.DatasetState attribute) FailedTest (class in tool_shed.utility_containers) failure() (in module galaxy.jobs.runners.state_handlers.resubmit) FailWorkflowEvaluation fake_dataset_association (galaxy.model.FakeDatasetAssociation attribute) FakeDatasetAssociation (class in galaxy.model) FallbackContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit) FallbackNoRequirementsContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit) FallbackNoRequirementsSingularityContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit) FallbackSingularityContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit) false_path (galaxy.tools.wrappers.DatasetFilenameWrapper attribute) family_name (galaxy.schema.schema.Person attribute) Fast5Archive (class in galaxy.datatypes.binary) Fast5ArchiveBz2 (class in galaxy.datatypes.binary) Fast5ArchiveGz (class in galaxy.datatypes.binary) Fast5ArchiveXz (class in galaxy.datatypes.binary) Fasta (class in galaxy.datatypes.sequence) fasta (galaxy.schema.schema.CreatedCustomBuild attribute) (galaxy.schema.schema.CustomBuildLenType attribute) fasta_hdas (galaxy.schema.schema.CustomBuildsMetadataResponse attribute) fasta_path (galaxy.model.GenomeIndexToolData attribute) FastaDataProvider (class in galaxy.datatypes.dataproviders.dataset) FastAPIAuthenticate (class in galaxy.webapps.galaxy.api.authenticate) FastAPIConfiguration (class in galaxy.webapps.galaxy.api.configuration) FastAPIDatatypes (class in galaxy.webapps.galaxy.api.datatypes) FastAPIDisplay (class in galaxy.webapps.galaxy.api.display_applications) FastAPIForms (class in galaxy.webapps.galaxy.api.forms) FastAPIGenomes (class in galaxy.webapps.galaxy.api.genomes) FastAPIGroupRoles (class in galaxy.webapps.galaxy.api.group_roles) FastAPIGroups (class in galaxy.webapps.galaxy.api.groups) FastAPIGroupUsers (class in galaxy.webapps.galaxy.api.group_users) FastAPILibraries (class in galaxy.webapps.galaxy.api.libraries) FastAPILibraryFolders (class in galaxy.webapps.galaxy.api.folders) FastAPILibraryFoldersContents (class in galaxy.webapps.galaxy.api.folder_contents) FastAPILicenses (class in galaxy.webapps.galaxy.api.licenses) FastAPIMetrics (class in galaxy.webapps.galaxy.api.metrics) FastAPIPages (class in galaxy.webapps.galaxy.api.pages) FastAPIQuota (class in galaxy.webapps.galaxy.api.quotas) FastAPIRemoteFiles (class in galaxy.webapps.galaxy.api.remote_files) FastAPIRoles (class in galaxy.webapps.galaxy.api.roles) FastAPIShortTermStorage (class in galaxy.webapps.galaxy.api.short_term_storage) FastAPITags (class in galaxy.webapps.galaxy.api.tags) FastAPITasks (class in galaxy.webapps.galaxy.api.tasks) FastAPIToolData (class in galaxy.webapps.galaxy.api.tool_data) FastAPIToolShedRepositories (class in galaxy.webapps.galaxy.api.tool_shed_repositories) FastAPITours (class in galaxy.webapps.galaxy.api.tours) FastAPIUsers (class in galaxy.webapps.galaxy.api.users) FastAPIVisualizations (class in galaxy.webapps.galaxy.api.visualizations) Fastg (class in galaxy.datatypes.sequence) Fastq (class in galaxy.datatypes.sequence) FastqCSSanger (class in galaxy.datatypes.sequence) FastqIllumina (class in galaxy.datatypes.sequence) FastqSanger (class in galaxy.datatypes.sequence) FastqSolexa (class in galaxy.datatypes.sequence) FastZipFile (class in galaxy.util.compression_utils) FATAL (galaxy.tool_util.parser.stdio.StdioErrorLevel attribute) FATAL_OOM (galaxy.tool_util.parser.stdio.StdioErrorLevel attribute) FavoriteObject (class in galaxy.schema.schema) FavoriteObjectsSummary (class in galaxy.schema.schema) FavoriteObjectType (class in galaxy.schema.schema) fax_number (galaxy.schema.schema.Creator attribute) FCS (class in galaxy.datatypes.flow) fda (galaxy.model.JobExportHistoryArchive property) FeatureLocationIndex (class in galaxy.datatypes.tabular) FeatureLocationIndexDataProvider (class in galaxy.visualization.data_providers.genome) FeatureXML (class in galaxy.datatypes.proteomics) feed() (galaxy.managers.pages.PageContentProcessor method) fetch() (galaxy_test.base.populators.BaseDatasetPopulator method) fetch_form() (galaxy.webapps.galaxy.api.tools.FetchTools method) fetch_hda() (galaxy_test.base.populators.BaseDatasetPopulator method) fetch_hdas() (galaxy_test.base.populators.BaseDatasetPopulator method) fetch_job_states() (in module galaxy.managers.jobs) fetch_json() (galaxy.webapps.galaxy.api.tools.FetchTools method) fetch_payload() (galaxy_test.base.populators.BaseDatasetPopulator method) fetch_repository_metadata() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) fetch_requests() (galaxy.web.proxy.JsonFileProxyIpc method) (galaxy.web.proxy.ProxyIpc method) (galaxy.web.proxy.SqliteProxyIpc method) fetch_single_url_to_folder() (galaxy_test.base.populators.LibraryPopulator method) FetchBaseModel (class in galaxy.schema.fetch_data) FetchDataFormPayload (class in galaxy.schema.fetch_data) FetchDataPayload (class in galaxy.schema.fetch_data) FetchTools (class in galaxy.webapps.galaxy.api.tools) FetchUploadToolAction (class in galaxy.tools.actions.upload) ff_dim (galaxy.tools.recommendations.ToolRecommendations attribute) ffprobe() (in module galaxy.datatypes.media) FIELD (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute) field_to_field_type() (in module galaxy.tool_util.cwl.representation) fields (galaxy.model.FormDefinition attribute) fields() (galaxy.util.form_builder.AddressField static method) (galaxy.web.form_builder.AddressField static method) file (galaxy.schema.schema.CustomBuildLenType attribute) (galaxy.schema.schema.HistoryImportArchiveSourceType attribute) file_ext (galaxy.datatypes.annotation.Augustus attribute) (galaxy.datatypes.annotation.SnapHmm attribute) (galaxy.datatypes.anvio.AnvioComposite attribute) (galaxy.datatypes.anvio.AnvioContigsDB attribute) (galaxy.datatypes.anvio.AnvioDB attribute) (galaxy.datatypes.anvio.AnvioGenomesDB attribute) (galaxy.datatypes.anvio.AnvioPanDB attribute) (galaxy.datatypes.anvio.AnvioProfileDB attribute) (galaxy.datatypes.anvio.AnvioSamplesDB attribute) (galaxy.datatypes.anvio.AnvioStructureDB attribute) (galaxy.datatypes.assembly.Amos attribute) (galaxy.datatypes.assembly.Roadmaps attribute) (galaxy.datatypes.assembly.Sequences attribute) (galaxy.datatypes.assembly.Velvet attribute) (galaxy.datatypes.binary.Ab1 attribute) (galaxy.datatypes.binary.Anndata attribute) (galaxy.datatypes.binary.BafTar attribute) (galaxy.datatypes.binary.Bam attribute) (galaxy.datatypes.binary.BamInputSorted attribute) (galaxy.datatypes.binary.BamNative attribute) (galaxy.datatypes.binary.BamQuerynameSorted attribute) (galaxy.datatypes.binary.Bcf attribute) (galaxy.datatypes.binary.BcfUncompressed attribute) (galaxy.datatypes.binary.BigBed attribute) (galaxy.datatypes.binary.BigWig attribute) (galaxy.datatypes.binary.Binary attribute) (galaxy.datatypes.binary.Biom2 attribute) (galaxy.datatypes.binary.BlibSQlite attribute) (galaxy.datatypes.binary.Bref3 attribute) (galaxy.datatypes.binary.Cel attribute) (galaxy.datatypes.binary.ChiraSQLite attribute) (galaxy.datatypes.binary.CompressedArchive attribute) (galaxy.datatypes.binary.CompressedZipArchive attribute) (galaxy.datatypes.binary.Cool attribute) (galaxy.datatypes.binary.Cpt attribute) (galaxy.datatypes.binary.CRAM attribute) (galaxy.datatypes.binary.CuffDiffSQlite attribute) (galaxy.datatypes.binary.DAA attribute) (galaxy.datatypes.binary.Dcd attribute) (galaxy.datatypes.binary.DlibSQlite attribute) (galaxy.datatypes.binary.DMND attribute) (galaxy.datatypes.binary.Edr attribute) (galaxy.datatypes.binary.ElibSQlite attribute) (galaxy.datatypes.binary.ExcelXls attribute) (galaxy.datatypes.binary.Fast5Archive attribute) (galaxy.datatypes.binary.Fast5ArchiveBz2 attribute) (galaxy.datatypes.binary.Fast5ArchiveGz attribute) (galaxy.datatypes.binary.Fast5ArchiveXz attribute) (galaxy.datatypes.binary.FITS attribute) (galaxy.datatypes.binary.GAFASQLite attribute) (galaxy.datatypes.binary.GeminiSQLite attribute) (galaxy.datatypes.binary.GeneNoteBook attribute) (galaxy.datatypes.binary.GenericAsn1Binary attribute) (galaxy.datatypes.binary.GmxBinary attribute) (galaxy.datatypes.binary.Grib attribute) (galaxy.datatypes.binary.H5 attribute) (galaxy.datatypes.binary.H5MLM attribute) (galaxy.datatypes.binary.HexrdEtaOmeNpz attribute) (galaxy.datatypes.binary.HexrdImagesNpz attribute) (galaxy.datatypes.binary.HexrdMaterials attribute) (galaxy.datatypes.binary.ICM attribute) (galaxy.datatypes.binary.Idat attribute) (galaxy.datatypes.binary.IdpDB attribute) (galaxy.datatypes.binary.JP2 attribute) (galaxy.datatypes.binary.Loom attribute) (galaxy.datatypes.binary.LudwigModel attribute) (galaxy.datatypes.binary.MashSketch attribute) (galaxy.datatypes.binary.MassHunterTar attribute) (galaxy.datatypes.binary.MassLynxTar attribute) (galaxy.datatypes.binary.MCool attribute) (galaxy.datatypes.binary.Meryldb attribute) (galaxy.datatypes.binary.MongoDBArchive attribute) (galaxy.datatypes.binary.MzSQlite attribute) (galaxy.datatypes.binary.NcbiTaxonomySQlite attribute) (galaxy.datatypes.binary.NetCDF attribute) (galaxy.datatypes.binary.Npz attribute) (galaxy.datatypes.binary.Numpy attribute) (galaxy.datatypes.binary.OSW attribute) (galaxy.datatypes.binary.OxliCountGraph attribute) (galaxy.datatypes.binary.OxliGraphLabels attribute) (galaxy.datatypes.binary.OxliNodeGraph attribute) (galaxy.datatypes.binary.OxliStopTags attribute) (galaxy.datatypes.binary.OxliSubset attribute) (galaxy.datatypes.binary.OxliTagSet attribute) (galaxy.datatypes.binary.Parquet attribute) (galaxy.datatypes.binary.PostgresqlArchive attribute) (galaxy.datatypes.binary.PQP attribute) (galaxy.datatypes.binary.Pretext attribute) (galaxy.datatypes.binary.ProBam attribute) (galaxy.datatypes.binary.RData attribute) (galaxy.datatypes.binary.RDS attribute) (galaxy.datatypes.binary.RMA6 attribute) (galaxy.datatypes.binary.Scf attribute) (galaxy.datatypes.binary.SearchGuiArchive attribute) (galaxy.datatypes.binary.Sff attribute) (galaxy.datatypes.binary.SQlite attribute) (galaxy.datatypes.binary.SQmass attribute) (galaxy.datatypes.binary.Sra attribute) (galaxy.datatypes.binary.TdfTar attribute) (galaxy.datatypes.binary.Trr attribute) (galaxy.datatypes.binary.TwoBit attribute) (galaxy.datatypes.binary.Vel attribute) (galaxy.datatypes.binary.Visium attribute) (galaxy.datatypes.binary.Wiff2Tar attribute) (galaxy.datatypes.binary.WiffTar attribute) (galaxy.datatypes.binary.Xlsx attribute) (galaxy.datatypes.binary.Xtc attribute) (galaxy.datatypes.binary.YepTar attribute) (galaxy.datatypes.blast.BlastDomainDb attribute) (galaxy.datatypes.blast.BlastDomainDb5 attribute) (galaxy.datatypes.blast.BlastNucDb attribute) (galaxy.datatypes.blast.BlastNucDb5 attribute) (galaxy.datatypes.blast.BlastProtDb attribute) (galaxy.datatypes.blast.BlastProtDb5 attribute) (galaxy.datatypes.blast.BlastXml attribute) (galaxy.datatypes.blast.LastDb attribute) (galaxy.datatypes.chrominfo.ChromInfo attribute) (galaxy.datatypes.constructive_solid_geometry.GmshGeo attribute) (galaxy.datatypes.constructive_solid_geometry.GmshMsh attribute) (galaxy.datatypes.constructive_solid_geometry.NeperMultiScaleCell attribute) (galaxy.datatypes.constructive_solid_geometry.NeperPoints attribute) (galaxy.datatypes.constructive_solid_geometry.NeperPointsTabular attribute) (galaxy.datatypes.constructive_solid_geometry.NeperTesr attribute) (galaxy.datatypes.constructive_solid_geometry.NeperTess attribute) (galaxy.datatypes.constructive_solid_geometry.PlyAscii attribute) (galaxy.datatypes.constructive_solid_geometry.PlyBinary attribute) (galaxy.datatypes.constructive_solid_geometry.STL attribute) (galaxy.datatypes.constructive_solid_geometry.VtkAscii attribute) (galaxy.datatypes.constructive_solid_geometry.VtkBinary attribute) (galaxy.datatypes.constructive_solid_geometry.ZsetGeof attribute) (galaxy.datatypes.coverage.LastzCoverage attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.data.GenericAsn1 attribute) (galaxy.datatypes.data.Newick attribute) (galaxy.datatypes.data.Nexus attribute) (galaxy.datatypes.data.Text attribute) (galaxy.datatypes.flow.FCS attribute) (galaxy.datatypes.genetics.Affybatch attribute) (galaxy.datatypes.genetics.AllegroLOD attribute) (galaxy.datatypes.genetics.DataIn attribute) (galaxy.datatypes.genetics.Eigenstratgeno attribute) (galaxy.datatypes.genetics.Eigenstratpca attribute) (galaxy.datatypes.genetics.Eset attribute) (galaxy.datatypes.genetics.Fped attribute) (galaxy.datatypes.genetics.Fphe attribute) (galaxy.datatypes.genetics.GenomeGraphs attribute) (galaxy.datatypes.genetics.GenotypeMatrix attribute) (galaxy.datatypes.genetics.IdeasPre attribute) (galaxy.datatypes.genetics.ldIndep attribute) (galaxy.datatypes.genetics.Lped attribute) (galaxy.datatypes.genetics.MAlist attribute) (galaxy.datatypes.genetics.MarkerMap attribute) (galaxy.datatypes.genetics.Pbed attribute) (galaxy.datatypes.genetics.Phe attribute) (galaxy.datatypes.genetics.Pheno attribute) (galaxy.datatypes.genetics.Pphe attribute) (galaxy.datatypes.genetics.RexpBase attribute) (galaxy.datatypes.genetics.Rgenetics attribute) (galaxy.datatypes.genetics.rgFeatureList attribute) (galaxy.datatypes.genetics.rgSampleList attribute) (galaxy.datatypes.genetics.rgTabList attribute) (galaxy.datatypes.genetics.SNPMatrix attribute) (galaxy.datatypes.genetics.Snptest attribute) (galaxy.datatypes.gis.Shapefile attribute) (galaxy.datatypes.goldenpath.GoldenPath attribute) (galaxy.datatypes.graph.Sif attribute) (galaxy.datatypes.graph.Xgmml attribute) (galaxy.datatypes.hdf5.HDF5SummarizedExperiment attribute) (galaxy.datatypes.images.Analyze75 attribute) (galaxy.datatypes.images.Bmp attribute) (galaxy.datatypes.images.Eps attribute) (galaxy.datatypes.images.Gif attribute) (galaxy.datatypes.images.Gifti attribute) (galaxy.datatypes.images.Gmaj attribute) (galaxy.datatypes.images.Hamamatsu attribute) (galaxy.datatypes.images.Im attribute) (galaxy.datatypes.images.Image attribute) (galaxy.datatypes.images.Jpg attribute) (galaxy.datatypes.images.Mirax attribute) (galaxy.datatypes.images.Mrc2014 attribute) (galaxy.datatypes.images.Nifti1 attribute) (galaxy.datatypes.images.Nifti2 attribute) (galaxy.datatypes.images.Nrrd attribute) (galaxy.datatypes.images.OMETiff attribute) (galaxy.datatypes.images.Pbm attribute) (galaxy.datatypes.images.Pcd attribute) (galaxy.datatypes.images.Pcx attribute) (galaxy.datatypes.images.Pdf attribute) (galaxy.datatypes.images.Pgm attribute) (galaxy.datatypes.images.Png attribute) (galaxy.datatypes.images.Ppm attribute) (galaxy.datatypes.images.Psd attribute) (galaxy.datatypes.images.Rast attribute) (galaxy.datatypes.images.Rgb attribute) (galaxy.datatypes.images.Sakura attribute) (galaxy.datatypes.images.Star attribute) (galaxy.datatypes.images.Tck attribute) (galaxy.datatypes.images.Tiff attribute) (galaxy.datatypes.images.Trk attribute) (galaxy.datatypes.images.Xbm attribute) (galaxy.datatypes.images.Xpm attribute) (galaxy.datatypes.interval.Bed attribute) (galaxy.datatypes.interval.Bed12 attribute) (galaxy.datatypes.interval.Bed6 attribute) (galaxy.datatypes.interval.BedGraph attribute) (galaxy.datatypes.interval.BedStrict attribute) (galaxy.datatypes.interval.BedTabix attribute) (galaxy.datatypes.interval.ChromatinInteractions attribute) (galaxy.datatypes.interval.CustomTrack attribute) (galaxy.datatypes.interval.ENCODEPeak attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Gff3 attribute) (galaxy.datatypes.interval.GffTabix attribute) (galaxy.datatypes.interval.Gtf attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.interval.IntervalTabix attribute) (galaxy.datatypes.interval.JuicerMediumTabix attribute) (galaxy.datatypes.interval.ProBed attribute) (galaxy.datatypes.interval.ScIdx attribute) (galaxy.datatypes.interval.Wiggle attribute) (galaxy.datatypes.isa.IsaJson attribute) (galaxy.datatypes.isa.IsaTab attribute) (galaxy.datatypes.media.Flv attribute) (galaxy.datatypes.media.Mkv attribute) (galaxy.datatypes.media.Mp3 attribute) (galaxy.datatypes.media.Mp4 attribute) (galaxy.datatypes.media.Mpg attribute) (galaxy.datatypes.media.Wav attribute) (galaxy.datatypes.metacyto.mStats attribute) (galaxy.datatypes.metacyto.mSummary attribute) (galaxy.datatypes.microarrays.Gal attribute) (galaxy.datatypes.microarrays.Gpr attribute) (galaxy.datatypes.molecules.AtomicStructFile attribute) (galaxy.datatypes.molecules.Cell attribute) (galaxy.datatypes.molecules.CIF attribute) (galaxy.datatypes.molecules.CML attribute) (galaxy.datatypes.molecules.DRF attribute) (galaxy.datatypes.molecules.ExtendedXYZ attribute) (galaxy.datatypes.molecules.FPS attribute) (galaxy.datatypes.molecules.grd attribute) (galaxy.datatypes.molecules.grdtgz attribute) (galaxy.datatypes.molecules.GRO attribute) (galaxy.datatypes.molecules.InChI attribute) (galaxy.datatypes.molecules.Magres attribute) (galaxy.datatypes.molecules.MOL attribute) (galaxy.datatypes.molecules.MOL2 attribute) (galaxy.datatypes.molecules.OBFS attribute) (galaxy.datatypes.molecules.PDB attribute) (galaxy.datatypes.molecules.PDBQT attribute) (galaxy.datatypes.molecules.PHAR attribute) (galaxy.datatypes.molecules.PQR attribute) (galaxy.datatypes.molecules.SDF attribute) (galaxy.datatypes.molecules.SMILES attribute) (galaxy.datatypes.molecules.XYZ attribute) (galaxy.datatypes.mothur.AccNos attribute) (galaxy.datatypes.mothur.AlignCheck attribute) (galaxy.datatypes.mothur.AlignReport attribute) (galaxy.datatypes.mothur.Axes attribute) (galaxy.datatypes.mothur.ConsensusTaxonomy attribute) (galaxy.datatypes.mothur.CountTable attribute) (galaxy.datatypes.mothur.DistanceMatrix attribute) (galaxy.datatypes.mothur.Frequency attribute) (galaxy.datatypes.mothur.Group attribute) (galaxy.datatypes.mothur.GroupAbund attribute) (galaxy.datatypes.mothur.LaneMask attribute) (galaxy.datatypes.mothur.LowerTriangleDistanceMatrix attribute) (galaxy.datatypes.mothur.Names attribute) (galaxy.datatypes.mothur.Oligos attribute) (galaxy.datatypes.mothur.Otu attribute) (galaxy.datatypes.mothur.PairwiseDistanceMatrix attribute) (galaxy.datatypes.mothur.Quantile attribute) (galaxy.datatypes.mothur.RefTaxonomy attribute) (galaxy.datatypes.mothur.Sabund attribute) (galaxy.datatypes.mothur.SecondaryStructureMap attribute) (galaxy.datatypes.mothur.SffFlow attribute) (galaxy.datatypes.mothur.SquareDistanceMatrix attribute) (galaxy.datatypes.mothur.Summary attribute) (galaxy.datatypes.mothur.TaxonomySummary attribute) (galaxy.datatypes.msa.Hmmer2 attribute) (galaxy.datatypes.msa.Hmmer3 attribute) (galaxy.datatypes.msa.HmmerPress attribute) (galaxy.datatypes.msa.InfernalCM attribute) (galaxy.datatypes.msa.MauveXmfa attribute) (galaxy.datatypes.msa.Msf attribute) (galaxy.datatypes.msa.Stockholm_1_0 attribute) (galaxy.datatypes.neo4j.Neo4jDB attribute) (galaxy.datatypes.neo4j.Neo4jDBzip attribute) (galaxy.datatypes.ngsindex.BowtieBaseIndex attribute) (galaxy.datatypes.ngsindex.BowtieColorIndex attribute) (galaxy.datatypes.phylip.Phylip attribute) (galaxy.datatypes.plant_tribes.PlantTribesKsComponents attribute) (galaxy.datatypes.plant_tribes.Smat attribute) (galaxy.datatypes.proteomics.ConsensusXML attribute) (galaxy.datatypes.proteomics.Dta attribute) (galaxy.datatypes.proteomics.Dta2d attribute) (galaxy.datatypes.proteomics.Edta attribute) (galaxy.datatypes.proteomics.FeatureXML attribute) (galaxy.datatypes.proteomics.IdXML attribute) (galaxy.datatypes.proteomics.ImzML attribute) (galaxy.datatypes.proteomics.Kroenik attribute) (galaxy.datatypes.proteomics.MascotDat attribute) (galaxy.datatypes.proteomics.MascotXML attribute) (galaxy.datatypes.proteomics.Mgf attribute) (galaxy.datatypes.proteomics.Ms2 attribute) (galaxy.datatypes.proteomics.Msp attribute) (galaxy.datatypes.proteomics.MzData attribute) (galaxy.datatypes.proteomics.MzIdentML attribute) (galaxy.datatypes.proteomics.MzML attribute) (galaxy.datatypes.proteomics.MzQuantML attribute) (galaxy.datatypes.proteomics.MzTab attribute) (galaxy.datatypes.proteomics.MzTab2 attribute) (galaxy.datatypes.proteomics.MzXML attribute) (galaxy.datatypes.proteomics.NmrML attribute) (galaxy.datatypes.proteomics.ParamXml attribute) (galaxy.datatypes.proteomics.PEFF attribute) (galaxy.datatypes.proteomics.PepList attribute) (galaxy.datatypes.proteomics.PepXml attribute) (galaxy.datatypes.proteomics.PepXmlReport attribute) (galaxy.datatypes.proteomics.ProtXML attribute) (galaxy.datatypes.proteomics.ProtXmlReport attribute) (galaxy.datatypes.proteomics.PSMS attribute) (galaxy.datatypes.proteomics.QCML attribute) (galaxy.datatypes.proteomics.Sf3 attribute) (galaxy.datatypes.proteomics.SPLib attribute) (galaxy.datatypes.proteomics.SPLibNoIndex attribute) (galaxy.datatypes.proteomics.TandemXML attribute) (galaxy.datatypes.proteomics.ThermoRAW attribute) (galaxy.datatypes.proteomics.TrafoXML attribute) (galaxy.datatypes.proteomics.TraML attribute) (galaxy.datatypes.proteomics.UniProtXML attribute) (galaxy.datatypes.proteomics.Wiff attribute) (galaxy.datatypes.proteomics.Wiff2 attribute) (galaxy.datatypes.proteomics.XHunterAslFormat attribute) (galaxy.datatypes.proteomics.XquestSpecXML attribute) (galaxy.datatypes.proteomics.XquestXML attribute) (galaxy.datatypes.qiime2.QIIME2Artifact attribute) (galaxy.datatypes.qiime2.QIIME2Metadata attribute) (galaxy.datatypes.qiime2.QIIME2Visualization attribute) (galaxy.datatypes.qualityscore.QualityScore attribute) (galaxy.datatypes.qualityscore.QualityScore454 attribute) (galaxy.datatypes.qualityscore.QualityScoreIllumina attribute) (galaxy.datatypes.qualityscore.QualityScoreSolexa attribute) (galaxy.datatypes.qualityscore.QualityScoreSOLiD attribute) (galaxy.datatypes.sequence.Axt attribute) (galaxy.datatypes.sequence.BaseFastq attribute) (galaxy.datatypes.sequence.csFasta attribute) (galaxy.datatypes.sequence.DotBracket attribute) (galaxy.datatypes.sequence.Fasta attribute) (galaxy.datatypes.sequence.Fastg attribute) (galaxy.datatypes.sequence.Fastq attribute) (galaxy.datatypes.sequence.FastqCSSanger attribute) (galaxy.datatypes.sequence.FastqIllumina attribute) (galaxy.datatypes.sequence.FastqSanger attribute) (galaxy.datatypes.sequence.FastqSolexa attribute) (galaxy.datatypes.sequence.Genbank attribute) (galaxy.datatypes.sequence.Lav attribute) (galaxy.datatypes.sequence.Maf attribute) (galaxy.datatypes.sequence.MafCustomTrack attribute) (galaxy.datatypes.sequence.MemePsp attribute) (galaxy.datatypes.sequence.RNADotPlotMatrix attribute) (galaxy.datatypes.sequence.SequenceSplitLocations attribute) (galaxy.datatypes.spaln.SpalnNuclDb attribute) (galaxy.datatypes.spaln.SpalnProtDb attribute) (galaxy.datatypes.speech.BPF attribute) (galaxy.datatypes.speech.TextGrid attribute) (galaxy.datatypes.tabular.CMAP attribute) (galaxy.datatypes.tabular.ConnectivityTable attribute) (galaxy.datatypes.tabular.CSV attribute) (galaxy.datatypes.tabular.Eland attribute) (galaxy.datatypes.tabular.ElandMulti attribute) (galaxy.datatypes.tabular.FeatureLocationIndex attribute) (galaxy.datatypes.tabular.MatrixMarket attribute) (galaxy.datatypes.tabular.Pileup attribute) (galaxy.datatypes.tabular.Psl attribute) (galaxy.datatypes.tabular.Sam attribute) (galaxy.datatypes.tabular.SraManifest attribute) (galaxy.datatypes.tabular.Tabular attribute) (galaxy.datatypes.tabular.Taxonomy attribute) (galaxy.datatypes.tabular.TSV attribute) (galaxy.datatypes.tabular.Vcf attribute) (galaxy.datatypes.tabular.VcfGz attribute) (galaxy.datatypes.text.Arff attribute) (galaxy.datatypes.text.BCSLmodel attribute) (galaxy.datatypes.text.BCSLts attribute) (galaxy.datatypes.text.Biom1 attribute) (galaxy.datatypes.text.Castep attribute) (galaxy.datatypes.text.CTLresult attribute) (galaxy.datatypes.text.DataManagerJson attribute) (galaxy.datatypes.text.ExpressionJson attribute) (galaxy.datatypes.text.FormattedDensity attribute) (galaxy.datatypes.text.GeoJson attribute) (galaxy.datatypes.text.Gfa1 attribute) (galaxy.datatypes.text.Gfa2 attribute) (galaxy.datatypes.text.Html attribute) (galaxy.datatypes.text.ImgtJson attribute) (galaxy.datatypes.text.Ipynb attribute) (galaxy.datatypes.text.IQTree attribute) (galaxy.datatypes.text.Json attribute) (galaxy.datatypes.text.Obo attribute) (galaxy.datatypes.text.Paf attribute) (galaxy.datatypes.text.Param attribute) (galaxy.datatypes.text.PithyaModel attribute) (galaxy.datatypes.text.PithyaProperty attribute) (galaxy.datatypes.text.PithyaResult attribute) (galaxy.datatypes.text.SnpEffDb attribute) (galaxy.datatypes.text.SnpSiftDbNSFP attribute) (galaxy.datatypes.text.StormCheck attribute) (galaxy.datatypes.text.StormSample attribute) (galaxy.datatypes.text.Yaml attribute) (galaxy.datatypes.tracks.GeneTrack attribute) (galaxy.datatypes.tracks.UCSCTrackHub attribute) (galaxy.datatypes.triples.HDT attribute) (galaxy.datatypes.triples.Jsonld attribute) (galaxy.datatypes.triples.N3 attribute) (galaxy.datatypes.triples.NTriples attribute) (galaxy.datatypes.triples.Rdf attribute) (galaxy.datatypes.triples.Sbol attribute) (galaxy.datatypes.triples.Triples attribute) (galaxy.datatypes.triples.Turtle attribute) (galaxy.datatypes.xml.CisML attribute) (galaxy.datatypes.xml.Dzi attribute) (galaxy.datatypes.xml.GenericXml attribute) (galaxy.datatypes.xml.MEMEXml attribute) (galaxy.datatypes.xml.Owl attribute) (galaxy.datatypes.xml.Phyloxml attribute) (galaxy.datatypes.xml.Sbml attribute) (galaxy.schema.schema.FileLibraryFolderItem attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) (galaxy.tools.wrappers.DatasetFilenameWrapper property)

file_ext_export_alias (galaxy.datatypes.tabular.VcfGz attribute) file_iter() (in module galaxy.util.compression_utils) file_name (galaxy.schema.schema.ExportHistoryArchivePayload attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) (galaxy.tools.wrappers.DatasetFilenameWrapper property) file_path (galaxy.model.Dataset attribute) file_reader() (in module galaxy.util) file_ready() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.cloud.Cloud method) (galaxy.objectstore.irods.IRODSObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.pulsar.PulsarObjectStore method) (galaxy.objectstore.s3.S3ObjectStore method) file_size (galaxy.datatypes.sniff.FilePrefix property) (galaxy.model.Dataset attribute) (galaxy.model.store.DatasetAttributeImportModel attribute) (galaxy.schema.schema.DatasetSummary attribute) (galaxy.schema.schema.FileLibraryFolderItem attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) file_source (galaxy.files.FileSourcePath attribute) (galaxy.files.FileSourceScore attribute) file_source_root (galaxy.model.store.BaseDirectoryImportModelStore property) (galaxy.model.store.ModelImportStore property) file_source_uri (galaxy.model.store.BagArchiveModelExportStore attribute) (galaxy.model.store.ROCrateArchiveModelExportStore attribute) (galaxy.model.store.TarModelExportStore attribute) file_sources (galaxy.files.DictFileSourcesUserContext property) (galaxy.files.FileSourceDictifiable property) (galaxy.files.ProvidesUserFileSourcesUserContext property) (galaxy.job_execution.setup.JobIO property) (galaxy.managers.tool_data.ToolDataImportManager attribute) (galaxy.model.store.BagDirectoryModelExportStore attribute) (galaxy.model.store.BcoModelExportStore attribute) (galaxy.model.store.DirectoryModelExportStore attribute) (galaxy.model.store.ROCrateModelExportStore attribute) (galaxy.model.store.StoreAppProtocol attribute) (galaxy.model.store.WorkflowInvocationOnlyExportStore attribute) (galaxy.model.unittest_utils.data_app.GalaxyDataTestApp attribute) (galaxy.model.unittest_utils.GalaxyDataTestApp attribute) (galaxy.structured_app.MinimalManagerApp attribute) (galaxy.structured_app.MinimalToolApp attribute) (galaxy.tools.data_fetch.UploadConfig property) (galaxy.tools.remote_tool_eval.ToolApp attribute) file_sources_config (galaxy.files.sources.FilesSourceProperties attribute) file_sources_dict (galaxy.tools.evaluation.PartialToolEvaluator attribute) (galaxy.tools.evaluation.RemoteToolEvaluator attribute) file_states (tool_shed.webapp.model.Repository attribute) file_type (galaxy.schema.schema.MetadataFile attribute) (galaxy.tools.parameters.grouping.Dataset attribute) FileDataElement (class in galaxy.schema.fetch_data) FileDataResolver (class in galaxy.tool_util.verify.test_data) FileDefaultsAction (class in galaxy.workflow.refactor.schema) FileLibraryFolderItem (class in galaxy.schema.schema) FileLiteralTarget (class in galaxy.tool_util.cwl.util) FileLock (class in galaxy.util.filelock) FileLockException filename (galaxy.schema.fetch_data.FilesPayload attribute) filename_ (galaxy.managers.display_applications.DisplayApplication attribute) filename_in (galaxy.model.JobExternalOutputMetadata attribute) filename_kwds (galaxy.model.JobExternalOutputMetadata attribute) filename_out (galaxy.model.JobExternalOutputMetadata attribute) filename_override_metadata (galaxy.model.JobExternalOutputMetadata attribute) filename_results_code (galaxy.model.JobExternalOutputMetadata attribute) filenames (galaxy.tools.data.RefgenieToolDataTable attribute) (galaxy.tools.data.TabularToolDataTable attribute) (galaxy.tools.data.ToolDataTable attribute) FileParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) FilePatternDatasetCollectionDescription (class in galaxy.tool_util.parser.output_collection_def) FilePrefix (class in galaxy.datatypes.sniff) files (galaxy.schema.fetch_data.ItemsFromSrc attribute) (galaxy.schema.fetch_data.Src attribute) (galaxy.schema.remote_files.RemoteFilesDisableMode attribute) files() (in module galaxy.util.resources) files_contains() (in module galaxy.tool_util.verify) files_delta() (in module galaxy.tool_util.verify) files_diff() (in module galaxy.tool_util.verify) files_image_diff() (in module galaxy.tool_util.verify) files_re_match() (in module galaxy.tool_util.verify) files_re_match_multiline() (in module galaxy.tool_util.verify) FileSourceDictifiable (class in galaxy.files) FileSourcePath (class in galaxy.files) FileSourceScore (class in galaxy.files) FilesPayload (class in galaxy.schema.fetch_data) FilesSource (class in galaxy.files.sources) FilesSourceOptions (class in galaxy.files.sources) FilesSourcePlugin (class in galaxy.schema.remote_files) FilesSourcePluginList (class in galaxy.schema.remote_files) FilesSourceProperties (class in galaxy.files.sources) filesystem_safe_string() (in module galaxy.util) FileToolParameter (class in galaxy.tools.parameters.basic) FileTracebackException FileUploadTarget (class in galaxy.tool_util.cwl.util) fill() (galaxy.selenium.has_driver.HasDriver method) fill_defaults (galaxy.managers.workflows.WorkflowStateResolutionOptions attribute) fill_input_fields() (galaxy_test.selenium.test_change_password.TestChangePassword method) fill_login_and_submit() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) fill_region_alignment() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) fill_template() (galaxy.app_unittest_utils.galaxy_mock.MockTrans method) (galaxy.webapps.base.webapp.GalaxyWebTransaction method) (in module galaxy.util.template) fill_template_mako() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) FillStepDefaultsAction (class in galaxy.workflow.refactor.schema) Filter (class in galaxy.tools.parameters.dynamic_options) filter (galaxy.managers.base.ParsedFilter attribute) filter() (galaxy.datatypes.dataproviders.base.FilteredDataProvider method) (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) (galaxy.datatypes.dataproviders.line.BlockDataProvider method) (galaxy.datatypes.dataproviders.line.FilteredLineDataProvider method) (galaxy.datatypes.dataproviders.line.RegexLineDataProvider method) (galaxy.web.legacy_framework.grids.CommunityTagsColumn method) (galaxy.web.legacy_framework.grids.DeletedColumn method) (galaxy.web.legacy_framework.grids.GridColumn method) (galaxy.web.legacy_framework.grids.MulticolFilterColumn method) (galaxy.web.legacy_framework.grids.SharingStatusColumn method) (galaxy.web.legacy_framework.grids.StateColumn method) (galaxy.web.legacy_framework.grids.TextColumn method) (galaxy.web_stack.ApplicationStackLogFilter method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.DestinationIdColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.EmailColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.SpecifiedDateColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.StateColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.ToolColumn method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.EmailColumn method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.SpecifiedDateColumn method) (tool_shed.grids.admin_grids.UserGrid.EmailColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.EmailColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.RepositoryCategoryColumn method) (tool_shed.grids.repository_grids.ValidRepositoryGrid.RepositoryCategoryColumn method) filter_accessible() (galaxy.managers.secured.AccessibleManagerMixin method) filter_annotation_contains() (galaxy.managers.annotatable.AnnotatableFilterMixin method) filter_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method) filter_by_columns() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) filter_by_dataset() (galaxy.datatypes.display_applications.application.DisplayApplication method) (galaxy.datatypes.display_applications.application.DisplayApplicationLink method) filter_by_latest_downloadable_changeset_revision_that_has_missing_tool_test_components() (in module tool_shed.grids.util) filter_by_latest_metadata_changeset_revision_that_has_invalid_tools() (in module tool_shed.grids.util) filter_by_regex() (galaxy.datatypes.dataproviders.line.RegexLineDataProvider method) filter_file_fields() (galaxy.tools.data.TabularToolDataTable method) filter_only_if_compiling_contained_td() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) filter_options() (galaxy.tool_util.parser.output_actions.BooleanFilter method) (galaxy.tool_util.parser.output_actions.ColumnReplaceFilter method) (galaxy.tool_util.parser.output_actions.ColumnStripFilter method) (galaxy.tool_util.parser.output_actions.InsertColumnToolOutputActionOptionFilter method) (galaxy.tool_util.parser.output_actions.MetadataValueFilter method) (galaxy.tool_util.parser.output_actions.MultipleSplitterFilter method) (galaxy.tool_util.parser.output_actions.ParamValueToolOutputActionOptionFilter method) (galaxy.tool_util.parser.output_actions.StringFunctionFilter method) (galaxy.tool_util.parser.output_actions.ToolOutputActionOptionFilter method) (galaxy.tools.parameters.dynamic_options.AdditionalValueFilter method) (galaxy.tools.parameters.dynamic_options.AttributeValueSplitterFilter method) (galaxy.tools.parameters.dynamic_options.DataMetaFilter method) (galaxy.tools.parameters.dynamic_options.Filter method) (galaxy.tools.parameters.dynamic_options.MultipleSplitterFilter method) (galaxy.tools.parameters.dynamic_options.ParamValueFilter method) (galaxy.tools.parameters.dynamic_options.RegexpFilter method) (galaxy.tools.parameters.dynamic_options.RemoveValueFilter method) (galaxy.tools.parameters.dynamic_options.SortByColumnFilter method) (galaxy.tools.parameters.dynamic_options.StaticValueFilter method) (galaxy.tools.parameters.dynamic_options.UniqueValueFilter method) filter_output() (in module galaxy.tools.actions) filter_owned() (galaxy.managers.secured.OwnableManagerMixin method) filter_template (galaxy.auth.util.Authenticator attribute) filter_type (galaxy.managers.base.ParsedFilter attribute) (in module galaxy.tool_util.parser.output_actions) FilterableMixin (class in galaxy.visualization.data_providers.genome) FilterDatasetsTool (class in galaxy.tools) FilteredDataProvider (class in galaxy.datatypes.dataproviders.base) FilteredLineDataProvider (class in galaxy.datatypes.dataproviders.line) FilterEmptyDatasetsTool (class in galaxy.tools) FilterFactory (class in galaxy.tool_util.toolbox.filters) FilterFailedDatasetsTool (class in galaxy.tools) FilterFromFileTool (class in galaxy.tools) FilterQueryParams (class in galaxy.schema) filters (tool_shed.grids.repository_grid_filter_manager.RepositoryGridFilterManager attribute) final() (tool_shed.webapp.search.repo_search.RepoWeighting method) final_path (galaxy.util.renamed_temporary_file.RenamedTemporaryFile attribute) finalize() (galaxy.model.DatasetCollection method) finalize_config() (galaxy.web.framework.base.WebApplication method) finalize_storage() (galaxy.model.store.discover.ModelPersistenceContext method) find() (galaxy.util.Element method) find_anaconda_versions() (in module galaxy.tool_util.deps.mulled.get_tests) find_best_container_description() (galaxy.tool_util.deps.containers.ContainerFinder method) (galaxy.tool_util.deps.containers.ContainerRegistry method) find_best_match() (galaxy.files.ConfiguredFileSources method) find_class() (galaxy.util.aliaspickler.AliasUnpickler method) find_config() (in module galaxy.main_config) find_config_file() (in module galaxy.util.properties) find_container() (galaxy.tool_util.deps.containers.ContainerFinder method) (galaxy.tool_util.deps.containers.NullContainerFinder method) find_conversion_destination() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) find_conversion_destination_for_dataset_by_extensions() (galaxy.datatypes.registry.Registry method) find_dce() (galaxy.model.store.ObjectImportTracker method) find_dep() (galaxy.tool_util.deps.DependencyManager method) (galaxy.tool_util.deps.NullDependencyManager method) find_element_by_id() (galaxy.selenium.has_driver.HasDriver method) find_element_by_link_text() (galaxy.selenium.has_driver.HasDriver method) find_element_by_selector() (galaxy.selenium.has_driver.HasDriver method) find_element_by_sizzle() (in module galaxy.selenium.sizzle) find_element_by_xpath() (galaxy.selenium.has_driver.HasDriver method) find_elements() (galaxy.selenium.has_driver.HasDriver method) find_elements_by_sizzle() (in module galaxy.selenium.sizzle) find_engine() (in module galaxy.tools.expressions) (in module galaxy.tools.expressions.util) find_files() (galaxy.job_execution.output_collect.BaseJobContext method) find_hda() (galaxy.model.store.ObjectImportTracker method) find_hdca() (galaxy.model.store.ObjectImportTracker method) find_implicit_input_collection() (galaxy.model.HistoryDatasetCollectionAssociation method) find_ingress_object_by_name() (in module galaxy.jobs.runners.util.pykube_util) find_instance_nested() (in module galaxy.util) find_job_object_by_name() (in module galaxy.jobs.runners.util.pykube_util) find_output_def() (galaxy.tools.Tool method) find_pod_object_by_name() (in module galaxy.jobs.runners.util.pykube_util) find_possible_tools_from_path() (in module galaxy.tool_util.loader_directory) find_required_files() (galaxy.tool_util.parser.interface.RequiredFiles method) (galaxy.tool_util.parser.RequiredFiles method) find_root() (in module galaxy.config) find_section_id() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) find_service_object_by_name() (in module galaxy.jobs.runners.util.pykube_util) find_tools() (tool_shed.webapp.controllers.repository.RepositoryController method) findall() (galaxy.util.Element method) finish() (galaxy.jobs.TaskWrapper method) (galaxy.selenium.cli.DriverWrapper method) (galaxy.workflow.render.WorkflowCanvas method) finish_job() (galaxy.jobs.runners.AsynchronousJobRunner method) (galaxy.jobs.runners.chronos.ChronosJobRunner method) (galaxy.jobs.runners.kubernetes.KubernetesJobRunner method) finished (galaxy.model.Job property) finished_states (galaxy.model.Job attribute) first_changeset_hash (in module tool_shed.test.functional.test_0420_citable_urls_for_repositories) first_dataset_element (galaxy.model.DatasetCollection property) first_dataset_instance() (galaxy.model.DatasetCollectionElement method) FITS (class in galaxy.datatypes.binary) fix_url_for() (in module galaxy.webapps.galaxy.api) FixedModuleCodeCompiler (class in galaxy.util.template) FLAGS_W_ARGS (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider attribute) FLAGS_WO_ARGS (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider attribute) flakey() (in module galaxy_test.base.populators) flat (galaxy.schema.remote_files.RemoteFilesFormat attribute) flat_map() (in module galaxy.util.rules_dsl) flat_to_nested_state() (in module galaxy.tools.parameters.wrapped) flatten() (galaxy.util.Params method) FlattenTool (class in galaxy.tools) FLOAT (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute) float_nan() (in module galaxy.visualization.data_providers.genome) FloatToolParameter (class in galaxy.tools.parameters.basic) FluentTraceLogger (class in galaxy.util.custom_logging.fluent_log) flush() (galaxy.datatypes.util.maf_utilities.RegionAlignment method) (galaxy.datatypes.util.maf_utilities.TempFileHandler method) (galaxy.job_execution.output_collect.JobContext method) (galaxy.model.StorableObject method) (galaxy.model.store.discover.ModelPersistenceContext method) (galaxy.model.store.discover.SessionlessModelPersistenceContext method) (galaxy.model.store.SessionlessContext method) (galaxy.tools.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.TempFileHandler method) (in module tool_shed.test.base.test_db_util) flush_per_n_datasets (galaxy.job_execution.output_collect.JobContext property) (galaxy.model.store.discover.ModelPersistenceContext property) (galaxy.model.store.discover.SessionlessModelPersistenceContext property) Flv (class in galaxy.datatypes.media) fn_filter_parsers (galaxy.managers.annotatable.AnnotatableFilterMixin attribute) (galaxy.managers.base.ModelFilterParser attribute) (galaxy.managers.datasets.DatasetAssociationFilterParser attribute) (galaxy.managers.hdas.HDAFilterParser attribute) (galaxy.managers.histories.HistoryFilters attribute) (galaxy.managers.history_contents.HistoryContentsFilters attribute) (galaxy.managers.sharable.SharableModelFilters attribute) (galaxy.managers.users.AdminUserFilterParser attribute) fname (galaxy.datatypes.goldenpath.AGPFile property) folder (galaxy.model.LibraryDataset attribute) (galaxy.model.LibraryDatasetCollectionAssociation attribute) (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryFolderPermissions attribute) (galaxy.tools.actions.upload_common.LibraryParams attribute) folder_contents (galaxy.schema.schema.LibraryFolderContentsIndexResult attribute) folder_description (galaxy.schema.schema.LibraryFolderMetadata attribute) folder_id (galaxy.model.LibraryDataset attribute) (galaxy.model.LibraryDatasetCollectionAssociation attribute) (galaxy.schema.schema.CreateNewCollectionPayload attribute) folder_is_public() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) folder_is_unrestricted() (galaxy.model.security.GalaxyRBACAgent method) folder_name (galaxy.schema.schema.LibraryFolderMetadata attribute) FolderLibraryFolderItem (class in galaxy.schema.schema) FolderManager (class in galaxy.managers.folders) folders (galaxy.model.LibraryFolder attribute) (galaxy.schema.remote_files.RemoteFilesDisableMode attribute) for_collection_type() (galaxy.model.dataset_collections.type_description.CollectionTypeDescriptionFactory method) for_collections() (galaxy.model.dataset_collections.matching.MatchingCollections static method) for_dataset_collection() (galaxy.model.dataset_collections.structure.Tree static method) for_direct_import() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) for_library (galaxy.schema.tasks.ImportModelStoreTaskRequest attribute) for_state() (galaxy.tools.test.ParamContext method) (galaxy.tools.test.RootParamContext method) FORBID (galaxy.model.store.ImportDiscardedDataType attribute) FORCE (galaxy.model.store.ImportDiscardedDataType attribute) force (galaxy.schema.schema.ExportHistoryArchivePayload attribute) force_bed_field_count() (in module galaxy.datatypes.converters.interval_to_bedstrict_converter) force_symlink() (in module galaxy.util) foreign_key_exists() (in module galaxy.model.migrations.util) foreign_key_name (galaxy.managers.base.ModelManager attribute) (galaxy.managers.cloudauthzs.CloudAuthzManager attribute) (galaxy.managers.datasets.DatasetManager attribute) (galaxy.managers.hdas.HDAManager attribute) (galaxy.managers.hdcas.HDCAManager attribute) (galaxy.managers.histories.HistoryManager attribute) (galaxy.managers.lddas.LDDAManager attribute) (galaxy.managers.library_datasets.LibraryDatasetsManager attribute) (galaxy.managers.pages.PageManager attribute) (galaxy.managers.roles.RoleManager attribute) (galaxy.managers.tools.DynamicToolManager attribute) (galaxy.managers.users.UserManager attribute) (galaxy.managers.visualizations.VisualizationManager attribute) (galaxy.managers.workflows.WorkflowsManager attribute) fork_pool (galaxy.celery.GalaxyCelery attribute) form_definition (galaxy.model.FormValues attribute) form_definition_current (galaxy.model.FormDefinition attribute) form_definition_current_id (galaxy.model.FormDefinition attribute) form_definition_id (galaxy.model.FormValues attribute) (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryInfoAssociation attribute) form_manager (galaxy.webapps.galaxy.api.forms.FastAPIForms attribute) form_values_id (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryInfoAssociation attribute) (galaxy.model.User attribute) format (galaxy.tool_util.parser.output_objects.ChangeFormatModel attribute) (galaxy.web.framework.middleware.translogger.TransLogger attribute) (galaxy.workflow.modules.InputModuleState attribute) format() (galaxy.job_metrics.formatting.JobMetricFormatter method) Format2ConverterGalaxyInterface (class in galaxy.managers.workflows) format_attrs() (in module galaxy.web.framework.helpers.tags) format_for_summary() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) format_param() (in module galaxy.workflow.modules) format_return_as_json() (in module galaxy.web) (in module galaxy.web.framework.decorators) format_version (galaxy.schema.schema.WorkflowToExport attribute) formats (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter property) formatted() (galaxy.webapps.reports.controllers.tools.Tools method) FormattedDensity (class in galaxy.datatypes.text) FormattedMetric (class in galaxy.job_metrics.formatting) formatter (galaxy.job_metrics.instrumenters.cgroup.CgroupPlugin attribute) (galaxy.job_metrics.instrumenters.core.CorePlugin attribute) (galaxy.job_metrics.instrumenters.cpuinfo.CpuInfoPlugin attribute) (galaxy.job_metrics.instrumenters.env.EnvPlugin attribute) (galaxy.job_metrics.instrumenters.InstrumentPlugin attribute) (galaxy.job_metrics.instrumenters.meminfo.MemInfoPlugin attribute) (galaxy.job_metrics.instrumenters.uname.UnamePlugin attribute) FormatToolOutputAction (class in galaxy.tool_util.parser.output_actions) FormDataApiRoute (class in galaxy.webapps.galaxy.api.tools) FormDefinition (class in galaxy.model) FormDefinition.types (class in galaxy.model) FormDefinitionAddressFieldFactory (class in galaxy.forms.forms) FormDefinitionAPIController (class in galaxy.webapps.galaxy.api.forms) FormDefinitionCurrent (class in galaxy.model) FormDefinitionFactory (class in galaxy.forms.forms) FormDefinitionFieldFactory (class in galaxy.forms.forms) FormDefinitionHistoryFieldFactory (class in galaxy.forms.forms) FormDefinitionPasswordFieldFactory (class in galaxy.forms.forms) FormDefinitionSelectFieldFactory (class in galaxy.forms.forms) FormDefinitionTextFieldFactory (class in galaxy.forms.forms) FormDefinitionWorkflowFieldFactory (class in galaxy.forms.forms) FormDefinitionWorkflowMappingFieldFactory (class in galaxy.forms.forms) Forms (class in galaxy.webapps.galaxy.controllers.forms) forms (galaxy.model.FormDefinitionCurrent attribute) forms_grid (galaxy.webapps.galaxy.controllers.forms.Forms attribute) forms_list() (galaxy.webapps.galaxy.controllers.forms.Forms method) FormsGrid (class in galaxy.webapps.galaxy.controllers.forms) FormsGrid.DescriptionColumn (class in galaxy.webapps.galaxy.controllers.forms) FormsGrid.NameColumn (class in galaxy.webapps.galaxy.controllers.forms) FormsGrid.TypeColumn (class in galaxy.webapps.galaxy.controllers.forms) FormValues (class in galaxy.model) found_errors (galaxy.tool_util.lint.LintContext property) found_warns (galaxy.tool_util.lint.LintContext property) Fped (class in galaxy.datatypes.genetics) Fphe (class in galaxy.datatypes.genetics) FPS (class in galaxy.datatypes.molecules) framework_tool_and_types (galaxy_test.performance.test_workflow_framework_performance.TestWorkflowFrameworkPerformance attribute) FrameworkRouter (class in galaxy.webapps.galaxy.api) freebayes_repository_long_description (in module tool_shed.test.functional.test_0430_browse_utilities) Frequency (class in galaxy.datatypes.mothur) from_app() (galaxy.security.vault.VaultFactory static method) (galaxy.tools.repositories.ValidationContext static method) from_app_config() (galaxy.files.ConfiguredFileSources static method) (galaxy.files.ConfiguredFileSourcesConfig static method) from_args() (galaxy.tool_util.deps.brew_exts.RecipeContext static method) from_code() (galaxy.exceptions.MessageException static method) from_collection_type() (galaxy.tools.parameters.history_query.HistoryQuery static method) from_collection_types() (galaxy.tools.parameters.history_query.HistoryQuery static method) from_cwl() (in module galaxy.workflow.modules) from_dict() (galaxy.files.ConfiguredFileSources static method) (galaxy.files.ConfiguredFileSourcesConfig static method) (galaxy.job_execution.setup.JobIO class method) (galaxy.job_metrics.JobInstrumenter static method) (galaxy.model.WorkflowComment method) (galaxy.selenium.driver_factory.ConfiguredDriver static method) (galaxy.tool_util.deps.dependencies.DependenciesDescription class method) (galaxy.tool_util.deps.requirements.ContainerDescription class method) (galaxy.tool_util.deps.requirements.RequirementSpecification class method) (galaxy.tool_util.deps.requirements.ToolRequirement class method) (galaxy.tool_util.deps.resolvers.RequirementMapping static method) (galaxy.tool_util.parser.interface.RequiredFiles static method) (galaxy.tool_util.parser.interface.TestCollectionDef static method) (galaxy.tool_util.parser.interface.TestCollectionOutputDef static method) (galaxy.tool_util.parser.output_objects.ToolOutput static method) (galaxy.tool_util.parser.output_objects.ToolOutputCollection static method) (galaxy.tool_util.parser.output_objects.ToolOutputCollectionStructure static method) (galaxy.tool_util.parser.RequiredFiles static method) (galaxy.tool_util.toolbox.views.definitions.StaticToolBoxView static method) (galaxy.tools.data.ToolDataTable class method) (galaxy.visualization.genomes.GenomeRegion static method) (galaxy.workflow.modules.SubWorkflowModule class method) (galaxy.workflow.modules.ToolModule class method) (galaxy.workflow.modules.WorkflowModule class method) (galaxy.workflow.modules.WorkflowModuleFactory method) from_elem() (galaxy.datatypes.display_applications.application.DisplayApplication class method) (galaxy.datatypes.display_applications.application.DisplayApplicationLink class method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter class method) (galaxy.forms.forms.FormDefinitionAddressFieldFactory method) (galaxy.forms.forms.FormDefinitionFactory method) (galaxy.forms.forms.FormDefinitionFieldFactory method) (galaxy.forms.forms.FormDefinitionHistoryFieldFactory method) (galaxy.forms.forms.FormDefinitionPasswordFieldFactory method) (galaxy.forms.forms.FormDefinitionSelectFieldFactory method) (galaxy.forms.forms.FormDefinitionTextFieldFactory method) (galaxy.forms.forms.FormDefinitionWorkflowFieldFactory method) (galaxy.forms.forms.FormDefinitionWorkflowMappingFieldFactory method) (galaxy.tool_util.parser.output_actions.ToolOutputAction class method) (galaxy.tool_util.parser.output_actions.ToolOutputActionConditionalWhen class method) (galaxy.tool_util.parser.output_actions.ToolOutputActionOption class method) (galaxy.tool_util.parser.output_actions.ToolOutputActionOptionFilter class method) from_element() (galaxy.tools.parameters.dynamic_options.Filter class method) (galaxy.tools.parameters.input_translation.ToolInputTranslator class method) (galaxy.tools.parameters.sanitize.ToolParameterSanitizer class method) (galaxy.tools.parameters.validation.DatasetEmptyValidator class method) (galaxy.tools.parameters.validation.DatasetExtraFilesPathEmptyValidator class method) (galaxy.tools.parameters.validation.DatasetOkValidator class method) (galaxy.tools.parameters.validation.EmptyTextfieldValidator class method) (galaxy.tools.parameters.validation.ExpressionValidator class method) (galaxy.tools.parameters.validation.InRangeValidator class method) (galaxy.tools.parameters.validation.LengthValidator class method) (galaxy.tools.parameters.validation.MetadataEqualValidator class method) (galaxy.tools.parameters.validation.MetadataInDataTableColumnValidator class method) (galaxy.tools.parameters.validation.MetadataInFileColumnValidator class method) (galaxy.tools.parameters.validation.MetadataInRangeValidator class method) (galaxy.tools.parameters.validation.MetadataValidator class method) (galaxy.tools.parameters.validation.NoOptionsValidator class method) (galaxy.tools.parameters.validation.RegexValidator class method) (galaxy.tools.parameters.validation.UnspecifiedBuildValidator class method) (galaxy.tools.parameters.validation.Validator class method) (galaxy.tools.parameters.validation.ValueInDataTableColumnValidator class method) from_external_value() (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.model.metadata.FileParameter method) (galaxy.model.metadata.MetadataParameter method) from_file() (galaxy.datatypes.display_applications.application.DisplayApplication class method) (galaxy.job_metrics.JobInstrumenter static method) (galaxy.tools.error_reports.ErrorPlugin static method) from_hda_id (galaxy.schema.schema.CreateLibraryFilePayload attribute) from_hdca_id (galaxy.schema.schema.CreateLibraryFilePayload attribute) from_JSON() (galaxy.datatypes.metadata.MetadataTempFile class method) from_json() (galaxy.job_execution.setup.JobIO class method) from_JSON() (galaxy.model.metadata.MetadataTempFile class method) from_json() (galaxy.tool_util.biotools.interface.BiotoolsEntry static method) (galaxy.tools.parameters.basic.BaseURLToolParameter method) (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.FileToolParameter method) (galaxy.tools.parameters.basic.FloatToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.IntegerToolParameter method) (galaxy.tools.parameters.basic.SelectTagParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.DataCollectionToolParameter method) (galaxy.tools.parameters.DataToolParameter method) (galaxy.tools.parameters.SelectToolParameter method) from_JSON_dict() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataCollection method) from_list() (galaxy.tool_util.deps.requirements.ToolRequirements class method) from_order_index (galaxy.workflow.refactor.schema.RefactorActionExecutionMessage attribute) from_parameter() (galaxy.tools.parameters.history_query.HistoryQuery static method) from_path (galaxy.model.StoredWorkflow attribute) from_step_label (galaxy.workflow.refactor.schema.RefactorActionExecutionMessage attribute) from_str() (galaxy.tool_util.deps.container_volumes.ContainerVolume method) (galaxy.tool_util.deps.container_volumes.DockerVolume class method) (galaxy.visualization.genomes.GenomeRegion static method) from_tool() (galaxy.tool_util.toolbox.lineages.interface.ToolLineage static method) (galaxy.tool_util.toolbox.lineages.ToolLineage static method) from_tool_form (galaxy.managers.workflows.WorkflowStateResolutionOptions attribute) from_url (galaxy.tools.parameters.dynamic_options.FromUrlOptions attribute) from_vault_type() (galaxy.security.vault.VaultFactory static method) from_workflow_step() (galaxy.workflow.modules.SubWorkflowModule class method) (galaxy.workflow.modules.ToolModule class method) (galaxy.workflow.modules.WorkflowModule class method) (galaxy.workflow.modules.WorkflowModuleFactory method) from_xml() (galaxy.objectstore.BaseObjectStore class method) (galaxy.objectstore.DistributedObjectStore class method) (galaxy.tool_util.parser.interface.TestCollectionDef static method) FromDataTableOutputActionOption (class in galaxy.tool_util.parser.output_actions) FromFileToolOutputActionOption (class in galaxy.tool_util.parser.output_actions) FromParamToolOutputActionOption (class in galaxy.tool_util.parser.output_actions) FromUrlOptions (class in galaxy.tools.parameters.dynamic_options) ftp_dir (galaxy.files.DictFileSourcesUserContext property) (galaxy.files.ProvidesUserFileSourcesUserContext property) ftp_import (galaxy.schema.fetch_data.ItemsFromSrc attribute) (galaxy.schema.fetch_data.Src attribute) ftp_path (galaxy.schema.fetch_data.FtpImportElement attribute) (galaxy.schema.fetch_data.FtpImportTarget attribute) (galaxy.schema.fetch_data.ItemsFromModel attribute) ftpdir (galaxy.schema.remote_files.RemoteFilesTarget attribute) FtpFilesSource (class in galaxy.files.sources.ftp) FTPFileToolParameter (class in galaxy.tools.parameters.basic) FtpImportElement (class in galaxy.schema.fetch_data) FtpImportTarget (class in galaxy.schema.fetch_data) full_delete() (galaxy.model.Dataset method) full_path (galaxy.schema.schema.LibraryFolderMetadata attribute) func_std_string() (in module galaxy.web.framework.middleware.profile) function (galaxy.tool_util.biotools.interface.BiotoolsEntry attribute) FunctionalTestCase (class in galaxy_test.base.testcase) futurize_preprocessor() (in module galaxy.util.template) fuzzy_root (galaxy.schema.fetch_data.ExtraFiles attribute)

G

ga_refresh() (in module tool_shed.test.base.test_db_util) GAFASQLite (class in galaxy.datatypes.binary) Gal (class in galaxy.datatypes.microarrays) galactic_job_json() (in module galaxy.tool_util.cwl.util) galaxy module galaxy.actions module galaxy.actions.library module galaxy.app module galaxy.app_unittest_utils module galaxy.app_unittest_utils.galaxy_mock module galaxy.app_unittest_utils.tools_support module galaxy.auth module galaxy.auth.providers module galaxy.auth.providers.alwaysreject module galaxy.auth.providers.ldap_ad module galaxy.auth.providers.localdb module galaxy.auth.providers.pam_auth module galaxy.auth.util module galaxy.authnz module galaxy.authnz.custos_authnz module galaxy.authnz.managers module galaxy.authnz.psa_authnz module galaxy.celery module galaxy.celery.tasks module galaxy.config module galaxy.config.config_manage module galaxy.config.schema module galaxy.config.script module galaxy.config_watchers module galaxy.datatypes module galaxy.datatypes.annotation module galaxy.datatypes.anvio module galaxy.datatypes.assembly module galaxy.datatypes.binary module galaxy.datatypes.blast module galaxy.datatypes.checkers module galaxy.datatypes.chrominfo module galaxy.datatypes.constructive_solid_geometry module galaxy.datatypes.converters module galaxy.datatypes.converters.bed_to_gff_converter module galaxy.datatypes.converters.fasta_to_len module galaxy.datatypes.converters.fasta_to_tabular_converter module galaxy.datatypes.converters.fastq_to_fqtoc module galaxy.datatypes.converters.fastqsolexa_to_fasta_converter module galaxy.datatypes.converters.fastqsolexa_to_qual_converter module galaxy.datatypes.converters.gff_to_bed_converter module galaxy.datatypes.converters.gff_to_interval_index_converter module galaxy.datatypes.converters.interval_to_bed_converter module galaxy.datatypes.converters.interval_to_bedstrict_converter module galaxy.datatypes.converters.interval_to_fli module galaxy.datatypes.converters.interval_to_interval_index_converter module galaxy.datatypes.converters.lped_to_fped_converter module galaxy.datatypes.converters.lped_to_pbed_converter module galaxy.datatypes.converters.maf_to_fasta_converter module galaxy.datatypes.converters.maf_to_interval_converter module galaxy.datatypes.converters.parquet_to_csv_converter module galaxy.datatypes.converters.pbed_ldreduced_converter module galaxy.datatypes.converters.pbed_to_lped_converter module galaxy.datatypes.converters.picard_interval_list_to_bed6_converter module galaxy.datatypes.converters.pileup_to_interval_index_converter module galaxy.datatypes.converters.ref_to_seq_taxonomy_converter module galaxy.datatypes.converters.tabular_csv module galaxy.datatypes.converters.vcf_to_interval_index_converter module galaxy.datatypes.converters.wiggle_to_simple_converter module galaxy.datatypes.coverage module galaxy.datatypes.data module galaxy.datatypes.dataproviders module galaxy.datatypes.dataproviders.base module galaxy.datatypes.dataproviders.chunk module galaxy.datatypes.dataproviders.column module galaxy.datatypes.dataproviders.dataset module galaxy.datatypes.dataproviders.decorators module galaxy.datatypes.dataproviders.exceptions module galaxy.datatypes.dataproviders.external module galaxy.datatypes.dataproviders.hierarchy module galaxy.datatypes.dataproviders.line module galaxy.datatypes.display_applications module galaxy.datatypes.display_applications.application module galaxy.datatypes.display_applications.parameters module galaxy.datatypes.display_applications.util module galaxy.datatypes.flow module galaxy.datatypes.genetics module galaxy.datatypes.gis module galaxy.datatypes.goldenpath module galaxy.datatypes.graph module galaxy.datatypes.hdf5 module galaxy.datatypes.images module galaxy.datatypes.interval module galaxy.datatypes.isa module galaxy.datatypes.media module galaxy.datatypes.metacyto module galaxy.datatypes.metadata module galaxy.datatypes.microarrays module galaxy.datatypes.molecules module galaxy.datatypes.mothur module galaxy.datatypes.msa module galaxy.datatypes.neo4j module galaxy.datatypes.ngsindex module galaxy.datatypes.phylip module galaxy.datatypes.plant_tribes module galaxy.datatypes.proteomics module galaxy.datatypes.qiime2 module galaxy.datatypes.qualityscore module galaxy.datatypes.registry module galaxy.datatypes.sequence module galaxy.datatypes.sniff module galaxy.datatypes.spaln module galaxy.datatypes.speech module galaxy.datatypes.tabular module galaxy.datatypes.text module galaxy.datatypes.tracks module galaxy.datatypes.triples module galaxy.datatypes.upload_util module galaxy.datatypes.util module galaxy.datatypes.util.generic_util module galaxy.datatypes.util.gff_util module galaxy.datatypes.util.maf_utilities module galaxy.datatypes.xml module galaxy.dependencies module galaxy.di module galaxy.exceptions module galaxy.exceptions.error_codes module galaxy.files module galaxy.files.sources module galaxy.files.sources.anvil module galaxy.files.sources.basespace module galaxy.files.sources.dropbox module galaxy.files.sources.ftp module galaxy.files.sources.galaxy module galaxy.files.sources.googlecloudstorage module galaxy.files.sources.googledrive module galaxy.files.sources.onedata module galaxy.files.sources.posix module galaxy.files.sources.s3fs module galaxy.files.sources.ssh module galaxy.files.sources.webdav module galaxy.files.unittest_utils module galaxy.files.uris module galaxy.forms module galaxy.forms.forms module galaxy.job_execution module galaxy.job_execution.actions module galaxy.job_execution.actions.post module galaxy.job_execution.compute_environment module galaxy.job_execution.datasets module galaxy.job_execution.output_collect module galaxy.job_execution.ports module galaxy.job_execution.ports.view module galaxy.job_execution.setup module galaxy.job_metrics module galaxy.job_metrics.formatting module galaxy.job_metrics.instrumenters module galaxy.job_metrics.instrumenters.cgroup module galaxy.job_metrics.instrumenters.core module galaxy.job_metrics.instrumenters.cpuinfo module galaxy.job_metrics.instrumenters.env module galaxy.job_metrics.instrumenters.hostname module galaxy.job_metrics.instrumenters.meminfo module galaxy.job_metrics.instrumenters.uname module galaxy.job_metrics.safety module galaxy.jobs module galaxy.jobs.command_factory module galaxy.jobs.dynamic_tool_destination module galaxy.jobs.handler module galaxy.jobs.manager module galaxy.jobs.mapper module galaxy.jobs.rule_helper module galaxy.jobs.rules module galaxy.jobs.runners module galaxy.jobs.runners.chronos module galaxy.jobs.runners.cli module galaxy.jobs.runners.condor module galaxy.jobs.runners.drmaa module galaxy.jobs.runners.godocker module galaxy.jobs.runners.kubernetes module galaxy.jobs.runners.local module galaxy.jobs.runners.pbs module galaxy.jobs.runners.pulsar module galaxy.jobs.runners.slurm module galaxy.jobs.runners.state_handler_factory module galaxy.jobs.runners.state_handlers module galaxy.jobs.runners.state_handlers.resubmit module galaxy.jobs.runners.tasks module galaxy.jobs.runners.univa module galaxy.jobs.runners.util module galaxy.jobs.runners.util.cli module galaxy.jobs.runners.util.cli.factory module galaxy.jobs.runners.util.cli.job module galaxy.jobs.runners.util.cli.job.lsf module galaxy.jobs.runners.util.cli.job.pbs module galaxy.jobs.runners.util.cli.job.slurm module galaxy.jobs.runners.util.cli.job.slurm_torque module galaxy.jobs.runners.util.cli.job.torque module galaxy.jobs.runners.util.cli.shell module galaxy.jobs.runners.util.cli.shell.local module galaxy.jobs.runners.util.cli.shell.rsh module galaxy.jobs.runners.util.condor module galaxy.jobs.runners.util.env module galaxy.jobs.runners.util.external module galaxy.jobs.runners.util.job_script module galaxy.jobs.runners.util.kill module galaxy.jobs.runners.util.process_groups module galaxy.jobs.runners.util.pykube_util module galaxy.jobs.runners.util.sudo module galaxy.jobs.splitters module galaxy.jobs.splitters.basic module galaxy.jobs.splitters.multi module galaxy.jobs.stock_rules module galaxy.main module galaxy.main_config module galaxy.managers module galaxy.managers.annotatable module galaxy.managers.api_keys module galaxy.managers.base module galaxy.managers.citations module galaxy.managers.cloud module galaxy.managers.cloudauthzs module galaxy.managers.collections module galaxy.managers.collections_util module galaxy.managers.configuration module galaxy.managers.context module galaxy.managers.datasets module galaxy.managers.datatypes module galaxy.managers.deletable module galaxy.managers.display_applications module galaxy.managers.executables module galaxy.managers.folders module galaxy.managers.genomes module galaxy.managers.group_roles module galaxy.managers.group_users module galaxy.managers.groups module galaxy.managers.hdas module galaxy.managers.hdcas module galaxy.managers.histories module galaxy.managers.history_contents module galaxy.managers.interactivetool module galaxy.managers.jobs module galaxy.managers.lddas module galaxy.managers.libraries module galaxy.managers.library_datasets module galaxy.managers.licenses module galaxy.managers.markdown_parse module galaxy.managers.markdown_util module galaxy.managers.metrics module galaxy.managers.model_stores module galaxy.managers.pages module galaxy.managers.quotas module galaxy.managers.ratable module galaxy.managers.rbac_secured module galaxy.managers.remote_files module galaxy.managers.roles module galaxy.managers.secured module galaxy.managers.session module galaxy.managers.sharable module galaxy.managers.taggable module galaxy.managers.tags module galaxy.managers.tool_data module galaxy.managers.tools module galaxy.managers.users module galaxy.managers.visualizations module galaxy.managers.workflows module galaxy.metadata module galaxy.metadata.set_metadata module galaxy.model module galaxy.model.base module galaxy.model.custom_types module galaxy.model.database_heartbeat module galaxy.model.database_utils module galaxy.model.dataset_collections module galaxy.model.dataset_collections.builder module galaxy.model.dataset_collections.matching module galaxy.model.dataset_collections.registry module galaxy.model.dataset_collections.structure module galaxy.model.dataset_collections.subcollections module galaxy.model.dataset_collections.type_description module galaxy.model.dataset_collections.types module galaxy.model.dataset_collections.types.list module galaxy.model.dataset_collections.types.paired module galaxy.model.deferred module galaxy.model.index_filter_util module galaxy.model.item_attrs module galaxy.model.mapping module galaxy.model.metadata module galaxy.model.migrations module galaxy.model.migrations.scripts module galaxy.model.migrations.util module galaxy.model.none_like module galaxy.model.orm module galaxy.model.orm.engine_factory module galaxy.model.orm.now module galaxy.model.orm.scripts module galaxy.model.orm.util module galaxy.model.scoped_session module galaxy.model.security module galaxy.model.store module galaxy.model.store.build_objects module galaxy.model.store.discover module galaxy.model.store.load_objects module galaxy.model.tags module galaxy.model.tool_shed_install module galaxy.model.tool_shed_install.mapping module galaxy.model.triggers module galaxy.model.triggers.history_update_time_field module galaxy.model.triggers.update_audit_table module galaxy.model.triggers.utils module galaxy.model.unittest_utils module galaxy.model.unittest_utils.data_app module galaxy.model.unittest_utils.store_fixtures module galaxy.objectstore module galaxy.objectstore.azure_blob module galaxy.objectstore.cloud module galaxy.objectstore.irods module galaxy.objectstore.pithos module galaxy.objectstore.pulsar module galaxy.objectstore.s3 module galaxy.objectstore.s3_multipart_upload module galaxy.objectstore.unittest_utils module galaxy.queue_worker module galaxy.queues module galaxy.quota module galaxy.schema module galaxy.schema.fetch_data module galaxy.schema.fields module galaxy.schema.remote_files module galaxy.schema.schema module galaxy.schema.tasks module galaxy.schema.types module galaxy.security module galaxy.security.idencoding module galaxy.security.object_wrapper module galaxy.security.passwords module galaxy.security.ssh_util module galaxy.security.validate_user_input module galaxy.security.vault module galaxy.selenium module galaxy.selenium.cli module galaxy.selenium.context module galaxy.selenium.driver_factory module galaxy.selenium.has_driver module galaxy.selenium.jupyter_context module galaxy.selenium.navigates_galaxy module galaxy.selenium.scripts module galaxy.selenium.scripts.dump_tour module galaxy.selenium.sizzle module galaxy.selenium.smart_components module galaxy.selenium.toolbox module galaxy.selenium.toolbox.filters module galaxy.structured_app module galaxy.tool_shed module galaxy.tool_shed.galaxy_install module galaxy.tool_shed.galaxy_install.install_manager module galaxy.tool_shed.galaxy_install.installed_repository_manager module galaxy.tool_shed.galaxy_install.metadata module galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager module galaxy.tool_shed.galaxy_install.repository_dependencies module galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager module galaxy.tool_shed.galaxy_install.tools module galaxy.tool_shed.galaxy_install.tools.data_manager module galaxy.tool_shed.galaxy_install.tools.tool_panel_manager module galaxy.tool_shed.galaxy_install.update_repository_manager module galaxy.tool_shed.metadata module galaxy.tool_shed.metadata.metadata_generator module galaxy.tool_shed.repository_type module galaxy.tool_shed.tools module galaxy.tool_shed.tools.data_table_manager module galaxy.tool_shed.tools.tool_validator module galaxy.tool_shed.util module galaxy.tool_shed.util.basic_util module galaxy.tool_shed.util.container_util module galaxy.tool_shed.util.hg_util module galaxy.tool_shed.util.metadata_util module galaxy.tool_shed.util.repository_util module galaxy.tool_shed.util.shed_util_common module galaxy.tool_shed.util.tool_dependency_util module galaxy.tool_shed.util.tool_util module galaxy.tool_util module galaxy.tool_util.biotools module galaxy.tool_util.biotools.interface module galaxy.tool_util.biotools.source module galaxy.tool_util.client module galaxy.tool_util.client.staging module galaxy.tool_util.cwl module galaxy.tool_util.cwl.cwltool_deps module galaxy.tool_util.cwl.parser module galaxy.tool_util.cwl.representation module galaxy.tool_util.cwl.runnable module galaxy.tool_util.cwl.runtime_actions module galaxy.tool_util.cwl.schema module galaxy.tool_util.cwl.util module galaxy.tool_util.deps module galaxy.tool_util.deps.brew_exts module galaxy.tool_util.deps.brew_util module galaxy.tool_util.deps.commands module galaxy.tool_util.deps.conda_compat module galaxy.tool_util.deps.conda_util module galaxy.tool_util.deps.container_classes module galaxy.tool_util.deps.container_resolvers module galaxy.tool_util.deps.container_resolvers.explicit module galaxy.tool_util.deps.container_resolvers.mulled module galaxy.tool_util.deps.container_volumes module galaxy.tool_util.deps.containers module galaxy.tool_util.deps.dependencies module galaxy.tool_util.deps.docker_util module galaxy.tool_util.deps.dockerfiles module galaxy.tool_util.deps.installable module galaxy.tool_util.deps.mulled module galaxy.tool_util.deps.mulled.get_tests module galaxy.tool_util.deps.mulled.mulled_build module galaxy.tool_util.deps.mulled.mulled_build_channel module galaxy.tool_util.deps.mulled.mulled_build_files module galaxy.tool_util.deps.mulled.mulled_build_tool module galaxy.tool_util.deps.mulled.mulled_hash module galaxy.tool_util.deps.mulled.mulled_list module galaxy.tool_util.deps.mulled.mulled_search module galaxy.tool_util.deps.mulled.mulled_update_singularity_containers module galaxy.tool_util.deps.mulled.util module galaxy.tool_util.deps.requirements module galaxy.tool_util.deps.resolvers module galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages module galaxy.tool_util.deps.resolvers.conda module galaxy.tool_util.deps.resolvers.galaxy_packages module galaxy.tool_util.deps.resolvers.homebrew module galaxy.tool_util.deps.resolvers.lmod module galaxy.tool_util.deps.resolvers.modules module galaxy.tool_util.deps.resolvers.resolver_mixins module galaxy.tool_util.deps.resolvers.tool_shed_packages module galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages module galaxy.tool_util.deps.singularity_util module galaxy.tool_util.deps.views module galaxy.tool_util.edam_util module galaxy.tool_util.fetcher module galaxy.tool_util.lint module galaxy.tool_util.linters module galaxy.tool_util.linters.citations module galaxy.tool_util.linters.command module galaxy.tool_util.linters.cwl module galaxy.tool_util.linters.general module galaxy.tool_util.linters.help module galaxy.tool_util.linters.inputs module galaxy.tool_util.linters.stdio module galaxy.tool_util.linters.tests module galaxy.tool_util.linters.xml_order module galaxy.tool_util.loader module galaxy.tool_util.loader_directory module galaxy.tool_util.locations module galaxy.tool_util.locations.dockstore module galaxy.tool_util.locations.file module galaxy.tool_util.locations.http module galaxy.tool_util.ontologies module galaxy.tool_util.ontologies.ontology_data module galaxy.tool_util.output_checker module galaxy.tool_util.parser module galaxy.tool_util.parser.cwl module galaxy.tool_util.parser.factory module galaxy.tool_util.parser.interface module galaxy.tool_util.parser.output_actions module galaxy.tool_util.parser.output_collection_def module galaxy.tool_util.parser.output_objects module galaxy.tool_util.parser.stdio module galaxy.tool_util.parser.util module galaxy.tool_util.parser.xml module galaxy.tool_util.parser.yaml module galaxy.tool_util.provided_metadata module galaxy.tool_util.toolbox module galaxy.tool_util.toolbox.base module galaxy.tool_util.toolbox.filters module galaxy.tool_util.toolbox.integrated_panel module galaxy.tool_util.toolbox.lineages module galaxy.tool_util.toolbox.lineages.factory module galaxy.tool_util.toolbox.lineages.interface module galaxy.tool_util.toolbox.panel module galaxy.tool_util.toolbox.parser module galaxy.tool_util.toolbox.views module galaxy.tool_util.toolbox.views.definitions module galaxy.tool_util.toolbox.views.edam module galaxy.tool_util.toolbox.views.interface module galaxy.tool_util.toolbox.views.sources module galaxy.tool_util.toolbox.views.static module galaxy.tool_util.toolbox.watcher module galaxy.tool_util.unittest_utils module galaxy.tool_util.unittest_utils.sample_data module galaxy.tool_util.verify module galaxy.tool_util.verify.asserts module galaxy.tool_util.verify.asserts.archive module galaxy.tool_util.verify.asserts.hdf5 module galaxy.tool_util.verify.asserts.size module galaxy.tool_util.verify.asserts.tabular module galaxy.tool_util.verify.asserts.text module galaxy.tool_util.verify.asserts.xml module galaxy.tool_util.verify.interactor module galaxy.tool_util.verify.script module galaxy.tool_util.verify.test_data module galaxy.tool_util.verify.wait module galaxy.tools module galaxy.tools.actions module galaxy.tools.actions.data_manager module galaxy.tools.actions.data_source module galaxy.tools.actions.history_imp_exp module galaxy.tools.actions.metadata module galaxy.tools.actions.model_operations module galaxy.tools.actions.upload module galaxy.tools.actions.upload_common module galaxy.tools.biotools module galaxy.tools.cache module galaxy.tools.data module galaxy.tools.data_fetch module galaxy.tools.data_manager module galaxy.tools.data_manager.manager module galaxy.tools.error_reports module galaxy.tools.error_reports.plugins module galaxy.tools.error_reports.plugins.base_git module galaxy.tools.error_reports.plugins.email module galaxy.tools.error_reports.plugins.github module galaxy.tools.error_reports.plugins.gitlab module galaxy.tools.error_reports.plugins.influxdb module galaxy.tools.error_reports.plugins.json module galaxy.tools.error_reports.plugins.sentry module galaxy.tools.errors module galaxy.tools.evaluation module galaxy.tools.exception_handling module galaxy.tools.execute module galaxy.tools.expressions module galaxy.tools.expressions.evaluation module galaxy.tools.expressions.script module galaxy.tools.expressions.util module galaxy.tools.filters module galaxy.tools.imp_exp module galaxy.tools.imp_exp.export_history module galaxy.tools.imp_exp.unpack_tar_gz_archive module galaxy.tools.parameters module galaxy.tools.parameters.basic module galaxy.tools.parameters.dataset_matcher module galaxy.tools.parameters.dynamic_options module galaxy.tools.parameters.grouping module galaxy.tools.parameters.history_query module galaxy.tools.parameters.input_translation module galaxy.tools.parameters.meta module galaxy.tools.parameters.sanitize module galaxy.tools.parameters.validation module galaxy.tools.parameters.wrapped module galaxy.tools.parameters.wrapped_json module galaxy.tools.recommendations module galaxy.tools.remote_tool_eval module galaxy.tools.repositories module galaxy.tools.search module galaxy.tools.special_tools module galaxy.tools.test module galaxy.tools.util module galaxy.tools.util.galaxyops module galaxy.tools.util.maf_utilities module galaxy.tools.wrappers module galaxy.tours module galaxy.tours.validate module galaxy.util module galaxy.util.aliaspickler module galaxy.util.bool_expressions module galaxy.util.bunch module galaxy.util.bytesize module galaxy.util.checkers module galaxy.util.commands module galaxy.util.compression_utils module galaxy.util.custom_logging module galaxy.util.custom_logging.fluent_log module galaxy.util.dictifiable module galaxy.util.dynamic module galaxy.util.expressions module galaxy.util.facts module galaxy.util.filelock module galaxy.util.form_builder module galaxy.util.hash_util module galaxy.util.heartbeat module galaxy.util.image_util module galaxy.util.inflection module galaxy.util.json module galaxy.util.jstree module galaxy.util.lazy_process module galaxy.util.monitors module galaxy.util.odict module galaxy.util.oset module galaxy.util.path module galaxy.util.path.ntpath module galaxy.util.path.posixpath module galaxy.util.permutations module galaxy.util.plugin_config module galaxy.util.properties module galaxy.util.renamed_temporary_file module galaxy.util.resources module galaxy.util.rules_dsl module galaxy.util.sanitize_html module galaxy.util.script module galaxy.util.search module galaxy.util.simplegraph module galaxy.util.sleeper module galaxy.util.sockets module galaxy.util.specs module galaxy.util.sqlite module galaxy.util.submodules module galaxy.util.task module galaxy.util.template module galaxy.util.tool_shed module galaxy.util.tool_shed.common_util module galaxy.util.tool_shed.encoding_util module galaxy.util.tool_shed.xml_util module galaxy.util.tool_version module galaxy.util.topsort module galaxy.util.ucsc module galaxy.util.validation module galaxy.util.watcher module galaxy.util.xml_macros module galaxy.util.yaml_util module galaxy.util.zipstream module galaxy.version module galaxy.visualization module galaxy.visualization.data_providers module galaxy.visualization.data_providers.basic module galaxy.visualization.data_providers.cigar module galaxy.visualization.data_providers.genome module galaxy.visualization.data_providers.phyloviz module galaxy.visualization.data_providers.phyloviz.baseparser module galaxy.visualization.data_providers.phyloviz.newickparser module galaxy.visualization.data_providers.phyloviz.nexusparser module galaxy.visualization.data_providers.phyloviz.phyloxmlparser module galaxy.visualization.data_providers.registry module galaxy.visualization.genome module galaxy.visualization.genomes module galaxy.visualization.plugins module galaxy.visualization.plugins.config_parser module galaxy.visualization.plugins.plugin module galaxy.visualization.plugins.registry module galaxy.visualization.plugins.resource_parser module galaxy.visualization.plugins.utils module galaxy.visualization.tracks module galaxy.web module galaxy.web.form_builder module galaxy.web.framework module galaxy.web.framework.base module galaxy.web.framework.decorators module galaxy.web.framework.helpers module galaxy.web.framework.helpers.grids module galaxy.web.framework.helpers.tags module galaxy.web.framework.middleware module galaxy.web.framework.middleware.error module galaxy.web.framework.middleware.profile module galaxy.web.framework.middleware.remoteuser module galaxy.web.framework.middleware.request_id module galaxy.web.framework.middleware.sqldebug module galaxy.web.framework.middleware.static module galaxy.web.framework.middleware.statsd module galaxy.web.framework.middleware.translogger module galaxy.web.framework.middleware.xforwardedhost module galaxy.web.legacy_framework module galaxy.web.legacy_framework.grids module galaxy.web.proxy module galaxy.web.statsd_client module galaxy.web_stack module galaxy.web_stack.gunicorn_config module galaxy.web_stack.handlers module galaxy.web_stack.message module galaxy.web_stack.transport module galaxy.webapps module galaxy.webapps.base module galaxy.webapps.base.api module galaxy.webapps.base.controller module galaxy.webapps.base.webapp module galaxy.webapps.galaxy module galaxy.webapps.galaxy.api module galaxy.webapps.galaxy.api.annotations module galaxy.webapps.galaxy.api.authenticate module galaxy.webapps.galaxy.api.cloudauthz module galaxy.webapps.galaxy.api.common module galaxy.webapps.galaxy.api.configuration module galaxy.webapps.galaxy.api.container_resolution module galaxy.webapps.galaxy.api.datatypes module galaxy.webapps.galaxy.api.display_applications module galaxy.webapps.galaxy.api.dynamic_tools module galaxy.webapps.galaxy.api.extended_metadata module galaxy.webapps.galaxy.api.folder_contents module galaxy.webapps.galaxy.api.folders module galaxy.webapps.galaxy.api.forms module galaxy.webapps.galaxy.api.genomes module galaxy.webapps.galaxy.api.group_roles module galaxy.webapps.galaxy.api.group_users module galaxy.webapps.galaxy.api.groups module galaxy.webapps.galaxy.api.job_files module galaxy.webapps.galaxy.api.job_lock module galaxy.webapps.galaxy.api.job_ports module galaxy.webapps.galaxy.api.libraries module galaxy.webapps.galaxy.api.library_contents module galaxy.webapps.galaxy.api.library_datasets module galaxy.webapps.galaxy.api.licenses module galaxy.webapps.galaxy.api.metrics module galaxy.webapps.galaxy.api.page_revisions module galaxy.webapps.galaxy.api.pages module galaxy.webapps.galaxy.api.plugins module galaxy.webapps.galaxy.api.provenance module galaxy.webapps.galaxy.api.quotas module galaxy.webapps.galaxy.api.remote_files module galaxy.webapps.galaxy.api.roles module galaxy.webapps.galaxy.api.sanitize_allow module galaxy.webapps.galaxy.api.short_term_storage module galaxy.webapps.galaxy.api.tags module galaxy.webapps.galaxy.api.tasks module galaxy.webapps.galaxy.api.tool_data module galaxy.webapps.galaxy.api.tool_dependencies module galaxy.webapps.galaxy.api.tool_entry_points module galaxy.webapps.galaxy.api.tool_shed_repositories module galaxy.webapps.galaxy.api.tools module galaxy.webapps.galaxy.api.toolshed module galaxy.webapps.galaxy.api.tours module galaxy.webapps.galaxy.api.trs_consumer module galaxy.webapps.galaxy.api.trs_search module galaxy.webapps.galaxy.api.uploads module galaxy.webapps.galaxy.api.users module galaxy.webapps.galaxy.api.visualizations module galaxy.webapps.galaxy.api.webhooks module galaxy.webapps.galaxy.buildapp module galaxy.webapps.galaxy.controllers module galaxy.webapps.galaxy.controllers.admin module galaxy.webapps.galaxy.controllers.admin_toolshed module galaxy.webapps.galaxy.controllers.async module galaxy.webapps.galaxy.controllers.authnz module galaxy.webapps.galaxy.controllers.data_manager module galaxy.webapps.galaxy.controllers.error module galaxy.webapps.galaxy.controllers.forms module galaxy.webapps.galaxy.controllers.history module galaxy.webapps.galaxy.controllers.page module galaxy.webapps.galaxy.controllers.root module galaxy.webapps.galaxy.controllers.shed_tool_static module galaxy.webapps.galaxy.controllers.tag module galaxy.webapps.galaxy.controllers.tool_runner module galaxy.webapps.galaxy.controllers.user module galaxy.webapps.galaxy.controllers.visualization module galaxy.webapps.galaxy.controllers.workflow module galaxy.webapps.galaxy.fast_app module galaxy.webapps.galaxy.fast_factory module galaxy.webapps.galaxy.services module galaxy.webapps.galaxy.services.authenticate module galaxy.webapps.galaxy.services.base module galaxy.webapps.galaxy.services.histories module galaxy.webapps.galaxy.services.libraries module galaxy.webapps.galaxy.services.library_folder_contents module galaxy.webapps.galaxy.services.library_folders module galaxy.webapps.galaxy.services.pages module galaxy.webapps.galaxy.services.quotas module galaxy.webapps.galaxy.services.sharable module galaxy.webapps.galaxy.services.tools module galaxy.webapps.galaxy.services.users module galaxy.webapps.galaxy.services.visualizations module galaxy.webapps.galaxy.workers module galaxy.webapps.openapi module galaxy.webapps.openapi.utils module galaxy.webapps.reports module galaxy.webapps.reports.api module galaxy.webapps.reports.app module galaxy.webapps.reports.buildapp module galaxy.webapps.reports.config module galaxy.webapps.reports.controllers module galaxy.webapps.reports.controllers.history module galaxy.webapps.reports.controllers.home module galaxy.webapps.reports.controllers.jobs module galaxy.webapps.reports.controllers.query module galaxy.webapps.reports.controllers.root module galaxy.webapps.reports.controllers.system module galaxy.webapps.reports.controllers.tools module galaxy.webapps.reports.controllers.users module galaxy.webapps.reports.controllers.workflows module galaxy.webapps.reports.fast_app module galaxy.webapps.reports.fast_factory module galaxy.webapps.util module galaxy.webhooks module galaxy.work module galaxy.work.context module galaxy.workflow module galaxy.workflow.extract module galaxy.workflow.modules module galaxy.workflow.refactor module galaxy.workflow.refactor.execute module galaxy.workflow.refactor.schema module galaxy.workflow.render module galaxy.workflow.reports module galaxy.workflow.reports.generators module galaxy.workflow.reports.generators.markdown module galaxy.workflow.resources module galaxy.workflow.run module galaxy.workflow.run_request module galaxy.workflow.schedulers module galaxy.workflow.schedulers.core module galaxy.workflow.scheduling_manager module galaxy.workflow.steps module galaxy.workflow.trs_proxy module galaxy_data_manager_data_path (galaxy.config.GalaxyAppConfiguration attribute) (galaxy.tools.remote_tool_eval.ToolAppConfig attribute) galaxy_directory() (in module galaxy.util) galaxy_driver_class (galaxy_test.base.testcase.FunctionalTestCase attribute) (galaxy_test.driver.testcase.DrivenFunctionalTestCase attribute) galaxy_ext module galaxy_ext.container_monitor module galaxy_ext.container_monitor.monitor module galaxy_ext.expressions module galaxy_ext.expressions.handle_job module galaxy_ext.metadata module galaxy_ext.metadata.set_metadata module galaxy_infrastructure_url (galaxy.config.GalaxyAppConfiguration attribute) galaxy_instance_id() (in module galaxy.jobs.runners.util.pykube_util) galaxy_interactor (galaxy_test.base.api.UsesApiTestCaseMixin property) (galaxy_test.base.populators.BaseDatasetPopulator attribute) (galaxy_test.base.populators.BasePopulator attribute) (galaxy_test.base.populators.DatasetPopulator attribute) (galaxy_test.base.populators.GalaxyInteractorHttpMixin attribute) (galaxy_test.base.populators.WorkflowPopulator attribute) galaxy_param_type (galaxy.tool_util.cwl.representation.TypeRepresentation attribute) galaxy_samples_directory() (in module galaxy.util) galaxy_scoped_session (class in galaxy.model.scoped_session) galaxy_session (galaxy.managers.context.ProvidesUserContext attribute) (galaxy.model.Event attribute) (galaxy.model.GalaxySessionToHistoryAssociation attribute) (galaxy.model.Job attribute) galaxy_sessions (galaxy.model.History attribute) (galaxy.model.User attribute) (tool_shed.webapp.model.User attribute) galaxy_task() (in module galaxy.celery) galaxy_test module galaxy_test.api module galaxy_test.api.cwl module galaxy_test.api.sharable module galaxy_test.api.test_authenticate module galaxy_test.api.test_configuration module galaxy_test.api.test_dataset_collections module galaxy_test.api.test_datasets module galaxy_test.api.test_datatypes module galaxy_test.api.test_display_applications module galaxy_test.api.test_folder_contents module galaxy_test.api.test_folders module galaxy_test.api.test_framework module galaxy_test.api.test_group_roles module galaxy_test.api.test_group_users module galaxy_test.api.test_groups module galaxy_test.api.test_histories module galaxy_test.api.test_history_contents module galaxy_test.api.test_history_contents_provenance module galaxy_test.api.test_jobs module galaxy_test.api.test_libraries module galaxy_test.api.test_licenses module galaxy_test.api.test_page_revisions module galaxy_test.api.test_pages module galaxy_test.api.test_roles module galaxy_test.api.test_tool_data module galaxy_test.api.test_tools module galaxy_test.api.test_tools_upload module galaxy_test.api.test_tours module galaxy_test.api.test_users module galaxy_test.api.test_visualizations module galaxy_test.api.test_webhooks module galaxy_test.api.test_workflow_extraction module galaxy_test.api.test_workflows module galaxy_test.api.test_workflows_cwl module galaxy_test.api.test_workflows_from_yaml module galaxy_test.base module galaxy_test.base.api module galaxy_test.base.api_asserts module galaxy_test.base.api_util module galaxy_test.base.constants module galaxy_test.base.env module galaxy_test.base.interactor module galaxy_test.base.populators module galaxy_test.base.rules_test_data module galaxy_test.base.testcase module galaxy_test.base.workflow_fixtures module galaxy_test.conftest module galaxy_test.driver module galaxy_test.driver.driver_util module galaxy_test.driver.integration_setup module galaxy_test.driver.integration_util module galaxy_test.driver.test_logging module galaxy_test.driver.testcase module galaxy_test.performance module galaxy_test.performance.test_workflow_framework_performance module galaxy_test.selenium module galaxy_test.selenium.conftest module galaxy_test.selenium.framework module galaxy_test.selenium.jupyter module galaxy_test.selenium.jupyter_context module galaxy_test.selenium.test_admin_app module galaxy_test.selenium.test_anon_history module galaxy_test.selenium.test_change_password module galaxy_test.selenium.test_collection_builders module galaxy_test.selenium.test_collection_edit module galaxy_test.selenium.test_custom_builds module galaxy_test.selenium.test_data_source_tools module galaxy_test.selenium.test_dataset_metadata_download module galaxy_test.selenium.test_histories_list module galaxy_test.selenium.test_history_copy_elements module galaxy_test.selenium.test_history_dataset_state module galaxy_test.selenium.test_history_multi_view module galaxy_test.selenium.test_history_options module galaxy_test.selenium.test_history_panel module galaxy_test.selenium.test_history_panel_collections module galaxy_test.selenium.test_history_sharing module galaxy_test.selenium.test_invocation_grid module galaxy_test.selenium.test_library_contents module galaxy_test.selenium.test_library_landing module galaxy_test.selenium.test_library_to_collections module galaxy_test.selenium.test_login module galaxy_test.selenium.test_navigates_galaxy module galaxy_test.selenium.test_pages module galaxy_test.selenium.test_personal_information module galaxy_test.selenium.test_registration module galaxy_test.selenium.test_sign_out module galaxy_test.selenium.test_sizzle_loading module galaxy_test.selenium.test_stock_tours module galaxy_test.selenium.test_tool_describing_tours module galaxy_test.selenium.test_tool_form module galaxy_test.selenium.test_uploads module galaxy_test.selenium.test_workflow_editor module galaxy_test.selenium.test_workflow_invocation_details module galaxy_test.selenium.test_workflow_management module galaxy_test.selenium.test_workflow_run module galaxy_test.selenium.test_workflow_sharing module galaxy_url (galaxy.model.store.BcoExportOptions attribute) (galaxy.schema.tasks.BcoGenerationTaskParametersMixin attribute) galaxy_url() (galaxy.job_execution.compute_environment.ComputeEnvironment method) (galaxy.job_execution.compute_environment.SharedComputeEnvironment method) galaxy_version (galaxy.model.Job attribute) (galaxy.model.store.BcoExportOptions attribute) (galaxy.schema.schema.JobBaseModel attribute) GalaxyAbstractRequest (class in galaxy.work.context) GalaxyAbstractResponse (class in galaxy.work.context) GalaxyAppConfiguration (class in galaxy.config) GalaxyASGIRequest (class in galaxy.webapps.galaxy.api) GalaxyASGIResponse (class in galaxy.webapps.galaxy.api) GalaxyCelery (class in galaxy.celery) GalaxyConfigBuilder (class in galaxy.main) GalaxyDataTestApp (class in galaxy.model.unittest_utils) (class in galaxy.model.unittest_utils.data_app) GalaxyDataTestConfig (class in galaxy.model.unittest_utils) (class in galaxy.model.unittest_utils.data_app) GalaxyFileResponse (class in galaxy.webapps.base.api) GalaxyInteractorApi (class in galaxy.tool_util.verify.interactor) GalaxyInteractorHttpMixin (class in galaxy_test.base.populators) GalaxyInteractorToolShedInstallationClient (class in tool_shed.test.base.twilltestcase) GalaxyLargeBinary (class in galaxy.model.custom_types) GalaxyManagerApplication (class in galaxy.app) GalaxyMetadataGenerator (class in galaxy.tool_shed.metadata.metadata_generator) GalaxyModelMapping (class in galaxy.model.mapping) GalaxyOutput (class in galaxy.tool_util.cwl.util) GalaxyPackageDependency (class in galaxy.tool_util.deps.resolvers.galaxy_packages) GalaxyPackageDependencyResolver (class in galaxy.tool_util.deps.resolvers.galaxy_packages) GalaxyQueueWorker (class in galaxy.queue_worker) GalaxyRBACAgent (class in galaxy.model.security) GalaxySeleniumContext (class in galaxy.selenium.context) GalaxySeleniumContextImpl (class in galaxy.selenium.context) GalaxySession (class in galaxy.model) (class in tool_shed.webapp.model) (galaxy.model.base.SharedModelMapping attribute) (galaxy.model.mapping.GalaxyModelMapping attribute) GalaxySessionlessTagHandler (class in galaxy.model.tags)

GalaxySessionManager (class in galaxy.managers.session) GalaxySessionToHistoryAssociation (class in galaxy.model) GalaxyStatsdClient (in module galaxy.web.statsd_client) GalaxyTagHandler (class in galaxy.model.tags) GalaxyTagHandlerSession (class in galaxy.model.tags) GalaxyTask (class in galaxy.celery) GalaxyTypeDepends (class in galaxy.webapps.galaxy.api) GalaxyWebApplication (class in galaxy.webapps.galaxy.buildapp) GalaxyWebTransaction (class in galaxy.webapps.base.webapp) gbrowse_links() (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Wiggle method) GeminiSQLite (class in galaxy.datatypes.binary) gen_edge_dicts() (galaxy.util.simplegraph.SimpleGraph method) gen_image() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) gen_node_dicts() (galaxy.util.simplegraph.SimpleGraph method) gen_task_name() (galaxy.celery.GalaxyCelery method) Genbank (class in galaxy.datatypes.sequence) GeneNoteBook (class in galaxy.datatypes.binary) generate_clone_url_for_installed_repository() (in module galaxy.util.tool_shed.common_util) (in module tool_shed.util.common_util) generate_clone_url_for_repository_in_tool_shed() (in module tool_shed.util.common_util) generate_clone_url_from_repo_info_tup() (in module galaxy.util.tool_shed.common_util) (in module tool_shed.util.common_util) generate_complex_dependency_xml() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) generate_contents_url() (galaxy.managers.hdcas.HDCASerializer method) generate_elements() (galaxy.model.dataset_collections.types.DatasetCollectionType method) (galaxy.model.dataset_collections.types.list.ListDatasetCollectionType method) (galaxy.model.dataset_collections.types.paired.PairedDatasetCollectionType method) generate_environment_dependency_metadata() (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator method) generate_message_for_invalid_tools() (in module galaxy.tool_shed.util.tool_util) (in module tool_shed.util.tool_util) generate_message_for_repository_type_change() (in module tool_shed.repository_types.util) generate_metadata_for_changeset_revision() (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator method) generate_package_dependency_metadata() (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator method) generate_primary_file() (galaxy.datatypes.anvio.AnvioComposite method) (galaxy.datatypes.assembly.Velvet method) (galaxy.datatypes.binary.LudwigModel method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.genetics.IdeasPre method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.genetics.Rgenetics method) (galaxy.datatypes.gis.Shapefile method) (galaxy.datatypes.hdf5.HDF5SummarizedExperiment method) (galaxy.datatypes.images.Analyze75 method) (galaxy.datatypes.neo4j.Neo4j method) (galaxy.datatypes.ngsindex.BowtieIndex method) (galaxy.datatypes.proteomics.ImzML method) (galaxy.datatypes.proteomics.SPLib method) (galaxy.datatypes.proteomics.Wiff method) (galaxy.datatypes.proteomics.Wiff2 method) (galaxy.datatypes.text.SnpSiftDbNSFP method) (galaxy.datatypes.tracks.UCSCTrackHub method) generate_report() (in module galaxy.workflow.reports) generate_report_json() (galaxy.workflow.reports.generators.WorkflowMarkdownGeneratorPlugin method) (galaxy.workflow.reports.generators.WorkflowReportGeneratorPlugin method) generate_report_pdf() (galaxy.workflow.reports.generators.WorkflowMarkdownGeneratorPlugin method) (galaxy.workflow.reports.generators.WorkflowReportGeneratorPlugin method) generate_repository_dependencies_key_for_repository() (in module galaxy.tool_shed.util.container_util) (in module tool_shed.util.container_util) generate_repository_dependency_metadata() (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator method) generate_repository_info_elem() (galaxy.tool_shed.tools.data_table_manager.ShedToolDataTableManager method) (tool_shed.tools.data_table_manager.ShedToolDataTableManager method) generate_repository_info_elem_from_repository() (galaxy.tool_shed.tools.data_table_manager.ShedToolDataTableManager method) (tool_shed.tools.data_table_manager.ShedToolDataTableManager method) generate_sharable_link_for_repository_in_tool_shed() (in module tool_shed.util.repository_util) generate_simple_dependency_xml() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) generate_ssh_keys() (in module galaxy.security.ssh_util) generate_statistics() (tool_shed.webapp.util.shed_statistics.ShedCounter method) generate_temp_path() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) generate_time (galaxy.schema.schema.PageDetails attribute) generate_tool_dependencies_key() (tool_shed.utility_containers.ToolShedUtilityContainerManager method) generate_tool_dependency_metadata() (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator method) generate_tool_elem() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_guid() (in module galaxy.tool_shed.util.shed_util_common) generate_tool_metadata() (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator method) generate_tool_panel_dict_for_new_install() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_panel_dict_for_tool_config() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_panel_dict_from_shed_tool_conf_entries() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_panel_elem_list() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_section_dicts() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_section_element_from_dict() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_shed_repository_install_dir() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) generate_version (galaxy.schema.schema.PageDetails attribute) GenerateHistoryContentDownload (class in galaxy.schema.tasks) GenerateHistoryDownload (class in galaxy.schema.tasks) GenerateInvocationDownload (class in galaxy.schema.tasks) generateJsonableDict() (galaxy.visualization.data_providers.phyloviz.baseparser.PhyloTree method) GeneratePdfDownload (class in galaxy.schema.tasks) generic (galaxy.tool_util.toolbox.views.definitions.StaticToolBoxViewTypeEnum attribute) (galaxy.tool_util.toolbox.views.interface.ToolPanelViewModelType attribute) GENERIC_ERROR (galaxy.tool_util.output_checker.DETECTED_JOB_STATE attribute) GenericAsn1 (class in galaxy.datatypes.data) GenericAsn1Binary (class in galaxy.datatypes.binary) GenericMicroarrayFile (class in galaxy.datatypes.microarrays) GenericMolFile (class in galaxy.datatypes.molecules) GenericS3ObjectStore (class in galaxy.objectstore.s3) GenericXml (class in galaxy.datatypes.xml) GeneTrack (class in galaxy.datatypes.tracks) Genome (class in galaxy.visualization.genomes) genome_build (galaxy.model.History attribute) (galaxy.model.LibraryFolder attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDASummary attribute) (galaxy.schema.schema.HistoryDetailed attribute) (galaxy.schema.schema.LibraryFolderDetails attribute) genome_build() (galaxy.managers.base.ModelValidator static method) genome_builds (galaxy.structured_app.MinimalManagerApp attribute) GenomeBuildParameter (class in galaxy.tools.parameters.basic) GenomeDataProvider (class in galaxy.visualization.data_providers.genome) GenomeFilterMixin (class in galaxy.managers.genomes) GenomeGraphs (class in galaxy.datatypes.genetics) GenomeIndexToolData (class in galaxy.model) GenomeRegion (class in galaxy.visualization.genomes) Genomes (class in galaxy.visualization.genomes) genomes (galaxy.structured_app.MinimalManagerApp attribute) GenomesManager (class in galaxy.managers.genomes) genomic_region_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.tabular.BaseVcf method) (galaxy.datatypes.tabular.Pileup method) (galaxy.datatypes.tabular.Sam method) genomic_region_dict_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.tabular.BaseVcf method) (galaxy.datatypes.tabular.Pileup method) (galaxy.datatypes.tabular.Sam method) GenomicRegionAlignment (class in galaxy.datatypes.util.maf_utilities) (class in galaxy.tools.util.maf_utilities) GenomicRegionDataProvider (class in galaxy.datatypes.dataproviders.dataset) GenotypeMatrix (class in galaxy.datatypes.genetics) geographical_server_location_name (galaxy.config.GalaxyAppConfiguration attribute) GeoJson (class in galaxy.datatypes.text) get (galaxy.webapps.galaxy.api.RestVerb attribute) get() (galaxy.config.CommonConfigurationMixin method) (galaxy.datatypes.metadata.MetadataElementSpec method) (galaxy.managers.cloud.CloudManager method) (galaxy.managers.datasets.DatasetRBACPermissions method) (galaxy.managers.folders.FolderManager method) (galaxy.managers.interactivetool.InteractiveToolSqlite method) (galaxy.managers.lddas.LDDAManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.managers.library_datasets.LibraryDatasetsManager method) (galaxy.managers.licenses.LicensesManager method) (galaxy.managers.roles.RoleManager method) (galaxy.model.dataset_collections.registry.DatasetCollectionTypesRegistry method) (galaxy.model.metadata.MetadataElementSpec method) (galaxy.model.PSAAssociation class method) (galaxy.model.store.SessionlessContext method) (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) (galaxy.tool_util.biotools.source.InMemoryCache method) (galaxy.tool_util.cwl.cwltool_deps.CommentedMap method) (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) (galaxy.tool_util.parser.yaml.YamlInputSource method) (galaxy.tool_util.toolbox.lineages.factory.LineageMap method) (galaxy.tool_util.toolbox.lineages.LineageMap method) (galaxy.tools.cache.ToolDocumentCache method) (galaxy.tools.wrappers.DatasetFilenameWrapper.MetadataWrapper method) (galaxy.util.bunch.Bunch method) (galaxy.util.Params method) (galaxy.webapps.galaxy.api.FrameworkRouter method) (galaxy.webapps.galaxy.api.licenses.FastAPILicenses method) (galaxy.webapps.reports.config.Configuration method) (galaxy_test.base.api.ApiTestInteractor method) (tool_shed.managers.groups.GroupManager method) get_absolute_path_to_file_in_repository() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_accepted_filters() (galaxy.web.legacy_framework.grids.DeletedColumn method) (galaxy.web.legacy_framework.grids.GridColumn method) (galaxy.web.legacy_framework.grids.SharingStatusColumn method) (galaxy.web.legacy_framework.grids.StateColumn method) get_access_roles() (galaxy.managers.libraries.LibraryManager method) (galaxy.model.Dataset method) (galaxy.model.HistoryDatasetAssociation method) (galaxy.model.Library method) (galaxy.model.LibraryDatasetDatasetAssociation method) get_accessible() (galaxy.managers.secured.AccessibleManagerMixin method) get_accessible_job() (galaxy.managers.jobs.JobManager method) get_accessible_libraries() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) get_action() (galaxy.security.RBACAgent method) (tool_shed.webapp.security.RBACAgent method) get_actions() (galaxy.security.RBACAgent method) (tool_shed.webapp.security.RBACAgent method) get_actions_for_items() (galaxy.model.security.GalaxyRBACAgent method) get_active_count() (galaxy.managers.histories.HistoryManager method) get_active_folders() (galaxy.model.Library method) get_active_processes() (galaxy.model.database_heartbeat.DatabaseHeartbeat method) get_add_roles() (galaxy.managers.libraries.LibraryManager method) get_address_input_field() (galaxy_test.selenium.test_personal_information.TestManageInformation method) get_admin_api_key() (in module galaxy_test.base.api_util) get_admin_user() (in module galaxy.webapps.galaxy.api) get_alembic_cfg() (in module galaxy.model.migrations.scripts) get_alembic_manager() (in module galaxy.model.migrations) (in module galaxy.model.migrations.scripts) get_all_dependencies() (in module tool_shed.util.metadata_util) get_all_forms() (galaxy.webapps.base.controller.UsesFormDefinitionsMixin method) get_all_inputs() (galaxy.workflow.modules.InputModule method) (galaxy.workflow.modules.PauseModule method) (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_all_installed_repositories() (in module tool_shed.test.base.test_db_util) (tool_shed.test.base.twilltestcase.GalaxyInteractorToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) (tool_shed.test.base.twilltestcase.StandaloneToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ToolShedInstallationClient method) get_all_outputs() (galaxy.workflow.modules.InputDataCollectionModule method) (galaxy.workflow.modules.InputDataModule method) (galaxy.workflow.modules.InputParameterModule method) (galaxy.workflow.modules.PauseModule method) (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_all_repositories() (in module tool_shed.test.base.test_db_util) get_all_roles() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) get_all_staging_paths() (galaxy.tools.wrappers.DatasetCollectionWrapper method) get_all_tools() (galaxy.managers.workflows.WorkflowContentsManager method) get_allowed_idps() (galaxy.authnz.managers.AuthnzManager method) get_alternative_versions() (in module galaxy.tool_util.deps.mulled.get_tests) get_amount() (galaxy.model.Quota method) get_anaconda_url() (in module galaxy.tool_util.deps.mulled.get_tests) get_api_key() (galaxy.managers.api_keys.ApiKeyManager method) (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) (galaxy.webapps.galaxy.api.authenticate.FastAPIAuthenticate method) (galaxy.webapps.galaxy.api.users.FastAPIUsers method) (galaxy.webapps.galaxy.services.authenticate.AuthenticationService method) (galaxy.webapps.galaxy.services.users.UsersService method) get_api_url() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) get_api_user() (in module galaxy.webapps.galaxy.api) get_app() (in module galaxy.webapps.galaxy.api) get_app_kwds() (galaxy.web_stack.ApplicationStack class method) (in module galaxy.web_stack) get_app_option() (galaxy.config.schema.Schema method) (galaxy.tool_util.deps.DependencyManager method) get_app_properties() (in module galaxy.celery) get_app_with_request_session() (in module galaxy.webapps.galaxy.api) get_archive_download_path() (galaxy.webapps.galaxy.services.histories.HistoriesService method) get_archive_media_type() (galaxy.webapps.galaxy.services.histories.HistoriesService method) get_archived() (galaxy.managers.base.StorageCleanerManager method) (galaxy.managers.histories.HistoryStorageCleanerManager method) get_archived_histories() (galaxy.webapps.galaxy.services.histories.HistoriesService method) (galaxy_test.base.populators.BaseDatasetPopulator method) get_archived_summary() (galaxy.managers.base.StorageCleanerManager method) (galaxy.managers.histories.HistoryStorageCleanerManager method) get_attribute() (galaxy.datatypes.binary.H5MLM method) get_attributes_from_fasta_header() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_authenticated_user() (galaxy.webapps.galaxy.services.base.ServiceBase method) get_authenticators() (in module galaxy.auth.util) get_available_tracks() (galaxy.datatypes.registry.Registry method) get_ave_item_rating_data() (galaxy.model.item_attrs.UsesItemRatings method) get_base_dir() (galaxy.tools.data.TabularToolDataField method) get_base_path() (galaxy.tools.data.TabularToolDataField method) get_beacon() (galaxy.webapps.galaxy.api.users.FastAPIUsers method) get_before_flush_handler() (in module galaxy.model.base) get_bibtex() (galaxy.managers.citations.DoiCache method) get_biocompute_object() (galaxy_test.base.populators.BaseWorkflowPopulator method) get_biotools_metadata() (galaxy.tool_util.biotools.BiotoolsMetadataSource method) (galaxy.tool_util.biotools.source.ApiBiotoolsMetadataSource method) (galaxy.tool_util.biotools.source.BiotoolsMetadataSource method) (galaxy.tool_util.biotools.source.CascadingBiotoolsMetadataSource method) (galaxy.tool_util.biotools.source.GitContentBiotoolsMetadataSource method) get_biotools_metadata_source() (in module galaxy.tool_util.biotools) (in module galaxy.tool_util.biotools.source) get_blurb() (galaxy.datatypes.constructive_solid_geometry.Vtk method) get_bool() (galaxy.config.CommonConfigurationMixin method) (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) (galaxy.tool_util.parser.yaml.YamlInputSource method) get_bounds() (in module galaxy.visualization.data_providers.genome) get_browsable() (galaxy.files.sources.BaseFilesSource method) (galaxy.files.sources.FilesSource method) get_build() (galaxy.visualization.genomes.Genomes method) get_cache_region() (galaxy.tools.ToolBox method) get_cache_value() (galaxy.work.context.WorkRequestContext method) get_categories() (in module tool_shed.util.shed_util_common) get_category() (in module tool_shed.util.shed_util_common) get_category_by_name() (in module tool_shed.util.shed_util_common) get_certified_level_one_clause_list() (tool_shed.repository_registry.Registry method) get_certified_level_one_tuple() (tool_shed.repository_registry.Registry method) get_certified_repositories_with_user() (in module tool_shed.repository_registry) get_change_datatype_actions() (galaxy.model.Job method) get_change_lines_in_file_for_tag() (in module tool_shed.util.commit_util) get_changectx_for_changeset() (in module galaxy.tool_shed.util.hg_util) (in module tool_shed.util.hg_util) get_changeset_revision_and_ctx_rev() (tool_shed.webapp.controllers.repository.RepositoryController method) get_changesets_for_setting_metadata() (tool_shed.repository_types.metadata.Metadata method) (tool_shed.repository_types.metadata.TipOnly method) (tool_shed.webapp.model.Repository method) get_charset_from_http_headers() (in module galaxy.util) get_children() (galaxy.datatypes.dataproviders.hierarchy.XMLDataProvider method) get_chopped_blocks_for_region() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_chopped_blocks_with_index_offset_for_region() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_chrom_info() (galaxy.tools.actions.ToolExecutionCache method) get_chunk() (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.tabular.ConnectivityTable method) (galaxy.datatypes.tabular.TabularData method) get_cilogon_idps() (galaxy.webapps.galaxy.controllers.authnz.OIDC method) get_class() (galaxy.webapps.galaxy.services.base.ServiceBase method) (in module galaxy.managers.base) get_class_by_label() (tool_shed.repository_types.registry.Registry method) get_cli_plugins() (galaxy.jobs.runners.cli.ShellJobRunner method) get_cloud_access_credentials() (galaxy.authnz.managers.AuthnzManager method) get_cloud_access_credentials_in_file() (galaxy.authnz.managers.AuthnzManager method) get_code() (galaxy.model.PSACode class method) get_collection_contents() (galaxy.managers.collections.DatasetCollectionManager method) get_column_list() (galaxy.tools.parameters.basic.ColumnListParameter method) get_column_metadata_from_dataset() (galaxy.datatypes.dataproviders.dataset.DatasetDataProvider class method) get_column_name_list() (galaxy.tools.data.TabularToolDataTable method) get_column_names() (galaxy.datatypes.qiime2.QIIME2Metadata method) (galaxy.datatypes.tabular.SraManifest method) (galaxy.datatypes.tabular.Tabular method) get_column_type() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) get_command_line() (galaxy.jobs.TaskWrapper method) (galaxy.model.Job method) (galaxy.model.Task method) get_commands_from_yaml() (in module galaxy.tool_util.deps.mulled.get_tests) get_community_tags() (galaxy.model.tags.TagHandler method) get_component_associations() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) get_components_by_src() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_components_by_src_start() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_components_from_key() (in module galaxy.tool_shed.util.container_util) (in module tool_shed.util.container_util) get_composite_dataset_name() (galaxy.tools.parameters.grouping.UploadDataset method) get_composite_extensions() (galaxy.datatypes.registry.Registry method) get_composite_files() (galaxy.datatypes.data.Data method) get_compressed_formats() (in module galaxy.tool_util.verify) get_concrete_store_badges() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) get_concrete_store_by_object_store_id() (galaxy.objectstore.DistributedObjectStore method) (galaxy.objectstore.ObjectStore method) get_concrete_store_description_markdown() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) get_concrete_store_name() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) get_conda_envs() (in module galaxy.tool_util.deps.mulled.mulled_list) get_conda_target_installed_path() (galaxy.tool_util.deps.conda_util.CondaContext method) get_conditional_requirements() (galaxy.dependencies.ConditionalDependencies method) get_config() (in module galaxy.celery) (in module galaxy.model.orm.scripts) get_config_form() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_config_from_disk() (in module galaxy.tool_shed.util.hg_util) (in module tool_shed.util.hg_util) get_config_string() (galaxy.datatypes.binary.H5MLM method) get_configuration() (galaxy.managers.configuration.ConfigurationManager method) (galaxy_test.base.populators.BaseDatasetPopulator method) (in module galaxy.model.migrations.scripts) get_configuration_from_file() (in module galaxy.model.migrations.scripts) get_configured_job_handler() (galaxy.tools.Tool method) get_configured_plugin() (galaxy.job_metrics.JobInstrumenter method) get_conformance_test() (galaxy_test.base.populators.CwlPopulator method) get_consumers() (galaxy.queue_worker.GalaxyQueueWorker method) get_containing_library_from_library_dataset() (in module galaxy.managers.libraries) get_containing_repository_for_tool_dependency() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_content_id() (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_content_type() (galaxy.work.context.GalaxyAbstractResponse method) get_contents() (galaxy.managers.folders.FolderManager method) get_converted_dataset() (galaxy.model.DatasetInstance method) get_converted_dataset_deps() (galaxy.model.DatasetInstance method) get_converted_files_by_type() (galaxy.model.DatasetInstance method) get_converter_by_target_type() (galaxy.datatypes.registry.Registry method) get_converter_types() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) get_converters_by_datatype() (galaxy.datatypes.registry.Registry method) get_converters_for_collection() (galaxy.managers.collections.DatasetCollectionManager method) get_cookie() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) (galaxy.webapps.galaxy.api.GalaxyASGIRequest method) (galaxy.work.context.GalaxyAbstractRequest method) get_copied_from_job_id() (galaxy.model.Job method) get_count() (in module galaxy.managers.folders) (in module galaxy.managers.histories) (in module galaxy.managers.pages) (in module galaxy.managers.workflows) get_cram_version() (galaxy.datatypes.binary.CRAM method) get_created_from_basename() (galaxy.model.DatasetInstance method) get_ctx_file_path_from_manifest() (in module galaxy.tool_shed.util.hg_util) (in module tool_shed.util.hg_util) get_ctx_rev() (in module galaxy.tool_shed.util.shed_util_common) (tool_shed.webapp.controllers.repository.RepositoryController method) get_curr_item() (in module galaxy.webapps.reports.controllers.jobs) get_current() (galaxy.managers.histories.HistoryManager method) get_current_case() (galaxy.tools.parameters.grouping.Conditional method) get_current_email_alert_repositories() (in module tool_shed.webapp.controllers.repository) get_current_form() (galaxy.webapps.galaxy.controllers.forms.Forms method) get_current_groups() (in module tool_shed.util.admin_util) get_current_history_from_session() (in module galaxy.webapps.galaxy.api) get_current_item() (galaxy.web.legacy_framework.grids.Grid method) (tool_shed.grids.admin_grids.UserGrid method) get_current_repositories() (in module tool_shed.metadata.repository_metadata_manager) (in module tool_shed.webapp.controllers.repository) get_current_repository_metadata_for_changeset_revision() (in module tool_shed.util.metadata_util) get_current_roles() (galaxy.managers.folders.FolderManager method) (galaxy.managers.libraries.LibraryManager method) (in module tool_shed.util.admin_util) get_current_thread_object_dict() (in module galaxy.util.heartbeat) get_current_user_roles() (galaxy.managers.context.ProvidesUserContext method) (galaxy.work.context.WorkRequestContext method) get_current_users() (in module tool_shed.util.admin_util) get_custom_builds() (galaxy.webapps.galaxy.api.users.FastAPIUsers method) (galaxy_test.selenium.test_custom_builds.TestCustomBuilds method) get_custom_builds_metadata() (galaxy.webapps.galaxy.services.histories.HistoriesService method) get_data() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.visualization.data_providers.basic.BaseDataProvider method) (galaxy.visualization.data_providers.basic.ColumnDataProvider method) (galaxy.visualization.data_providers.genome.BBIDataProvider method) (galaxy.visualization.data_providers.genome.FeatureLocationIndexDataProvider method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) (galaxy.visualization.data_providers.phyloviz.PhylovizDataProvider method) get_data_dir() (in module galaxy.util.properties) get_data_inputs() (galaxy.workflow.modules.WorkflowModule method) get_data_outputs() (galaxy.workflow.modules.WorkflowModule method) get_data_provider() (galaxy.visualization.data_providers.registry.DataProviderRegistry method) get_database_engine_options() (in module galaxy.config) (in module galaxy.webapps.reports.config) get_dataset_by_hid() (galaxy.model.History method) get_dataset_collection() (galaxy.managers.collections.DatasetCollectionManager method) get_dataset_collection_instance() (galaxy.managers.collections.DatasetCollectionManager method) get_dataset_finish_context() (galaxy.jobs.TaskWrapper method) get_dataset_hash() (in module galaxy.managers.datasets) get_dataset_info() (galaxy.datatypes.molecules.AtomicStructFile method) get_dataset_matcher_factory() (in module galaxy.tools.parameters.dataset_matcher) get_dataset_meta() (galaxy.tool_util.provided_metadata.BaseToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.LegacyToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.ToolProvidedMetadata method) get_datasets_for_group() (galaxy.tools.wrappers.DatasetCollectionWrapper method) (galaxy.tools.wrappers.DatasetListWrapper method) get_datasources() (galaxy.model.DatasetInstance method) get_datatype() (galaxy.tools.parameters.grouping.UploadDataset method) get_datatype_by_extension() (galaxy.datatypes.registry.Registry method) get_datatype_class_by_name() (galaxy.datatypes.registry.Registry method) get_datatype_ext() (galaxy.tools.parameters.grouping.UploadDataset method) get_datatype_from_filename() (galaxy.datatypes.registry.Registry method) get_dbkey() (galaxy.model.DatasetInstance method) (galaxy.tools.parameters.grouping.UploadDataset method) get_dbkeys() (galaxy.managers.genomes.GenomesManager method) (galaxy.visualization.genomes.Genomes method) get_default_history_by_trans() (galaxy.tools.DataManagerTool method) (galaxy.tools.Tool method) get_default_max_vals() (galaxy.visualization.data_providers.genome.ChromatinInteractionsDataProvider method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) get_default_parsers() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) get_definitions() (galaxy.tool_util.toolbox.views.sources.StaticToolBoxViewSources method) get_dependencies() (galaxy.model.Job method) (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.SelectTagParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.DataToolParameter method) (galaxy.tools.parameters.SelectToolParameter method) get_dependencies_for_metadata_revision() (in module tool_shed.util.metadata_util) get_dependencies_for_repository() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_dependency_name() (galaxy.tools.parameters.dynamic_options.DataMetaFilter method) (galaxy.tools.parameters.dynamic_options.Filter method) (galaxy.tools.parameters.dynamic_options.ParamValueFilter method) (galaxy.tools.parameters.dynamic_options.UniqueValueFilter method) get_dependency_names() (galaxy.tools.parameters.dynamic_options.DynamicOptions method) get_destination() (galaxy.jobs.JobConfiguration method) get_destination_configuration() (galaxy.model.Job method) get_destination_info_for_container_type() (galaxy.tool_util.deps.DependencyManager method) get_destination_list_from_job_config() (in module galaxy.jobs.dynamic_tool_destination) get_destinations() (galaxy.jobs.JobConfiguration method) get_device_id() (galaxy.objectstore.DeviceSourceMap method) get_device_source_map() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ConcreteObjectStore method) (galaxy.objectstore.DistributedObjectStore method) (galaxy.objectstore.ObjectStore method) get_directory() (galaxy.tool_util.verify.test_data.TestDataResolver method) get_discarded() (galaxy.managers.base.StorageCleanerManager method) (galaxy.managers.hdas.HDAStorageCleanerManager method) (galaxy.managers.histories.HistoryStorageCleanerManager method) get_discarded_summary() (galaxy.managers.base.StorageCleanerManager method) (galaxy.managers.hdas.HDAStorageCleanerManager method) (galaxy.managers.histories.HistoryStorageCleanerManager method) get_disk_usage() (galaxy.model.GalaxySession method) (galaxy.model.User method) (galaxy.webapps.reports.controllers.system.System method) (tool_shed.webapp.model.User method) get_display_application() (galaxy.datatypes.data.Data method) get_display_applications() (galaxy.model.DatasetInstance method) get_display_applications_by_dataset() (galaxy.datatypes.data.Data method) get_display_label() (galaxy.datatypes.data.Data method) get_display_links() (galaxy.datatypes.data.Data method) get_display_name() (galaxy.model.HasName method) get_display_sites() (galaxy.datatypes.registry.Registry method) get_display_text() (galaxy.tools.wrappers.ToolParameterValueWrapper method) get_display_types() (galaxy.datatypes.data.Data method) get_display_url() (galaxy.datatypes.display_applications.application.DisplayApplicationLink method) get_edit_distance() (in module galaxy.jobs.dynamic_tool_destination) get_element_position() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) get_element_size() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) get_elements() (galaxy.util.topsort.CycleError method) get_empty_field_by_name() (galaxy.tools.data.ToolDataTable method) get_entries() (galaxy.tools.data.TabularToolDataTable method) get_entry() (galaxy.tools.data.TabularToolDataTable method) (tool_shed.util.hgweb_config.HgWebConfigManager method) get_entry_point_path() (galaxy.managers.interactivetool.InteractiveToolManager method) get_entry_point_subdomain() (galaxy.managers.interactivetool.InteractiveToolManager method) get_envs() (galaxy.jobs.JobConfiguration static method) get_error_response_for_request() (in module galaxy.webapps.base.api) get_errors() (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_estimated_display_viewport() (galaxy.datatypes.interval.BedGraph method) (galaxy.datatypes.interval.CustomTrack method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.Wiggle method) get_exit_code() (galaxy.jobs.TaskWrapper method) get_expanded_tool_source() (galaxy.tools.ToolBox method) get_export_dataset_extra_files_dir_name() (in module galaxy.model.store) get_export_dataset_filename() (in module galaxy.model.store) get_export_state() (galaxy.workflow.modules.InputModule method) (galaxy.workflow.modules.InputParameterModule method) (galaxy.workflow.modules.WorkflowModule method) get_export_store_factory() (in module galaxy.model.store) get_export_url() (galaxy_test.base.populators.BaseDatasetPopulator method) get_exports() (galaxy.managers.histories.HistoryExportManager method) get_ext() (in module galaxy.util.path) get_ext_or_implicit_ext() (in module galaxy.tools.actions) get_extension() (galaxy.datatypes.registry.Registry method) get_external_output_metadata() (galaxy.model.Job method) (galaxy.model.Task method) get_externally_referenced_paths() (galaxy.tools.Tool class method) get_extra_files_path() (galaxy.model.Dataset method) get_facts() (in module galaxy.util.facts) get_failure_reason() (galaxy.jobs.runners.util.cli.job.BaseJobExec method) (galaxy.jobs.runners.util.cli.job.lsf.LSF method) get_fasta_hdas_by_history() (in module galaxy.webapps.galaxy.services.histories) get_fasta_header() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_field() (galaxy.datatypes.metadata.ColumnParameter method) (galaxy.datatypes.metadata.DBKeyParameter method) (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.datatypes.metadata.PythonObjectParameter method) (galaxy.datatypes.metadata.RangeParameter method) (galaxy.datatypes.metadata.SelectParameter method) (galaxy.model.metadata.ColumnParameter method) (galaxy.model.metadata.DBKeyParameter method) (galaxy.model.metadata.FileParameter method) (galaxy.model.metadata.MetadataParameter method) (galaxy.model.metadata.PythonObjectParameter method) (galaxy.model.metadata.RangeParameter method) (galaxy.model.metadata.SelectParameter method) (galaxy.tools.data.TabularToolDataTable method) get_field_by_name_for_value() (galaxy.tools.parameters.dynamic_options.DynamicOptions method) get_field_file_path() (galaxy.managers.tool_data.ToolDataManager method) get_fields() (galaxy.tools.data.TabularToolDataTable method) (galaxy.tools.parameters.dynamic_options.DynamicOptions method) get_fields_by_value() (galaxy.tools.parameters.dynamic_options.DynamicOptions method) get_file_base_name() (galaxy.tools.parameters.grouping.UploadDataset method) get_file_contents() (tool_shed.webapp.controllers.repository.RepositoryController method) get_file_context_from_ctx() (in module galaxy.tool_shed.util.hg_util) (in module tool_shed.util.hg_util) get_file_count() (galaxy.tools.parameters.grouping.UploadDataset method) get_file_name (galaxy.datatypes.display_applications.parameters.DatasetLikeObject attribute) get_file_name() (galaxy.datatypes.metadata.MetadataTempFile method) (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) (galaxy.model.FakeDatasetAssociation method) (galaxy.model.metadata.MetadataTempFile method) (galaxy.model.MetadataFile method) (galaxy.model.none_like.NoneDataset method) get_file_peek() (galaxy.datatypes.genetics.RexpBase method) (in module galaxy.datatypes.data) get_file_size() (in module galaxy.util) get_file_source_path() (galaxy.files.ConfiguredFileSources method) get_file_sources() (in module galaxy.tools.data_fetch) (in module galaxy.tools.imp_exp.export_history) (in module galaxy.tools.imp_exp.unpack_tar_gz_archive) get_file_sources_dict() (galaxy.job_execution.compute_environment.ComputeEnvironment method) (galaxy.job_execution.compute_environment.SharedComputeEnvironment method) get_file_type() (galaxy.tools.parameters.grouping.UploadDataset method) get_file_type_str() (in module galaxy.tool_shed.util.basic_util) (in module tool_shed.util.basic_util) get_filecontent() (galaxy.tool_util.verify.test_data.TestDataResolver method) get_filename() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.tool_util.verify.test_data.TestDataResolver method) (galaxy_test.base.testcase.FunctionalTestCase method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_filename_for_source() (galaxy.tools.data.TabularToolDataTable method) get_fileobj() (in module galaxy.util.compression_utils) get_fileobj_raw() (in module galaxy.util.compression_utils) get_files() (galaxy.tools.data.TabularToolDataField method) get_files_from_conda_package() (in module galaxy.tool_util.deps.mulled.util) get_files_source_plugins() (galaxy.managers.remote_files.RemoteFilesManager method) get_filesize_map() (galaxy.tools.data.TabularToolDataField method) get_filter() (galaxy.web.legacy_framework.grids.CommunityTagsColumn method) (galaxy.web.legacy_framework.grids.IndividualTagsColumn method) (galaxy.web.legacy_framework.grids.TextColumn method) (tool_shed.grids.repository_grid_filter_manager.RepositoryGridFilterManager method) get_filter_query_params() (in module galaxy.webapps.galaxy.api.common) get_filter_set() (galaxy.workflow.modules.InputDataModule method) get_filtered_repositories() (in module tool_shed.metadata.repository_metadata_manager) get_filters() (galaxy.visualization.data_providers.genome.BamDataProvider method) (galaxy.visualization.data_providers.genome.ENCODEPeakTabixDataProvider method) (galaxy.visualization.data_providers.genome.FilterableMixin method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) get_fingerprint() (galaxy.tools.data.TabularToolDataField method) get_first_line() (in module galaxy.tool_util.verify.asserts.tabular) get_first_repository_metadata() (in module tool_shed.webapp.controllers.repository) get_folder() (in module galaxy.managers.folders) get_folder_dict() (galaxy.managers.folders.FolderManager method) get_foreign_key() (in module galaxy.model.item_attrs) get_form_values() (galaxy.webapps.base.controller.UsesFormDefinitionsMixin method) get_func_list() (in module galaxy.web.framework.middleware.profile) get_galaxy_app() (in module galaxy.celery) get_galaxy_biotools_metadata_source() (in module galaxy.tools.biotools) get_galaxy_session() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) (galaxy.webapps.base.webapp.GalaxyWebTransaction method) (galaxy.work.context.SessionRequestContext method) get_genome() (galaxy.managers.genomes.GenomesManager method) get_genome_data() (galaxy.visualization.data_providers.genome.GenomeDataProvider method) get_genomic_region_indeces() (galaxy.datatypes.dataproviders.dataset.DatasetDataProvider method) get_grabbable_handler_assignment_method() (galaxy.jobs.handler.ItemGrabber static method) get_grid_entry_names() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) get_grid_title() (tool_shed.grids.repository_grid_filter_manager.RepositoryGridFilterManager method) get_group() (in module galaxy.webapps.galaxy.controllers.admin) (in module tool_shed.util.admin_util) get_group_by_name() (in module galaxy.managers.groups) (in module tool_shed.managers.groups) get_group_id() (in module tool_shed.util.admin_util) get_group_role() (in module galaxy.managers.group_roles) get_group_user() (in module galaxy.managers.group_users) get_gxy_db_version() (galaxy.model.migrations.scripts.LegacyManageDb method) get_gxy_metadata() (in module galaxy.model.migrations) get_gxy_version() (galaxy.model.migrations.scripts.LegacyManageDb method) get_handler() (galaxy.model.Job method) get_hashed_dependencies_path() (galaxy.tool_util.deps.CachedDependencyManager method) get_hdas() (in module galaxy.managers.context) get_hdca() (galaxy.job_execution.output_collect.JobContext method) (galaxy.job_execution.output_collect.SessionlessJobContext method) (galaxy.model.store.discover.SessionlessModelPersistenceContext method) get_headers() (galaxy.util.zipstream.ZipstreamWrapper method) (in module galaxy.datatypes.sniff) get_hg_repo() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_histories() (galaxy_test.base.populators.BaseDatasetPopulator method) (galaxy_test.selenium.test_histories_list.TestSavedHistories method) get_history() (galaxy.app_unittest_utils.galaxy_mock.MockTrans method) (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) (galaxy.webapps.base.webapp.GalaxyWebTransaction method) (galaxy.work.context.WorkRequestContext method) get_history_collection_details() (galaxy_test.base.populators.BaseDatasetPopulator method) get_history_contents() (galaxy_test.base.populators.BaseDatasetPopulator method) get_history_dataset_content() (galaxy_test.base.populators.BaseDatasetPopulator method) get_history_dataset_details() (galaxy_test.base.populators.BaseDatasetPopulator method) get_history_dataset_details_raw() (galaxy_test.base.populators.BaseDatasetPopulator method) get_history_dataset_extra_files() (galaxy_test.base.populators.BaseDatasetPopulator method) get_history_dataset_source_transform_actions() (galaxy_test.base.populators.BaseDatasetPopulator method) get_history_export_tasks() (galaxy_test.base.populators.BaseDatasetPopulator method) get_hook() (galaxy.tools.Tool method) get_html_repr() (galaxy.datatypes.binary.H5MLM method) get_id() (galaxy.tool_util.cwl.runnable.CwlWorkflowOutput method) (galaxy.tool_util.cwl.runnable.ToolOutput method) (in module galaxy.webapps.galaxy.api.genomes) get_id_col_in_item_tag_assoc_table() (galaxy.model.tags.TagHandler method) get_id_tag() (galaxy.jobs.TaskWrapper method) (galaxy.model.Job method) (galaxy.model.Task method) get_id_to_source_pairs() (galaxy.objectstore.QuotaSourceMap method) get_id_token() (galaxy.model.UserAuthnzToken method) get_identifier() (galaxy.model.SerializationOptions method) get_identifier_for_id() (galaxy.model.SerializationOptions method) get_ids() (galaxy.web.legacy_framework.grids.Grid method) get_ids_of_tool_shed_repositories_being_installed() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_image_metric() (in module galaxy.tool_util.verify) get_implicit_collection_jobs_association_id() (galaxy.job_execution.output_collect.JobContext method) (galaxy.job_execution.output_collect.SessionlessJobContext method) (galaxy.model.store.discover.ModelPersistenceContext method) (galaxy.model.store.discover.SessionlessModelPersistenceContext method) get_import_model_store_for_dict() (in module galaxy.model.store) get_import_model_store_for_directory() (in module galaxy.model.store) get_imported() (galaxy.model.Job method) get_indeces_by_column_names() (galaxy.datatypes.dataproviders.dataset.DatasetDataProvider method) get_index() (galaxy.tools.test.RootParamContext method) (galaxy.webapps.galaxy.services.users.UsersService method) get_index_flag() (galaxy.datatypes.binary.Bam method) get_indexes() (galaxy.managers.genomes.GenomesManager method) get_info() (galaxy.model.Job method) (galaxy.model.LibraryDataset method) (galaxy.model.Task method) get_informal_replacement_parameters() (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_information() (galaxy.webapps.galaxy.api.users.UserAPIController method) get_inital_values() (galaxy.datatypes.display_applications.application.DisplayApplicationLink method) get_initial_value() (galaxy.tools.parameters.basic.BaseDataToolParameter method) (galaxy.tools.parameters.basic.BaseURLToolParameter method) (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.ColorToolParameter method) (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.FloatToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.HiddenToolParameter method) (galaxy.tools.parameters.basic.IntegerToolParameter method) (galaxy.tools.parameters.basic.SelectTagParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.SimpleTextToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.grouping.Conditional method) (galaxy.tools.parameters.grouping.Group method) (galaxy.tools.parameters.grouping.Repeat method) (galaxy.tools.parameters.grouping.Section method) (galaxy.tools.parameters.grouping.UploadDataset method) (galaxy.tools.parameters.SelectToolParameter method) get_input() (galaxy.model.WorkflowStep method) get_input_dataset_fnames() (galaxy.job_execution.setup.JobIO method) get_input_datasets() (galaxy.job_execution.setup.JobIO method) (galaxy.model.Job method) get_input_default_value() (galaxy.model.WorkflowStep method) get_input_fnames() (galaxy.job_execution.setup.JobIO method) get_input_library_datasets() (galaxy.model.Job method) get_input_object() (galaxy.model.WorkflowInvocation method) get_input_path() (galaxy.job_execution.setup.JobIO method) get_input_paths() (galaxy.job_execution.setup.JobIO method) get_input_source() (in module galaxy.tool_util.parser) (in module galaxy.tool_util.parser.factory) get_inputs() (galaxy.workflow.modules.InputDataCollectionModule method) (galaxy.workflow.modules.InputDataModule method) (galaxy.workflow.modules.InputParameterModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_install_info() (in module tool_shed.managers.repositories) get_install_info_from_tool_shed() (in module galaxy.tool_shed.galaxy_install.install_manager) get_installable_revisions() (tool_shed.webapp.api.repositories.RepositoriesController method) get_installed_and_missing_repository_dependencies() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_installed_and_missing_repository_dependencies_for_new_or_updated_install() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_installed_and_missing_tool_dependencies_for_repository() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_installed_repositories_by_name_owner() (tool_shed.test.base.twilltestcase.GalaxyInteractorToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.StandaloneToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ToolShedInstallationClient method) get_installed_repository() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.test.base.twilltestcase) (in module tool_shed.util.repository_util) get_installed_repository_by_id() (in module tool_shed.test.base.test_db_util) get_installed_repository_by_name_owner() (in module tool_shed.test.base.test_db_util) (tool_shed.test.base.twilltestcase.GalaxyInteractorToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.StandaloneToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ToolShedInstallationClient method) get_installed_repository_for() (tool_shed.test.base.twilltestcase.GalaxyInteractorToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.StandaloneToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ToolShedInstallationClient method) get_installed_tool_shed_repository() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_interesting_stack_frame() (galaxy.util.heartbeat.Heartbeat method) get_internal_version() (galaxy.model.StoredWorkflow method) get_invalid_file_tups() (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator method) get_invocation() (galaxy.managers.workflows.WorkflowsManager method) (galaxy_test.base.populators.BaseWorkflowPopulator method) get_invocation_jobs() (galaxy_test.base.populators.BaseWorkflowPopulator method) get_invocation_report() (galaxy.managers.workflows.WorkflowsManager method) get_invocation_step() (galaxy.managers.workflows.WorkflowsManager method) get_ip() (in module galaxy.util.sockets) get_ip_address() (in module galaxy_test.base.env) get_item() (galaxy.webapps.base.controller.SharableMixin method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) get_item_actions() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) (tool_shed.webapp.security.RBACAgent method) get_item_annotation_obj() (galaxy.model.item_attrs.UsesAnnotations method) get_item_annotation_str() (galaxy.model.item_attrs.UsesAnnotations method) get_item_extended_metadata_obj() (galaxy.webapps.base.controller.UsesExtendedMetadataMixin method) get_iterator() (galaxy.visualization.data_providers.basic.BaseDataProvider method) (galaxy.visualization.data_providers.genome.BamDataProvider method) (galaxy.visualization.data_providers.genome.BedDataProvider method) (galaxy.visualization.data_providers.genome.ChromatinInteractionsTabixDataProvider method) (galaxy.visualization.data_providers.genome.ENCODEPeakDataProvider method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) (galaxy.visualization.data_providers.genome.IntervalDataProvider method) (galaxy.visualization.data_providers.genome.IntervalIndexDataProvider method) (galaxy.visualization.data_providers.genome.RawBedDataProvider method) (galaxy.visualization.data_providers.genome.RawGFFDataProvider method) (galaxy.visualization.data_providers.genome.RawVcfDataProvider method) (galaxy.visualization.data_providers.genome.TabixDataProvider method) get_iuc_group() (in module tool_shed.webapp.security) get_job() (galaxy.jobs.TaskWrapper method) (galaxy.model.Job method) (galaxy.model.store.discover.ModelPersistenceContext method) (galaxy.model.Task method) (in module galaxy.managers.jobs) (in module galaxy.webapps.reports.controllers.jobs) get_job_destination() (galaxy.jobs.mapper.JobRunnerMapper method) (galaxy.tools.Tool method) get_job_details() (galaxy_test.base.populators.BaseDatasetPopulator method) get_job_file() (galaxy.jobs.runners.BaseJobRunner method) get_job_id() (galaxy.job_execution.output_collect.BaseJobContext method) (galaxy.job_execution.output_collect.JobContext method) (galaxy.job_execution.output_collect.SessionlessJobContext method) get_job_interface() (galaxy.jobs.runners.util.cli.CliInterface method) get_job_runner() (galaxy.jobs.handler.DefaultJobDispatcher method) get_job_runner_external_id() (galaxy.model.Job method) (galaxy.model.Task method) get_job_runner_name() (galaxy.model.Job method) (galaxy.model.Task method) get_job_runner_plugins() (galaxy.jobs.JobConfiguration method) get_job_stdio() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) get_job_tool_configurations() (galaxy.jobs.JobConfiguration method) get_jobs_to_check_at_startup() (in module galaxy.managers.jobs) get_key_for_repository_changeset_revision() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) get_keys_from_dict() (in module galaxy.jobs.dynamic_tool_destination) get_label() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) (galaxy.tools.error_reports.plugins.github.GithubPlugin method) (galaxy.tools.parameters.basic.HiddenToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) get_last_sqlalchemymigrate_version() (in module galaxy.model.migrations) get_latest_changeset_revision() (in module tool_shed.util.metadata_util) get_latest_downloadable_changeset_revision() (in module tool_shed.util.metadata_util) (tool_shed.webapp.controllers.repository.RepositoryController method) get_latest_downloadable_repository_metadata() (in module tool_shed.grids.util) get_latest_downloadable_repository_metadata_if_it_includes_tools() (in module tool_shed.grids.util) get_latest_repository_metadata() (in module tool_shed.grids.util) (in module tool_shed.util.metadata_util) get_latest_repository_metadata_if_it_includes_invalid_tools() (in module tool_shed.grids.util) get_latest_tool_config_revision_from_repository_manifest() (tool_shed.tools.tool_validator.ToolValidator method) get_ldda_by_dataset() (in module tool_shed.util.admin_util) get_legacy_sites_by_build() (galaxy.datatypes.registry.Registry method) get_legal_names() (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.SelectToolParameter method) get_legal_values() (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.GenomeBuildParameter method) (galaxy.tools.parameters.basic.SelectTagParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.SelectToolParameter method) get_legitimate_roles() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) get_level() (galaxy.model.dataset_collections.builder.CollectionBuilder method) get_libraries() (galaxy_test.base.populators.LibraryPopulator method) get_libraries_for_admins() (in module galaxy.managers.libraries) get_libraries_for_nonadmins() (in module galaxy.managers.libraries) get_library() (in module galaxy.managers.libraries) get_library_by_folder() (in module tool_shed.util.admin_util) get_library_contents() (galaxy_test.base.populators.LibraryPopulator method) get_library_contents_with_path() (galaxy_test.base.populators.LibraryPopulator method) get_library_dataset() (in module galaxy.managers.library_datasets) get_library_dict() (galaxy.managers.libraries.LibraryManager method) get_library_folder() (galaxy.job_execution.output_collect.JobContext method) (galaxy.model.store.discover.SessionlessModelPersistenceContext method) get_library_ids() (in module galaxy.managers.libraries) get_library_permissions_by_role() (in module galaxy.managers.libraries) get_license_by_id() (galaxy.managers.licenses.LicensesManager method) get_licenses() (galaxy.managers.licenses.LicensesManager method) get_link() (galaxy.datatypes.display_applications.application.DisplayApplication method) (galaxy.web.legacy_framework.grids.GridColumn method) (galaxy.web.legacy_framework.grids.PublicURLColumn method) (galaxy.web.legacy_framework.grids.SharingStatusColumn method) get_lint_context_for_tool_source() (in module galaxy.tool_util.lint) get_list_from_file() (in module galaxy.tool_util.deps.mulled.mulled_update_singularity_containers) get_list_of_copied_sample_files() (tool_shed.tools.tool_validator.ToolValidator method) get_loaded_tools_by_lineage() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) get_local_driver() (in module galaxy.selenium.driver_factory) get_logged_in_user() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) get_logger() (in module galaxy.util.custom_logging) get_logout_url() (galaxy.webapps.galaxy.controllers.authnz.OIDC method) get_manage_permissions_roles() (galaxy.model.Dataset method) (galaxy.model.LibraryDatasetDatasetAssociation method) get_manage_roles() (galaxy.managers.libraries.LibraryManager method) get_manager() (galaxy.tools.data_manager.manager.DataManagers method) get_mapping_by_name() (galaxy.tools.parameters.sanitize.ToolParameterSanitizer class method) get_matcher() (galaxy.datatypes.molecules.PQR method) get_max_optional_metadata_filesize() (galaxy.datatypes.data.Data method) get_mercurial_default_options_dict() (in module tool_shed.webapp.controllers.repository) get_message() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) get_message_for_no_shed_tool_config() (in module galaxy.webapps.galaxy.api.tool_shed_repositories) get_metadata() (galaxy.model.DatasetInstance method) (in module galaxy.model.migrations) (in module tool_shed.util.search_util) get_metadata_by_changeset() (in module tool_shed.util.metadata_util) get_metadata_column_index_by_name() (galaxy.datatypes.dataproviders.dataset.DatasetDataProvider method) get_metadata_column_names() (galaxy.datatypes.dataproviders.dataset.DatasetDataProvider method) get_metadata_column_types() (galaxy.datatypes.dataproviders.dataset.DatasetDataProvider method) get_metadata_compute_strategy() (in module galaxy.metadata) get_metadata_dataset() (galaxy.model.DatasetInstance method) get_metadata_dict() (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator method) get_metadata_file_paths_and_extensions() (galaxy.model.DatasetInstance method) get_metadata_parameter() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataCollection method) get_metadata_params() (in module galaxy.metadata.set_metadata) get_metadata_revisions() (in module tool_shed.util.metadata_util) get_metadata_source() (galaxy.job_execution.output_collect.MetadataSourceProvider method) (galaxy.model.store.discover.MetadataSourceProvider method) (galaxy.model.store.discover.UnusedMetadataSourceProvider method) get_mime() (galaxy.datatypes.anvio.AnvioComposite method) (galaxy.datatypes.binary.Binary method) (galaxy.datatypes.binary.ExcelXls method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.data.Text method) (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.genetics.Rgenetics method) (galaxy.datatypes.genetics.rgTabList method) (galaxy.datatypes.hdf5.HDF5SummarizedExperiment method) (galaxy.datatypes.images.Gmaj method) (galaxy.datatypes.media.Wav method) (galaxy.datatypes.microarrays.GenericMicroarrayFile method) (galaxy.datatypes.molecules.GenericMolFile method) (galaxy.datatypes.molecules.OBFS method) (galaxy.datatypes.neo4j.Neo4j method) (galaxy.datatypes.text.Html method) (galaxy.datatypes.text.Json method) (galaxy.datatypes.text.Yaml method) (galaxy.model.DatasetInstance method) get_mimetype_by_extension() (galaxy.datatypes.registry.Registry method) get_missing_containers() (in module galaxy.tool_util.deps.mulled.mulled_list) get_missing_envs() (in module galaxy.tool_util.deps.mulled.mulled_list) get_model_db_head() (galaxy.model.migrations.AlembicManager method) get_model_script_head() (galaxy.model.migrations.AlembicManager method) get_modify_roles() (galaxy.managers.libraries.LibraryManager method) get_modules() (galaxy.workflow.modules.SubWorkflowModule method) get_monitor_id() (in module galaxy.webapps.reports.controllers.jobs) get_most_recent_history() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) get_mutable() (galaxy.managers.secured.OwnableManagerMixin method) get_mutable_output_fnames() (galaxy.job_execution.setup.JobIO method) get_name() (galaxy.model.LibraryDataset method) (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_named_fields_list() (galaxy.tools.data.TabularToolDataTable method) get_named_tmpfile_from_ctx() (in module tool_shed.util.hg_util) get_native_spec() (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) get_new_dataset_meta_by_basename() (galaxy.tool_util.provided_metadata.BaseToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.LegacyToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.ToolProvidedMetadata method) get_new_datasets() (galaxy.tool_util.provided_metadata.BaseToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.LegacyToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.ToolProvidedMetadata method) get_new_datasets_for_metadata_collection() (galaxy.tool_util.provided_metadata.BaseToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.LegacyToolProvidedMetadata method) get_new_guid() (galaxy.security.idencoding.IdEncodingHelper method) get_next_downloadable_changeset_revision() (in module tool_shed.util.metadata_util) get_next_line() (in module galaxy.datatypes.constructive_solid_geometry) get_next_prior_import_or_install_required_dict_entry() (in module galaxy.tool_shed.util.shed_util_common) get_node_position() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) get_non_anonymous_user_full() (galaxy.webapps.galaxy.services.users.UsersService method) get_nonterminal_for_user_by_trans() (galaxy.managers.interactivetool.InteractiveToolManager method) get_not_deleted_groups() (in module galaxy.managers.groups) get_object() (galaxy.webapps.galaxy.services.base.ServiceBase method) (galaxy.webapps.galaxy.services.library_folder_contents.LibraryFolderContentsService method) (in module galaxy.managers.base) get_object_session() (in module galaxy.model.orm.util) get_object_store() (in module galaxy.metadata.set_metadata) get_object_store_id() (galaxy.model.DatasetInstance method) get_object_url() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) get_observer_class() (in module galaxy.util.watcher) get_oidc_token() (galaxy.tools.evaluation.ToolEvaluator method) get_oidc_tokens() (galaxy.model.User method) get_open_tempfile() (galaxy.datatypes.util.maf_utilities.TempFileHandler method) (galaxy.tools.util.maf_utilities.TempFileHandler method) get_openapi() (in module galaxy.webapps.openapi.utils) get_openapi_schema() (in module tool_shed.webapp.fast_app) get_option() (galaxy.tools.data_fetch.UploadConfig method) get_option_from_dataset() (galaxy.tools.parameters.dynamic_options.DynamicOptions method) get_options() (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.GenomeBuildParameter method) (galaxy.tools.parameters.basic.SelectTagParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.dynamic_options.DynamicOptions method) (galaxy.tools.parameters.SelectToolParameter method) get_options_filter_attribute() (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.DataToolParameter method) get_or_add_input() (galaxy.model.WorkflowStep method) get_or_create_api_key() (galaxy.managers.api_keys.ApiKeyManager method) (galaxy.webapps.galaxy.api.users.FastAPIUsers method) (galaxy.webapps.galaxy.services.users.UsersService method) get_or_create_default_history() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) (tool_shed.webapp.buildapp.ToolShedGalaxyWebTransaction method) get_or_create_index() (in module galaxy.tools.search) get_or_create_remote_user() (galaxy.managers.users.UserManager method) get_or_create_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_or_create_section() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) get_or_create_tool_section() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) get_or_create_tool_shed_repository() (galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) get_ordered_installable_revisions() (in module tool_shed.managers.repositories) (tool_shed.webapp.api.repositories.RepositoriesController method) get_oriented_chopped_blocks_for_region() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_oriented_chopped_blocks_with_index_offset_for_region() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_outdir() (galaxy.tool_util.cwl.cwltool_deps.RuntimeContext method) get_output_as_object() (galaxy_test.base.populators.CwlRun method) get_output_basenames() (galaxy.job_execution.setup.JobIO method) get_output_datasets() (galaxy.model.Job method) get_output_destination() (galaxy.jobs.TaskWrapper method) get_output_file_id() (galaxy.job_execution.setup.JobIO method) (galaxy.jobs.TaskWrapper method) get_output_fnames() (galaxy.job_execution.setup.JobIO method) get_output_hdas_and_fnames() (galaxy.job_execution.setup.JobIO method) get_output_library_datasets() (galaxy.model.Job method) get_output_name() (galaxy.tools.actions.DefaultToolAction method) (in module galaxy.managers.jobs) get_output_object() (galaxy.model.WorkflowInvocation method) get_output_path() (galaxy.job_execution.setup.JobIO method) get_outputs() (in module galaxy.tool_util.cwl.runnable) get_owned() (galaxy.managers.secured.OwnableManagerMixin method) get_owned_ids() (galaxy.managers.hdas.HDAManager method) get_owned_workflow() (galaxy.managers.workflows.WorkflowsManager method) get_page() (galaxy.webapps.galaxy.controllers.page.PageController method) (in module galaxy.managers.pages) get_page_identifiers() (in module galaxy.managers.pages) get_page_revision() (in module galaxy.managers.pages) get_pairlist() (galaxy.util.topsort.CycleError method) get_panel_section() (galaxy.tools.Tool method) get_param() (galaxy.tools.Tool method) get_param_filename() (galaxy.model.Job method) get_param_name_by_url() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) get_param_value() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) get_param_values() (galaxy.model.Job method) (galaxy.model.Task method) get_parameters() (galaxy.model.Job method) (galaxy.model.Task method) get_params() (galaxy.jobs.JobConfiguration static method) (galaxy.model.Job method) get_params_and_input_name() (in module galaxy.datatypes.data) get_parent() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataCollection method) get_partial() (galaxy.util.topsort.CycleError method) get_password() (galaxy.webapps.galaxy.api.users.UserAPIController method) get_path_key() (in module galaxy.managers.jobs) get_path_rewriter() (in module galaxy.job_execution.datasets) get_peek() (galaxy.datatypes.genetics.RexpBase method) get_percent() (galaxy.quota.NoQuotaAgent method) get_permissions() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) (galaxy.webapps.galaxy.api.folders.FastAPILibraryFolders method) (galaxy.webapps.galaxy.api.libraries.FastAPILibraries method) (galaxy.webapps.galaxy.api.users.UserAPIController method) (galaxy.webapps.galaxy.services.libraries.LibrariesService method) (galaxy.webapps.galaxy.services.library_folders.LibraryFoldersService method) (galaxy_test.base.populators.LibraryPopulator method) get_permitted_actions() (in module galaxy.security) (in module tool_shed.webapp.security) get_permitted_libraries() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) get_phecols() (galaxy.datatypes.genetics.RexpBase method) get_pheno() (galaxy.datatypes.genetics.RexpBase method) get_plugin() (galaxy.visualization.plugins.registry.VisualizationsRegistry method) get_plugins() (galaxy.jobs.runners.util.cli.CliInterface method) (galaxy.visualization.plugins.registry.VisualizationsRegistry method) get_posix_file_source_config() (in module galaxy_test.driver.integration_setup) get_post_job_actions() (galaxy.model.Job method) (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_pred_counts() (galaxy.util.topsort.CycleError method) get_predictions() (galaxy.tools.recommendations.ToolRecommendations method) get_preds() (galaxy.util.topsort.CycleError method) get_preferred_handler_assignment_method() (galaxy.web_stack.ApplicationStack method) get_prefix() (galaxy.files.sources.BaseFilesSource method) (galaxy.files.sources.galaxy.LibraryImportFilesSource method) (galaxy.files.sources.galaxy.UserFtpFilesSource method) (galaxy.files.sources.galaxy.UserLibraryImportFilesSource method) get_prepare_input_files_cmd() (galaxy.model.Task method) get_prepare_steps() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) get_present_histories() (galaxy_test.selenium.test_histories_list.TestSavedHistories method) get_previous_metadata_changeset_revision() (in module tool_shed.util.metadata_util) get_prior_import_or_install_required_dict() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_prior_installation_required_and_only_if_compiling_contained_td() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) get_private_user_role() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) (tool_shed.webapp.security.RBACAgent method) get_protocol_from_tool_shed_url() (in module galaxy.util.tool_shed.common_util) (in module tool_shed.util.common_util) get_quay_containers() (in module galaxy.tool_util.deps.mulled.mulled_list) get_query_filters_with_relations() (galaxy.managers.history_contents.HistoryContentsFilters method) get_query_for_setting_metadata_on_repositories() (galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) get_query_parameters_from_request_excluding() (in module galaxy.webapps.galaxy.api.common) get_quota() (galaxy.managers.quotas.QuotaManager method) (galaxy.quota.NoQuotaAgent method) (in module galaxy.webapps.galaxy.controllers.admin) get_quota_agent() (in module galaxy.quota) get_quota_source_info() (galaxy.objectstore.QuotaSourceMap method) get_quota_source_label() (galaxy.model.DatasetInstance method) (galaxy.objectstore.QuotaSourceMap method) get_quota_source_labels() (galaxy.objectstore.QuotaSourceMap method) get_quota_source_map() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ConcreteObjectStore method) (galaxy.objectstore.DistributedObjectStore method) (galaxy.objectstore.HierarchicalObjectStore method) (galaxy.objectstore.ObjectStore method) get_quotas() (galaxy_test.base.populators.BaseDatasetPopulator method) (in module galaxy.webapps.galaxy.services.quotas) get_random_name() (galaxy_test.base.populators.BaseDatasetPopulator method) get_readable_ctx_date() (in module tool_shed.util.hg_util) get_readme_files() (tool_shed.webapp.controllers.repository.RepositoryController method) get_readme_files_dict_for_display() (in module tool_shed.util.readme_util) get_ready_history_export() (galaxy.webapps.galaxy.services.histories.HistoriesService method) get_ready_history_export_file_path() (galaxy.managers.histories.HistoryManager method) get_ready_jeha() (galaxy.managers.histories.HistoryExportManager method) get_record_metadata() (galaxy.managers.histories.HistoryExportManager method) get_ref() (galaxy.tool_util.parser.output_actions.ToolOutputActionConditionalWhen method) get_ref_based_read_seq_and_cigar() (in module galaxy.visualization.data_providers.cigar) get_region_alignment() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_relative_path_to_repository_file() (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator method) get_remote_driver() (in module galaxy.selenium.driver_factory) get_remote_files() (galaxy_test.base.populators.BaseDatasetPopulator method) get_removed_tool() (galaxy.tools.cache.ToolCache method) get_repo_cat_associations() (in module tool_shed.util.shed_index) get_repo_info_dict() (in module tool_shed.util.repository_util) get_repo_info_tuple_contents() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repo_path() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_repos() (in module tool_shed.util.shed_index) get_repositories() (in module tool_shed.repository_registry) (tool_shed.webapp.api.categories.CategoriesController method) get_repositories_by_category() (in module tool_shed.util.repository_util) get_repositories_category_api() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_repositories_for_indexing() (in module tool_shed.util.shed_index) get_repositories_for_setting_metadata() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) get_repositories_with_alerts() (in module tool_shed.util.commit_util) get_repositories_with_user() (in module tool_shed.repository_registry) get_repository() (in module tool_shed.metadata.repository_metadata_manager) get_repository_admin_role_name() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repository_and_repository_dependencies_from_repo_info_dict() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repository_by_id() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.test.base.test_db_util) (in module tool_shed.util.repository_util) get_repository_by_name() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repository_by_name_and_owner() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.test.base.test_db_util) (in module tool_shed.util.repository_util) get_repository_changelog_tuples() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_repository_dependencies() (in module galaxy.util.tool_shed.common_util) (in module tool_shed.util.common_util) (tool_shed.webapp.controllers.repository.RepositoryController method) (tool_shed.webapp.model.Repository method) get_repository_dependencies_for_changeset_revision() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) get_repository_dependencies_for_installed_tool_shed_repository() (galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) get_repository_dependency_as_key() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) get_repository_dependency_by_repository_id() (galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) get_repository_dependency_tups_for_installed_repository() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_repository_dependency_tups_from_repository_metadata() (in module tool_shed.util.metadata_util) get_repository_dependency_types() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repository_file_contents() (in module tool_shed.util.shed_util_common) get_repository_file_list() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_repository_first_revision() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_repository_for_dependency_relationship() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repository_heads() (in module tool_shed.util.hg_util) get_repository_id() (tool_shed.webapp.controllers.repository.RepositoryController method) get_repository_ids_requiring_prior_import_or_install() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repository_in_tool_shed() (in module tool_shed.util.repository_util) get_repository_information() (tool_shed.webapp.controllers.repository.RepositoryController method) get_repository_install_dir() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_repository_metadata() (in module tool_shed.metadata.repository_metadata_manager) (in module tool_shed.webapp.api.repository_revisions) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_repository_metadata_by_changeset_revision() (in module tool_shed.util.metadata_util) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_repository_metadata_by_id() (in module tool_shed.util.metadata_util) get_repository_metadata_by_repository_id_changeset_revision() (in module tool_shed.test.base.test_db_util) (in module tool_shed.util.metadata_util) get_repository_metadata_dict() (in module tool_shed.managers.repositories) get_repository_metadata_for_db_object() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_repository_metadata_for_management() (in module tool_shed.managers.repositories) get_repository_metadata_revisions() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_repository_owner() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repository_owner_from_clone_url() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repository_query() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repository_revision_install_info() (tool_shed.webapp.api.repositories.RepositoriesController method) get_repository_role_association() (in module tool_shed.test.base.test_db_util) get_repository_tip() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_repository_tools_tups() (galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) get_repository_tuple_for_installed_repository_manager() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_repository_type() (tool_shed.webapp.controllers.repository.RepositoryController method) get_repr() (galaxy.datatypes.binary.H5MLM method) get_required_enctype() (galaxy.tools.parameters.basic.FileToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) get_required_item() (in module galaxy.model.store.discover) get_required_repo_info_dict() (tool_shed.webapp.controllers.repository.RepositoryController method) get_required_repo_info_dicts() (galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) get_requirements_status() (galaxy.tool_util.deps.views.DependencyResolversView method) get_reset_token() (galaxy.managers.users.UserManager method) get_resolution_cache() (galaxy.tool_util.deps.containers.ContainerRegistry method) get_resolver_option() (galaxy.tool_util.deps.DependencyManager method) get_resource_group() (galaxy.jobs.JobToolConfiguration method) get_resource_mapper_function() (in module galaxy.workflow.resources) get_resubmits() (galaxy.jobs.JobConfiguration static method) get_rev_label_changeset_revision_from_repository_metadata() (in module tool_shed.util.hg_util) get_rev_label_from_changeset_revision() (in module tool_shed.util.hg_util) get_reversed_changelog_changesets() (in module tool_shed.util.hg_util) get_revision_label() (in module tool_shed.util.hg_util) get_revision_label_from_ctx() (in module tool_shed.util.hg_util) get_ro_crate() (galaxy_test.base.populators.BaseWorkflowPopulator method) get_role() (galaxy.model.security.GalaxyRBACAgent method) (in module galaxy.webapps.galaxy.controllers.admin) (in module tool_shed.test.base.test_db_util) (in module tool_shed.util.admin_util) get_role_by_id() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_role_id() (in module tool_shed.util.admin_util) get_roles() (galaxy_test.base.populators.BaseDatasetPopulator method) get_roles_by_ids() (in module galaxy.managers.roles) get_roles_for_action() (galaxy.model.security.GalaxyRBACAgent method) get_rules_specification() (in module galaxy.util.rules_dsl) get_run_test() (in module galaxy.tool_util.deps.mulled.get_tests) get_runtime_inputs() (galaxy.workflow.modules.InputDataCollectionModule method) (galaxy.workflow.modules.InputDataModule method) (galaxy.workflow.modules.InputParameterModule method) (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_runtime_state() (galaxy.workflow.modules.InputModule method) (galaxy.workflow.modules.InputParameterModule method) (galaxy.workflow.modules.PauseModule method) (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_safe_version() (in module galaxy.tools) get_sample_files_from_disk() (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator method) get_scheme() (galaxy.files.sources.BaseFilesSource method) (galaxy.files.sources.galaxy.LibraryImportFilesSource method) (galaxy.files.sources.galaxy.UserFtpFilesSource method) (galaxy.files.sources.galaxy.UserLibraryImportFilesSource method) get_section() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) get_section_for_tool() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) get_section_for_tool_id() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) get_sections() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) get_sequence() (galaxy.datatypes.util.maf_utilities.RegionAlignment method) (galaxy.datatypes.util.maf_utilities.SplicedAlignment method) (galaxy.managers.genomes.GenomesManager method) (galaxy.tools.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.SplicedAlignment method) get_sequence_reverse_complement() (galaxy.datatypes.util.maf_utilities.RegionAlignment method) (galaxy.datatypes.util.maf_utilities.SplicedAlignment method) (galaxy.tools.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.SplicedAlignment method) get_sequences_per_file() (galaxy.datatypes.sequence.Sequence static method) get_server() (galaxy.auth.providers.ldap_ad.LDAP3 method) (galaxy.workflow.trs_proxy.TrsProxy method) get_servers() (galaxy.webapps.galaxy.api.trs_consumer.TrsConsumeAPIController method) (galaxy.workflow.trs_proxy.TrsProxy method) get_session() (in module galaxy.webapps.galaxy.api) get_session_from_session_key() (galaxy.managers.session.GalaxySessionManager method) get_session_id() (galaxy.jobs.TaskWrapper method) (galaxy.model.Job method) (galaxy.model.Task method) get_session_manager() (in module galaxy.webapps.galaxy.api) get_setting() (galaxy.authnz.psa_authnz.Strategy method) get_sharable_url() (galaxy.model.tool_shed_install.ToolShedRepository method) get_share_assocs() (galaxy.managers.sharable.SharableModelManager method) get_shared_pages() (in module galaxy.managers.pages) get_sharing_extra_information() (galaxy.managers.histories.HistoryManager method) (galaxy.managers.sharable.SharableModelManager method) get_sharing_roles() (galaxy.model.security.GalaxyRBACAgent method) get_shed_config_dict() (galaxy.model.tool_shed_install.ToolShedRepository method) get_shed_config_dict_by_filename() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) get_shed_tool_conf_dict() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) get_shell() (in module galaxy.jobs.runners.util.cli.factory) get_shell_plugin() (galaxy.jobs.runners.util.cli.CliInterface method) get_short_str() (galaxy.job_execution.actions.post.ActionBox class method) (galaxy.job_execution.actions.post.ChangeDatatypeAction class method) (galaxy.job_execution.actions.post.ColumnSetAction class method) (galaxy.job_execution.actions.post.DefaultJobAction class method) (galaxy.job_execution.actions.post.DeleteDatasetAction class method) (galaxy.job_execution.actions.post.DeleteIntermediatesAction class method) (galaxy.job_execution.actions.post.EmailAction class method) (galaxy.job_execution.actions.post.HideDatasetAction class method) (galaxy.job_execution.actions.post.RenameDatasetAction class method) (galaxy.job_execution.actions.post.TagDatasetAction class method) (galaxy.job_execution.actions.post.ValidateOutputsAction class method) get_showable_folders() (galaxy.model.security.GalaxyRBACAgent method) get_signature_file() (galaxy.datatypes.binary.BafTar method) (galaxy.datatypes.binary.MassHunterTar method) (galaxy.datatypes.binary.MassLynxTar method) (galaxy.datatypes.binary.TdfTar method) (galaxy.datatypes.binary.YepTar method) get_single_filter() (galaxy.web.legacy_framework.grids.BooleanColumn method) (galaxy.web.legacy_framework.grids.IntegerColumn method) (galaxy.web.legacy_framework.grids.OwnerAnnotationColumn method) (galaxy.web.legacy_framework.grids.TextColumn method) get_single_status() (galaxy.jobs.runners.util.cli.job.BaseJobExec method) (galaxy.jobs.runners.util.cli.job.lsf.LSF method) (galaxy.jobs.runners.util.cli.job.pbs.OpenPBS method) (galaxy.jobs.runners.util.cli.job.slurm.Slurm method) (galaxy.jobs.runners.util.cli.job.torque.Torque method) get_singularity_containers() (in module galaxy.tool_util.deps.mulled.mulled_list) get_singularity_target_kwds() (galaxy.tool_util.deps.container_classes.SingularityContainer method) get_size() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) get_social_auth() (galaxy.model.UserAuthnzToken class method) get_social_auth_for_user() (galaxy.model.UserAuthnzToken class method) get_spark_time() (in module galaxy.webapps.reports.controllers.jobs) get_species_in_block() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_species_in_maf() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_species_names() (galaxy.datatypes.util.maf_utilities.RegionAlignment method) (galaxy.datatypes.util.maf_utilities.SplicedAlignment method) (galaxy.tools.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.SplicedAlignment method) get_spliced_region_alignment() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_split_commands_sequential() (galaxy.datatypes.sequence.Sequence static method) get_split_commands_with_toc() (galaxy.datatypes.sequence.Sequence static method) get_stage_in_out() (galaxy.jobs.runners.pbs.PBSJobRunner method) get_stagedir() (galaxy.tool_util.cwl.cwltool_deps.RuntimeContext method) get_staging_path() (galaxy.tools.wrappers.DatasetFilenameWrapper method) get_starts_ends_fields_from_gene_bed() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_state() (galaxy.jobs.TaskWrapper method) (galaxy.model.Job method) (galaxy.model.Task method) (galaxy.workflow.modules.WorkflowModule method) get_static_param_values() (galaxy.tools.Tool method) get_status() (galaxy.jobs.runners.util.cli.job.BaseJobExec method) (galaxy.jobs.runners.util.cli.job.lsf.LSF method) (galaxy.jobs.runners.util.cli.job.pbs.OpenPBS method) (galaxy.jobs.runners.util.cli.job.slurm.Slurm method) (galaxy.jobs.runners.util.cli.job.slurm_torque.SlurmTorque method) (galaxy.jobs.runners.util.cli.job.torque.Torque method) get_step_map_over() (galaxy.managers.workflows.WorkflowContentsManager static method) get_store_by() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) get_store_usage_percent() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) get_stored_accessible_workflow() (galaxy.managers.workflows.WorkflowsManager method) get_stored_workflow() (galaxy.managers.workflows.WorkflowsManager method) get_structure() (in module galaxy.model.dataset_collections.structure) get_structured_content() (galaxy.datatypes.binary.Binary method) (galaxy.datatypes.binary.H5 method) get_subworkflow_invocation_association_for_step() (galaxy.model.WorkflowInvocation method) get_subworkflow_invocation_for_step() (galaxy.model.WorkflowInvocation method) get_succs() (galaxy.util.topsort.CycleError method) get_tag_assoc_class() (galaxy.model.tags.TagHandler method) get_tag_by_id() (galaxy.model.tags.TagHandler method) get_tag_by_name() (galaxy.model.tags.GalaxySessionlessTagHandler method) (galaxy.model.tags.TagHandler method) get_tag_list() (galaxy.tools.parameters.basic.SelectTagParameter method) get_tags_list() (galaxy.model.tags.TagHandler method) get_tags_str() (galaxy.model.tags.TagHandler method) get_target_install_dir() (galaxy.tool_shed.tools.data_table_manager.ShedToolDataTableManager method) (tool_shed.tools.data_table_manager.ShedToolDataTableManager method) get_task() (galaxy.jobs.runners.godocker.GodockerJobRunner method) (galaxy.jobs.TaskWrapper method) get_task_export_by_id() (galaxy.managers.histories.HistoryExportManager method) get_task_exports() (galaxy.managers.histories.HistoryExportManager method) get_task_runner_external_id() (galaxy.model.Task method) get_task_runner_name() (galaxy.model.Task method) get_task_status() (galaxy.jobs.runners.godocker.GodockerJobRunner method) get_tasks() (galaxy.model.Job method) get_test_config() (galaxy.tool_util.verify.interactor.DictClientTestConfig method) (galaxy.tool_util.verify.interactor.NullClientTestConfig method) (galaxy.tool_util.verify.interactor.TestConfig method) get_test_fname() (in module galaxy.datatypes.data) (in module galaxy.datatypes.sniff) get_test_from_anaconda() (in module galaxy.tool_util.deps.mulled.get_tests) get_tests_summary() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) get_timer() (galaxy.app.ExecutionTimerFactory method) get_timestamp_drop_sql() (in module galaxy.model.triggers.history_update_time_field) get_timestamp_install_sql() (in module galaxy.model.triggers.history_update_time_field) get_timings() (in module galaxy_test.conftest) get_tmpdir() (galaxy.tool_util.cwl.cwltool_deps.RuntimeContext method) get_tool() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) (galaxy.tool_util.toolbox.base.ToolBoxRegistryImpl method) (galaxy.tool_util.toolbox.views.interface.ToolBoxRegistry method) (galaxy.tools.cache.ToolCache method) (galaxy.webapps.galaxy.api.trs_consumer.TrsConsumeAPIController method) (galaxy.workflow.trs_proxy.TrsServer method) get_tool_by_id() (galaxy.managers.tools.DynamicToolManager method) (galaxy.tools.cache.ToolCache method) get_tool_by_tool_id() (galaxy.managers.tools.DynamicToolManager method) get_tool_by_uuid() (galaxy.managers.tools.DynamicToolManager method) get_tool_components() (galaxy.tools.ToolBox method) get_tool_conf_watcher() (in module galaxy.tool_util.toolbox.watcher) get_tool_dependencies() (tool_shed.webapp.controllers.repository.RepositoryController method) (tool_shed.webapp.model.Repository method) get_tool_dependencies_config_contents() (tool_shed.webapp.controllers.repository.RepositoryController method) get_tool_dependency() (in module galaxy.tool_shed.util.tool_dependency_util) get_tool_dependency_by_name_type_repository() (in module galaxy.tool_shed.util.tool_dependency_util) get_tool_dependency_by_name_version_type() (in module galaxy.tool_shed.util.tool_dependency_util) get_tool_dependency_by_name_version_type_repository() (in module galaxy.tool_shed.util.tool_dependency_util) get_tool_dependency_definition_metadata() (tool_shed.webapp.controllers.repository.RepositoryController method) get_tool_dependency_ids() (in module galaxy.tool_shed.util.tool_dependency_util) get_tool_id() (galaxy.model.Job method) get_tool_index_sample_files() (galaxy.tool_shed.tools.data_table_manager.ShedToolDataTableManager method) (tool_shed.tools.data_table_manager.ShedToolDataTableManager method) get_tool_names() (tool_shed.test.base.twilltestcase.GalaxyInteractorToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.StandaloneToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ToolShedInstallationClient method) get_tool_panel_config_tool_path_install_dir() (in module galaxy.tool_shed.util.shed_util_common) get_tool_provided_job_metadata() (galaxy.jobs.TaskWrapper method) get_tool_relative_path() (galaxy.model.tool_shed_install.ToolShedRepository method) (galaxy.tool_util.toolbox.base.ToolConfRepository method) get_tool_repository_from_xml_item() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) get_tool_resource_xml() (galaxy.jobs.JobConfiguration method) get_tool_shed_api_key() (tool_shed.webapp.api.authenticate.ToolShedAuthenticationController method) get_tool_shed_from_clone_url() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_tool_shed_repository_by_id() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_tool_shed_repository_ids() (in module galaxy.util.tool_shed.common_util) (in module tool_shed.util.common_util) get_tool_shed_repository_info_dict() (galaxy.tools.data_manager.manager.DataManager method) get_tool_shed_repository_url() (in module galaxy.util.tool_shed.common_util) (in module tool_shed.util.common_util) get_tool_shed_status_for_installed_repository() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_tool_shed_url_from_tool_shed_registry() (in module galaxy.util.tool_shed.common_util) (in module tool_shed.util.common_util) get_tool_source() (in module galaxy.tool_util.parser) (in module galaxy.tool_util.parser.factory) get_tool_source_from_representation() (in module galaxy.tool_util.parser) get_tool_source_path() (galaxy.tool_util.locations.dockstore.DockStoreResolver method) (galaxy.tool_util.locations.file.HttpToolResolver method) (galaxy.tool_util.locations.http.HttpToolResolver method) (galaxy.tool_util.locations.ToolLocationResolver method) get_tool_state() (galaxy.workflow.modules.WorkflowModule method) get_tool_tags() (galaxy.model.tags.TagHandler method) get_tool_tests() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) get_tool_to_dict() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) get_tool_version() (galaxy.model.Job method) get_tool_versions() (tool_shed.webapp.controllers.repository.RepositoryController method) get_tool_watcher() (in module galaxy.tool_util.toolbox.watcher) get_tool_with_id() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) get_toolbox() (galaxy.managers.context.ProvidesAppContext method) get_toolbox_filters() (galaxy.webapps.galaxy.api.users.UserAPIController method) get_toolbox_parser() (in module galaxy.tool_util.toolbox.parser) get_tools() (galaxy.workflow.trs_proxy.TrsServer method) get_tools_from_repository_metadata() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_tooltip() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_tooltip_text() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) get_total_job_count_per_destination() (galaxy.jobs.handler.JobHandlerQueue method) get_total_size() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) get_tours() (galaxy.tours.ToursRegistry method) get_trans() (in module galaxy.webapps.galaxy.api) get_trigger_name() (in module galaxy.model.triggers.history_update_time_field) (in module galaxy.model.triggers.update_audit_table) get_tsi_metadata() (in module galaxy.model.migrations) get_type() (galaxy.datatypes.binary.BafTar method) (galaxy.datatypes.binary.MassHunterTar method) (galaxy.datatypes.binary.MassLynxTar method) (galaxy.datatypes.binary.TdfTar method) (galaxy.datatypes.binary.Wiff2Tar method) (galaxy.datatypes.binary.WiffTar method) (galaxy.datatypes.binary.YepTar method) (galaxy.workflow.modules.WorkflowModule method) get_type_class() (tool_shed.webapp.model.Repository method) get_typo_correction() (in module galaxy.jobs.dynamic_tool_destination) get_unique_slug() (galaxy.managers.sharable.SharableModelManager method) get_unnamed_outputs() (galaxy.tool_util.provided_metadata.BaseToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.LegacyToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.ToolProvidedMetadata method) get_update_permission_payload() (in module galaxy.webapps.galaxy.api.common) get_update_to_changeset_revision_and_ctx_rev() (galaxy.tool_shed.galaxy_install.update_repository_manager.UpdateRepositoryManager method) get_updated_changeset_revisions() (in module tool_shed.util.metadata_util) get_updated_changeset_revisions_for_repository_dependencies() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) get_updated_changeset_revisions_from_tool_shed() (in module galaxy.tool_shed.util.metadata_util) get_updated_repository_information() (tool_shed.webapp.controllers.repository.RepositoryController method) get_upload_metadata_params() (galaxy.datatypes.registry.Registry method) get_uploaded_datasets() (galaxy.tools.parameters.grouping.UploadDataset method) (in module galaxy.tools.actions.upload_common) get_uri_root() (galaxy.files.sources.BaseFilesSource method) (galaxy.files.sources.SupportsBrowsing method) get_url_args() (galaxy.web.legacy_framework.grids.DisplayByUsernameAndSlugGridOperation method) (galaxy.web.legacy_framework.grids.GridColumnFilter method) (galaxy.web.legacy_framework.grids.GridOperation method) get_usage() (galaxy_test.base.populators.BaseDatasetPopulator method) get_usage_for() (galaxy_test.base.populators.BaseDatasetPopulator method) get_user() (galaxy.app_unittest_utils.galaxy_mock.MockTrans method) (galaxy.managers.context.ProvidesUserContext method) (galaxy.managers.model_stores.ModelStoreUserContext method) (galaxy.model.Job method) (galaxy.model.UserAuthnzToken class method) (galaxy.webapps.base.webapp.GalaxyWebTransaction method) (galaxy.webapps.galaxy.services.users.UsersService method) (galaxy.work.context.WorkRequestContext method) (in module galaxy.tool_shed.util.shed_util_common) (in module galaxy.webapps.galaxy.api) (in module galaxy.webapps.galaxy.controllers.admin) (in module tool_shed.test.base.test_db_util) (in module tool_shed.util.admin_util) (in module tool_shed.util.shed_util_common) get_user_api_key() (in module galaxy_test.base.api_util) get_user_by_email() (in module galaxy.managers.users) get_user_by_identity() (galaxy.managers.users.UserManager method) get_user_by_username() (in module galaxy.managers.users) (in module tool_shed.metadata.repository_metadata_manager) get_user_data_tables() (galaxy.model.User method) get_user_email() (galaxy.model.Job method) (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) get_user_emails_by_prefix() (in module tool_shed.util.admin_util) get_user_full() (galaxy.webapps.galaxy.services.users.UsersService method) get_user_id() (galaxy.model.Job method) (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) get_user_item_rating() (galaxy.model.item_attrs.UsesItemRatings method) get_user_job_count() (galaxy.jobs.handler.JobHandlerQueue method) get_user_job_count_per_destination() (galaxy.jobs.handler.JobHandlerQueue method) get_user_options() (galaxy.tools.parameters.dynamic_options.DynamicOptions method) get_user_repositories() (in module tool_shed.webapp.api.groups) get_user_tags_used() (galaxy.webapps.base.controller.UsesTagsMixin method) get_username() (galaxy.model.UserAuthnzToken class method) get_users_by_email() (galaxy.model.UserAuthnzToken class method) get_users_by_ids() (in module galaxy.managers.users) get_uuid() (in module galaxy.model) get_valid_by_name() (galaxy.tools.parameters.sanitize.ToolParameterSanitizer class method) get_valid_roles() (galaxy.model.security.GalaxyRBACAgent method) get_value() (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationTemplateParameter method) (galaxy.tool_util.deps.requirements.ResourceRequirement method) (galaxy.tool_util.parser.output_actions.FromDataTableOutputActionOption method) (galaxy.tool_util.parser.output_actions.FromFileToolOutputActionOption method) (galaxy.tool_util.parser.output_actions.FromParamToolOutputActionOption method) (galaxy.tool_util.parser.output_actions.NullToolOutputActionOption method) (galaxy.tool_util.parser.output_actions.ToolOutputActionOption method) (galaxy.web.framework.helpers.grids.GridColumn method) (galaxy.web.legacy_framework.grids.CommunityRatingColumn method) (galaxy.web.legacy_framework.grids.CommunityTagsColumn method) (galaxy.web.legacy_framework.grids.GridColumn method) (galaxy.web.legacy_framework.grids.IndividualTagsColumn method) (galaxy.web.legacy_framework.grids.OwnerAnnotationColumn method) (galaxy.web.legacy_framework.grids.OwnerColumn method) (galaxy.web.legacy_framework.grids.SharingStatusColumn method) (galaxy.web.legacy_framework.grids.StateColumn method) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid.RolesColumn method) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid.UsersColumn method) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.AmountColumn method) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.DefaultTypeColumn method) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.GroupsColumn method) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.UsersColumn method) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid.GroupsColumn method) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid.UsersColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.DiskUsageColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.GroupsColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.LastLoginColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.RolesColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.StatusColumn method) (galaxy.webapps.galaxy.controllers.forms.FormsGrid.DescriptionColumn method) (galaxy.webapps.galaxy.controllers.forms.FormsGrid.NameColumn method) (galaxy.webapps.galaxy.controllers.forms.FormsGrid.TypeColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.CreateTimeColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.JobIdColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.StateColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.ToolColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.UserColumn method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.CreateTimeColumn method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.UserColumn method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.WorkflowNameColumn method) (tool_shed.grids.admin_grids.AdminRepositoryGrid.DeletedColumn method) (tool_shed.grids.admin_grids.GroupGrid.NameColumn method) (tool_shed.grids.admin_grids.GroupGrid.RolesColumn method) (tool_shed.grids.admin_grids.GroupGrid.StatusColumn method) (tool_shed.grids.admin_grids.GroupGrid.UsersColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.DatatypesColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.DeletedColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.DeprecatedColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.IdColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.MaliciousColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.NameColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.OwnerColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.RevisionColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.ToolsColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.WorkflowsColumn method) (tool_shed.grids.admin_grids.RoleGrid.DescriptionColumn method) (tool_shed.grids.admin_grids.RoleGrid.GroupsColumn method) (tool_shed.grids.admin_grids.RoleGrid.NameColumn method) (tool_shed.grids.admin_grids.RoleGrid.RepositoriesColumn method) (tool_shed.grids.admin_grids.RoleGrid.StatusColumn method) (tool_shed.grids.admin_grids.RoleGrid.TypeColumn method) (tool_shed.grids.admin_grids.RoleGrid.UsersColumn method) (tool_shed.grids.admin_grids.UserGrid.ExternalColumn method) (tool_shed.grids.admin_grids.UserGrid.GroupsColumn method) (tool_shed.grids.admin_grids.UserGrid.LastLoginColumn method) (tool_shed.grids.admin_grids.UserGrid.RolesColumn method) (tool_shed.grids.admin_grids.UserGrid.StatusColumn method) (tool_shed.grids.admin_grids.UserGrid.UserLoginColumn method) (tool_shed.grids.admin_grids.UserGrid.UserNameColumn method) (tool_shed.grids.repository_grids.CategoryGrid.DescriptionColumn method) (tool_shed.grids.repository_grids.CategoryGrid.NameColumn method) (tool_shed.grids.repository_grids.CategoryGrid.RepositoriesColumn method) (tool_shed.grids.repository_grids.DatatypesGrid.DatatypesColumn method) (tool_shed.grids.repository_grids.MatchedRepositoryGrid.DescriptionColumn method) (tool_shed.grids.repository_grids.MatchedRepositoryGrid.NameColumn method) (tool_shed.grids.repository_grids.MatchedRepositoryGrid.RevisionColumn method) (tool_shed.grids.repository_grids.MatchedRepositoryGrid.UserColumn method) (tool_shed.grids.repository_grids.RepositoriesWithInvalidToolsGrid.InvalidToolConfigColumn method) (tool_shed.grids.repository_grids.RepositoryDependenciesGrid.RequiredRepositoryColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.CategoryColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.DeprecatedColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.DescriptionColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.EmailAlertsColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.HeadsColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.LatestInstallableRevisionColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.MetadataRevisionColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.NameColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.TipRevisionColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.TypeColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.UserColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.ChangesetRevisionColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.DownloadableColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.HasRepositoryDependenciesColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.IncludesDatatypesColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.IncludesToolDependenciesColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.IncludesToolsColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.IncludesWorkflowsColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.MaliciousColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.RepositoryNameColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.RepositoryOwnerColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.RepositoryTypeColumn method) (tool_shed.grids.repository_grids.ToolDependenciesGrid.ToolDependencyColumn method) (tool_shed.grids.repository_grids.ToolsGrid.ToolsColumn method) (tool_shed.grids.repository_grids.ValidCategoryGrid.RepositoriesColumn method) (tool_shed.grids.repository_grids.ValidRepositoryGrid.CategoryColumn method) (tool_shed.grids.repository_grids.ValidRepositoryGrid.InstallableRevisionColumn method) get_value_filter_query_params() (in module galaxy.webapps.galaxy.api.common) get_value_mapper() (in module tool_shed.managers.repositories) get_version() (galaxy.webapps.galaxy.api.trs_consumer.TrsConsumeAPIController method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) (galaxy.workflow.trs_proxy.TrsServer method) get_version_descriptor() (galaxy.workflow.trs_proxy.TrsServer method) get_version_fields() (galaxy.tools.data.TabularToolDataTable method) get_version_ids() (galaxy.tool_util.toolbox.lineages.interface.ToolLineage method) (galaxy.tool_util.toolbox.lineages.ToolLineage method) get_version_lineage_for_tool() (tool_shed.tools.tool_version_manager.ToolVersionManager method) get_versions() (galaxy.tool_util.toolbox.lineages.interface.ToolLineage method) (galaxy.tool_util.toolbox.lineages.ToolLineage method) (galaxy.webapps.galaxy.api.trs_consumer.TrsConsumeAPIController method) (galaxy.workflow.trs_proxy.TrsServer method) get_visualization() (galaxy.visualization.plugins.registry.VisualizationsRegistry method) get_visualizations() (galaxy.app_unittest_utils.galaxy_mock.MockVisualizationsRegistry method) (galaxy.visualization.plugins.registry.VisualizationsRegistry method) get_volume_mounts_for_job() (in module galaxy.jobs.runners.util.pykube_util) get_watcher() (in module galaxy.util.watcher) get_webapp_global_conf() (in module galaxy_test.driver.driver_util) get_work_dir_outputs() (galaxy.jobs.runners.BaseJobRunner method) get_workflow() (galaxy.tool_util.toolbox.base.ToolBoxRegistryImpl method) (galaxy.tool_util.toolbox.views.interface.ToolBoxRegistry method) (in module galaxy.webapps.reports.controllers.workflows) get_workflow_parameter_list() (in module galaxy.workflow.resources) get_workflow_svg() (galaxy.managers.workflows.WorkflowsManager method) get_workflow_svg_from_id() (galaxy.managers.workflows.WorkflowsManager method) get_working_directory() (galaxy.model.Task method) get_writable() (galaxy.files.sources.BaseFilesSource method) (galaxy.files.sources.SingleFileSource method) get_writable_files_for_dataset() (galaxy.datatypes.data.Data method) get_xml_default() (galaxy.web_stack.handlers.ConfiguresHandlers static method) GetCustosBasedAuthProvider() (galaxy.authnz.custos_authnz.CustosAuthFactory static method) getdefault() (in module galaxy.tool_util.cwl.cwltool_deps) getmember() (galaxy.util.compression_utils.CompressedFile method) getmembers() (galaxy.util.compression_utils.CompressedFile method) getmembers_tar() (galaxy.util.compression_utils.CompressedFile method) getmembers_zip() (galaxy.util.compression_utils.CompressedFile method) getMissval() (in module galaxy.datatypes.converters.lped_to_pbed_converter) getModuleCode() (galaxy.util.template.FixedModuleCodeCompiler method) getname() (galaxy.util.compression_utils.CompressedFile method) getname_tar() (galaxy.util.compression_utils.CompressedFile method) getname_zip() (galaxy.util.compression_utils.CompressedFile method) getroot() (galaxy.util.ElementTree method) getSnpeffVersionFromFile() (galaxy.datatypes.text.SnpEffDb method) Gfa1 (class in galaxy.datatypes.text) Gfa2 (class in galaxy.datatypes.text) Gff (class in galaxy.datatypes.interval) Gff3 (class in galaxy.datatypes.interval) gff_attributes_to_str() (in module galaxy.datatypes.util.gff_util) GFFFeature (class in galaxy.datatypes.util.gff_util) GFFInterval (class in galaxy.datatypes.util.gff_util) GFFIntervalToBEDReaderWrapper (class in galaxy.datatypes.util.gff_util) GFFReaderWrapper (class in galaxy.datatypes.util.gff_util) GffTabix (class in galaxy.datatypes.interval) GiDatasetCollectionPopulator (class in galaxy_test.base.populators) GiDatasetPopulator (class in galaxy_test.base.populators) GIE_SPAWN (galaxy.selenium.navigates_galaxy.WAIT_TYPES attribute) Gif (class in galaxy.datatypes.images) Gifti (class in galaxy.datatypes.images) GiHttpMixin (class in galaxy_test.base.populators) git_default_repo_name (galaxy.tools.error_reports.plugins.base_git.BaseGitPlugin attribute) git_default_repo_only (galaxy.tools.error_reports.plugins.base_git.BaseGitPlugin attribute) git_default_repo_owner (galaxy.tools.error_reports.plugins.base_git.BaseGitPlugin attribute) git_execute() (in module galaxy.tool_util.deps.brew_exts) git_project_cache (galaxy.tools.error_reports.plugins.base_git.BaseGitPlugin attribute) git_username_id_cache (galaxy.tools.error_reports.plugins.base_git.BaseGitPlugin attribute) GitContentBiotoolsMetadataSource (class in galaxy.tool_util.biotools.source) GitDataResolver (class in galaxy.tool_util.verify.test_data) GithubPlugin (class in galaxy.tools.error_reports.plugins.github) gitlab_connect() (galaxy.tools.error_reports.plugins.gitlab.GitLabPlugin method) GitLabPlugin (class in galaxy.tools.error_reports.plugins.gitlab) givenName (galaxy.schema.schema.Person attribute) GiWorkflowPopulator (class in galaxy_test.base.populators) glob() (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method) global_actions (galaxy.web.legacy_framework.grids.Grid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.ManageCategoryGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.EmailAlertsRepositoryGrid attribute) global_conf (galaxy.main_config.WebappConfig attribute) global_conf() (galaxy.main.GalaxyConfigBuilder method) global_tool_logs() (in module galaxy.tools.evaluation) GlobusSecureShell (class in galaxy.jobs.runners.util.cli.shell.rsh) Gmaj (class in galaxy.datatypes.images) GmshGeo (class in galaxy.datatypes.constructive_solid_geometry) GmshMsh (class in galaxy.datatypes.constructive_solid_geometry) GmxBinary (class in galaxy.datatypes.binary) go_to_history_sharing() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) go_to_trs_by_id() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) go_to_trs_search() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) go_to_workflow_export() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) go_to_workflow_sharing() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) GodockerJobRunner (class in galaxy.jobs.runners.godocker) GolangProxyLauncher (class in galaxy.web.proxy) GoldenPath (class in galaxy.datatypes.goldenpath) GoogleCloudStorageFilesSource (class in galaxy.files.sources.googlecloudstorage) GoogleDriveFilesSource (class in galaxy.files.sources.googledrive) Gpr (class in galaxy.datatypes.microarrays) grab_model (galaxy.jobs.handler.InvocationGrabber attribute) (galaxy.jobs.handler.ItemGrabber attribute) (galaxy.jobs.handler.JobGrabber attribute) grab_unhandled_items() (galaxy.jobs.handler.ItemGrabber method) grant() (galaxy.managers.rbac_secured.AccessDatasetRBACPermission method) (galaxy.managers.rbac_secured.ManageDatasetRBACPermission method) (galaxy.managers.rbac_secured.RBACPermission method) grant_role_to_user() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) grant_write_access() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) grd (class in galaxy.datatypes.molecules) grdtgz (class in galaxy.datatypes.molecules) Grib (class in galaxy.datatypes.binary) Grid (class in galaxy.web.legacy_framework.grids) grid_fields() (galaxy.model.FormDefinition method) GridAction (class in galaxy.web.legacy_framework.grids) GridColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.web.legacy_framework.grids) GridColumnFilter (class in galaxy.web.legacy_framework.grids) GridData (class in galaxy.web.framework.helpers.grids) GridOperation (class in galaxy.web.legacy_framework.grids) GRO (class in galaxy.datatypes.molecules) groom_dataset_content() (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.data.Data method) Group (class in galaxy.datatypes.mothur) (class in galaxy.model) (class in galaxy.tools.parameters.grouping) (class in tool_shed.webapp.controllers.groups) (class in tool_shed.webapp.model) group (galaxy.model.GroupQuotaAssociation attribute) (galaxy.model.GroupRoleAssociation attribute) (galaxy.model.UserGroupAssociation attribute) (tool_shed.webapp.model.GroupRoleAssociation attribute) (tool_shed.webapp.model.UserGroupAssociation attribute) group_assoc (galaxy.managers.roles.RoleManager attribute) group_by_day() (galaxy.webapps.reports.controllers.query.ReportQueryBuilder method) group_by_month() (galaxy.webapps.reports.controllers.query.ReportQueryBuilder method) group_id (galaxy.model.GroupQuotaAssociation attribute) (galaxy.model.GroupRoleAssociation attribute) (galaxy.model.UserGroupAssociation attribute) (tool_shed.webapp.model.GroupRoleAssociation attribute) (tool_shed.webapp.model.UserGroupAssociation attribute) group_ids (galaxy.schema.schema.RoleDefinitionModel attribute) group_list_grid (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) (tool_shed.util.admin_util.Admin attribute) (tool_shed.webapp.controllers.admin.AdminController attribute) group_names (galaxy.files.DictFileSourcesUserContext property) (galaxy.files.FileSourceDictifiable property) (galaxy.files.ProvidesUserFileSourcesUserContext property) group_role_to_model() (in module galaxy.webapps.galaxy.api.group_roles) group_title() (galaxy.tools.parameters.grouping.UploadDataset method) group_user_to_model() (in module galaxy.webapps.galaxy.api.group_users) GroupAbund (class in galaxy.datatypes.mothur) GroupGrid (class in tool_shed.grids.admin_grids) GroupGrid.NameColumn (class in tool_shed.grids.admin_grids) GroupGrid.RolesColumn (class in tool_shed.grids.admin_grids) GroupGrid.StatusColumn (class in tool_shed.grids.admin_grids) GroupGrid.UsersColumn (class in tool_shed.grids.admin_grids) GroupListGrid (class in galaxy.webapps.galaxy.controllers.admin) GroupListGrid.RolesColumn (class in galaxy.webapps.galaxy.controllers.admin) GroupListGrid.UsersColumn (class in galaxy.webapps.galaxy.controllers.admin) GroupManager (class in tool_shed.managers.groups) GroupModel (class in galaxy.schema.schema) GroupQuotaAssociation (class in galaxy.model) GroupRoleAssociation (class in galaxy.model) (class in tool_shed.webapp.model) GroupRoleListResponse (class in galaxy.schema.schema) GroupRoleResponse (class in galaxy.schema.schema) GroupRolesManager (class in galaxy.managers.group_roles) groups (galaxy.model.Quota attribute) (galaxy.model.Role attribute) (galaxy.model.User attribute) (tool_shed.webapp.model.Role attribute) (tool_shed.webapp.model.User attribute) groups() (tool_shed.util.admin_util.Admin method) groups_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) GroupsController (class in tool_shed.webapp.api.groups) GroupsManager (class in galaxy.managers.groups) GroupUserListResponse (class in galaxy.schema.schema) GroupUserResponse (class in galaxy.schema.schema) GroupUsersManager (class in galaxy.managers.group_users) Gtf (class in galaxy.datatypes.interval) GtfTabixDataProvider (class in galaxy.visualization.data_providers.genome) guess_artifact_type() (in module galaxy.tool_util.cwl.util) guess_derived_permissions() (galaxy.model.security.GalaxyRBACAgent method) guess_derived_permissions_for_datasets() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) guess_ext() (in module galaxy.datatypes.sniff) guess_ext_from_file_name() (in module galaxy.datatypes.sniff) guess_shed_config() (galaxy.model.tool_shed_install.ToolShedRepository method) guess_type() (galaxy.datatypes.tabular.TabularData method) guid_to_repository() (in module tool_shed.managers.repositories) GUID_TYPE (galaxy.tools.data_manager.manager.DataManager attribute) GunicornApplicationStack (class in galaxy.web_stack) GzDynamicCompressedArchive (class in galaxy.datatypes.binary) gzip (galaxy.schema.schema.ExportHistoryArchivePayload attribute) GzipDataProvider (class in galaxy.datatypes.dataproviders.external)

H

H5 (class in galaxy.datatypes.binary) H5MLM (class in galaxy.datatypes.binary) HaltableContainer (class in galaxy.app) haltables (galaxy.app.HaltableContainer attribute) Hamamatsu (class in galaxy.datatypes.images) handle (galaxy.model.PSAAssociation attribute) handle_bz2() (in module tool_shed.util.commit_util) handle_charref() (galaxy.managers.pages.PageContentProcessor method) handle_circular_repository_dependency() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) handle_comment() (galaxy.managers.pages.PageContentProcessor method) handle_complex_dependency_elem() (tool_shed.dependencies.attribute_handlers.RepositoryDependencyAttributeHandler method) handle_composite_file() (in module galaxy.datatypes.sniff) handle_compressed_file() (in module galaxy.datatypes.sniff) handle_controller_exception() (galaxy.web.framework.base.WebApplication method) (galaxy.webapps.base.webapp.WebApplication method) handle_current_repository_dependency() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) handle_data() (galaxy.managers.pages.PageContentProcessor method) (galaxy.webapps.galaxy.controllers.workflow.SingleTagContentsParser method) handle_dataset_as_image() (galaxy.datatypes.data.Data method) (galaxy.datatypes.images.Image method) handle_decl() (galaxy.managers.pages.PageContentProcessor method) handle_directory_changes() (in module tool_shed.util.commit_util) handle_elem() (tool_shed.dependencies.attribute_handlers.RepositoryDependencyAttributeHandler method) handle_email_alerts() (in module tool_shed.util.shed_util_common) handle_endtag() (galaxy.managers.pages.PageContentProcessor method) handle_entityref() (galaxy.managers.pages.PageContentProcessor method) handle_exception() (in module galaxy.web.framework.middleware.error) handle_existing_tool_dependencies_that_changed_in_update() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) handle_found_index_file() (galaxy.tools.data.TabularToolDataTable method) handle_galaxy_config_kwds() (galaxy_test.base.api.UsesCeleryTasks class method) (galaxy_test.driver.integration_setup.PosixFileSourceSetup class method) handle_galaxy_url() (in module galaxy.util.tool_shed.common_util) (in module tool_shed.util.common_util) handle_gzip() (in module tool_shed.util.commit_util) handle_incoming() (galaxy.job_execution.actions.post.ActionBox class method) handle_incoming_errors() (galaxy.tools.Tool method) handle_input() (galaxy.tools.Tool method) handle_key_rd_dicts_for_repository() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) handle_last_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method) handle_library_params() (in module galaxy.tools.actions.upload_common) handle_metadata_externally() (galaxy.jobs.runners.cli.ShellJobRunner method) handle_missing_data_table_entry() (galaxy.tool_shed.tools.data_table_manager.ShedToolDataTableManager method) (tool_shed.tools.data_table_manager.ShedToolDataTableManager method) handle_missing_index_file() (in module galaxy.tool_shed.util.tool_util) handle_next_repository_dependency() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) handle_operation() (galaxy.web.legacy_framework.grids.Grid method) handle_outputs() (in module galaxy.tool_util.cwl) (in module galaxy.tool_util.cwl.runtime_actions) handle_pi() (galaxy.managers.pages.PageContentProcessor method) handle_population_failed() (galaxy.model.DatasetCollection method) handle_repository_elem() (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator method) (galaxy.tool_shed.metadata.metadata_generator.GalaxyMetadataGenerator method) (tool_shed.metadata.repository_metadata_manager.ToolShedMetadataGenerator method) handle_request() (galaxy.web.framework.base.WebApplication method) (tool_shed.webapp.controllers.hg.HgController method) handle_requests() (galaxy.web.proxy.JsonFileProxyIpc method) (galaxy.web.proxy.ProxyIpc method) (galaxy.web.proxy.RestGolangProxyIpc method) (galaxy.web.proxy.SqliteProxyIpc method) handle_role_associations() (in module tool_shed.util.repository_util) handle_sample_files_and_load_tool_from_disk() (tool_shed.tools.tool_validator.ToolValidator method) handle_sample_files_and_load_tool_from_tmp_config() (tool_shed.tools.tool_validator.ToolValidator method) handle_sample_tool_data_table_conf_file() (galaxy.tool_shed.tools.data_table_manager.ShedToolDataTableManager method) (tool_shed.tools.data_table_manager.ShedToolDataTableManager method) handle_signal() (in module galaxy.main) handle_single_execution() (galaxy.tools.Tool method) handle_starttag() (galaxy.managers.pages.PageContentProcessor method) (galaxy.webapps.galaxy.controllers.workflow.SingleTagContentsParser method) handle_step() (galaxy.selenium.navigates_galaxy.NullTourCallback method) (galaxy.selenium.scripts.dump_tour.DumpTourCallback method) (galaxy_test.selenium.test_stock_tours.TourCallback method) handle_stop() (galaxy.jobs.runners.AsynchronousJobRunner method) handle_sub_elem() (tool_shed.dependencies.attribute_handlers.RepositoryDependencyAttributeHandler method) handle_tag_attributes() (tool_shed.dependencies.attribute_handlers.RepositoryDependencyAttributeHandler method) (tool_shed.dependencies.attribute_handlers.ToolDependencyAttributeHandler method) handle_tags() (galaxy.tool_util.toolbox.AbstractToolTagManager method) (galaxy.tool_util.toolbox.base.AbstractToolTagManager method) (galaxy.tool_util.toolbox.base.NullToolTagManager method) (galaxy.tools.NullToolTagManager method) (galaxy.tools.PersistentToolTagManager method) handle_tool_panel_section() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) handle_tool_panel_selection() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) handle_tool_shed_repositories() (galaxy.tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) handle_tool_shed_url_protocol() (in module galaxy.util.tool_shed.common_util) (in module tool_shed.util.common_util) handle_upload() (in module galaxy.datatypes.upload_util) handle_uploaded_dataset_file() (in module galaxy.datatypes.sniff) handle_uploaded_dataset_file_internal() (in module galaxy.datatypes.sniff) handle_url_for() (in module galaxy.web.framework) handle_user_login() (galaxy.app_unittest_utils.galaxy_mock.MockTrans method) (galaxy.webapps.base.webapp.GalaxyWebTransaction method) handle_user_logout() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) HandleCompressedFileResponse (class in galaxy.datatypes.sniff) handler (galaxy.model.Job attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.schema.schema.JobSummary attribute) HANDLER_ASSIGNMENT_METHODS (class in galaxy.web_stack.handlers) handler_count (galaxy.web_stack.message.ApplicationStackMessageDispatcher property) handler_runner_plugins (galaxy.jobs.JobConfiguration attribute) handler_tags (galaxy.web_stack.handlers.ConfiguresHandlers property) HandlerAssignmentError HandlerAssignmentSkip handlers (galaxy.jobs.JobConfiguration attribute) HandleUploadedDatasetFileInternalResponse (class in galaxy.datatypes.sniff) HandleUploadResponse (class in galaxy.datatypes.upload_util) hapmapmart() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) HarmonizeTool (class in galaxy.tools) has_access_permission() (galaxy.managers.datasets.DatasetManager method) has_accessible_folders() (galaxy.model.security.GalaxyRBACAgent method) has_accessible_library_datasets() (galaxy.model.security.GalaxyRBACAgent method) has_base_pool() (galaxy.web_stack.ApplicationStack method) has_been_resubmitted() (galaxy.managers.hdas.HDAManager method) has_class() (galaxy.selenium.smart_components.SmartTarget method) has_collections() (galaxy.model.dataset_collections.matching.CollectionsToMatch method) has_cycles (galaxy.model.Workflow attribute) has_cycles() (in module galaxy.workflow.steps) has_data() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) (galaxy.visualization.data_providers.basic.BaseDataProvider method) (galaxy.visualization.data_providers.genome.BBIDataProvider method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) has_dataprovider() (galaxy.datatypes.data.Data method) has_dataproviders() (in module galaxy.datatypes.dataproviders.decorators) has_deferred_data (galaxy.model.DatasetCollection property) (galaxy.model.DatasetCollectionElement property) (galaxy.model.DatasetCollectionInstance property) (galaxy.model.DatasetInstance property) has_doi() (galaxy.managers.citations.BaseCitation method) (galaxy.managers.citations.DoiCitation method) has_env() (galaxy.tool_util.deps.conda_util.CondaContext method) has_errors (galaxy.model.Workflow attribute) (galaxy.util.rules_dsl.RuleSet property) has_ext() (in module galaxy.util.path) has_failed_outputs() (galaxy.tool_util.provided_metadata.BaseToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.LegacyToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.ToolProvidedMetadata method) has_input_for_step() (galaxy.model.WorkflowInvocation method) has_item_recursive() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) has_manage_permissions_roles() (galaxy.model.Dataset method) (galaxy.model.LibraryDatasetDatasetAssociation method) has_metadata_files (galaxy.model.DatasetInstance property) has_outputs_defined() (galaxy.model.Workflow method) has_pool() (galaxy.web_stack.ApplicationStack method) has_possible_members (galaxy.model.History property) has_readme_files (galaxy.model.tool_shed_install.ToolShedRepository property) has_reference_data() (galaxy.visualization.genomes.Genomes method) has_reloaded() (galaxy.tools.ToolBox method) has_repository_dependencies (galaxy.model.tool_shed_install.ToolShedRepository property) (tool_shed.webapp.model.RepositoryMetadata attribute) has_repository_dependencies_only_if_compiling_contained_td (galaxy.model.tool_shed_install.ToolShedRepository property) has_resolution (galaxy.datatypes.data.Data property) has_subcollections (galaxy.model.DatasetCollection property) has_subcollections() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) has_subcollections_of_type() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) has_tool() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) (galaxy.tool_util.toolbox.base.ToolBoxRegistryImpl method) (galaxy.tool_util.toolbox.views.interface.ToolBoxRegistry method) has_tool_with_id() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) has_value() (galaxy.web_stack.handlers.HANDLER_ASSIGNMENT_METHODS class method) HasAModelManager (class in galaxy.managers.base) HasAnonymousGalaxyInteractor (class in galaxy_test.base.api) HasDatasets (class in galaxy.tools.wrappers) HasDockerLikeVolumes (class in galaxy.tool_util.deps.container_classes) HasDriver (class in galaxy.selenium.has_driver) hash (galaxy.tools.cache.ToolHash property) hash_dependencies() (galaxy.tool_util.deps.CachedDependencyManager method) hash_equals() (galaxy.tools.cache.ToolHash method) hash_function (galaxy.model.DatasetHash attribute) (galaxy.model.DatasetSourceHash attribute) (galaxy.schema.schema.DatasetHash attribute) (galaxy.schema.tasks.ComputeDatasetHashTaskRequest attribute) hash_password() (in module galaxy.security.passwords) hash_password_PBKDF2() (in module galaxy.security.passwords) hash_value (galaxy.model.DatasetHash attribute) (galaxy.model.DatasetSourceHash attribute) (galaxy.schema.schema.DatasetHash attribute) hashed_test_search() (in module galaxy.tool_util.deps.mulled.get_tests) hashes (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance property) (galaxy.model.DatasetSource attribute) (galaxy.model.store.discover.JsonCollectedDatasetMatch property) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) HashFunctionNames (class in galaxy.schema.schema) HashicorpVault (class in galaxy.security.vault) HasItems (class in galaxy.tool_util.toolbox.views.definitions) HasName (class in galaxy.model) HasPanelItems (class in galaxy.tool_util.toolbox.panel) HasSettings (class in galaxy.datatypes.dataproviders.base) HasTags (class in galaxy.model) HasToolBox (class in galaxy.model.tool_shed_install) have_shed_tool_conf_for_install() (in module galaxy.tool_shed.util.shed_util_common) hda (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.HistoryDatasetAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociationSubset attribute) (galaxy.schema.schema.ColletionSourceType attribute) (galaxy.schema.schema.DataItemSourceType attribute) (galaxy.schema.schema.DatasetSourceType attribute) (galaxy.schema.schema.DCEType attribute) (galaxy.schema.schema.HistoryContentSource attribute) hda_click_details() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) hda_click_primary_action_button() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) hda_copied_from_sinks (galaxy.model.store.ObjectImportTracker attribute) hda_id (galaxy.model.CleanupEventHistoryDatasetAssociationAssociation attribute) (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) (galaxy.model.MetadataFile attribute) (galaxy.model.WorkflowInvocationMessage attribute) hda_ldda (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) (galaxy.schema.schema.HDAObject attribute) hda_manager (galaxy.app_unittest_utils.galaxy_mock.MockApp attribute) (galaxy.structured_app.MinimalManagerApp attribute) (galaxy.webapps.galaxy.api.annotations.HistoryContentAnnotationsController attribute) (galaxy.webapps.galaxy.api.extended_metadata.HistoryDatasetExtendMetadataController attribute) (galaxy.webapps.galaxy.api.plugins.PluginsController attribute) (galaxy.webapps.galaxy.api.provenance.HDAProvenanceController attribute) (galaxy.webapps.galaxy.api.provenance.LDDAProvenanceController attribute) (galaxy.webapps.galaxy.api.tools.ToolsController attribute) (galaxy.webapps.galaxy.controllers.page.PageController attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController attribute) hda_parent_id (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) hda_to_table_entries() (galaxy.tools.parameters.dynamic_options.DynamicOptions static method) HDABasicInfo (class in galaxy.schema.schema) HDACommon (class in galaxy.schema.schema) HDACustom (class in galaxy.schema.schema) HDADeserializer (class in galaxy.managers.hdas) HdaDestination (class in galaxy.schema.fetch_data) HDADetailed (class in galaxy.schema.schema) HDAExtended (class in galaxy.schema.schema) HDAFilterParser (class in galaxy.managers.hdas) HDAInaccessible (class in galaxy.schema.schema) HDAManager (class in galaxy.managers.hdas) HDAObject (class in galaxy.schema.schema) HDAProvenanceController (class in galaxy.webapps.galaxy.api.provenance) hdas (galaxy.schema.fetch_data.DestinationType attribute) hdas_by_id (galaxy.model.store.ObjectImportTracker attribute) hdas_by_key (galaxy.model.store.ObjectImportTracker attribute) HDASerializer (class in galaxy.managers.hdas) HDAStorageCleanerManager (class in galaxy.managers.hdas) HDASummary (class in galaxy.schema.schema) hdca (galaxy.schema.schema.ColletionSourceType attribute) (galaxy.schema.schema.DataItemSourceType attribute) (galaxy.schema.schema.HistoryContentSource attribute) hdca_copied_from_sinks (galaxy.model.store.ObjectImportTracker attribute) hdca_id (galaxy.model.WorkflowInvocationMessage attribute) hdca_manager (galaxy.webapps.galaxy.api.tools.ToolsController attribute) HDCACommon (class in galaxy.schema.schema) HdcaDataItemsFromTarget (class in galaxy.schema.fetch_data) HdcaDataItemsTarget (class in galaxy.schema.fetch_data) HdcaDestination (class in galaxy.schema.fetch_data) HDCADetailed (class in galaxy.schema.schema) HDCAManager (class in galaxy.managers.hdcas) hdcas (galaxy.schema.fetch_data.DestinationType attribute) hdcas_by_id (galaxy.model.store.ObjectImportTracker attribute) hdcas_by_key (galaxy.model.store.ObjectImportTracker attribute) HDCASerializer (class in galaxy.managers.hdcas) HDCASummary (class in galaxy.schema.schema) HDCJobStateSummary (class in galaxy.schema.schema) HDF5SummarizedExperiment (class in galaxy.datatypes.hdf5) HDT (class in galaxy.datatypes.triples) head (galaxy.webapps.galaxy.api.RestVerb attribute) head() (galaxy.webapps.galaxy.api.FrameworkRouter method) (galaxy_test.base.api.ApiTestInteractor method) header (galaxy.datatypes.speech.TextGrid attribute) header_check() (galaxy.datatypes.genetics.AllegroLOD method) (galaxy.datatypes.genetics.GenotypeMatrix method) (galaxy.datatypes.genetics.MarkerMap method) header_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.tabular.Sam method) header_regexp (galaxy.datatypes.tabular.ConnectivityTable attribute) headers (galaxy.webapps.galaxy.api.GalaxyASGIRequest property) (galaxy.webapps.galaxy.api.GalaxyASGIResponse property) (galaxy.work.context.GalaxyAbstractResponse property) Heartbeat (class in galaxy.util.heartbeat) height (galaxy.schema.schema.WorkflowStepLayoutPosition attribute) help (galaxy.tools.Tool property) help() (tool_shed.webapp.controllers.repository.RepositoryController method) HelpEmpty (class in galaxy.tool_util.linters.help) HelpInvalidRST (class in galaxy.tool_util.linters.help) HelpMissing (class in galaxy.tool_util.linters.help) HelpPresent (class in galaxy.tool_util.linters.help) HelpTODO (class in galaxy.tool_util.linters.help) HelpValidRST (class in galaxy.tool_util.linters.help) hex_to_lowercase_alphanum() (in module galaxy.util) hexlify (tool_shed.managers.repositories.UpdatesRequest attribute) HexrdEtaOmeNpz (class in galaxy.datatypes.binary) HexrdImagesNpz (class in galaxy.datatypes.binary) HexrdMaterials (class in galaxy.datatypes.binary) hg_repo (tool_shed.webapp.model.Repository property) HgController (class in tool_shed.webapp.controllers.hg) hgweb_config (tool_shed.util.hgweb_config.HgWebConfigManager property) hgweb_config_manager (tool_shed.webapp.app.UniverseApplication attribute) HgWebConfigManager (class in tool_shed.util.hgweb_config) hid (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.schema.schema.EncodedJobParameterHistoryItem attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HistoryItemBase attribute) (galaxy.selenium.navigates_galaxy.HistoryEntry attribute) hid_counter (galaxy.model.History attribute) hid_to_history_item() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) hidden (galaxy.model.DynamicTool attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.schema.schema.HistoryActiveContentCounts attribute) (galaxy.schema.schema.StoredWorkflowSummary attribute) hidden_beneath_collection_instance (galaxy.model.HistoryDatasetAssociation attribute) hidden_beneath_collection_instance_id (galaxy.model.HistoryDatasetAssociation attribute) HiddenDataToolParameter (class in galaxy.tools.parameters.basic) HiddenToolParameter (class in galaxy.tools.parameters.basic) hide (galaxy.schema.schema.HistoryContentItemOperation attribute) hide_outputs() (galaxy.model.Job method) hide_source_items (galaxy.schema.schema.CreateNewCollectionPayload attribute) HideDatasetAction (class in galaxy.job_execution.actions.post) HierarchalDataProvider (class in galaxy.datatypes.dataproviders.hierarchy) HierarchicalObjectStore (class in galaxy.objectstore) histories (galaxy.model.GalaxySession attribute) (galaxy.model.User attribute) histories_click_advanced_search() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) HistoriesService (class in galaxy.webapps.galaxy.services.histories) History (class in galaxy.model) (class in galaxy.webapps.reports.controllers.history) history (galaxy.managers.context.ProvidesHistoryContext property) History (galaxy.managers.tags.TaggableItemClass attribute) history (galaxy.model.DataManagerHistoryAssociation attribute) (galaxy.model.DefaultHistoryPermissions attribute) (galaxy.model.Event attribute) (galaxy.model.GalaxySessionToHistoryAssociation attribute) (galaxy.model.HistoryAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.HistoryRatingAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.HistoryUserShareAssociation attribute) (galaxy.model.Job attribute) (galaxy.model.JobExportHistoryArchive attribute) (galaxy.model.JobImportHistoryArchive attribute) (galaxy.model.WorkflowInvocation attribute)

HISTORY (galaxy.schema.schema.ExportObjectType attribute) history (galaxy.webapps.base.webapp.GalaxyWebTransaction property) (galaxy.work.context.WorkRequestContext property) history_and_dataset_per_user() (galaxy.webapps.reports.controllers.history.History method) history_and_dataset_type() (galaxy.webapps.reports.controllers.history.History method) history_associations (galaxy.model.Dataset attribute) history_attrs_filename (galaxy.model.JobExportHistoryArchive attribute) history_click_create_new() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_click_editor_save() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_content_id (galaxy.tool_util.cwl.util.GalaxyOutput attribute) history_content_type (galaxy.model.HistoryDatasetAssociation property) (galaxy.model.HistoryDatasetCollectionAssociation property) (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) (galaxy.schema.schema.HDACommon attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDCACommon attribute) (galaxy.schema.schema.HistoryContentItemBase attribute) (galaxy.schema.schema.UpdateContentItem attribute) (galaxy.selenium.navigates_galaxy.HistoryEntry attribute) (galaxy.tool_util.cwl.util.GalaxyOutput attribute) history_contents() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_data() (galaxy.webapps.galaxy.controllers.history.HistoryController method) history_dataset (galaxy.model.MetadataFile attribute) history_dataset_association (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization attribute) (galaxy.model.HistoryDatasetAssociationRatingAssociation attribute) (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.JobExternalOutputMetadata attribute) history_dataset_association_id (galaxy.model.HistoryDatasetAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization attribute) (galaxy.model.HistoryDatasetAssociationHistory attribute) (galaxy.model.HistoryDatasetAssociationRatingAssociation attribute) (galaxy.model.HistoryDatasetAssociationSubset attribute) (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.JobExternalOutputMetadata attribute) history_dataset_association_subset_id (galaxy.model.HistoryDatasetAssociationSubset attribute) history_dataset_collection (galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation attribute) history_dataset_collection_association_id (galaxy.schema.tasks.PrepareDatasetCollectionDownload attribute) history_dataset_collection_associations (galaxy.model.Job attribute) history_dataset_collection_id (galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetCollectionRatingAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) history_dataset_collections() (galaxy.managers.collections.DatasetCollectionManager method) history_element() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_get_default_permissions() (galaxy.model.security.GalaxyRBACAgent method) history_id (galaxy.model.CleanupEventHistoryAssociation attribute) (galaxy.model.DataManagerHistoryAssociation attribute) (galaxy.model.DefaultHistoryPermissions attribute) (galaxy.model.Event attribute) (galaxy.model.GalaxySessionToHistoryAssociation attribute) (galaxy.model.HistoryAnnotationAssociation attribute) (galaxy.model.HistoryAudit attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.HistoryRatingAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.HistoryUserShareAssociation attribute) (galaxy.model.Job attribute) (galaxy.model.JobExportHistoryArchive attribute) (galaxy.model.JobImportHistoryArchive attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowInvocationMessage property) (galaxy.schema.fetch_data.BaseDataPayload attribute) (galaxy.schema.schema.CreateHistoryPayload attribute) (galaxy.schema.schema.CreateNewCollectionPayload attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDAObject attribute) (galaxy.schema.schema.HistoryItemBase attribute) (galaxy.schema.schema.InvocationIndexQueryPayload attribute) (galaxy.schema.schema.JobBaseModel attribute) (galaxy.schema.schema.JobIndexQueryPayload attribute) (galaxy.schema.schema.MaterializeDatasetInstanceRequest attribute) (galaxy.schema.tasks.GenerateHistoryDownload attribute) (galaxy.schema.tasks.ImportModelStoreTaskRequest attribute) (galaxy.schema.tasks.MaterializeDatasetInstanceTaskRequest attribute) (galaxy.schema.tasks.SetupHistoryExportJob attribute) (galaxy.schema.tasks.WriteHistoryTo attribute) (galaxy.tool_util.cwl.util.GalaxyOutput attribute) (galaxy_test.api.test_workflow_extraction.RunJobsSummary attribute) (galaxy_test.base.populators.RunJobsSummary attribute) history_id() (galaxy_test.driver.integration_util.IntegrationInstance method) history_invocations() (galaxy_test.base.populators.BaseWorkflowPopulator method) history_item_dict_to_python() (in module galaxy.tools.parameters.basic) history_item_to_json() (in module galaxy.tools.parameters.basic) history_item_wait_for() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_jobs() (galaxy_test.base.populators.BaseDatasetPopulator method) history_jobs_for_tool() (galaxy_test.base.populators.BaseDatasetPopulator method) history_length() (galaxy_test.base.populators.BaseDatasetPopulator method) history_manager (galaxy.app_unittest_utils.galaxy_mock.MockApp attribute) (galaxy.structured_app.MinimalManagerApp attribute) (galaxy.tools.Tool property) (galaxy.webapps.galaxy.api.annotations.HistoryAnnotationsController attribute) (galaxy.webapps.galaxy.api.plugins.PluginsController attribute) (galaxy.webapps.galaxy.api.tools.ToolsController attribute) (galaxy.webapps.galaxy.controllers.history.HistoryController attribute) (galaxy.webapps.galaxy.controllers.page.PageController attribute) (galaxy.webapps.galaxy.controllers.root.RootController attribute) history_model_store_dict() (in module galaxy.model.unittest_utils.store_fixtures) history_multi_view_display_collection_contents() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_names() (galaxy_test.base.populators.BaseDatasetPopulator method) history_panel_add_tags() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_click_copy_elements() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_click_item_title() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_click_to_rename() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_collection_name_element() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_collection_rename() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_create_new() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_create_new_with_name() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_ensure_showing_item_details() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_expand_collection() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_item_available_visualizations() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_item_available_visualizations_elements() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_item_body_component() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_item_click_visualization() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_item_click_visualization_menu() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_item_component() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_item_edit() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_item_get_tags() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_item_selector() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_item_showing_details() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_item_view_dataset_details() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_muli_operation_select_hid() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_multi_operation_action_click() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_multi_operations_show() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_name() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_name_element() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_name_input() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_refresh_click() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_rename() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_wait_for_hid_deferred() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_wait_for_hid_hidden() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_wait_for_hid_ok() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_wait_for_hid_state() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_wait_for_hid_visible() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_wait_for_history_loaded() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_per_user() (galaxy.webapps.reports.controllers.users.Users method) HISTORY_POLL (galaxy.selenium.navigates_galaxy.WAIT_TYPES attribute) history_serializer (galaxy.webapps.galaxy.controllers.history.HistoryController attribute) (galaxy.webapps.galaxy.controllers.page.PageController attribute) history_set_default_permissions() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) HistoryActiveContentCounts (class in galaxy.schema.schema) HistoryAnnotationAssociation (class in galaxy.model) HistoryAnnotationsController (class in galaxy.webapps.galaxy.api.annotations) HistoryAudit (class in galaxy.model) HistoryContentAnnotationsController (class in galaxy.webapps.galaxy.api.annotations) HistoryContentBulkOperationPayload (class in galaxy.schema.schema) HistoryContentBulkOperationResult (class in galaxy.schema.schema) HistoryContentItem (class in galaxy.schema.schema) HistoryContentItemBase (class in galaxy.schema.schema) HistoryContentItemOperation (class in galaxy.schema.schema) HistoryContentsArchiveDryRunResult (class in galaxy.schema.schema) HistoryContentsFilters (class in galaxy.managers.history_contents) HistoryContentsManager (class in galaxy.managers.history_contents) HistoryContentSource (class in galaxy.schema.schema) HistoryContentsResult (class in galaxy.schema.schema) HistoryContentsSerializer (class in galaxy.managers.history_contents) HistoryContentStats (class in galaxy.schema.schema) HistoryContentsWithStatsResult (class in galaxy.schema.schema) HistoryContentType (class in galaxy.schema.schema) HistoryController (class in galaxy.webapps.galaxy.controllers.history) HistoryDatasetAssociation (class in galaxy.model) (galaxy.managers.tags.TaggableItemClass attribute) HistoryDatasetAssociationAnnotationAssociation (class in galaxy.model) HistoryDatasetAssociationDisplayAtAuthorization (class in galaxy.model) HistoryDatasetAssociationHistory (class in galaxy.model) HistoryDatasetAssociationNoHistoryException HistoryDatasetAssociationRatingAssociation (class in galaxy.model) HistoryDatasetAssociationSubset (class in galaxy.model) HistoryDatasetAssociationTagAssociation (class in galaxy.model) HistoryDatasetCollectionAssociation (class in galaxy.model) (galaxy.managers.tags.TaggableItemClass attribute) HistoryDatasetCollectionAssociationAnnotationAssociation (class in galaxy.model) HistoryDatasetCollectionRatingAssociation (class in galaxy.model) HistoryDatasetCollectionTagAssociation (class in galaxy.model) HistoryDatasetExtendMetadataController (class in galaxy.webapps.galaxy.api.extended_metadata) HistoryDeserializer (class in galaxy.managers.histories) HistoryDetailed (class in galaxy.schema.schema) HistoryEntry (class in galaxy.selenium.navigates_galaxy) HistoryExportManager (class in galaxy.managers.histories) HistoryField (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) HistoryFilters (class in galaxy.managers.histories) HistoryImportArchiveSourceType (class in galaxy.schema.schema) HistoryItemBase (class in galaxy.schema.schema) HistoryItemCommon (class in galaxy.schema.schema) HistoryManager (class in galaxy.managers.histories) HistoryQuery (class in galaxy.tools.parameters.history_query) HistoryRatingAssociation (class in galaxy.model) HistorySerializer (class in galaxy.managers.histories) HistoryStorageCleanerManager (class in galaxy.managers.histories) HistorySummary (class in galaxy.schema.schema) HistoryTagAssociation (class in galaxy.model) HistoryUserShareAssociation (class in galaxy.model) hmac_new() (in module galaxy.util.hash_util) Hmmer (class in galaxy.datatypes.msa) Hmmer2 (class in galaxy.datatypes.msa) Hmmer3 (class in galaxy.datatypes.msa) HmmerPress (class in galaxy.datatypes.msa) home() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) home_directory() (galaxy.job_execution.compute_environment.ComputeEnvironment method) (galaxy.job_execution.compute_environment.SharedComputeEnvironment method) HomebrewDependency (class in galaxy.tool_util.deps.resolvers.resolver_mixins) HomebrewDependencyResolver (class in galaxy.tool_util.deps.resolvers.homebrew) HomebrewRecipe (class in galaxy.tool_util.deps.brew_util) HomebrewToolShedDependencyResolver (class in galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages) HomePage (class in galaxy.webapps.reports.controllers.home) homepage_url (tool_shed.webapp.model.Repository attribute) honorific_prefix (galaxy.schema.schema.Person attribute) honorific_suffix (galaxy.schema.schema.Person attribute) hooks() (galaxy.webapps.galaxy.api.uploads.UploadsAPIController method) host (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.web.proxy.ProxyMapping attribute) (galaxy.webapps.galaxy.api.GalaxyASGIRequest property) (galaxy.work.context.GalaxyAbstractRequest property) (galaxy.work.context.SessionRequestContext property) (galaxy_test.api.test_pages.TestPagesApi attribute) (galaxy_test.api.test_workflows.TestAdminWorkflowsApi attribute) (galaxy_test.api.test_workflows_cwl.BaseCwlWorkflowsApiTestCase attribute) (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi attribute) (galaxy_test.base.testcase.FunctionalTestCase attribute) (galaxy_test.driver.testcase.DrivenFunctionalTestCase attribute) (galaxy_test.selenium.test_admin_app.TestAdminApp attribute) (galaxy_test.selenium.test_anon_history.TestAnonymousHistories attribute) (galaxy_test.selenium.test_change_password.TestChangePassword attribute) (galaxy_test.selenium.test_collection_builders.TestCollectionBuilders attribute) (galaxy_test.selenium.test_collection_edit.TestCollectionEdit attribute) (galaxy_test.selenium.test_data_source_tools.TestDataSource attribute) (galaxy_test.selenium.test_dataset_metadata_download.TestHistoryDatasetState attribute) (galaxy_test.selenium.test_histories_list.TestSavedHistories attribute) (galaxy_test.selenium.test_history_copy_elements.TestHistoryCopyElements attribute) (galaxy_test.selenium.test_history_dataset_state.TestHistoryDatasetState attribute) (galaxy_test.selenium.test_history_multi_view.TestHistoryMultiView attribute) (galaxy_test.selenium.test_history_options.TestHistoryOptions attribute) (galaxy_test.selenium.test_history_panel.TestHistoryPanel attribute) (galaxy_test.selenium.test_history_panel_collections.TestHistoryPanelCollections attribute) (galaxy_test.selenium.test_history_sharing.TestHistoryRequiresLoginSelenium attribute) (galaxy_test.selenium.test_history_sharing.TestHistorySharing attribute) (galaxy_test.selenium.test_invocation_grid.TestInvocationGridSelenium attribute) (galaxy_test.selenium.test_library_contents.TestLibraryContents attribute) (galaxy_test.selenium.test_library_landing.TestLibraryLanding attribute) (galaxy_test.selenium.test_library_to_collections.TestLibraryToCollections attribute) (galaxy_test.selenium.test_login.TestLogin attribute) (galaxy_test.selenium.test_navigates_galaxy.TestNavigatesGalaxySelenium attribute) (galaxy_test.selenium.test_pages.TestPages attribute) (galaxy_test.selenium.test_personal_information.TestDeleteCurrentAccount attribute) (galaxy_test.selenium.test_personal_information.TestManageInformation attribute) (galaxy_test.selenium.test_registration.TestRegistration attribute) (galaxy_test.selenium.test_sign_out.TestSignOut attribute) (galaxy_test.selenium.test_sizzle_loading.TestSizzleLoading attribute) (galaxy_test.selenium.test_stock_tours.TestStockToursTestCase attribute) (galaxy_test.selenium.test_tool_describing_tours.TestToolDescribingTours attribute) (galaxy_test.selenium.test_tool_form.TestLoggedInToolForm attribute) (galaxy_test.selenium.test_tool_form.TestToolForm attribute) (galaxy_test.selenium.test_uploads.TestUploads attribute) (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor attribute) (galaxy_test.selenium.test_workflow_invocation_details.TestWorkflowInvocationDetails attribute) (galaxy_test.selenium.test_workflow_management.TestWorkflowManagement attribute) (galaxy_test.selenium.test_workflow_run.TestWorkflowRun attribute) (galaxy_test.selenium.test_workflow_sharing.TestWorkflowSharing attribute) (galaxy_test.selenium.test_workflow_sharing.TestWorkflowSharingRedirect attribute) (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures attribute) (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository attribute) (tool_shed.test.functional.test_0020_basic_repository_dependencies.TestBasicRepositoryDependencies attribute) (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions attribute) (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies attribute) (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels attribute) (tool_shed.test.functional.test_0070_invalid_tool.TestBismarkRepository attribute) (tool_shed.test.functional.test_0080_advanced_circular_dependencies.TestRepositoryCircularDependencies attribute) (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain attribute) (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies attribute) (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies attribute) (tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners.TestRepositoryMultipleOwners attribute) (tool_shed.test.functional.test_0140_tool_help_images.TestToolHelpImages attribute) (tool_shed.test.functional.test_0150_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_0160_circular_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_0170_complex_prior_installation_required.TestComplexPriorInstallation attribute) (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata attribute) (tool_shed.test.functional.test_0310_hg_api_features.TestHgWebFeatures attribute) (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs attribute) (tool_shed.test.functional.test_0430_browse_utilities.TestToolShedBrowseUtilities attribute) (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies attribute) (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision attribute) (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance attribute) (tool_shed.test.functional.test_0480_tool_dependency_xml_verification.TestDependencyDefinitionValidation attribute) (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole attribute) (tool_shed.test.functional.test_0550_metadata_updated_dependencies.TestGetUpdatedMetadata attribute) (tool_shed.test.functional.test_1000_install_basic_repository.TestBasicToolShedFeatures attribute) (tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies.TestToolWithToolDependencies attribute) (tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies.TestToolWithRepositoryDependencies attribute) (tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions.TestRepositoryWithDependencyRevisions attribute) (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies attribute) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies attribute) (tool_shed.test.functional.test_1070_invalid_tool.TestFreebayesRepository attribute) (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies attribute) (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies attribute) (tool_shed.test.functional.test_1100_install_updated_repository_dependencies.TestRepositoryDependencies attribute) (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies attribute) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies attribute) (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners attribute) (tool_shed.test.functional.test_1160_tool_help_images.TestToolHelpImages attribute) (tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_1190_complex_prior_installation_required.TestComplexPriorInstallation attribute) (tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository.TestUninstallingAndReinstallingRepositories attribute) (tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies.TestUninstallingAndReinstallingRepositories attribute) (tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions.TestUninstallingAndReinstallingRepositories attribute) (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata attribute) (tool_shed.test.functional.test_1410_update_manager.TestUpdateManager attribute) (tool_shed.test.functional.test_1430_repair_installed_repository.TestRepairRepository attribute) (tool_shed.test.functional.test_1460_data_managers.TestDataManagers attribute) (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository attribute) host_security_agent (galaxy.structured_app.MinimalApp attribute) HostAgent (class in galaxy.model.security) hostname (galaxy.model.WorkerProcess attribute) HostnamePlugin (class in galaxy.job_metrics.instrumenters.hostname) hours_between_check (galaxy.config.GalaxyAppConfiguration attribute) hover_over() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) href (galaxy.schema.schema.Hyperlink attribute) Html (class in galaxy.datatypes.images) (class in galaxy.datatypes.text) html (galaxy.schema.schema.PageContentFormat attribute) html() (galaxy.authnz.psa_authnz.Strategy method) html_table (galaxy.datatypes.genetics.RexpBase attribute) HTTP_REPR (galaxy.datatypes.binary.H5MLM attribute) HTTPBadRequest HttpsToolResolver (class in galaxy.tool_util.locations.http) HttpToolResolver (class in galaxy.tool_util.locations.file) (class in galaxy.tool_util.locations.http) Hyperlink (class in galaxy.schema.schema) HYPERPARAMETER (galaxy.datatypes.binary.H5MLM attribute)

I

iam_client_secret (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute) icda_id (galaxy.model.CleanupEventImplicitlyConvertedDatasetAssociationAssociation attribute) ICM (class in galaxy.datatypes.binary) id (galaxy.files.sources.FilesSourceProperties attribute) (galaxy.managers.api_keys.IsUserModel attribute) (galaxy.managers.display_applications.DisplayApplication attribute) (galaxy.model.APIKeys attribute) (galaxy.model.CleanupEvent attribute) (galaxy.model.CleanupEventDatasetAssociation attribute) (galaxy.model.CleanupEventHistoryAssociation attribute) (galaxy.model.CleanupEventHistoryDatasetAssociationAssociation attribute) (galaxy.model.CleanupEventImplicitlyConvertedDatasetAssociationAssociation attribute) (galaxy.model.CleanupEventLibraryAssociation attribute) (galaxy.model.CleanupEventLibraryDatasetAssociation attribute) (galaxy.model.CleanupEventLibraryDatasetDatasetAssociationAssociation attribute) (galaxy.model.CleanupEventLibraryFolderAssociation attribute) (galaxy.model.CleanupEventMetadataFileAssociation attribute) (galaxy.model.CloudAuthz attribute) (galaxy.model.CustosAuthnzToken attribute) (galaxy.model.DataManagerHistoryAssociation attribute) (galaxy.model.DataManagerJobAssociation attribute) (galaxy.model.Dataset attribute) (galaxy.model.DatasetCollection attribute) (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.DatasetHash attribute) (galaxy.model.DatasetPermissions attribute) (galaxy.model.DatasetSource attribute) (galaxy.model.DatasetSourceHash attribute) (galaxy.model.DefaultHistoryPermissions attribute) (galaxy.model.DefaultQuotaAssociation attribute) (galaxy.model.DefaultUserPermissions attribute) (galaxy.model.DynamicTool attribute) (galaxy.model.Event attribute) (galaxy.model.ExtendedMetadata attribute) (galaxy.model.ExtendedMetadataIndex attribute) (galaxy.model.FormDefinition attribute) (galaxy.model.FormDefinitionCurrent attribute) (galaxy.model.FormValues attribute) (galaxy.model.GalaxySession attribute) (galaxy.model.GalaxySessionToHistoryAssociation attribute) (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.Group attribute) (galaxy.model.GroupQuotaAssociation attribute) (galaxy.model.GroupRoleAssociation attribute) (galaxy.model.History attribute) (galaxy.model.HistoryAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization attribute) (galaxy.model.HistoryDatasetAssociationHistory attribute) (galaxy.model.HistoryDatasetAssociationRatingAssociation attribute) (galaxy.model.HistoryDatasetAssociationSubset attribute) (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetCollectionRatingAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryRatingAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.HistoryUserShareAssociation attribute) (galaxy.model.ImplicitCollectionJobs attribute) (galaxy.model.ImplicitCollectionJobsJobAssociation attribute) (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) (galaxy.model.ImplicitlyCreatedDatasetCollectionInput attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.Job attribute) (galaxy.model.JobContainerAssociation attribute) (galaxy.model.JobExportHistoryArchive attribute) (galaxy.model.JobExternalOutputMetadata attribute) (galaxy.model.JobImportHistoryArchive attribute) (galaxy.model.JobMetricNumeric attribute) (galaxy.model.JobMetricText attribute) (galaxy.model.JobParameter attribute) (galaxy.model.JobStateHistory attribute) (galaxy.model.JobToImplicitOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetAssociation attribute) (galaxy.model.JobToInputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetCollectionElementAssociation attribute) (galaxy.model.JobToInputLibraryDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToOutputLibraryDatasetAssociation attribute) (galaxy.model.Library attribute) (galaxy.model.LibraryDataset attribute) (galaxy.model.LibraryDatasetCollectionAnnotationAssociation attribute) (galaxy.model.LibraryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetCollectionRatingAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationPermissions attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) (galaxy.model.LibraryDatasetPermissions attribute) (galaxy.model.LibraryFolder attribute) (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryFolderPermissions attribute) (galaxy.model.LibraryInfoAssociation attribute) (galaxy.model.LibraryPermissions attribute) (galaxy.model.MetadataFile attribute) (galaxy.model.Notification attribute) (galaxy.model.Page attribute) (galaxy.model.PageAnnotationAssociation attribute) (galaxy.model.PageRatingAssociation attribute) (galaxy.model.PageRevision attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.PageUserShareAssociation attribute) (galaxy.model.PostJobAction attribute) (galaxy.model.PostJobActionAssociation attribute) (galaxy.model.PSAAssociation attribute) (galaxy.model.PSACode attribute) (galaxy.model.PSANonce attribute) (galaxy.model.PSAPartial attribute) (galaxy.model.Quota attribute) (galaxy.model.RepresentById attribute) (galaxy.model.Role attribute) (galaxy.model.Serializable attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.StoredWorkflowAnnotationAssociation attribute) (galaxy.model.StoredWorkflowMenuEntry attribute) (galaxy.model.StoredWorkflowRatingAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.StoredWorkflowUserShareAssociation attribute) (galaxy.model.StoreExportAssociation attribute) (galaxy.model.Tag attribute) (galaxy.model.Task attribute) (galaxy.model.TaskMetricNumeric attribute) (galaxy.model.TaskMetricText attribute) (galaxy.model.tool_shed_install.RepositoryDependency attribute) (galaxy.model.tool_shed_install.RepositoryRepositoryDependencyAssociation attribute) (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.model.tool_shed_install.ToolVersion attribute) (galaxy.model.tool_shed_install.ToolVersionAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.User attribute) (galaxy.model.UserAction attribute) (galaxy.model.UserAddress attribute) (galaxy.model.UserAuthnzToken attribute) (galaxy.model.UserGroupAssociation attribute) (galaxy.model.UserNotificationAssociation attribute) (galaxy.model.UserPreference attribute) (galaxy.model.UserQuotaAssociation attribute) (galaxy.model.UserQuotaSourceUsage attribute) (galaxy.model.UserRoleAssociation attribute) (galaxy.model.Visualization attribute) (galaxy.model.VisualizationAnnotationAssociation attribute) (galaxy.model.VisualizationRatingAssociation attribute) (galaxy.model.VisualizationRevision attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.VisualizationUserShareAssociation attribute) (galaxy.model.WorkerProcess attribute) (galaxy.model.Workflow attribute) (galaxy.model.WorkflowComment attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowInvocationMessage attribute) (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationOutputValue attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute) (galaxy.model.WorkflowOutput attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.model.WorkflowRequestInputStepParameter attribute) (galaxy.model.WorkflowRequestStepState attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowStep attribute) (galaxy.model.WorkflowStepAnnotationAssociation attribute) (galaxy.model.WorkflowStepConnection attribute) (galaxy.model.WorkflowStepInput attribute) (galaxy.model.WorkflowStepTagAssociation attribute) (galaxy.schema.BootstrapAdminUser attribute) (galaxy.schema.remote_files.FilesSourcePlugin attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.ArchivedHistorySummary attribute) (galaxy.schema.schema.AsyncTaskResultSummary attribute) (galaxy.schema.schema.BaseUserModel attribute) (galaxy.schema.schema.BasicRoleModel attribute) (galaxy.schema.schema.CollectionElementIdentifier attribute) (galaxy.schema.schema.CustomBuildModel attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.DatasetHash attribute) (galaxy.schema.schema.DatasetSource attribute) (galaxy.schema.schema.DatasetSourceId attribute) (galaxy.schema.schema.DatasetSummary attribute) (galaxy.schema.schema.DCESummary attribute) (galaxy.schema.schema.DCObject attribute) (galaxy.schema.schema.DCSummary attribute) (galaxy.schema.schema.DeleteHistoryContentResult attribute) (galaxy.schema.schema.EncodedDataItemSourceId attribute) (galaxy.schema.schema.EncodedDatasetSourceId attribute) (galaxy.schema.schema.EncodedHistoryContentItem attribute) (galaxy.schema.schema.FileLibraryFolderItem attribute) (galaxy.schema.schema.FolderLibraryFolderItem attribute) (galaxy.schema.schema.GroupModel attribute) (galaxy.schema.schema.GroupRoleResponse attribute) (galaxy.schema.schema.GroupUserResponse attribute) (galaxy.schema.schema.HDABasicInfo attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDAObject attribute) (galaxy.schema.schema.HistoryContentItem attribute) (galaxy.schema.schema.HistoryItemBase attribute) (galaxy.schema.schema.HistorySummary attribute) (galaxy.schema.schema.ImportToolDataBundleDatasetSource attribute) (galaxy.schema.schema.InputConnection attribute) (galaxy.schema.schema.InstalledToolShedRepository attribute) (galaxy.schema.schema.ItemStateSummary attribute) (galaxy.schema.schema.JobBaseModel attribute) (galaxy.schema.schema.LibraryFolderDetails attribute) (galaxy.schema.schema.LibraryLegacySummary attribute) (galaxy.schema.schema.LimitedUserModel attribute) (galaxy.schema.schema.ObjectExportResponseBase attribute) (galaxy.schema.schema.PageSummary attribute) (galaxy.schema.schema.SharingStatus attribute) (galaxy.schema.schema.StoredWorkflowSummary attribute) (galaxy.schema.schema.UpdateContentItem attribute) (galaxy.schema.schema.UserEmail attribute) (galaxy.schema.schema.WorkflowStepBase attribute) (galaxy.schema.schema.WorkflowStepToExportBase attribute) (galaxy.selenium.navigates_galaxy.HistoryEntry attribute) (galaxy.tool_shed.metadata.metadata_generator.RepositoryProtocol attribute) (galaxy.tool_util.toolbox.views.definitions.Label attribute) (galaxy.tool_util.toolbox.views.definitions.Section attribute) (galaxy.tool_util.toolbox.views.definitions.StaticToolBoxView attribute) (galaxy.tool_util.toolbox.views.definitions.Tool attribute) (galaxy.tool_util.toolbox.views.definitions.Workflow attribute) (galaxy.tool_util.toolbox.views.interface.ToolPanelViewModel attribute) (galaxy.tools.data_manager.manager.DataManager property) (galaxy.tours.Tour attribute) (galaxy.util.jstree.Path attribute) (tool_shed.webapp.model.APIKeys attribute) (tool_shed.webapp.model.Category attribute) (tool_shed.webapp.model.GalaxySession attribute) (tool_shed.webapp.model.Group attribute) (tool_shed.webapp.model.GroupRoleAssociation attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.RepositoryCategoryAssociation attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) (tool_shed.webapp.model.RepositoryRatingAssociation attribute) (tool_shed.webapp.model.RepositoryRoleAssociation attribute) (tool_shed.webapp.model.Role attribute) (tool_shed.webapp.model.Tag attribute) (tool_shed.webapp.model.User attribute) (tool_shed.webapp.model.UserGroupAssociation attribute) (tool_shed.webapp.model.UserRoleAssociation attribute) id_based (galaxy.tool_util.toolbox.lineages.interface.ToolLineageVersion property) id_seq_qual_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.tabular.Sam method) id_token (galaxy.model.CustosAuthnzToken attribute) IdAsLowercaseAlphanumEncodingHelper (class in galaxy.security.idencoding) Idat (class in galaxy.datatypes.binary) IdeasPre (class in galaxy.datatypes.genetics) IdEncodingHelper (class in galaxy.security.idencoding) identifier (galaxy.schema.schema.Creator attribute) identifier() (galaxy.tools.wrappers.ElementIdentifierMapper method) identifier_columns (galaxy.util.rules_dsl.RuleSet property) IdentityProvider (class in galaxy.authnz) IdpDB (class in galaxy.datatypes.binary) ids_per_quota_source() (galaxy.objectstore.QuotaSourceMap method) IdXML (class in galaxy.datatypes.proteomics) iff() (in module galaxy.web.framework.helpers) ignore_result (galaxy.celery.GalaxyTask attribute) ignored (galaxy.schema.schema.AsyncTaskResultSummary attribute) Im (class in galaxy.datatypes.images) Image (class in galaxy.datatypes.images) image (galaxy.schema.schema.Creator attribute) image_name() (in module galaxy.tool_util.deps.mulled.util) image_type() (in module galaxy.util.image_util) ImgtJson (class in galaxy.datatypes.text) immediate_actions (galaxy.job_execution.actions.post.ActionBox attribute) imp() (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) impersonate() (galaxy.managers.users.UserManager method) (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) impl (galaxy.model.custom_types.JSONType attribute) (galaxy.model.custom_types.TrimmedString attribute) (galaxy.model.custom_types.UUIDType attribute) implicit_collection_jobs (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.ImplicitCollectionJobsJobAssociation attribute) (galaxy.model.WorkflowInvocationStep attribute) implicit_collection_jobs_association (galaxy.model.Job attribute) implicit_collection_jobs_id (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.ImplicitCollectionJobsJobAssociation attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.schema.schema.HDCADetailed attribute) (galaxy.schema.schema.JobIndexQueryPayload attribute) implicit_collection_jobs_properties() (galaxy.model.store.BaseDirectoryImportModelStore method) (galaxy.model.store.DictImportModelStore method) (galaxy.model.store.ModelImportStore method) implicit_dataset_conversion_properties() (galaxy.model.store.BaseDirectoryImportModelStore method) (galaxy.model.store.DictImportModelStore method) (galaxy.model.store.ModelImportStore method) implicit_input_collections (galaxy.model.HistoryDatasetCollectionAssociation attribute) implicit_output_name (galaxy.model.HistoryDatasetCollectionAssociation attribute) ImplicitCollectionJobs (class in galaxy.model) (galaxy.schema.schema.JobSourceType attribute) ImplicitCollectionJobs.populated_states (class in galaxy.model) ImplicitCollectionJobsJobAssociation (class in galaxy.model) ImplicitCollectionJobsStateSummary (class in galaxy.schema.schema) ImplicitConversionRequired implicitly_converted_datasets (galaxy.model.DatasetInstance attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) implicitly_converted_parent_datasets (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) ImplicitlyConvertedDatasetAssociation (class in galaxy.model) ImplicitlyCreatedDatasetCollectionInput (class in galaxy.model) import_data_bundle_by_dataset() (galaxy.managers.tool_data.ToolDataImportManager method) import_data_bundle_by_uri() (galaxy.managers.tool_data.ToolDataImportManager method) import_history() (galaxy_test.base.populators.BaseDatasetPopulator method) import_history_and_wait_for_name() (galaxy_test.base.populators.BaseDatasetPopulator method) import_history_from_uri_async() (galaxy_test.base.populators.BaseDatasetPopulator method) import_model_store() (galaxy.managers.model_stores.ModelStoreManager method) import_submodules() (in module galaxy.util.submodules) import_test_to_command_list() (in module galaxy.tool_util.deps.mulled.get_tests) import_tool() (galaxy_test.base.populators.WorkflowPopulator method) import_tools (galaxy.managers.workflows.WorkflowCreateOptions attribute) import_workflow() (galaxy.managers.workflows.Format2ConverterGalaxyInterface method) (galaxy_test.api.test_workflows.BaseWorkflowsApiTestCase method) (galaxy_test.base.populators.WorkflowPopulator method) import_workflow_from_path() (galaxy_test.base.populators.BaseWorkflowPopulator method) import_workflow_from_path_raw() (galaxy_test.base.populators.BaseWorkflowPopulator method) importable (galaxy.managers.workflows.WorkflowCreateOptions attribute) (galaxy.model.History attribute) (galaxy.model.Page attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.Visualization attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.HistoryDetailed attribute) (galaxy.schema.schema.PageSummary attribute) (galaxy.schema.schema.SharingStatus attribute) importdir (galaxy.schema.remote_files.RemoteFilesTarget attribute) ImportDiscardedDataType (class in galaxy.model.store) imported (galaxy.model.Job attribute) imported_macro_paths() (in module galaxy.tool_util.loader) (in module galaxy.util.xml_macros) imported_store_for_metadata() (in module galaxy.model.store) importer() (in module galaxy.jobs.dynamic_tool_destination) ImportExportTests (class in galaxy_test.api.test_histories) ImportHistoryTool (class in galaxy.tools) ImportHistoryToolAction (class in galaxy.tools.actions.history_imp_exp) importing (galaxy.model.History attribute) ImportModelStoreTaskRequest (class in galaxy.schema.tasks) ImportOptions (class in galaxy.model.store) ImportToolDataBundle (class in galaxy.webapps.galaxy.api.tool_data) ImportToolDataBundleDatasetSource (class in galaxy.schema.schema) ImportToolDataBundleUriSource (class in galaxy.schema.schema) ImzML (class in galaxy.datatypes.proteomics) in_all_repository_dependencies() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) in_circular_repository_dependencies() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) in_directory() (in module galaxy.util) in_error_state (galaxy.model.tool_shed_install.ToolDependency property) (galaxy.model.tool_shed_install.ToolShedRepository property) in_key_rd_dicts() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) in_packages() (in module galaxy.util) in_pool() (galaxy.web_stack.ApplicationStack method) (galaxy.web_stack.WeblessApplicationStack method) in_ready_state() (galaxy.model.Dataset method) in_tool_dict() (in module tool_shed.util.search_util) InappropriateDatasetContentError InChI (class in galaxy.datatypes.molecules) include() (galaxy.util.yaml_util.OrderedLoader method) include_all_package_routers() (in module galaxy.webapps.base.api) include_deleted (galaxy.schema.schema.ExportHistoryArchivePayload attribute) (galaxy.schema.schema.ExportRecordData attribute) (galaxy.schema.schema.LibraryFolderContentsIndexQueryPayload attribute) (galaxy.schema.schema.StoreExportPayload attribute) (galaxy.schema.tasks.SetupHistoryExportJob attribute) include_files (galaxy.schema.schema.ExportRecordData attribute) (galaxy.schema.schema.StoreExportPayload attribute) (galaxy.schema.tasks.SetupHistoryExportJob attribute) include_hidden (galaxy.schema.schema.ExportHistoryArchivePayload attribute) (galaxy.schema.schema.ExportRecordData attribute) (galaxy.schema.schema.StoreExportPayload attribute) (galaxy.schema.tasks.SetupHistoryExportJob attribute) include_nested_invocations (galaxy.schema.schema.InvocationIndexQueryPayload attribute) include_terminal (galaxy.schema.schema.InvocationIndexQueryPayload attribute) include_test_data_dir (galaxy_test.driver.integration_setup.PosixFileSourceSetup attribute) included_collections (galaxy.model.store.BagDirectoryModelExportStore attribute) (galaxy.model.store.BcoModelExportStore attribute) (galaxy.model.store.ROCrateModelExportStore attribute) (galaxy.model.store.WorkflowInvocationOnlyExportStore attribute) included_datasets (galaxy.model.store.BagDirectoryModelExportStore attribute) (galaxy.model.store.BcoModelExportStore attribute) (galaxy.model.store.ROCrateModelExportStore attribute) (galaxy.model.store.WorkflowInvocationOnlyExportStore attribute) (galaxy.model.store.WriteCrates attribute) included_invocations (galaxy.model.store.BagDirectoryModelExportStore attribute) (galaxy.model.store.BcoModelExportStore attribute) (galaxy.model.store.ROCrateModelExportStore attribute) (galaxy.model.store.WorkflowInvocationOnlyExportStore attribute) (galaxy.model.store.WriteCrates attribute) included_libraries (galaxy.model.store.BagDirectoryModelExportStore attribute) (galaxy.model.store.BcoModelExportStore attribute) (galaxy.model.store.ROCrateModelExportStore attribute) (galaxy.model.store.WorkflowInvocationOnlyExportStore attribute) included_library_folders (galaxy.model.store.BagDirectoryModelExportStore attribute) (galaxy.model.store.BcoModelExportStore attribute) (galaxy.model.store.ROCrateModelExportStore attribute) (galaxy.model.store.WorkflowInvocationOnlyExportStore attribute) includes_data_managers (galaxy.model.tool_shed_install.ToolShedRepository property) includes_datatypes (galaxy.model.tool_shed_install.ToolShedRepository attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) includes_tool_dependencies (galaxy.model.tool_shed_install.ToolShedRepository property) (tool_shed.webapp.model.RepositoryMetadata attribute) includes_tools (galaxy.model.tool_shed_install.ToolShedRepository property) (tool_shed.webapp.model.RepositoryMetadata attribute) includes_tools_for_display_in_tool_panel (galaxy.model.tool_shed_install.ToolShedRepository property) (tool_shed.webapp.model.RepositoryMetadata property) includes_workflows (tool_shed.webapp.model.RepositoryMetadata attribute) InconsistentDatabase increase_running_job_count() (galaxy.jobs.handler.JobHandlerQueue method) increment_discovered_file_count() (galaxy.model.store.discover.ModelPersistenceContext method) index() (galaxy.managers.display_applications.DisplayApplicationsManager method) (galaxy.managers.group_roles.GroupRolesManager method) (galaxy.managers.group_users.GroupUsersManager method) (galaxy.managers.groups.GroupsManager method) (galaxy.managers.licenses.LicensesManager method) (galaxy.managers.remote_files.RemoteFilesManager method) (galaxy.managers.tool_data.ToolDataManager method) (galaxy.tool_util.deps.views.ContainerResolutionView method) (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController method) (galaxy.webapps.galaxy.api.cloudauthz.CloudAuthzController method) (galaxy.webapps.galaxy.api.configuration.FastAPIConfiguration method) (galaxy.webapps.galaxy.api.container_resolution.ContainerResolutionAPIController method) (galaxy.webapps.galaxy.api.datatypes.FastAPIDatatypes method) (galaxy.webapps.galaxy.api.display_applications.FastAPIDisplay method) (galaxy.webapps.galaxy.api.dynamic_tools.DynamicToolsController method) (galaxy.webapps.galaxy.api.extended_metadata.BaseExtendedMetadataController method) (galaxy.webapps.galaxy.api.folder_contents.FastAPILibraryFoldersContents method) (galaxy.webapps.galaxy.api.forms.FormDefinitionAPIController method) (galaxy.webapps.galaxy.api.genomes.FastAPIGenomes method) (galaxy.webapps.galaxy.api.group_roles.FastAPIGroupRoles method) (galaxy.webapps.galaxy.api.group_users.FastAPIGroupUsers method) (galaxy.webapps.galaxy.api.groups.FastAPIGroups method) (galaxy.webapps.galaxy.api.job_files.JobFilesAPIController method) (galaxy.webapps.galaxy.api.libraries.FastAPILibraries method) (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method) (galaxy.webapps.galaxy.api.licenses.FastAPILicenses method) (galaxy.webapps.galaxy.api.page_revisions.PageRevisionsController method) (galaxy.webapps.galaxy.api.pages.FastAPIPages method) (galaxy.webapps.galaxy.api.plugins.PluginsController method) (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method) (galaxy.webapps.galaxy.api.quotas.FastAPIQuota method) (galaxy.webapps.galaxy.api.remote_files.FastAPIRemoteFiles method) (galaxy.webapps.galaxy.api.roles.FastAPIRoles method) (galaxy.webapps.galaxy.api.sanitize_allow.SanitizeAllowController method) (galaxy.webapps.galaxy.api.tool_data.FastAPIToolData method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) (galaxy.webapps.galaxy.api.tool_entry_points.ToolEntryPointsAPIController method) (galaxy.webapps.galaxy.api.tool_shed_repositories.FastAPIToolShedRepositories method) (galaxy.webapps.galaxy.api.tools.ToolsController method) (galaxy.webapps.galaxy.api.toolshed.ToolShedController method) (galaxy.webapps.galaxy.api.tours.FastAPITours method) (galaxy.webapps.galaxy.api.trs_search.TrsSearchAPIController method) (galaxy.webapps.galaxy.api.users.FastAPIUsers method) (galaxy.webapps.galaxy.api.visualizations.FastAPIVisualizations method) (galaxy.webapps.galaxy.controllers.async.ASync method) (galaxy.webapps.galaxy.controllers.authnz.OIDC method) (galaxy.webapps.galaxy.controllers.error.Error method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.root.RootController method) (galaxy.webapps.galaxy.controllers.shed_tool_static.ShedToolStatic method) (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) (galaxy.webapps.galaxy.services.histories.HistoriesService method) (galaxy.webapps.galaxy.services.libraries.LibrariesService method) (galaxy.webapps.galaxy.services.library_folder_contents.LibraryFolderContentsService method) (galaxy.webapps.galaxy.services.pages.PagesService method) (galaxy.webapps.galaxy.services.quotas.QuotasService method) (galaxy.webapps.galaxy.services.visualizations.VisualizationsService method) (galaxy.webapps.reports.controllers.root.Report method) (galaxy.webapps.reports.controllers.system.System method) (galaxy_test.base.populators.BaseWorkflowPopulator method) (tool_shed.util.admin_util.Admin method) (tool_shed.webapp.api.categories.CategoriesController method) (tool_shed.webapp.api.groups.GroupsController method) (tool_shed.webapp.api.repositories.RepositoriesController method) (tool_shed.webapp.api.repository_revisions.RepositoryRevisionsController method) (tool_shed.webapp.api.tools.ToolsController method) (tool_shed.webapp.api.users.UsersController method) (tool_shed.webapp.controllers.groups.Group method) (tool_shed.webapp.controllers.repository.RepositoryController method) (tool_shed.webapp.controllers.user.User method) index_deleted() (galaxy.webapps.galaxy.api.libraries.FastAPILibraries method) (galaxy.webapps.galaxy.api.quotas.FastAPIQuota method) (galaxy.webapps.galaxy.api.users.FastAPIUsers method) index_exists() (in module galaxy.model.migrations.util) index_exports() (galaxy.webapps.galaxy.services.histories.HistoriesService method) index_ids() (galaxy_test.base.populators.BaseWorkflowPopulator method) index_of_tool_id() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) index_query() (galaxy.managers.histories.HistoryManager method) (galaxy.managers.jobs.JobManager method) (galaxy.managers.pages.PageManager method) (galaxy.managers.visualizations.VisualizationManager method) (galaxy.managers.workflows.WorkflowsManager method) (galaxy.webapps.galaxy.services.histories.HistoriesService method) index_repositories() (in module tool_shed.managers.repositories) index_tool_ids() (in module tool_shed.managers.repositories) indexer (galaxy.model.GenomeIndexToolData attribute) indexes() (galaxy.webapps.galaxy.api.genomes.FastAPIGenomes method) IndexQueryTag (class in galaxy.webapps.galaxy.api) IndividualTagsColumn (class in galaxy.web.legacy_framework.grids) InfernalCM (class in galaxy.datatypes.msa) Inflector (class in galaxy.util.inflection) InfluxDBPlugin (class in galaxy.tools.error_reports.plugins.influxdb) info (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.Job attribute) (galaxy.model.JobStateHistory attribute) (galaxy.model.LibraryDataset property) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryInfoAssociation attribute) (galaxy.model.store.discover.DiscoveredResultState attribute) (galaxy.model.Task attribute) (galaxy.schema.fetch_data.BaseDataElement attribute) INFO (galaxy.tool_util.lint.LintLevel attribute) info() (galaxy.tool_util.lint.LintContext method) info_message() (galaxy.tool_util.verify.script.Results method) info_messages (galaxy.tool_util.lint.LintContext property) info_text (galaxy.web.legacy_framework.grids.Grid attribute) ingress_object_dict() (in module galaxy.jobs.runners.util.pykube_util) inheritable (galaxy.model.LibraryDatasetDatasetInfoAssociation property) (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryInfoAssociation attribute) init() (in module galaxy.model.mapping) (in module galaxy.model.tool_shed_install.mapping) (in module galaxy.selenium.context) (in module galaxy.selenium.jupyter_context) (in module galaxy_test.selenium.jupyter_context) (in module tool_shed.webapp.model.mapping) init_celery_app() (in module galaxy.celery) init_datatypes() (galaxy.model.unittest_utils.data_app.GalaxyDataTestApp method) (galaxy.model.unittest_utils.GalaxyDataTestApp method) init_fork_pool() (in module galaxy.celery) init_job_handling() (galaxy.web_stack.ApplicationStack method) init_late_prefork() (galaxy.web_stack.ApplicationStack method) (galaxy.web_stack.transport.ApplicationStackTransport method) init_meta() (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.binary.SQlite method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.hdf5.HDF5SummarizedExperiment method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.mothur.DistanceMatrix method) (galaxy.datatypes.mothur.GroupAbund method) (galaxy.datatypes.mothur.LowerTriangleDistanceMatrix method) (galaxy.datatypes.mothur.Sabund method) (galaxy.datatypes.mothur.SquareDistanceMatrix method) (galaxy.datatypes.sequence.Maf method) (galaxy.datatypes.tabular.Pileup method) (galaxy.model.DatasetInstance method) init_models_from_config() (in module galaxy.model.mapping) init_new_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method) init_on_load() (galaxy.model.History method) (galaxy.model.WorkflowStep method) init_repository() (in module tool_shed.util.hg_util) init_tag_associations() (galaxy.model.tags.GalaxyTagHandler class method) initial_metadata_dict() (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator method) (galaxy.tool_shed.metadata.metadata_generator.GalaxyMetadataGenerator method) (tool_shed.metadata.repository_metadata_manager.ToolShedMetadataGenerator method) initialize() (galaxy.tools.DefaultToolState method) initialize_all_repository_dependencies() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) initialize_fast_app() (in module galaxy.webapps.galaxy.fast_app) (in module galaxy.webapps.reports.fast_app) (in module tool_shed.webapp.fast_app) initiate_repository_installation() (galaxy.tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) inject() (galaxy.workflow.modules.WorkflowModuleInjector method) inject_all() (galaxy.workflow.modules.WorkflowModuleInjector method) inject_shed_browser() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) inject_validates() (in module galaxy.tool_util.parser.xml) injection_aware (galaxy.webapps.base.webapp.WebApplication attribute) (galaxy.webapps.galaxy.buildapp.GalaxyWebApplication attribute) (tool_shed.webapp.buildapp.CommunityWebApplication attribute) InMemoryCache (class in galaxy.tool_util.biotools.source) InnerCollectionFilter (class in galaxy.model) inp_data (galaxy.model.IoDicts attribute) Input (class in galaxy.schema.schema) input (galaxy.tool_util.parser.output_objects.ChangeFormatModel attribute) (galaxy.tools.wrappers.DatasetListWrapper attribute) (galaxy.tools.wrappers.InputValueWrapper attribute) (galaxy.tools.wrappers.RawObjectWrapper attribute) (galaxy.tools.wrappers.SelectToolParameterWrapper attribute) (galaxy.tools.wrappers.ToolParameterValueWrapper attribute) (galaxy.workflow.refactor.schema.ConnectAction attribute) (galaxy.workflow.refactor.schema.DisconnectAction attribute) (galaxy.workflow.refactor.schema.ExtractInputAction attribute)

input_associations (galaxy.model.WorkflowInvocation property) input_combinations (galaxy.tools.parameters.meta.WorkflowParameterExpansion attribute) input_connections (galaxy.model.WorkflowStep property) (galaxy.schema.schema.WorkflowStepToExportBase attribute) input_connections_by_name (galaxy.model.WorkflowStep property) input_dataset (galaxy.tool_util.parser.output_objects.ChangeFormatModel attribute) input_dataset_collection (galaxy.model.ImplicitlyCreatedDatasetCollectionInput attribute) input_dataset_collection_elements (galaxy.model.Job attribute) input_dataset_collection_id (galaxy.model.ImplicitlyCreatedDatasetCollectionInput attribute) input_dataset_collections (galaxy.model.Job attribute) (galaxy.model.WorkflowInvocation attribute) input_datasets (galaxy.model.Job attribute) (galaxy.model.WorkflowInvocation attribute) input_dbkey (galaxy.job_execution.output_collect.JobContext property) (galaxy.model.store.discover.ModelPersistenceContext property) input_default_value (galaxy.model.WorkflowStep property) input_extra_files_rewrite() (galaxy.job_execution.compute_environment.ComputeEnvironment method) (galaxy.job_execution.compute_environment.SharedComputeEnvironment method) input_library_datasets (galaxy.model.Job attribute) input_metadata_rewrite() (galaxy.job_execution.compute_environment.ComputeEnvironment method) (galaxy.job_execution.compute_environment.SharedComputeEnvironment method) input_name (galaxy.model.WorkflowStepConnection property) (galaxy.workflow.refactor.schema.InputReferenceByLabel attribute) (galaxy.workflow.refactor.schema.InputReferenceByOrderIndex attribute) (galaxy.workflow.refactor.schema.RefactorActionExecutionMessage attribute) input_optional (galaxy.model.WorkflowStep property) input_parameters (galaxy.model.WorkflowInvocation attribute) input_params (galaxy.tools.ApplyRulesTool attribute) (galaxy.tools.AsyncDataSourceTool attribute) (galaxy.tools.BuildListCollectionTool attribute) (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.DataDestinationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.DuplicateFileToCollectionTool attribute) (galaxy.tools.ExportHistoryTool attribute) (galaxy.tools.ExpressionTool attribute) (galaxy.tools.ExtractDatasetCollectionTool attribute) (galaxy.tools.FilterDatasetsTool attribute) (galaxy.tools.FilterEmptyDatasetsTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) (galaxy.tools.FilterFromFileTool attribute) (galaxy.tools.FlattenTool attribute) (galaxy.tools.HarmonizeTool attribute) (galaxy.tools.ImportHistoryTool attribute) (galaxy.tools.InteractiveTool attribute) (galaxy.tools.KeepSuccessDatasetsTool attribute) (galaxy.tools.MergeCollectionTool attribute) (galaxy.tools.OutputParameterJSONTool attribute) (galaxy.tools.RelabelFromFileTool attribute) (galaxy.tools.SortTool attribute) (galaxy.tools.TagFromFileTool attribute) (galaxy.tools.UnzipCollectionTool attribute) (galaxy.tools.ZipCollectionTool attribute) input_path_rewrite() (galaxy.job_execution.compute_environment.ComputeEnvironment method) (galaxy.job_execution.compute_environment.SharedComputeEnvironment method) input_step (galaxy.model.WorkflowStepConnection property) input_step_id (galaxy.model.WorkflowStepConnection property) input_step_input (galaxy.model.WorkflowStepConnection attribute) input_step_input_id (galaxy.model.WorkflowStepConnection attribute) input_step_parameters (galaxy.model.WorkflowInvocation attribute) input_step_types (galaxy.model.Workflow attribute) input_steps (galaxy.model.Workflow property) (galaxy.schema.schema.WorkflowStepBase attribute) input_subworkflow_step (galaxy.model.WorkflowStepConnection attribute) input_subworkflow_step_id (galaxy.model.WorkflowStepConnection attribute) (galaxy.schema.schema.InputConnection attribute) INPUT_TYPE (class in galaxy.tool_util.cwl.representation) input_type (galaxy.model.WorkflowStep property) InputConnection (class in galaxy.schema.schema) InputDataCollectionModule (class in galaxy.workflow.modules) InputDataCollectionStep (class in galaxy.schema.schema) InputDataModule (class in galaxy.workflow.modules) InputDataStep (class in galaxy.schema.schema) InputKey (class in galaxy.tools.parameters.meta) InputMatchedException InputModule (class in galaxy.workflow.modules) InputModuleState (class in galaxy.workflow.modules) InputNotFoundSyntaxError InputParameterModule (class in galaxy.workflow.modules) InputParameterStep (class in galaxy.schema.schema) InputProxy (class in galaxy.workflow.modules) InputReferenceByLabel (class in galaxy.workflow.refactor.schema) InputReferenceByOrderIndex (class in galaxy.workflow.refactor.schema) inputs (galaxy.model.WorkflowStep attribute) (galaxy.schema.schema.JobDetails attribute) (galaxy.schema.schema.WorkflowStepToExportBase attribute) (galaxy.tool_util.parser.interface.ToolSourceTest attribute) (galaxy.tool_util.verify.interactor.InvalidToolTestDict attribute) (galaxy.tool_util.verify.interactor.RunToolResponse attribute) (galaxy.tool_util.verify.interactor.ToolTestDescriptionDict attribute) (galaxy.tool_util.verify.interactor.ValidToolTestDict attribute) (galaxy_test.api.test_workflow_extraction.RunJobsSummary attribute) (galaxy_test.base.populators.RunJobsSummary attribute) inputs_by_name (galaxy.model.WorkflowStep property) inputs_by_page (galaxy.tools.ApplyRulesTool attribute) (galaxy.tools.AsyncDataSourceTool attribute) (galaxy.tools.BuildListCollectionTool attribute) (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.DataDestinationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.DuplicateFileToCollectionTool attribute) (galaxy.tools.ExportHistoryTool attribute) (galaxy.tools.ExpressionTool attribute) (galaxy.tools.ExtractDatasetCollectionTool attribute) (galaxy.tools.FilterDatasetsTool attribute) (galaxy.tools.FilterEmptyDatasetsTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) (galaxy.tools.FilterFromFileTool attribute) (galaxy.tools.FlattenTool attribute) (galaxy.tools.HarmonizeTool attribute) (galaxy.tools.ImportHistoryTool attribute) (galaxy.tools.InteractiveTool attribute) (galaxy.tools.KeepSuccessDatasetsTool attribute) (galaxy.tools.MergeCollectionTool attribute) (galaxy.tools.OutputParameterJSONTool attribute) (galaxy.tools.RelabelFromFileTool attribute) (galaxy.tools.SortTool attribute) (galaxy.tools.TagFromFileTool attribute) (galaxy.tools.UnzipCollectionTool attribute) (galaxy.tools.ZipCollectionTool attribute) inputs_defined (galaxy.tool_util.parser.interface.PagesSource property) (galaxy.tool_util.parser.xml.XmlPagesSource property) InputsBoolDistinctValues (class in galaxy.tool_util.linters.inputs) InputsBoolProblematic (class in galaxy.tool_util.linters.inputs) InputsDataFormat (class in galaxy.tool_util.linters.inputs) InputsDataOptionsAttrib (class in galaxy.tool_util.linters.inputs) InputsDataOptionsFilterAttribFiltersType (class in galaxy.tool_util.linters.inputs) InputsDataOptionsFiltersRef (class in galaxy.tool_util.linters.inputs) InputsDataOptionsFiltersType (class in galaxy.tool_util.linters.inputs) InputsDataOptionsMultiple (class in galaxy.tool_util.linters.inputs) InputsDatasourceTags (class in galaxy.tool_util.linters.inputs) InputsMissing (class in galaxy.tool_util.linters.inputs) InputsMissingDataSource (class in galaxy.tool_util.linters.inputs) InputsName (class in galaxy.tool_util.linters.inputs) InputsNameDuplicate (class in galaxy.tool_util.linters.inputs) InputsNameDuplicateOutput (class in galaxy.tool_util.linters.inputs) InputsNameEmpty (class in galaxy.tool_util.linters.inputs) InputsNameRedundantArgument (class in galaxy.tool_util.linters.inputs) InputsNameValid (class in galaxy.tool_util.linters.inputs) InputsNum (class in galaxy.tool_util.linters.inputs) InputSource (class in galaxy.tool_util.parser.interface) InputsSelectDynamicOptions (class in galaxy.tool_util.linters.inputs) InputsSelectMandatoryCheckboxes (class in galaxy.tool_util.linters.inputs) InputsSelectMultipleRadio (class in galaxy.tool_util.linters.inputs) InputsSelectOptionalRadio (class in galaxy.tool_util.linters.inputs) InputsSelectOptionDuplicateText (class in galaxy.tool_util.linters.inputs) InputsSelectOptionDuplicateValue (class in galaxy.tool_util.linters.inputs) InputsSelectOptionsDef (class in galaxy.tool_util.linters.inputs) InputsSelectOptionsDefConditional (class in galaxy.tool_util.linters.inputs) InputsSelectOptionsDefinesOptions (class in galaxy.tool_util.linters.inputs) InputsSelectOptionsDeprecatedAttr (class in galaxy.tool_util.linters.inputs) InputsSelectOptionsFromDatasetAndDatatable (class in galaxy.tool_util.linters.inputs) InputsSelectOptionsMetaFileKey (class in galaxy.tool_util.linters.inputs) InputsSelectOptionsMultiple (class in galaxy.tool_util.linters.inputs) InputsSelectOptionValueMissing (class in galaxy.tool_util.linters.inputs) InputsSelectSingleCheckboxes (class in galaxy.tool_util.linters.inputs) InputStep (class in galaxy.schema.schema) InputsTypeChildCombination (class in galaxy.tool_util.linters.inputs) InputValueWrapper (class in galaxy.tools.wrappers) InRangeValidator (class in galaxy.tools.parameters.validation) insert() (galaxy.model.custom_types.MutationList method) (galaxy.tool_util.cwl.cwltool_deps.CommentedMap method) (galaxy.util.odict.odict method) insert_tool() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) InsertColumnToolOutputActionOptionFilter (class in galaxy.tool_util.parser.output_actions) install() (galaxy.tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) (in module galaxy.model.triggers.update_audit_table) install_all() (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method) install_conda() (in module galaxy.tool_util.deps.conda_util) install_conda_target() (in module galaxy.tool_util.deps.conda_util) install_data_managers() (galaxy.tool_shed.galaxy_install.tools.data_manager.DataManagerHandler method) install_dependencies() (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tools.ToolsController method) install_dependency() (galaxy.tool_util.deps.resolvers.DependencyResolver method) (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) install_environment (galaxy.tool_util.deps.conda_util.CondaTarget property) install_matched_repository_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) install_model (galaxy.app.MinimalGalaxyApplication attribute) (galaxy.app_unittest_utils.galaxy_mock.MockApp attribute) (galaxy.managers.context.ProvidesAppContext property) (galaxy.structured_app.MinimalApp attribute) install_model_scoped_session (class in galaxy.model.scoped_session) install_options (galaxy.managers.workflows.WorkflowCreateOptions property) install_repositories() (galaxy.tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) install_repository() (tool_shed.test.base.twilltestcase.GalaxyInteractorToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.StandaloneToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ToolShedInstallationClient method) install_repository_dependencies (galaxy.managers.workflows.WorkflowCreateOptions attribute) install_repository_revision() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) install_repository_revisions() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) install_resolver_dependencies (galaxy.managers.workflows.WorkflowCreateOptions attribute) install_session() (in module tool_shed.test.base.test_db_util) install_timestamp_triggers() (in module galaxy.model.triggers.history_update_time_field) install_tool_data_tables() (galaxy.tool_shed.tools.data_table_manager.ShedToolDataTableManager method) (tool_shed.tools.data_table_manager.ShedToolDataTableManager method) install_tool_dependencies (galaxy.managers.workflows.WorkflowCreateOptions attribute) install_tool_shed_repository() (galaxy.tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) installable_description (galaxy.tool_util.deps.conda_util.CondaContext attribute) (galaxy.tool_util.deps.installable.InstallableContext property) installable_resolvers (galaxy.tool_util.deps.views.DependencyResolversView property) installable_revisions() (tool_shed.webapp.model.Repository method) InstallableContext (class in galaxy.tool_util.deps.installable) installation_directory() (galaxy.model.tool_shed_install.ToolDependency method) installation_status (galaxy.model.tool_shed_install.ToolDependency attribute) INSTALLED (galaxy.model.tool_shed_install.ToolShedRepository.installation_status attribute) installed_builds (galaxy.schema.schema.CustomBuildsMetadataResponse attribute) installed_changeset_revision (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.schema.schema.InstalledToolShedRepository attribute) installed_dependent_repositories_of_installed_repositories (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager attribute) installed_len_files (galaxy.webapps.galaxy.controllers.user.User attribute) installed_repository_dependencies (galaxy.model.tool_shed_install.ToolShedRepository property) installed_repository_dependencies_of_installed_repositories (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager attribute) installed_repository_dicts (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager attribute) installed_repository_extended_info() (tool_shed.test.base.twilltestcase.GalaxyInteractorToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.StandaloneToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ToolShedInstallationClient method) installed_repository_manager (galaxy.structured_app.MinimalManagerApp attribute) installed_tool_dependencies (galaxy.model.tool_shed_install.ToolShedRepository property) (galaxy.tools.Tool property) InstalledRepositoryManager (class in galaxy.tool_shed.galaxy_install.installed_repository_manager) InstalledRepositoryMetadataManager (class in galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager) InstalledRepositoryToolShedStatus (class in galaxy.schema.schema) InstalledToolShedRepositories (class in galaxy.schema.schema) InstalledToolShedRepository (class in galaxy.schema.schema) INSTALLING (galaxy.model.tool_shed_install.ToolDependency.states attribute) (galaxy.model.tool_shed_install.ToolShedRepository.states attribute) INSTALLING_REPOSITORY_DEPENDENCIES (galaxy.model.tool_shed_install.ToolShedRepository.installation_status attribute) INSTALLING_TOOL_DEPENDENCIES (galaxy.model.tool_shed_install.ToolShedRepository.installation_status attribute) InstallMatchedRepositoryGrid (class in tool_shed.grids.repository_grids) InstallRepositoryManager (class in galaxy.tool_shed.galaxy_install.install_manager) instance_type (galaxy.schema.schema.CreateNewCollectionPayload attribute) institution (galaxy.model.UserAddress attribute) InstrumentPlugin (class in galaxy.job_metrics.instrumenters) InsufficientPermissionsException int_range() (galaxy.managers.base.ModelValidator static method) int_to_octet() (in module galaxy.webapps.reports.controllers.history) (in module galaxy.webapps.reports.controllers.tools) INTEGER (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute) IntegerColumn (class in galaxy.web.legacy_framework.grids) IntegerToolParameter (class in galaxy.tools.parameters.basic) integrated_tool_panel_config (galaxy.config.GalaxyAppConfiguration attribute) integration_module_instance() (in module galaxy_test.driver.integration_util) integration_tool_runner() (in module galaxy_test.driver.integration_util) IntegrationInstance (class in galaxy_test.driver.integration_util) IntegrationTestCase (class in galaxy_test.driver.integration_util) InteractiveTool (class in galaxy.tools) interactivetool_entry_points (galaxy.model.Job attribute) interactivetool_manager (galaxy.structured_app.StructuredApp attribute) InteractiveToolEntryPoint (class in galaxy.model) InteractiveToolManager (class in galaxy.managers.interactivetool) interactivetools (galaxy.tools.evaluation.PartialToolEvaluator attribute) (galaxy.tools.evaluation.RemoteToolEvaluator attribute) interactivetools_enable (galaxy.tools.repositories.ValidationContextConfig attribute) InteractiveToolSqlite (class in galaxy.managers.interactivetool) InteractorStaging (class in galaxy.tool_util.client.staging) internal_galaxy_markdown_to_pdf() (in module galaxy.managers.markdown_util) InternalServerError InterruptedUpload intersection_over_union() (in module galaxy.tool_util.verify) Interval (class in galaxy.datatypes.interval) interval_dataprovider() (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) interval_dict_dataprovider() (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) IntervalDataProvider (class in galaxy.datatypes.dataproviders.dataset) (class in galaxy.visualization.data_providers.genome) IntervalIndexDataProvider (class in galaxy.visualization.data_providers.genome) IntervalTabix (class in galaxy.datatypes.interval) IntervalTabixDataProvider (class in galaxy.visualization.data_providers.genome) IntervalTask (class in galaxy.util.task) INVALID (galaxy.schema.schema.DatasetValidatedState attribute) invalid() (galaxy.datatypes.data.DatatypeValidation static method) invalid_file_tups (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator attribute) (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager attribute) (tool_shed.metadata.repository_metadata_manager.ToolShedMetadataGenerator attribute) invalid_tools_labels (tool_shed.test.base.twilltestcase.ShedTwillTestCase property) InvalidAuthnzConfigException InvalidDataProviderSource InvalidFileFormatError InvalidModelIdError InvalidRepositoryDependency (class in tool_shed.utility_containers) InvalidToolDependency (class in tool_shed.utility_containers) InvalidToolTestDict (class in galaxy.tool_util.verify.interactor) InvalidVaultConfigException InvalidVaultKeyException INVOCATION (galaxy.schema.schema.ExportObjectType attribute) invocation (galaxy_test.base.populators.RunJobsSummary attribute) invocation_counts() (galaxy.model.StoredWorkflow method) invocation_id (galaxy.schema.schema.CreatePagePayload attribute) (galaxy.schema.schema.JobIndexQueryPayload attribute) (galaxy.schema.tasks.GenerateInvocationDownload attribute) (galaxy.schema.tasks.WriteInvocationTo attribute) (galaxy_test.base.populators.RunJobsSummary attribute) invocation_index_table_elements() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) invocation_job_source_iter() (in module galaxy.managers.jobs) invocation_jobs() (galaxy_test.base.populators.BaseDatasetPopulator method) invocation_report (galaxy.schema.PdfDocumentType attribute) invocation_to_output() (in module galaxy.tool_util.cwl.util) InvocationGrabber (class in galaxy.jobs.handler) InvocationIndexQueryPayload (class in galaxy.schema.schema) invocations_properties() (galaxy.model.store.BaseDirectoryImportModelStore method) (galaxy.model.store.DictImportModelStore method) (galaxy.model.store.ModelImportStore method) InvocationSortByEnum (class in galaxy.schema.schema) invoke_alembic() (in module galaxy.model.migrations.scripts) invoke_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method) invoke_workflow_and_assert_ok() (galaxy_test.base.populators.BaseWorkflowPopulator method) invoke_workflow_and_wait() (galaxy_test.base.populators.BaseWorkflowPopulator method) invoke_workflow_raw() (galaxy_test.base.populators.BaseWorkflowPopulator method) involucro_path (galaxy.config.GalaxyAppConfiguration attribute) io_dicts() (galaxy.model.Job method) IoDicts (class in galaxy.model) Ipynb (class in galaxy.datatypes.text) IQTree (class in galaxy.datatypes.text) IRODSObjectStore (class in galaxy.objectstore.irods) IRREGULAR_WORDS (galaxy.util.inflection.Inflector attribute) is_a_yaml_with_class() (in module galaxy.tool_util.loader_directory) is_aborted() (in module galaxy.celery.tasks) is_absent (galaxy.selenium.smart_components.SmartTarget property) is_accessible() (galaxy.managers.datasets.DatasetAssociationManager method) (galaxy.managers.datasets.DatasetManager method) (galaxy.managers.hdas.HDAManager method) (galaxy.managers.secured.AccessibleManagerMixin method) (galaxy.managers.sharable.SharableModelManager method) is_active() (galaxy.model.User method) is_admin (galaxy.files.DictFileSourcesUserContext property) (galaxy.files.ProvidesUserFileSourcesUserContext property) (galaxy.managers.folders.SecurityParams attribute) (galaxy.schema.schema.DetailedUserModel attribute) is_admin() (galaxy.managers.users.UserManager method) is_admin_user (galaxy.tools.remote_tool_eval.ToolAppConfig attribute) is_admin_user() (galaxy.config.CommonConfigurationMixin method) is_anonymous() (galaxy.managers.users.UserManager method) is_authenticated() (galaxy.model.User method) is_auto_migrate (galaxy.model.migrations.DatabaseStateVerifier property) is_bag() (galaxy.schema.schema.ModelStoreFormat class method) is_bam() (galaxy.datatypes.binary.BamNative class method) is_binary (galaxy.datatypes.binary.Cel attribute) (galaxy.datatypes.binary.CompressedArchive attribute) (galaxy.datatypes.binary.MashSketch attribute) (galaxy.datatypes.constructive_solid_geometry.GmshMsh attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.data.Text attribute) (galaxy.datatypes.media.Wav attribute) (galaxy.datatypes.upload_util.HandleUploadResponse attribute) is_binary() (in module galaxy.util) is_bz2() (in module galaxy.datatypes.checkers) (in module galaxy.util.checkers) is_case() (galaxy.tool_util.parser.output_actions.DatatypeIsInstanceToolOutputActionConditionalWhen method) (galaxy.tool_util.parser.output_actions.ToolOutputActionConditionalWhen method) (galaxy.tool_util.parser.output_actions.ValueToolOutputActionConditionalWhen method) is_checked() (galaxy.util.form_builder.CheckboxField static method) (galaxy.web.form_builder.CheckboxField static method) is_circular_repository_dependency() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) is_collection (galaxy.model.DatasetCollectionElement property) (galaxy.tools.wrappers.DatasetCollectionWrapper property) (galaxy.tools.wrappers.DatasetFilenameWrapper property) is_column_based() (in module galaxy.datatypes.sniff) is_composite() (galaxy.managers.datasets.DatasetAssociationManager method) is_compressed (galaxy.datatypes.sniff.HandleCompressedFileResponse attribute) is_compressed() (galaxy.schema.schema.ModelStoreFormat class method) is_conda_installed() (galaxy.tool_util.deps.conda_util.CondaContext method) is_config_watcher (galaxy.model.database_heartbeat.DatabaseHeartbeat property) is_current_version() (galaxy.tools.data.ToolDataTable method) is_datatype_change_allowed() (galaxy.datatypes.data.Data class method) is_datatype_converter (galaxy.tools.Tool property) is_deactivated_or_installed (galaxy.model.tool_shed_install.ToolShedRepository property) is_deprecated_in_tool_shed (galaxy.model.tool_shed_install.ToolShedRepository property) is_dict() (in module galaxy.tool_util.parser.util) is_dir() (galaxy.util.resources.Traversable method) is_displayed (galaxy.selenium.smart_components.SmartTarget property) is_displayed() (galaxy.selenium.has_driver.HasDriver method) is_downloadable() (in module tool_shed.util.metadata_util) is_extension_unsniffable_binary() (galaxy.datatypes.registry.Registry method) is_fetch_with_celery_enabled() (galaxy.config.GalaxyAppConfiguration method) is_file() (galaxy.util.resources.Traversable method) is_file_empty() (galaxy.tools.parameters.basic.ColumnListParameter method) is_float() (galaxy.datatypes.tabular.TabularData method) is_gzip() (in module galaxy.datatypes.checkers) (in module galaxy.util.checkers) is_handler (galaxy.web_stack.handlers.ConfiguresHandlers property) is_hashable() (in module galaxy.util.hash_util) is_hda() (in module galaxy.model) is_history_shared_with() (galaxy.managers.histories.HistoryManager method) is_id() (galaxy.jobs.JobConfiguration method) is_importable (galaxy.managers.workflows.WorkflowCreateOptions property) is_in() (in module galaxy.util.specs) is_in_repo_info_dicts() (galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) is_input_supplied (galaxy.tools.wrappers.DatasetCollectionWrapper property) is_installed (galaxy.model.tool_shed_install.ToolDependency property) (galaxy.model.tool_shed_install.ToolShedRepository property) is_installed() (galaxy.tool_util.deps.conda_util.CondaContext method) (galaxy.tool_util.deps.installable.InstallableContext method) is_int() (galaxy.datatypes.tabular.TabularData method) is_integrity_error() (galaxy.authnz.psa_authnz.Storage class method) is_job_handler (galaxy.app.GalaxyManagerApplication property) (galaxy.structured_app.MinimalManagerApp property) is_JSONified_value() (galaxy.datatypes.metadata.MetadataTempFile class method) (galaxy.model.metadata.MetadataTempFile class method) is_latest_installable_revision (galaxy.model.tool_shed_install.ToolShedRepository property) is_latest_version (galaxy.tools.Tool property) is_leaf (galaxy.model.dataset_collections.structure.Leaf property) (galaxy.model.dataset_collections.structure.Tree property) (galaxy.model.dataset_collections.structure.UninitializedTree property) is_level_one_certified() (tool_shed.repository_registry.Registry method) is_logged_in() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) is_malicious() (in module tool_shed.util.metadata_util) is_mapped_over() (galaxy.model.dataset_collections.matching.MatchingCollections method) is_missing_shed_tool() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) is_named_collection_part_name() (galaxy.tool_util.parser.output_objects.ToolOutputCollectionPart static method) (galaxy.tool_util.parser.ToolOutputCollectionPart static method) is_new (galaxy.model.Dataset property) (galaxy.model.tool_shed_install.ToolShedRepository property) (galaxy.model.WorkflowInvocationStep property) is_new() (tool_shed.webapp.model.Repository method) is_new_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method) is_object_applicable() (galaxy.visualization.plugins.registry.VisualizationsRegistry method) is_of_type() (galaxy.tools.wrappers.DatasetFilenameWrapper method) is_ok (galaxy.model.DatasetInstance property) is_one_database() (in module galaxy.model.database_utils) is_optional() (in module galaxy.schema.fields) is_output_name_an_effective_output() (galaxy.model.WorkflowInvocationStepObjectStores method) is_outside_grace_period() (galaxy.webapps.galaxy.controllers.user.User method) is_over_quota() (galaxy.quota.NoQuotaAgent method) is_owner() (galaxy.managers.hdas.HDAManager method) (galaxy.managers.histories.HistoryManager method) (galaxy.managers.secured.OwnableManagerMixin method) (galaxy.managers.sharable.SharableModelManager method) is_package_installed() (galaxy.tool_util.deps.conda_util.CondaContext method) is_path_within_dependency_dir() (in module tool_shed.util.shed_util_common) is_path_within_repo() (in module tool_shed.util.shed_util_common) is_pending (galaxy.model.DatasetInstance property) is_permitted() (galaxy.managers.rbac_secured.AccessDatasetRBACPermission method) (galaxy.managers.rbac_secured.ManageDatasetRBACPermission method) (galaxy.managers.rbac_secured.RBACPermission method) is_pod_unschedulable() (in module galaxy.jobs.runners.util.pykube_util) is_postgres() (in module galaxy.model.database_utils) is_preload_app() (in module galaxy.web_stack.gunicorn_config) is_preparing() (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter method) is_private (galaxy.schema.schema.FileLibraryFolderItem attribute) is_private() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) is_public() (galaxy.managers.libraries.LibraryManager method) (galaxy.managers.rbac_secured.AccessDatasetRBACPermission method) is_read_only_query() (in module galaxy.util.sqlite) is_ready() (galaxy.schema.schema.ExportObjectMetadata method) (galaxy.webapps.galaxy.api.short_term_storage.FastAPIShortTermStorage method) is_registered_dbkey() (galaxy.managers.genomes.GenomesManager method) is_repository_admin_role (tool_shed.webapp.model.Role property) is_runtime_context() (in module galaxy.tools.parameters.basic) is_secure (galaxy.webapps.galaxy.api.GalaxyASGIRequest property) (galaxy.work.context.GalaxyAbstractRequest property) is_set() (galaxy.config.BaseAppConfiguration method) is_short_term() (galaxy.schema.schema.ExportObjectMetadata method) is_split_configuration (galaxy.model.WorkflowInvocationStepObjectStores property) is_subcollection_of_type() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) is_tag() (galaxy.jobs.JobConfiguration method) is_task (galaxy.jobs.TaskWrapper attribute) is_tool_load_error() (in module galaxy.tool_util.loader_directory) is_tool_shed_client() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) is_true() (in module galaxy.web.framework.helpers) is_under_version_control() (galaxy.model.migrations.AlembicManager method) is_unrestricted (galaxy.schema.schema.FileLibraryFolderItem attribute) is_up_to_date() (galaxy.model.migrations.AlembicManager method) is_url() (in module galaxy.util) is_uuid() (in module galaxy.util) is_v2 (tool_shed.test.base.twilltestcase.ShedTwillTestCase property) is_valid (galaxy.datatypes.sniff.HandleCompressedFileResponse attribute) (galaxy.model.GalaxySession attribute) (galaxy.model.JobExternalOutputMetadata attribute) (tool_shed.webapp.model.GalaxySession attribute) is_valid() (tool_shed.repository_registry.Registry method) is_valid_expression() (galaxy.util.bool_expressions.BooleanExpressionEvaluator class method) is_valid_filter() (tool_shed.grids.repository_grid_filter_manager.RepositoryGridFilterManager method) is_valid_for_type() (tool_shed.repository_types.metadata.Metadata method) (tool_shed.repository_types.repository_suite_definition.RepositorySuiteDefinition method) (tool_shed.repository_types.tool_dependency_definition.ToolDependencyDefinition method) (tool_shed.repository_types.unrestricted.Unrestricted method) is_valid_slug() (galaxy.managers.sharable.SharableModelManager method) (in module galaxy.managers.base) is_virtual_display_available() (in module galaxy.selenium.driver_factory) is_webapp (galaxy.app_unittest_utils.galaxy_mock.MockApp attribute) (galaxy.structured_app.MinimalApp attribute) (galaxy.structured_app.MinimalToolApp attribute) (galaxy.tools.remote_tool_eval.ToolApp attribute) (galaxy.tools.repositories.ValidationContext attribute) is_workflow_compatible (galaxy.tools.Tool property) is_xz() (in module galaxy.util.checkers) is_zip() (in module galaxy.util.checkers) IsaJson (class in galaxy.datatypes.isa) IsaTab (class in galaxy.datatypes.isa) isDeprecatedLicenseId (galaxy.managers.licenses.LicenseMetadataModel attribute) isdir() (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method) (galaxy.util.compression_utils.CompressedFile method) isdir_tar() (galaxy.util.compression_utils.CompressedFile method) isdir_zip() (galaxy.util.compression_utils.CompressedFile method) isfile() (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method) (galaxy.util.compression_utils.CompressedFile method) isinstance_datatype() (galaxy.managers.datasets.DatasetAssociationFilterParser method) isolate_galaxy_config (galaxy_test.driver.integration_util.IntegrationInstance attribute) isOsiApproved (galaxy.managers.licenses.LicenseMetadataModel attribute) issue_cache (galaxy.tools.error_reports.plugins.base_git.BaseGitPlugin attribute) issued (galaxy.model.PSAAssociation attribute) issuer (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute) IsUserModel (class in galaxy.managers.api_keys) item (galaxy.model.JobToOutputDatasetAssociation property) (galaxy.model.JobToOutputDatasetCollectionAssociation property) (galaxy.schema.schema.BulkOperationItemError attribute) item_class (galaxy.managers.tags.ItemTagsPayload attribute) item_count (galaxy.model.LibraryFolder attribute) (galaxy.schema.schema.LibraryFolderDetails attribute) item_has_tag() (galaxy.model.tags.TagHandler method) item_id (galaxy.managers.tags.ItemTagsPayload attribute) item_permission_map_for_add() (galaxy.model.security.GalaxyRBACAgent method) item_permission_map_for_manage() (galaxy.model.security.GalaxyRBACAgent method) item_permission_map_for_modify() (galaxy.model.security.GalaxyRBACAgent method) item_tags (galaxy.managers.tags.ItemTagsPayload attribute) ItemAccessibilityException ItemDeletionException ItemGrabber (class in galaxy.jobs.handler) ItemImmutableException ItemOwnershipException ItemRatingAssociation (class in galaxy.model) (class in tool_shed.webapp.model) ItemRatings (class in tool_shed.webapp.util.ratings_util) items (galaxy.schema.fetch_data.CompositeItems attribute) (galaxy.schema.fetch_data.DataElementsTarget attribute) (galaxy.schema.fetch_data.HdcaDataItemsTarget attribute) (galaxy.schema.fetch_data.NestedElement attribute) (galaxy.schema.schema.HistoryContentBulkOperationPayload attribute) (galaxy.schema.schema.UpdateHistoryContentsBatchPayload attribute) (galaxy.tool_util.toolbox.views.definitions.HasItems attribute) (galaxy.tool_util.toolbox.views.definitions.Section attribute) (galaxy.tool_util.toolbox.views.definitions.StaticToolBoxView attribute) items() (galaxy.model.dataset_collections.matching.CollectionsToMatch method) (galaxy.tool_util.cwl.cwltool_deps.CommentedMap method) (galaxy.tools.wrappers.DatasetFilenameWrapper.MetadataWrapper method) (galaxy.util.bunch.Bunch method) (galaxy.util.odict.odict method) items_expanded (galaxy.tool_util.toolbox.views.definitions.HasItems property) items_from (galaxy.schema.fetch_data.BaseDataElement attribute) (galaxy.schema.fetch_data.DataElementsFromTarget attribute) (galaxy.schema.fetch_data.ExtraFiles attribute) (galaxy.schema.fetch_data.FtpImportTarget attribute) (galaxy.schema.fetch_data.HdcaDataItemsFromTarget attribute) (galaxy.schema.fetch_data.PathDataElement attribute) (galaxy.tool_util.toolbox.views.definitions.ItemsFrom attribute) ItemsFrom (class in galaxy.tool_util.toolbox.views.definitions) ItemsFromModel (class in galaxy.schema.fetch_data) ItemsFromSrc (class in galaxy.schema.fetch_data) ItemStateSummary (class in galaxy.schema.schema) ItemTagAssociation (class in galaxy.model) ItemTagAssocInfo (class in galaxy.model.tags) ItemTagsPayload (class in galaxy.managers.tags) iter_blocks_split_by_species() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) iter_blocks_split_by_src() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) iter_components_by_src() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) iter_components_by_src_start() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) iter_fasta_alignment() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) iter_headers() (in module galaxy.datatypes.sniff) iter_start_of_line() (in module galaxy.util) iter_to_string() (in module galaxy.tools.parameters.basic) iterable_has_all() (in module galaxy.managers.rbac_secured) iterate_lines() (galaxy.datatypes.goldenpath.AGPFile method) (galaxy.datatypes.goldenpath.AGPObject method) iterate_objs() (galaxy.datatypes.goldenpath.AGPFile method) iterdir() (galaxy.util.resources.Traversable method) iteritems() (galaxy.util.odict.odict method) iterkeys() (galaxy.util.odict.odict method) ITERPARSE_ALL_EVENTS (galaxy.datatypes.dataproviders.hierarchy.XMLDataProvider attribute) itervalues() (galaxy.util.odict.odict method)

J

javascript_link() (in module galaxy.web.framework.helpers.tags) Job (class in galaxy.model) job (galaxy.job_execution.compute_environment.SharedComputeEnvironment attribute) (galaxy.job_execution.output_collect.JobContext property) (galaxy.job_execution.setup.JobIO property) (galaxy.model.DataManagerJobAssociation attribute) (galaxy.model.Dataset attribute) (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.ImplicitCollectionJobsJobAssociation attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.JobContainerAssociation attribute) (galaxy.model.JobExportHistoryArchive attribute) (galaxy.model.JobExternalOutputMetadata attribute) (galaxy.model.JobImportHistoryArchive attribute) (galaxy.model.JobToImplicitOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetAssociation attribute) (galaxy.model.JobToInputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetCollectionElementAssociation attribute) (galaxy.model.JobToInputLibraryDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToOutputLibraryDatasetAssociation attribute) (galaxy.model.PostJobActionAssociation attribute) (galaxy.model.store.discover.ModelPersistenceContext property) (galaxy.model.store.discover.SessionlessModelPersistenceContext property) (galaxy.model.Task attribute) (galaxy.model.WorkflowInvocationStep attribute) Job (galaxy.schema.schema.JobSourceType attribute) job (galaxy.tools.evaluation.PartialToolEvaluator attribute) (galaxy.tools.evaluation.RemoteToolEvaluator attribute) (galaxy.tools.evaluation.ToolEvaluator attribute) JOB_COMPLETION (galaxy.selenium.navigates_galaxy.WAIT_TYPES attribute) job_config (galaxy.app.MinimalGalaxyApplication attribute) (galaxy.structured_app.MinimalManagerApp attribute) job_count() (galaxy.jobs.rule_helper.RuleHelper method) job_destination (galaxy.jobs.JobWrapper property) job_failed() (galaxy.tools.InteractiveTool method) (galaxy.tools.SetMetadataTool method) (galaxy.tools.Tool method) job_handler (galaxy.jobs.manager.JobManager attribute) job_hash() (galaxy.jobs.rule_helper.RuleHelper method) job_id (galaxy.job_execution.compute_environment.SharedComputeEnvironment attribute) (galaxy.model.DataManagerJobAssociation attribute) (galaxy.model.Dataset attribute) (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.ImplicitCollectionJobsJobAssociation attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.JobContainerAssociation attribute) (galaxy.model.JobExportHistoryArchive attribute) (galaxy.model.JobExternalOutputMetadata attribute) (galaxy.model.JobImportHistoryArchive attribute) (galaxy.model.JobMetricNumeric attribute) (galaxy.model.JobMetricText attribute) (galaxy.model.JobParameter attribute) (galaxy.model.JobStateHistory attribute) (galaxy.model.JobToImplicitOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetAssociation attribute) (galaxy.model.JobToInputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetCollectionElementAssociation attribute) (galaxy.model.JobToInputLibraryDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToOutputLibraryDatasetAssociation attribute) (galaxy.model.PostJobActionAssociation attribute) (galaxy.model.Task attribute) (galaxy.model.WorkflowInvocationMessage attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.schema.schema.InvocationIndexQueryPayload attribute) (galaxy.schema.schema.JobExportHistoryArchiveModel attribute) (galaxy.schema.schema.JobIdResponse attribute) (galaxy.schema.tasks.SetupHistoryExportJob attribute) (galaxy_test.base.populators.CwlToolRun property) job_id() (galaxy.job_execution.output_collect.JobContext method) (galaxy.job_execution.output_collect.SessionlessJobContext method) (galaxy.model.store.discover.ModelPersistenceContext method) job_info (galaxy.tool_util.deps.container_classes.ContainerProtocol property) job_info() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) (galaxy.webapps.reports.controllers.jobs.Jobs method) job_list (galaxy.model.ImplicitCollectionJobs property) job_lock() (galaxy.managers.jobs.JobManager method) job_lock_status() (in module galaxy.webapps.galaxy.api.job_lock) job_manager (galaxy.structured_app.MinimalManagerApp attribute) job_messages (galaxy.model.Job attribute) (galaxy.model.Task attribute) (galaxy.schema.schema.JobFullDetails attribute) job_metrics (galaxy.app_unittest_utils.galaxy_mock.MockApp attribute) (galaxy.schema.schema.JobFullDetails attribute) (galaxy.structured_app.MinimalManagerApp attribute) JOB_NAME_PREFIX (galaxy.jobs.runners.chronos.ChronosJobRunner attribute) job_object_dict() (in module galaxy.jobs.runners.util.pykube_util) job_output_dataset_associations (galaxy.model.store.BagDirectoryModelExportStore attribute) (galaxy.model.store.BcoModelExportStore attribute) (galaxy.model.store.ROCrateModelExportStore attribute) (galaxy.model.store.WorkflowInvocationOnlyExportStore attribute) job_pair_for_id() (galaxy.jobs.handler.JobHandlerQueue method) job_properties() (galaxy.job_metrics.instrumenters.cgroup.CgroupPlugin method) (galaxy.job_metrics.instrumenters.core.CorePlugin method) (galaxy.job_metrics.instrumenters.cpuinfo.CpuInfoPlugin method) (galaxy.job_metrics.instrumenters.env.EnvPlugin method) (galaxy.job_metrics.instrumenters.hostname.HostnamePlugin method) (galaxy.job_metrics.instrumenters.InstrumentPlugin method) (galaxy.job_metrics.instrumenters.meminfo.MemInfoPlugin method) (galaxy.job_metrics.instrumenters.uname.UnamePlugin method) JOB_RESOURCE_CONDITIONAL_XML (galaxy.jobs.JobConfiguration attribute) job_rule_modules() (in module galaxy.queue_worker) job_rules_paths (galaxy.config_watchers.ConfigWatchers property) job_runner_external_id (galaxy.model.Job attribute) job_runner_external_pid (galaxy.model.JobExternalOutputMetadata attribute) job_runner_name (galaxy.model.Job attribute) (galaxy.schema.schema.JobSummary attribute) job_script() (in module galaxy.jobs.runners.util.job_script) job_script_kwargs() (galaxy.jobs.runners.util.cli.job.BaseJobExec method) (galaxy.jobs.runners.util.cli.job.lsf.LSF method) (galaxy.jobs.runners.util.cli.job.slurm.Slurm method) (galaxy.jobs.runners.util.cli.job.torque.Torque method) job_search (galaxy.app_unittest_utils.galaxy_mock.MockApp attribute) (galaxy.tools.ApplyRulesTool attribute) (galaxy.tools.AsyncDataSourceTool attribute) (galaxy.tools.BuildListCollectionTool attribute) (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.DataDestinationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.DuplicateFileToCollectionTool attribute) (galaxy.tools.ExportHistoryTool attribute) (galaxy.tools.ExpressionTool attribute) (galaxy.tools.ExtractDatasetCollectionTool attribute) (galaxy.tools.FilterDatasetsTool attribute) (galaxy.tools.FilterEmptyDatasetsTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) (galaxy.tools.FilterFromFileTool attribute) (galaxy.tools.FlattenTool attribute) (galaxy.tools.HarmonizeTool attribute) (galaxy.tools.ImportHistoryTool attribute) (galaxy.tools.InteractiveTool attribute) (galaxy.tools.KeepSuccessDatasetsTool attribute) (galaxy.tools.MergeCollectionTool attribute) (galaxy.tools.OutputParameterJSONTool attribute) (galaxy.tools.RelabelFromFileTool attribute) (galaxy.tools.SortTool attribute) (galaxy.tools.TagFromFileTool attribute) (galaxy.tools.Tool attribute) (galaxy.tools.UnzipCollectionTool attribute) (galaxy.tools.ZipCollectionTool attribute) job_source_id (galaxy.model.HistoryDatasetCollectionAssociation property) (galaxy.schema.schema.HDCASummary attribute) job_source_type (galaxy.model.HistoryDatasetCollectionAssociation property) (galaxy.schema.schema.HDCASummary attribute) job_state_summary (galaxy.model.HistoryDatasetCollectionAssociation property) (galaxy.schema.schema.HDCASummary attribute) job_state_summary_dict (galaxy.model.HistoryDatasetCollectionAssociation property) job_states (in module galaxy.jobs.runners.util.cli.job)

job_stderr (galaxy.model.Job attribute) (galaxy.model.Task attribute) (galaxy.schema.schema.JobFullDetails attribute) job_stdout (galaxy.model.Job attribute) (galaxy.model.Task attribute) (galaxy.schema.schema.JobFullDetails attribute) job_title (galaxy.schema.schema.Person attribute) job_tool_configurations (galaxy.tools.ApplyRulesTool attribute) (galaxy.tools.AsyncDataSourceTool attribute) (galaxy.tools.BuildListCollectionTool attribute) (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.DataDestinationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.DuplicateFileToCollectionTool attribute) (galaxy.tools.ExportHistoryTool attribute) (galaxy.tools.ExpressionTool attribute) (galaxy.tools.ExtractDatasetCollectionTool attribute) (galaxy.tools.FilterDatasetsTool attribute) (galaxy.tools.FilterEmptyDatasetsTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) (galaxy.tools.FilterFromFileTool attribute) (galaxy.tools.FlattenTool attribute) (galaxy.tools.HarmonizeTool attribute) (galaxy.tools.ImportHistoryTool attribute) (galaxy.tools.InteractiveTool attribute) (galaxy.tools.KeepSuccessDatasetsTool attribute) (galaxy.tools.MergeCollectionTool attribute) (galaxy.tools.OutputParameterJSONTool attribute) (galaxy.tools.RelabelFromFileTool attribute) (galaxy.tools.SortTool attribute) (galaxy.tools.TagFromFileTool attribute) (galaxy.tools.Tool attribute) (galaxy.tools.UnzipCollectionTool attribute) (galaxy.tools.ZipCollectionTool attribute) job_working_directory (galaxy.job_execution.output_collect.BaseJobContext attribute) (galaxy.job_execution.output_collect.JobContext attribute) (galaxy.job_execution.output_collect.SessionlessJobContext attribute) (galaxy.model.store.discover.ModelPersistenceContext attribute) (galaxy.model.store.discover.SessionlessModelPersistenceContext attribute) (galaxy.tools.wrappers.HasDatasets attribute) job_wrapper() (galaxy.jobs.handler.JobHandlerQueue method) JobBaseModel (class in galaxy.schema.schema) JobConfiguration (class in galaxy.jobs) JobContainerAssociation (class in galaxy.model) JobContext (class in galaxy.job_execution.output_collect) JobDestination (class in galaxy.jobs) JobDetails (class in galaxy.schema.schema) JobExportHistoryArchive (class in galaxy.model) JobExportHistoryArchiveListResponse (class in galaxy.schema.schema) JobExportHistoryArchiveModel (class in galaxy.schema.schema) JobExportHistoryArchiveWrapper (class in galaxy.tools.imp_exp) JobExternalOutputMetadata (class in galaxy.model) JobFilesAPIController (class in galaxy.webapps.galaxy.api.job_files) JobFullDetails (class in galaxy.schema.schema) JobGrabber (class in galaxy.jobs.handler) JobHandler (class in galaxy.jobs.handler) JobHandlerI (class in galaxy.jobs.handler) JobHandlerMessage (class in galaxy.web_stack.message) JobHandlerQueue (class in galaxy.jobs.handler) JobHandlerStopQueue (class in galaxy.jobs.handler) JobIdResponse (class in galaxy.schema.schema) JobImportHistoryArchive (class in galaxy.model) JobImportHistoryArchiveWrapper (class in galaxy.tools.imp_exp) JobImportHistoryResponse (class in galaxy.schema.schema) JobIndexQueryPayload (class in galaxy.schema.schema) JobIndexSortByEnum (class in galaxy.schema.schema) JobInfo (class in galaxy.tool_util.deps.dependencies) JobInstrumenter (class in galaxy.job_metrics) JobIO (class in galaxy.job_execution.setup) JobLike (class in galaxy.model) JobLock (class in galaxy.managers.jobs) JobManager (class in galaxy.jobs.manager) (class in galaxy.managers.jobs) JobMappingConfigurationException JobMappingException JobMetric (class in galaxy.schema.schema) JobMetricCollection (class in galaxy.schema.schema) JobMetricFormatter (class in galaxy.job_metrics.formatting) JobMetricNumeric (class in galaxy.model) JobMetricText (class in galaxy.model) JobNotReadyException JobOutput (class in galaxy.job_execution.setup) JobOutputs (class in galaxy.job_execution.setup) JobOutputsError JobParameter (class in galaxy.model) JobPortsAPIController (class in galaxy.webapps.galaxy.api.job_ports) JobPortsView (class in galaxy.job_execution.ports) (class in galaxy.job_execution.ports.view) JobRunnerMapper (class in galaxy.jobs.mapper) Jobs (class in galaxy.webapps.reports.controllers.jobs) jobs (galaxy.model.History attribute) (galaxy.model.ImplicitCollectionJobs attribute) (galaxy.model.WorkflowInvocationStep property) (galaxy.tool_util.verify.interactor.RunToolResponse attribute) (galaxy_test.api.test_workflow_extraction.RunJobsSummary attribute) (galaxy_test.base.populators.RunJobsSummary attribute) jobs_by_key (galaxy.model.store.ObjectImportTracker attribute) jobs_for_tool() (galaxy_test.base.populators.RunJobsSummary method) jobs_list() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) jobs_properties() (galaxy.model.store.BaseDirectoryImportModelStore method) (galaxy.model.store.DictImportModelStore method) (galaxy.model.store.ModelImportStore method) JobSearch (class in galaxy.managers.jobs) JobSourceType (class in galaxy.schema.schema) JobState (class in galaxy.jobs.runners) (class in galaxy.schema.schema) JobStateHistory (class in galaxy.model) JobStateSummary (class in galaxy.model) (class in galaxy.schema.schema) JobSummary (class in galaxy.schema.schema) JobToImplicitOutputDatasetCollectionAssociation (class in galaxy.model) JobToInputDatasetAssociation (class in galaxy.model) JobToInputDatasetCollectionAssociation (class in galaxy.model) JobToInputDatasetCollectionElementAssociation (class in galaxy.model) JobToInputLibraryDatasetAssociation (class in galaxy.model) JobToolConfiguration (class in galaxy.jobs) JobToOutputDatasetAssociation (class in galaxy.model) JobToOutputDatasetCollectionAssociation (class in galaxy.model) JobToOutputLibraryDatasetAssociation (class in galaxy.model) JobWrapper (class in galaxy.jobs) join() (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method) (in module galaxy.util.path) join_url_and_params() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) joinext() (in module galaxy.util.path) joinpath() (galaxy.util.resources.Traversable method) JP2 (class in galaxy.datatypes.binary) Jpg (class in galaxy.datatypes.images) js() (galaxy.app_unittest_utils.galaxy_mock.MockTemplateHelpers method) js_helper() (in module galaxy.web.framework.helpers) js_nullable() (in module galaxy.web.framework.helpers) Json (class in galaxy.datatypes.text) json() (in module galaxy.web) (in module galaxy.web.framework.decorators) json_pretty() (in module galaxy.web) (in module galaxy.web.framework.decorators) json_wrap() (in module galaxy.tools.parameters.wrapped_json) JsonApiRoute (class in galaxy.webapps.galaxy.api.tools) JsonCollectedDatasetMatch (class in galaxy.model.store.discover) jsonData() (galaxy.util.jstree.JSTree method) (galaxy.util.jstree.Node method) JsonFileProxyIpc (class in galaxy.web.proxy) Jsonld (class in galaxy.datatypes.triples) JsonPlugin (class in galaxy.tools.error_reports.plugins.json) JsonReportHooks (class in galaxy_test.conftest) jsonrpc_request() (in module galaxy.util.json) jsonrpc_response() (in module galaxy.util.json) JSONType (class in galaxy.model.custom_types) JSTree (class in galaxy.util.jstree) jstree (galaxy.schema.remote_files.RemoteFilesFormat attribute) JuicerMediumTabix (class in galaxy.datatypes.interval) JupyterContextImpl (class in galaxy.selenium.jupyter_context) JupyterTestContextImpl (class in galaxy_test.selenium.jupyter_context) jwks_uri (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute)

K

k8s_config_path() (in module galaxy_test.driver.integration_util) keep_outputs_dir (galaxy.tool_util.verify.interactor.GalaxyInteractorApi attribute) (galaxy_test.base.api.AnonymousGalaxyInteractor attribute) (galaxy_test.base.api.ApiTestInteractor attribute) (galaxy_test.base.interactor.TestCaseGalaxyInteractor attribute) keepOutdir (galaxy_test.api.test_pages.TestPagesApi attribute) (galaxy_test.api.test_workflows.TestAdminWorkflowsApi attribute) (galaxy_test.api.test_workflows_cwl.BaseCwlWorkflowsApiTestCase attribute) (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi attribute) (galaxy_test.base.testcase.FunctionalTestCase attribute) (galaxy_test.driver.testcase.DrivenFunctionalTestCase attribute) (galaxy_test.selenium.test_admin_app.TestAdminApp attribute) (galaxy_test.selenium.test_anon_history.TestAnonymousHistories attribute) (galaxy_test.selenium.test_change_password.TestChangePassword attribute) (galaxy_test.selenium.test_collection_builders.TestCollectionBuilders attribute) (galaxy_test.selenium.test_collection_edit.TestCollectionEdit attribute) (galaxy_test.selenium.test_data_source_tools.TestDataSource attribute) (galaxy_test.selenium.test_dataset_metadata_download.TestHistoryDatasetState attribute) (galaxy_test.selenium.test_histories_list.TestSavedHistories attribute) (galaxy_test.selenium.test_history_copy_elements.TestHistoryCopyElements attribute) (galaxy_test.selenium.test_history_dataset_state.TestHistoryDatasetState attribute) (galaxy_test.selenium.test_history_multi_view.TestHistoryMultiView attribute) (galaxy_test.selenium.test_history_options.TestHistoryOptions attribute) (galaxy_test.selenium.test_history_panel.TestHistoryPanel attribute) (galaxy_test.selenium.test_history_panel_collections.TestHistoryPanelCollections attribute) (galaxy_test.selenium.test_history_sharing.TestHistoryRequiresLoginSelenium attribute) (galaxy_test.selenium.test_history_sharing.TestHistorySharing attribute) (galaxy_test.selenium.test_invocation_grid.TestInvocationGridSelenium attribute) (galaxy_test.selenium.test_library_contents.TestLibraryContents attribute) (galaxy_test.selenium.test_library_landing.TestLibraryLanding attribute) (galaxy_test.selenium.test_library_to_collections.TestLibraryToCollections attribute) (galaxy_test.selenium.test_login.TestLogin attribute) (galaxy_test.selenium.test_navigates_galaxy.TestNavigatesGalaxySelenium attribute) (galaxy_test.selenium.test_pages.TestPages attribute) (galaxy_test.selenium.test_personal_information.TestDeleteCurrentAccount attribute) (galaxy_test.selenium.test_personal_information.TestManageInformation attribute) (galaxy_test.selenium.test_registration.TestRegistration attribute) (galaxy_test.selenium.test_sign_out.TestSignOut attribute) (galaxy_test.selenium.test_sizzle_loading.TestSizzleLoading attribute) (galaxy_test.selenium.test_stock_tours.TestStockToursTestCase attribute) (galaxy_test.selenium.test_tool_describing_tours.TestToolDescribingTours attribute) (galaxy_test.selenium.test_tool_form.TestLoggedInToolForm attribute) (galaxy_test.selenium.test_tool_form.TestToolForm attribute) (galaxy_test.selenium.test_uploads.TestUploads attribute) (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor attribute) (galaxy_test.selenium.test_workflow_invocation_details.TestWorkflowInvocationDetails attribute) (galaxy_test.selenium.test_workflow_management.TestWorkflowManagement attribute) (galaxy_test.selenium.test_workflow_run.TestWorkflowRun attribute) (galaxy_test.selenium.test_workflow_sharing.TestWorkflowSharing attribute) (galaxy_test.selenium.test_workflow_sharing.TestWorkflowSharingRedirect attribute) (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures attribute) (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository attribute) (tool_shed.test.functional.test_0020_basic_repository_dependencies.TestBasicRepositoryDependencies attribute) (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions attribute) (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies attribute) (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels attribute) (tool_shed.test.functional.test_0070_invalid_tool.TestBismarkRepository attribute) (tool_shed.test.functional.test_0080_advanced_circular_dependencies.TestRepositoryCircularDependencies attribute) (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain attribute) (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies attribute) (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies attribute) (tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners.TestRepositoryMultipleOwners attribute) (tool_shed.test.functional.test_0140_tool_help_images.TestToolHelpImages attribute) (tool_shed.test.functional.test_0150_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_0160_circular_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_0170_complex_prior_installation_required.TestComplexPriorInstallation attribute) (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata attribute) (tool_shed.test.functional.test_0310_hg_api_features.TestHgWebFeatures attribute) (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs attribute) (tool_shed.test.functional.test_0430_browse_utilities.TestToolShedBrowseUtilities attribute) (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies attribute) (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision attribute) (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance attribute) (tool_shed.test.functional.test_0480_tool_dependency_xml_verification.TestDependencyDefinitionValidation attribute) (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole attribute) (tool_shed.test.functional.test_0550_metadata_updated_dependencies.TestGetUpdatedMetadata attribute) (tool_shed.test.functional.test_1000_install_basic_repository.TestBasicToolShedFeatures attribute) (tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies.TestToolWithToolDependencies attribute) (tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies.TestToolWithRepositoryDependencies attribute) (tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions.TestRepositoryWithDependencyRevisions attribute) (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies attribute) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies attribute) (tool_shed.test.functional.test_1070_invalid_tool.TestFreebayesRepository attribute) (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies attribute) (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies attribute) (tool_shed.test.functional.test_1100_install_updated_repository_dependencies.TestRepositoryDependencies attribute) (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies attribute) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies attribute) (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners attribute) (tool_shed.test.functional.test_1160_tool_help_images.TestToolHelpImages attribute) (tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_1190_complex_prior_installation_required.TestComplexPriorInstallation attribute) (tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository.TestUninstallingAndReinstallingRepositories attribute) (tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies.TestUninstallingAndReinstallingRepositories attribute) (tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions.TestUninstallingAndReinstallingRepositories attribute) (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata attribute) (tool_shed.test.functional.test_1410_update_manager.TestUpdateManager attribute) (tool_shed.test.functional.test_1430_repair_installed_repository.TestRepairRepository attribute) (tool_shed.test.functional.test_1460_data_managers.TestDataManagers attribute) (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository attribute)

KeepSuccessDatasetsTool (class in galaxy.tools) key (galaxy.model.APIKeys attribute) (galaxy.model.Vault attribute) (galaxy.schema.APIKeyModel attribute) (galaxy.webapps.base.api.AccessLoggingMiddleware attribute) (tool_shed.webapp.model.APIKeys attribute) keys (galaxy.schema.SerializationParams attribute) (galaxy.selenium.has_driver.HasDriver attribute) keys() (galaxy.tool_util.cwl.cwltool_deps.CommentedMap method) (galaxy.tools.wrappers.DatasetCollectionWrapper method) (galaxy.util.bunch.Bunch method) (galaxy.util.odict.odict method) kill_command() (in module galaxy.tool_util.deps.docker_util) kill_pg() (in module galaxy.jobs.runners.util.process_groups) kill_pid() (in module galaxy.jobs.runners.util) (in module galaxy.jobs.runners.util.kill) known_outputs() (galaxy.tool_util.parser.output_objects.ToolOutputCollection method) Kroenik (class in galaxy.datatypes.proteomics) KubernetesJobRunner (class in galaxy.jobs.runners.kubernetes)

L

Label (class in galaxy.tool_util.toolbox.views.definitions) label (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute) (galaxy.files.sources.FilesSourceProperties attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.WorkflowOutput attribute) (galaxy.model.WorkflowStep attribute) (galaxy.objectstore.QuotaSourceInfo attribute) (galaxy.schema.remote_files.FilesSourcePlugin attribute) (galaxy.schema.schema.DisplayApp attribute) (galaxy.schema.schema.LabelValuePair attribute) (galaxy.schema.schema.WorkflowInput attribute) (galaxy.schema.schema.WorkflowOutput attribute) (galaxy.schema.schema.WorkflowStepToExportBase attribute) (galaxy.tool_util.cwl.representation.TypeRepresentation attribute) LABEL (galaxy.tool_util.toolbox.panel.panel_item_types attribute) (galaxy.tool_util.toolbox.panel_item_types attribute) label (galaxy.tool_util.toolbox.views.definitions.LabelShortcut attribute) (galaxy.tools.parameters.grouping.Conditional property) (galaxy.tools.parameters.grouping.Repeat property) (galaxy.tools.parameters.grouping.Section property) (galaxy.workflow.modules.InputDataCollectionModule attribute) (galaxy.workflow.modules.InputDataModule attribute) (galaxy.workflow.modules.InputModule attribute) (galaxy.workflow.modules.InputParameterModule attribute) (galaxy.workflow.modules.InputProxy property) (galaxy.workflow.modules.PauseModule attribute) (galaxy.workflow.modules.ToolModule attribute) (galaxy.workflow.modules.WorkflowModule attribute) (galaxy.workflow.refactor.schema.AddInputAction attribute) (galaxy.workflow.refactor.schema.AddStepAction attribute) (galaxy.workflow.refactor.schema.ExtractInputAction attribute) (galaxy.workflow.refactor.schema.ExtractUntypedParameter attribute) (galaxy.workflow.refactor.schema.StepReferenceByLabel attribute) (galaxy.workflow.refactor.schema.UpdateStepLabelAction attribute) label_cache (galaxy.tools.error_reports.plugins.base_git.BaseGitPlugin attribute) LABEL_END (galaxy.jobs.runners.kubernetes.KubernetesJobRunner attribute) LABEL_REGEX (galaxy.jobs.runners.kubernetes.KubernetesJobRunner attribute) LABEL_START (galaxy.jobs.runners.kubernetes.KubernetesJobRunner attribute) labels (galaxy.tools.ApplyRulesTool attribute) (galaxy.tools.AsyncDataSourceTool attribute) (galaxy.tools.BuildListCollectionTool attribute) (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.DataDestinationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.DuplicateFileToCollectionTool attribute) (galaxy.tools.ExportHistoryTool attribute) (galaxy.tools.ExpressionTool attribute) (galaxy.tools.ExtractDatasetCollectionTool attribute) (galaxy.tools.FilterDatasetsTool attribute) (galaxy.tools.FilterEmptyDatasetsTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) (galaxy.tools.FilterFromFileTool attribute) (galaxy.tools.FlattenTool attribute) (galaxy.tools.HarmonizeTool attribute) (galaxy.tools.ImportHistoryTool attribute) (galaxy.tools.InteractiveTool attribute) (galaxy.tools.KeepSuccessDatasetsTool attribute) (galaxy.tools.MergeCollectionTool attribute) (galaxy.tools.OutputParameterJSONTool attribute) (galaxy.tools.RelabelFromFileTool attribute) (galaxy.tools.SortTool attribute) (galaxy.tools.TagFromFileTool attribute) (galaxy.tools.UnzipCollectionTool attribute) (galaxy.tools.ZipCollectionTool attribute) LabelShortcut (class in galaxy.tool_util.toolbox.views.definitions) LabelValuePair (class in galaxy.schema.schema) Laj (class in galaxy.datatypes.images) LaneMask (class in galaxy.datatypes.mothur) language (galaxy.tool_util.parser.cwl.CwlToolSource attribute) (galaxy.tool_util.parser.interface.ToolSource attribute) (galaxy.tool_util.parser.ToolSource attribute) (galaxy.tool_util.parser.xml.XmlToolSource attribute) (galaxy.tool_util.parser.yaml.YamlToolSource attribute) last_access_date() (galaxy.webapps.reports.controllers.users.Users method) last_action (galaxy.model.GalaxySession attribute) (tool_shed.webapp.model.GalaxySession attribute) last_activity (galaxy.model.CloudAuthz attribute) last_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) last_password_change (galaxy.model.User attribute) (galaxy.schema.schema.UserModel attribute) last_scheduled_time (galaxy.model.CeleryUserRateLimit attribute) last_update (galaxy.model.CloudAuthz attribute) LastDb (class in galaxy.datatypes.blast) LastzCoverage (class in galaxy.datatypes.coverage) late_postfork() (galaxy.web_stack.GunicornApplicationStack class method) late_postfork_event (galaxy.web_stack.GunicornApplicationStack attribute) late_postfork_thread (galaxy.web_stack.GunicornApplicationStack attribute) latest_export (galaxy.model.History property) latest_form (galaxy.model.FormDefinitionCurrent attribute) latest_form_id (galaxy.model.FormDefinitionCurrent attribute) latest_history_entry() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) latest_history_item() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) latest_installable_revision (galaxy.schema.schema.InstalledRepositoryToolShedStatus attribute) latest_revision (galaxy.model.Page attribute) (galaxy.model.Visualization attribute) latest_revision_id (galaxy.model.Page attribute) (galaxy.model.Visualization attribute) (galaxy.schema.schema.PageSummary attribute) latest_version (galaxy.tools.Tool property) latest_workflow (galaxy.model.StoredWorkflow attribute) latest_workflow_id (galaxy.model.StoredWorkflow attribute) latest_workflow_uuid (galaxy.schema.schema.StoredWorkflowSummary attribute) launch_proxy_command() (galaxy.web.proxy.GolangProxyLauncher method) (galaxy.web.proxy.NodeProxyLauncher method) (galaxy.web.proxy.ProxyLauncher method) Lav (class in galaxy.datatypes.sequence) layout (galaxy.model.FormDefinition attribute) lazy_property (in module galaxy.web.framework.base) LazyProcess (class in galaxy.util.lazy_process) lda_id (galaxy.model.MetadataFile attribute) LDAP (class in galaxy.auth.providers.ldap_ad) LDAP3 (class in galaxy.auth.providers.ldap_ad) ldap_search() (galaxy.auth.providers.ldap_ad.LDAP method) (galaxy.auth.providers.ldap_ad.LDAP3 method) ldda (galaxy.model.DatasetCollectionElement attribute) (galaxy.schema.schema.ColletionSourceType attribute) (galaxy.schema.schema.DataItemSourceType attribute) (galaxy.schema.schema.DatasetSourceType attribute) ldda_id (galaxy.model.CleanupEventLibraryDatasetDatasetAssociationAssociation attribute) (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) (galaxy.model.JobToInputLibraryDatasetAssociation attribute) (galaxy.model.JobToOutputLibraryDatasetAssociation attribute) (galaxy.schema.schema.FileLibraryFolderItem attribute) ldda_message (galaxy.schema.schema.CreateLibraryFilePayload attribute) ldda_parent_id (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) LDDAManager (class in galaxy.managers.lddas) LDDAProvenanceController (class in galaxy.webapps.galaxy.api.provenance) lddas_by_key (galaxy.model.store.ObjectImportTracker attribute) ldIndep (class in galaxy.datatypes.genetics) Leaf (class in galaxy.model.dataset_collections.structure) left (galaxy.schema.schema.WorkflowStepLayoutPosition attribute) (galaxy.workflow.refactor.schema.Position attribute) legacy_alter_table() (in module galaxy.model.migrations.util) legacy_archive_download() (galaxy.webapps.galaxy.services.histories.HistoriesService method) legacy_biotools_external_reference() (in module galaxy.tool_util.ontologies.ontology_data) LEGACY_CONFIG_FILE_ARG_NAMES (galaxy.model.migrations.scripts.LegacyManageDb attribute) legacy_expose_api() (in module galaxy.web) (in module galaxy.web.framework.decorators) legacy_expose_api_anonymous() (in module galaxy.web) (in module galaxy.web.framework.decorators) legacy_expose_api_raw() (in module galaxy.web) (in module galaxy.web.framework.decorators) legacy_expose_api_raw_anonymous() (in module galaxy.web) (in module galaxy.web.framework.decorators) legacy_serve_ready_history_export() (galaxy.managers.histories.HistoryManager method) legacy_tool_shed_endpoint() (in module galaxy.webapps.galaxy.controllers.admin_toolshed) LegacyLibraryPermissionsPayload (class in galaxy.schema.schema) LegacyManageDb (class in galaxy.model.migrations.scripts) LegacyToolProvidedMetadata (class in galaxy.tool_util.provided_metadata) LegacyUnprefixedDict (class in galaxy.tools.parameters.wrapped) legal_values (galaxy.tools.parameters.basic.BooleanToolParameter property) legend (galaxy.web.legacy_framework.grids.Grid attribute) len (galaxy.schema.schema.CreatedCustomBuild attribute) len_file_path (galaxy.config.GalaxyAppConfiguration attribute) (galaxy.tools.remote_tool_eval.ToolAppConfig attribute) (galaxy.tools.repositories.ValidationContextConfig attribute) len_type (galaxy.schema.schema.CustomBuildCreationPayload attribute) len_value (galaxy.schema.schema.CustomBuildCreationPayload attribute) LengthValidator (class in galaxy.tools.parameters.validation) level (galaxy.managers.metrics.Metric attribute) (galaxy.tool_util.lint.LintContext attribute) libraries_by_key (galaxy.model.store.ObjectImportTracker attribute) libraries_click_dataset_import() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_dataset_import() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_dataset_import_from_history_click_ok() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_dataset_import_from_history_select() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_folder_create() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_index_click_search() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_index_create() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_index_search_for() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_index_sort_click() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_index_sort_selector() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_index_table_elements() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_open() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_open_with_name() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_table_elements() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) LibrariesService (class in galaxy.webapps.galaxy.services.libraries) Library (class in galaxy.model) library (galaxy.model.LibraryInfoAssociation attribute) (galaxy.model.LibraryPermissions attribute) (galaxy.schema.fetch_data.DestinationType attribute) (galaxy.schema.schema.HistoryContentSource attribute) LIBRARY_ACCESS_in (galaxy.schema.schema.LegacyLibraryPermissionsPayload attribute) LIBRARY_ADD_in (galaxy.schema.schema.LegacyLibraryPermissionsPayload attribute) library_associations (galaxy.model.Dataset attribute) library_dataset (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryDatasetPermissions attribute) (galaxy.model.MetadataFile attribute) library_dataset_collection_id (galaxy.model.LibraryDatasetCollectionAnnotationAssociation attribute) (galaxy.model.LibraryDatasetCollectionRatingAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) library_dataset_dataset_association (galaxy.model.JobExternalOutputMetadata attribute) (galaxy.model.LibraryDataset attribute) (galaxy.model.LibraryDatasetDatasetAssociationPermissions attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) library_dataset_dataset_association_id (galaxy.model.JobExternalOutputMetadata attribute) (galaxy.model.LibraryDataset attribute) (galaxy.model.LibraryDatasetDatasetAssociationPermissions attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) library_dataset_id (galaxy.model.CleanupEventLibraryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryDatasetPermissions attribute) library_folder (galaxy.model.Job attribute) (galaxy.schema.fetch_data.DestinationType attribute) (galaxy.schema.schema.HistoryContentSource attribute) library_folder_id (galaxy.model.CleanupEventLibraryFolderAssociation attribute) (galaxy.model.Job attribute) (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryFolderPermissions attribute) (galaxy.schema.fetch_data.LibraryFolderDestination attribute) library_folder_manager (galaxy.structured_app.MinimalManagerApp attribute) library_id (galaxy.model.CleanupEventLibraryAssociation attribute) (galaxy.model.LibraryInfoAssociation attribute) (galaxy.model.LibraryPermissions attribute) library_is_public() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) library_is_unrestricted() (galaxy.model.security.GalaxyRBACAgent method) LIBRARY_MANAGE_in (galaxy.schema.schema.LegacyLibraryPermissionsPayload attribute) library_manager (galaxy.structured_app.MinimalManagerApp attribute) LIBRARY_MODIFY_in (galaxy.schema.schema.LegacyLibraryPermissionsPayload attribute) library_path (galaxy.model.LibraryFolder property) (galaxy.schema.schema.LibraryFolderDetails attribute) library_properties() (galaxy.model.store.BaseDirectoryImportModelStore method) (galaxy.model.store.DictImportModelStore method) (galaxy.model.store.ModelImportStore method) library_root (galaxy.model.LibraryFolder attribute) LibraryActions (class in galaxy.actions.library) LibraryAvailablePermissions (class in galaxy.schema.schema) LibraryContentsController (class in galaxy.webapps.galaxy.api.library_contents) LibraryCurrentPermissions (class in galaxy.schema.schema) LibraryDataset (class in galaxy.model) LibraryDatasetCollectionAnnotationAssociation (class in galaxy.model) LibraryDatasetCollectionAssociation (class in galaxy.model) LibraryDatasetCollectionRatingAssociation (class in galaxy.model) LibraryDatasetCollectionTagAssociation (class in galaxy.model) LibraryDatasetDatasetAssociation (class in galaxy.model) (galaxy.managers.tags.TaggableItemClass attribute) LibraryDatasetDatasetAssociationPermissions (class in galaxy.model) LibraryDatasetDatasetAssociationTagAssociation (class in galaxy.model) LibraryDatasetDatasetInfoAssociation (class in galaxy.model) LibraryDatasetExtendMetadataController (class in galaxy.webapps.galaxy.api.extended_metadata) LibraryDatasetPermissions (class in galaxy.model) LibraryDatasetsController (class in galaxy.webapps.galaxy.api.library_datasets) LibraryDatasetsManager (class in galaxy.managers.library_datasets) LibraryDestination (class in galaxy.schema.fetch_data) LibraryFolder (class in galaxy.model) LibraryFolderContentsIndexQueryPayload (class in galaxy.schema.schema) LibraryFolderContentsIndexResult (class in galaxy.schema.schema) LibraryFolderContentsService (class in galaxy.webapps.galaxy.services.library_folder_contents) LibraryFolderCurrentPermissions (class in galaxy.schema.schema) LibraryFolderDestination (class in galaxy.schema.fetch_data) LibraryFolderDetails (class in galaxy.schema.schema) LibraryFolderInfoAssociation (class in galaxy.model) LibraryFolderItemBase (class in galaxy.schema.schema) LibraryFolderMetadata (class in galaxy.schema.schema) LibraryFolderPermissionAction (class in galaxy.schema.schema) LibraryFolderPermissions (class in galaxy.model) LibraryFolderPermissionsPayload (class in galaxy.schema.schema) LibraryFoldersService (class in galaxy.webapps.galaxy.services.library_folders) LibraryImportFilesSource (class in galaxy.files.sources.galaxy) LibraryInfoAssociation (class in galaxy.model) LibraryLegacySummary (class in galaxy.schema.schema) LibraryManager (class in galaxy.managers.libraries) LibraryParams (class in galaxy.tools.actions.upload_common) LibraryPermissionAction (class in galaxy.schema.schema) LibraryPermissions (class in galaxy.model) LibraryPermissionScope (class in galaxy.schema.schema) LibraryPermissionsPayload (class in galaxy.schema.schema) LibraryPermissionsPayloadBase (class in galaxy.schema.schema) LibraryPopulator (class in galaxy_test.base.populators) LibrarySummary (class in galaxy.schema.schema) LibrarySummaryList (class in galaxy.schema.schema) license (galaxy.model.Workflow attribute) (galaxy.schema.schema.WorkflowToExport attribute) (galaxy.workflow.refactor.schema.UpdateLicenseAction attribute) licenseId (galaxy.managers.licenses.LicenseMetadataModel attribute) LicenseMetadataModel (class in galaxy.managers.licenses) licenses_manager (galaxy.webapps.galaxy.api.licenses.FastAPILicenses attribute) LicensesManager (class in galaxy.managers.licenses) lifespan_context (galaxy.webapps.galaxy.api.Router attribute) lifetime (galaxy.model.PSAAssociation attribute) (galaxy.model.UserAuthnzToken attribute) limit (galaxy.schema.PaginationQueryParams attribute) (galaxy.schema.schema.InvocationIndexQueryPayload attribute) (galaxy.schema.schema.JobIndexQueryPayload attribute) (galaxy.schema.schema.LibraryFolderContentsIndexQueryPayload attribute) (galaxy.schema.schema.PageIndexQueryPayload attribute) (galaxy.schema.schema.WorkflowIndexQueryPayload attribute) LimitedOffsetDataProvider (class in galaxy.datatypes.dataproviders.base) LimitedUserModel (class in galaxy.schema.schema) line_class (galaxy.datatypes.data.Text attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.tabular.Pileup attribute) (galaxy.datatypes.tabular.Psl attribute) line_count (galaxy.datatypes.sniff.ConvertResult attribute) line_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.data.Text method) (galaxy.datatypes.tabular.Sam method) line_enumerator() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) line_iterator() (galaxy.datatypes.sniff.FilePrefix method) lineage (galaxy.tools.Tool property) LineageMap (class in galaxy.tool_util.toolbox.lineages) (class in galaxy.tool_util.toolbox.lineages.factory) lineages_by_id (galaxy.tool_util.toolbox.lineages.interface.ToolLineage attribute) (galaxy.tool_util.toolbox.lineages.ToolLineage attribute) LineCount (class in galaxy.datatypes.data) linecount (galaxy.schema.schema.CreatedCustomBuild attribute) lines() (galaxy.datatypes.util.gff_util.GFFFeature method) Link (class in galaxy.managers.display_applications) link_data (galaxy.model.store.discover.JsonCollectedDatasetMatch property)

link_data_only (galaxy.schema.fetch_data.PathDataElement attribute) (galaxy.schema.fetch_data.ServerDirElement attribute) link_to() (galaxy.model.DatasetInstance method) LinkageStudies (class in galaxy.datatypes.genetics) links (galaxy.managers.display_applications.DisplayApplication attribute) (galaxy.schema.schema.DisplayApp attribute) lint() (galaxy.tool_util.lint.LintContext method) (galaxy.tool_util.lint.Linter class method) (galaxy.tool_util.linters.citations.CitationsFound class method) (galaxy.tool_util.linters.citations.CitationsMissing class method) (galaxy.tool_util.linters.citations.CitationsNoText class method) (galaxy.tool_util.linters.citations.CitationsNoValid class method) (galaxy.tool_util.linters.command.CommandEmpty class method) (galaxy.tool_util.linters.command.CommandInfo class method) (galaxy.tool_util.linters.command.CommandInterpreterDeprecated class method) (galaxy.tool_util.linters.command.CommandMissing class method) (galaxy.tool_util.linters.command.CommandTODO class method) (galaxy.tool_util.linters.cwl.CWLDescriptionMissing class method) (galaxy.tool_util.linters.cwl.CWLDockerGood class method) (galaxy.tool_util.linters.cwl.CWLDockerMissing class method) (galaxy.tool_util.linters.cwl.CWLHelpTODO class method) (galaxy.tool_util.linters.cwl.CWLInValid class method) (galaxy.tool_util.linters.cwl.CWLValid class method) (galaxy.tool_util.linters.cwl.CWLVersionGood class method) (galaxy.tool_util.linters.cwl.CWLVersionMissing class method) (galaxy.tool_util.linters.cwl.CWLVersionUnknown class method) (galaxy.tool_util.linters.general.RequirementNameMissing class method) (galaxy.tool_util.linters.general.RequirementVersionMissing class method) (galaxy.tool_util.linters.general.RequirementVersionWhitespace class method) (galaxy.tool_util.linters.general.ResourceRequirementExpression class method) (galaxy.tool_util.linters.general.ToolIDMissing class method) (galaxy.tool_util.linters.general.ToolIDValid class method) (galaxy.tool_util.linters.general.ToolIDWhitespace class method) (galaxy.tool_util.linters.general.ToolNameMissing class method) (galaxy.tool_util.linters.general.ToolNameValid class method) (galaxy.tool_util.linters.general.ToolNameWhitespace class method) (galaxy.tool_util.linters.general.ToolProfileInvalid class method) (galaxy.tool_util.linters.general.ToolProfileLegacy class method) (galaxy.tool_util.linters.general.ToolProfileValid class method) (galaxy.tool_util.linters.general.ToolVersionMissing class method) (galaxy.tool_util.linters.general.ToolVersionPEP404 class method) (galaxy.tool_util.linters.general.ToolVersionValid class method) (galaxy.tool_util.linters.general.ToolVersionWhitespace class method) (galaxy.tool_util.linters.help.HelpEmpty class method) (galaxy.tool_util.linters.help.HelpInvalidRST class method) (galaxy.tool_util.linters.help.HelpMissing class method) (galaxy.tool_util.linters.help.HelpPresent class method) (galaxy.tool_util.linters.help.HelpTODO class method) (galaxy.tool_util.linters.help.HelpValidRST class method) (galaxy.tool_util.linters.inputs.ConditionalOptionMissing class method) (galaxy.tool_util.linters.inputs.ConditionalOptionMissingBoolean class method) (galaxy.tool_util.linters.inputs.ConditionalParamIncompatibleAttributes class method) (galaxy.tool_util.linters.inputs.ConditionalParamType class method) (galaxy.tool_util.linters.inputs.ConditionalParamTypeBool class method) (galaxy.tool_util.linters.inputs.ConditionalWhenMissing class method) (galaxy.tool_util.linters.inputs.InputsBoolDistinctValues class method) (galaxy.tool_util.linters.inputs.InputsBoolProblematic class method) (galaxy.tool_util.linters.inputs.InputsDataFormat class method) (galaxy.tool_util.linters.inputs.InputsDataOptionsAttrib class method) (galaxy.tool_util.linters.inputs.InputsDataOptionsFilterAttribFiltersType class method) (galaxy.tool_util.linters.inputs.InputsDataOptionsFiltersRef class method) (galaxy.tool_util.linters.inputs.InputsDataOptionsFiltersType class method) (galaxy.tool_util.linters.inputs.InputsDataOptionsMultiple class method) (galaxy.tool_util.linters.inputs.InputsDatasourceTags class method) (galaxy.tool_util.linters.inputs.InputsMissing class method) (galaxy.tool_util.linters.inputs.InputsMissingDataSource class method) (galaxy.tool_util.linters.inputs.InputsName class method) (galaxy.tool_util.linters.inputs.InputsNameDuplicate class method) (galaxy.tool_util.linters.inputs.InputsNameDuplicateOutput class method) (galaxy.tool_util.linters.inputs.InputsNameEmpty class method) (galaxy.tool_util.linters.inputs.InputsNameRedundantArgument class method) (galaxy.tool_util.linters.inputs.InputsNameValid class method) (galaxy.tool_util.linters.inputs.InputsNum class method) (galaxy.tool_util.linters.inputs.InputsSelectDynamicOptions class method) (galaxy.tool_util.linters.inputs.InputsSelectMandatoryCheckboxes class method) (galaxy.tool_util.linters.inputs.InputsSelectMultipleRadio class method) (galaxy.tool_util.linters.inputs.InputsSelectOptionalRadio class method) (galaxy.tool_util.linters.inputs.InputsSelectOptionDuplicateText class method) (galaxy.tool_util.linters.inputs.InputsSelectOptionDuplicateValue class method) (galaxy.tool_util.linters.inputs.InputsSelectOptionsDef class method) (galaxy.tool_util.linters.inputs.InputsSelectOptionsDefConditional class method) (galaxy.tool_util.linters.inputs.InputsSelectOptionsDefinesOptions class method) (galaxy.tool_util.linters.inputs.InputsSelectOptionsDeprecatedAttr class method) (galaxy.tool_util.linters.inputs.InputsSelectOptionsFromDatasetAndDatatable class method) (galaxy.tool_util.linters.inputs.InputsSelectOptionsMetaFileKey class method) (galaxy.tool_util.linters.inputs.InputsSelectOptionsMultiple class method) (galaxy.tool_util.linters.inputs.InputsSelectOptionValueMissing class method) (galaxy.tool_util.linters.inputs.InputsSelectSingleCheckboxes class method) (galaxy.tool_util.linters.inputs.InputsTypeChildCombination class method) (galaxy.tool_util.linters.inputs.ValidatorAttribIncompatible class method) (galaxy.tool_util.linters.inputs.ValidatorDatasetMetadataEqualValue class method) (galaxy.tool_util.linters.inputs.ValidatorDatasetMetadataEqualValueOrJson class method) (galaxy.tool_util.linters.inputs.ValidatorExpression class method) (galaxy.tool_util.linters.inputs.ValidatorExpressionFuture class method) (galaxy.tool_util.linters.inputs.ValidatorHasNoText class method) (galaxy.tool_util.linters.inputs.ValidatorHasText class method) (galaxy.tool_util.linters.inputs.ValidatorMetadataCheckSkip class method) (galaxy.tool_util.linters.inputs.ValidatorMetadataName class method) (galaxy.tool_util.linters.inputs.ValidatorMinMax class method) (galaxy.tool_util.linters.inputs.ValidatorParamIncompatible class method) (galaxy.tool_util.linters.inputs.ValidatorTableName class method) (galaxy.tool_util.linters.stdio.StdIOAbsence class method) (galaxy.tool_util.linters.stdio.StdIOAbsenceLegacy class method) (galaxy.tool_util.linters.stdio.StdIORegex class method) (galaxy.tool_util.linters.tests.TestsAssertsHasNQuant class method) (galaxy.tool_util.linters.tests.TestsAssertsHasSizeOrValueQuant class method) (galaxy.tool_util.linters.tests.TestsAssertsHasSizeQuant class method) (galaxy.tool_util.linters.tests.TestsAssertsMultiple class method) (galaxy.tool_util.linters.tests.TestsExpectNumOutputs class method) (galaxy.tool_util.linters.tests.TestsExpectNumOutputsFailing class method) (galaxy.tool_util.linters.tests.TestsHasExpectations class method) (galaxy.tool_util.linters.tests.TestsMissing class method) (galaxy.tool_util.linters.tests.TestsMissingDatasource class method) (galaxy.tool_util.linters.tests.TestsNoValid class method) (galaxy.tool_util.linters.tests.TestsOutputCheckDiscovered class method) (galaxy.tool_util.linters.tests.TestsOutputCollectionCheckDiscovered class method) (galaxy.tool_util.linters.tests.TestsOutputCollectionCheckDiscoveredNested class method) (galaxy.tool_util.linters.tests.TestsOutputCollectionCorresponding class method) (galaxy.tool_util.linters.tests.TestsOutputCompareAttrib class method) (galaxy.tool_util.linters.tests.TestsOutputCorresponding class method) (galaxy.tool_util.linters.tests.TestsOutputDefined class method) (galaxy.tool_util.linters.tests.TestsOutputFailing class method) (galaxy.tool_util.linters.tests.TestsOutputName class method) (galaxy.tool_util.linters.tests.TestsParamInInputs class method) (galaxy.tool_util.linters.tests.TestsValid class method) (galaxy.tool_util.linters.xml_order.XMLOrder class method) lint_message_class (galaxy.tool_util.lint.LintContext attribute) lint_tool_source() (in module galaxy.tool_util.lint) lint_tool_source_with() (in module galaxy.tool_util.lint) lint_tool_source_with_modules() (in module galaxy.tool_util.lint) lint_xml() (in module galaxy.tool_util.lint) lint_xml_with() (in module galaxy.tool_util.lint) LintContext (class in galaxy.tool_util.lint) Linter (class in galaxy.tool_util.lint) LintLevel (class in galaxy.tool_util.lint) LintMessage (class in galaxy.tool_util.lint) list() (galaxy.files.sources.BaseFilesSource method) (galaxy.files.sources.SupportsBrowsing method) (galaxy.managers.base.ModelManager method) (galaxy.managers.libraries.LibraryManager method) (tool_shed.managers.groups.GroupManager method) list_accessible() (galaxy.managers.secured.AccessibleManagerMixin method) list_dependencies() (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method) (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependencyResolver method) (galaxy.tool_util.deps.resolvers.ListableDependencyResolver method) list_displayable_roles() (galaxy.managers.roles.RoleManager method) list_dynamic_tools() (galaxy_test.base.populators.BaseDatasetPopulator method) list_identifiers() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method) list_linters() (galaxy.tool_util.lint.Linter class method) list_listers() (galaxy.tool_util.lint.Linter class method) list_of_pairs_export() (galaxy_test.selenium.test_library_to_collections.TestLibraryToCollections method) list_owned() (galaxy.managers.secured.OwnableManagerMixin method) list_published() (galaxy.managers.sharable.SharableModelManager method) list_secrets() (galaxy.security.vault.CustosVault method) (galaxy.security.vault.DatabaseVault method) (galaxy.security.vault.HashicorpVault method) (galaxy.security.vault.NullVault method) (galaxy.security.vault.UserVaultWrapper method) (galaxy.security.vault.Vault method) (galaxy.security.vault.VaultKeyPrefixWrapper method) (galaxy.security.vault.VaultKeyValidationWrapper method) list_shared_with() (galaxy.managers.sharable.SharableModelManager method) list_tools() (galaxy.managers.tools.DynamicToolManager method) ListableDependencyResolver (class in galaxy.tool_util.deps.resolvers) ListDatasetCollectionType (class in galaxy.model.dataset_collections.types.list) listdir() (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method) listify() (in module galaxy.util) listify_options (galaxy.config.BaseAppConfiguration attribute) (galaxy.config.GalaxyAppConfiguration attribute) listing (galaxy.tool_util.cwl.util.OutputPropertiesType attribute) ListJstreeResponse (class in galaxy.schema.remote_files) ListParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) ListParser (class in galaxy.visualization.plugins.config_parser) ListUriResponse (class in galaxy.schema.remote_files) literal_to_value() (in module galaxy.schema.fields) LmodDependencyResolver (class in galaxy.tool_util.deps.resolvers.lmod) load() (galaxy.model.PSAPartial class method) (galaxy.util.aliaspickler.AliasPickleModule method) (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method) (in module galaxy.util.xml_macros) load_app_kwds (galaxy.main_config.WebappConfig attribute) load_app_properties() (in module galaxy.util.properties) load_builtin_converters() (galaxy.tools.ToolBox method) load_certified_level_one_repository_and_suite_tuple() (tool_shed.repository_registry.Registry method) load_changeset_in_tool_shed() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) load_checkable_revisions() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) load_citable_url() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) load_data_dict() (in module galaxy_test.base.populators) load_datatype_converters() (galaxy.datatypes.registry.Registry method) load_datatype_sniffers() (galaxy.datatypes.registry.Registry method) load_datatypes() (galaxy.datatypes.registry.Registry method) load_dialect_impl() (galaxy.model.custom_types.JSONType method) (galaxy.model.custom_types.UUIDType method) load_display_applications() (galaxy.datatypes.registry.Registry method) load_display_tool_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) load_dynamic_tool() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) load_edam_tree() (in module galaxy.tool_util.edam_util) load_external_metadata_tool() (galaxy.datatypes.registry.Registry method) load_from_xml() (galaxy.tools.data_manager.manager.DataManagers method) load_galaxy_app() (in module galaxy.main) load_hidden_lib_tool() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) load_hidden_tool() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) load_invalid_tool() (tool_shed.webapp.controllers.repository.RepositoryController method) load_invalid_tool_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) load_item() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) load_job_metadata() (in module galaxy.metadata.set_metadata) load_job_proxy() (in module galaxy.tool_util.cwl.parser) load_lib_tools() (in module galaxy.tools.special_tools) load_manager_from_elem() (galaxy.tools.data_manager.manager.DataManagers method) load_metadata() (galaxy.metadata.ExtendedDirectoryMetadataGenerator method) (galaxy.metadata.MetadataCollectionStrategy method) (galaxy.metadata.PortableDirectoryMetadataGenerator method) load_module_sections() (in module galaxy.workflow.modules) load_one_dir() (in module tool_shed.util.shed_index) load_plugins() (in module galaxy.util.plugin_config) load_random_x2_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method) load_repository_and_suite_tuple() (tool_shed.repository_registry.Registry method) load_repository_and_suite_tuples() (tool_shed.repository_registry.Registry method) load_tool() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) (in module galaxy.tool_util.loader) load_tool_elements_from_path() (in module galaxy.tool_util.loader_directory) load_tool_from_cache() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) load_tool_from_changeset_revision() (tool_shed.tools.tool_validator.ToolValidator method) load_tool_from_config() (galaxy.tool_shed.tools.tool_validator.ToolValidator method) load_tool_from_tmp_config() (tool_shed.tools.tool_validator.ToolValidator method) load_tool_sources_from_path() (in module galaxy.tool_util.loader_directory) load_tool_with_refereces() (in module galaxy.tool_util.loader) load_tour() (galaxy.tours.ToursRegistry method) load_vault_config() (galaxy.security.vault.VaultFactory static method) load_versioned_deps() (in module galaxy.tool_util.deps.brew_exts) load_viewable_repositories_and_suites_by_category() (tool_shed.repository_registry.Registry method) load_webhook_from_config() (galaxy.webhooks.WebhooksRegistry method) load_webhooks() (galaxy.webhooks.WebhooksRegistry method) load_with_references() (in module galaxy.util.xml_macros) load_workflow() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) (galaxy_test.base.populators.BaseWorkflowPopulator method) load_workflow_from_resource() (galaxy_test.base.populators.BaseWorkflowPopulator method) loading_context (galaxy.tool_util.cwl.schema.RawProcessReference attribute) (galaxy.tool_util.cwl.schema.ResolvedProcessDefinition attribute) loading_context() (galaxy.tool_util.cwl.schema.SchemaLoader method) LOADING_PROPRIETARY_DATATYPES (galaxy.model.tool_shed_install.ToolShedRepository.installation_status attribute) LoadingContext (class in galaxy.tool_util.cwl.cwltool_deps) loads() (galaxy.util.aliaspickler.AliasPickleModule method) local_extra_dirs() (in module galaxy.objectstore) local_filename (galaxy.schema.fetch_data.FilesPayload attribute) local_storage() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) LocalDB (class in galaxy.auth.providers.localdb) LocalJobRunner (class in galaxy.jobs.runners.local) LocalShell (class in galaxy.jobs.runners.util.cli.shell.local) location (galaxy.model.HistoryDatasetAssociationSubset attribute) (galaxy.tool_util.cwl.util.OutputPropertiesType attribute) lock (galaxy.tool_util.toolbox.lineages.interface.ToolLineage attribute) (galaxy.tool_util.toolbox.lineages.ToolLineage attribute) LOG (galaxy.tool_util.parser.stdio.StdioErrorLevel attribute) log() (galaxy.util.custom_logging.fluent_log.FluentTraceLogger method) log_action() (galaxy.managers.context.ProvidesAppContext method) log_check_not_passed() (galaxy.model.migrations.util.AddColumn method) (galaxy.model.migrations.util.AlterColumn method) (galaxy.model.migrations.util.CreateForeignKey method) (galaxy.model.migrations.util.CreateIndex method) (galaxy.model.migrations.util.CreateTable method) (galaxy.model.migrations.util.CreateUniqueConstraint method) (galaxy.model.migrations.util.DDLOperation method) (galaxy.model.migrations.util.DropColumn method) (galaxy.model.migrations.util.DropConstraint method) (galaxy.model.migrations.util.DropIndex method) (galaxy.model.migrations.util.DropTable method) log_event() (galaxy.app_unittest_utils.galaxy_mock.MockTrans method) (galaxy.managers.context.ProvidesAppContext method) log_filter() (galaxy.web_stack.ApplicationStack class method) log_filter_class (galaxy.web_stack.ApplicationStack attribute) log_format (galaxy.web_stack.ApplicationStack attribute) log_request_query_counts() (in module galaxy.model.orm.engine_factory) log_startup() (galaxy.web_stack.ApplicationStack method) (galaxy.web_stack.GunicornApplicationStack method) log_str() (galaxy.model.JobLike method) (galaxy.model.Workflow method) (galaxy.model.WorkflowInvocation method) (galaxy.model.WorkflowStep method) LOGGING_CONFIG_DEFAULT (in module galaxy.config) login() (galaxy.jobs.runners.godocker.GodockerJobRunner method) (galaxy.webapps.galaxy.controllers.authnz.OIDC method) (galaxy.webapps.galaxy.controllers.root.RootController method) (galaxy.webapps.galaxy.controllers.user.User method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) (tool_shed.webapp.controllers.user.User method) logout() (galaxy.authnz.custos_authnz.OIDCAuthnzBase method) (galaxy.authnz.IdentityProvider method) (galaxy.authnz.managers.AuthnzManager method) (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) (galaxy.webapps.galaxy.controllers.authnz.OIDC method) (galaxy.webapps.galaxy.controllers.user.User method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) (tool_shed.webapp.controllers.user.User method) logout_if_needed() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) logs_command() (in module galaxy.tool_util.deps.docker_util) long_description (tool_shed.webapp.model.Repository attribute) looks_like_a_cwl_artifact() (in module galaxy.tool_util.loader_directory) looks_like_a_tool_cwl() (in module galaxy.tool_util.loader_directory) looks_like_a_tool_xml() (in module galaxy.tool_util.loader_directory) looks_like_a_tool_yaml() (in module galaxy.tool_util.loader_directory) looks_like_uri() (galaxy.files.ConfiguredFileSources method) looks_like_view_source_filename() (in module galaxy.tool_util.toolbox.views.sources) Loom (class in galaxy.datatypes.binary) lowercase_alphanum_to_hex() (in module galaxy.util) LowerTriangleDistanceMatrix (class in galaxy.datatypes.mothur) Lped (class in galaxy.datatypes.genetics) LSF (class in galaxy.jobs.runners.util.cli.job.lsf) LudwigModel (class in galaxy.datatypes.binary)

M

macro_paths (galaxy.tool_util.parser.interface.ToolSource property) (galaxy.tool_util.parser.ToolSource property) (galaxy.tool_util.parser.xml.XmlToolSource property) Maf (class in galaxy.datatypes.sequence) maf_index_by_uid() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) MafCustomTrack (class in galaxy.datatypes.sequence) magic_header() (galaxy.datatypes.sniff.FilePrefix method) magic_number (galaxy.datatypes.binary.Cpt attribute) (galaxy.datatypes.binary.Edr attribute) (galaxy.datatypes.binary.GmxBinary attribute) (galaxy.datatypes.binary.Trr attribute) (galaxy.datatypes.binary.Xtc attribute) Magres (class in galaxy.datatypes.molecules) main() (in module galaxy.config.config_manage) (in module galaxy.config.script) (in module galaxy.datatypes.converters.fastq_to_fqtoc) (in module galaxy.datatypes.converters.gff_to_interval_index_converter) (in module galaxy.datatypes.converters.interval_to_fli) (in module galaxy.datatypes.converters.interval_to_interval_index_converter) (in module galaxy.datatypes.converters.lped_to_fped_converter) (in module galaxy.datatypes.converters.lped_to_pbed_converter) (in module galaxy.datatypes.converters.pbed_ldreduced_converter) (in module galaxy.datatypes.converters.pbed_to_lped_converter) (in module galaxy.datatypes.converters.pileup_to_interval_index_converter) (in module galaxy.datatypes.converters.tabular_csv) (in module galaxy.datatypes.converters.vcf_to_interval_index_converter) (in module galaxy.datatypes.converters.wiggle_to_simple_converter) (in module galaxy.main) (in module galaxy.model.store.build_objects) (in module galaxy.model.store.load_objects) (in module galaxy.selenium.scripts.dump_tour) (in module galaxy.tool_util.deps.brew_exts) (in module galaxy.tool_util.deps.mulled.mulled_build) (in module galaxy.tool_util.deps.mulled.mulled_build_channel) (in module galaxy.tool_util.deps.mulled.mulled_build_files) (in module galaxy.tool_util.deps.mulled.mulled_build_tool) (in module galaxy.tool_util.deps.mulled.mulled_hash) (in module galaxy.tool_util.deps.mulled.mulled_list) (in module galaxy.tool_util.deps.mulled.mulled_search) (in module galaxy.tool_util.deps.mulled.mulled_update_singularity_containers) (in module galaxy.tool_util.verify.script) (in module galaxy.tools.data_fetch) (in module galaxy.tools.imp_exp.export_history) (in module galaxy.tools.imp_exp.unpack_tar_gz_archive) (in module galaxy.tools.remote_tool_eval) (in module galaxy.tours.validate) (in module galaxy.util.script) main_factory() (in module galaxy.util.script) main_panel() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) main_test_search() (in module galaxy.tool_util.deps.mulled.get_tests) make_accessible_and_publishable() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) make_accessible_to_shared (galaxy.managers.sharable.SharingOptions attribute) (galaxy.schema.schema.SharingOptions attribute) make_backup() (tool_shed.util.hgweb_config.HgWebConfigManager method) make_body_iterable() (galaxy.web.framework.base.WebApplication method) (galaxy.webapps.base.webapp.WebApplication method) make_catching_iter() (galaxy.web.framework.middleware.error.ErrorMiddleware method) make_copy() (galaxy.datatypes.metadata.DBKeyParameter method) (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.model.metadata.DBKeyParameter method) (galaxy.model.metadata.FileParameter method) (galaxy.model.metadata.MetadataParameter method) make_dataset_public() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) make_dataset_public_raw() (galaxy_test.base.populators.BaseDatasetPopulator method) make_dict_copy() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataCollection method) (in module galaxy.tools.parameters.wrapped) make_fast_zipfile() (in module galaxy.util.compression_utils) make_filter() (in module galaxy.web.framework.middleware.translogger) make_folder_public() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) make_html_peek_header() (galaxy.datatypes.tabular.TabularData method) make_html_peek_rows() (galaxy.datatypes.tabular.TabularData method) make_html_table() (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.mothur.SffFlow method) (galaxy.datatypes.sequence.Maf method) (galaxy.datatypes.tabular.Eland method) (galaxy.datatypes.tabular.TabularData method) make_importable() (galaxy.managers.sharable.SharableModelManager method) make_library_public() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) make_manager() (galaxy.model.database_utils.DatabaseManager static method) make_members_public() (galaxy.managers.histories.HistoryManager method) (galaxy.managers.sharable.SharableModelManager method) make_non_importable() (galaxy.managers.sharable.SharableModelManager method) make_page_public() (galaxy_test.base.populators.BaseDatasetPopulator method) make_private (galaxy.schema.schema.DatasetPermissionAction attribute) make_private() (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy_test.base.populators.BaseDatasetPopulator method) make_public (galaxy.managers.sharable.SharingOptions attribute) (galaxy.schema.schema.SharingOptions attribute) make_public() (galaxy.managers.libraries.LibraryManager method) (galaxy_test.base.populators.BaseDatasetPopulator method) make_same_length() (in module tool_shed.util.search_util) make_static() (in module galaxy.web.framework.middleware.static) make_tag_string_list() (galaxy.model.HasTags method) make_temp_fname() (in module galaxy.tool_util.verify) makeLDreduced() (in module galaxy.datatypes.converters.pbed_ldreduced_converter) makeNode() (galaxy.visualization.data_providers.phyloviz.baseparser.PhyloTree method) maketrans() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) MAKO_TEMPLATE (galaxy.visualization.plugins.plugin.ChartVisualizationPlugin attribute) (galaxy.visualization.plugins.plugin.ScriptVisualizationPlugin attribute) MalformedContents MalformedId MalformedYMLException malicious (tool_shed.webapp.model.RepositoryMetadata attribute) MAlist (class in galaxy.datatypes.genetics) manage (galaxy.schema.schema.DatasetPermissions attribute) (galaxy.webapps.galaxy.services.library_folder_contents.UserFolderPermissions attribute) manage_categories() (tool_shed.webapp.controllers.admin.AdminController method) manage_category_grid (tool_shed.webapp.controllers.admin.AdminController attribute) manage_dataset_roles (galaxy.schema.schema.DatasetAssociationRoles attribute) manage_db() (in module galaxy.model.orm.scripts) manage_dependency_relationships (galaxy.config.GalaxyAppConfiguration attribute) manage_email_alerts() (tool_shed.webapp.controllers.repository.RepositoryController method) manage_folder_role_list (galaxy.schema.schema.LibraryFolderCurrentPermissions attribute) manage_ids (galaxy.schema.schema.LibraryPermissionsPayloadBase attribute) (galaxy.schema.schema.UpdateDatasetPermissionsPayload attribute) manage_library_role_list (galaxy.schema.schema.LibraryCurrentPermissions attribute) manage_repository() (tool_shed.webapp.controllers.repository.RepositoryController method) manage_repository_admins() (tool_shed.webapp.controllers.repository.RepositoryController method) manage_repository_json() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) manage_role_associations() (tool_shed.webapp.controllers.admin.AdminController method) manage_roles_and_groups_for_user() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (tool_shed.util.admin_util.Admin method) manage_user_info() (tool_shed.webapp.controllers.user.User method) manage_users_and_groups_for_quota() (galaxy.managers.quotas.QuotaManager method) (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) manage_users_and_groups_for_role() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (tool_shed.util.admin_util.Admin method) manage_users_and_roles_for_group() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (tool_shed.util.admin_util.Admin method) ManageCategoryGrid (class in tool_shed.grids.admin_grids) managed_data_tables (galaxy.tools.data_manager.manager.DataManagers attribute) ManageDatasetRBACPermission (class in galaxy.managers.rbac_secured) manager (galaxy.managers.base.HasAModelManager property) (galaxy.webapps.base.controller.SharableMixin attribute) (galaxy.webapps.galaxy.api.display_applications.FastAPIDisplay attribute) (galaxy.webapps.galaxy.api.genomes.FastAPIGenomes attribute) (galaxy.webapps.galaxy.api.group_roles.FastAPIGroupRoles attribute) (galaxy.webapps.galaxy.api.group_users.FastAPIGroupUsers attribute) (galaxy.webapps.galaxy.api.groups.FastAPIGroups attribute) (galaxy.webapps.galaxy.api.metrics.FastAPIMetrics attribute) (galaxy.webapps.galaxy.api.page_revisions.PageRevisionsController attribute) (galaxy.webapps.galaxy.api.remote_files.FastAPIRemoteFiles attribute) (galaxy.webapps.galaxy.api.tags.FastAPITags attribute) (galaxy.webapps.galaxy.api.tasks.FastAPITasks attribute) manager_dependency() (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) manager_requirements() (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) ManagesIntegratedToolPanelMixin (class in galaxy.tool_util.toolbox.integrated_panel) mandatory_headers (galaxy.datatypes.speech.BPF attribute) map_datasets() (galaxy.managers.hdcas.HDCAManager method) (galaxy.managers.history_contents.HistoryContentsManager method) map_over_action_tuples() (galaxy.model.dataset_collections.matching.MatchingCollections method) map_over_collection_type() (in module galaxy.model.dataset_collections.type_description) map_tool_to_destination() (in module galaxy.jobs.dynamic_tool_destination) MappableDependencyResolver (class in galaxy.tool_util.deps.resolvers) mapped_over_output_actions (galaxy.job_execution.actions.post.ActionBox attribute) mapping() (galaxy.webapps.galaxy.api.datatypes.FastAPIDatatypes method) mapping_as_dict (galaxy.util.rules_dsl.RuleSet property) MAPPING_PRESET (galaxy.tools.parameters.sanitize.ToolParameterSanitizer attribute) MappingContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit) mark_as_failed() (galaxy.jobs.runners.AsynchronousJobRunner method) mark_as_finished() (galaxy.jobs.runners.AsynchronousJobRunner method) mark_as_populated() (galaxy.model.DatasetCollection method) mark_as_queued() (galaxy.jobs.runners.BaseJobRunner method) mark_as_resubmitted() (galaxy.jobs.runners.BaseJobRunner method) mark_cancelled() (galaxy.model.WorkflowInvocation method) mark_category_deleted() (tool_shed.webapp.controllers.admin.AdminController method) mark_deleted() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) (galaxy.model.Job method) mark_failed() (galaxy.model.Job method) mark_group_deleted() (tool_shed.util.admin_util.Admin method) mark_role_deleted() (tool_shed.util.admin_util.Admin method) mark_stopped() (galaxy.model.Job method) mark_undeleted() (galaxy.model.DatasetInstance method) mark_unhidden() (galaxy.model.DatasetInstance method) mark_user_deleted() (tool_shed.util.admin_util.Admin method) markdown (galaxy.schema.schema.PageContentFormat attribute) (galaxy.workflow.refactor.schema.Report attribute) MarkdownWorkflowMarkdownReportGeneratorPlugin (class in galaxy.workflow.reports.generators.markdown) MarkerMap (class in galaxy.datatypes.genetics) marshal() (galaxy.datatypes.metadata.FileParameter class method) (galaxy.datatypes.metadata.MetadataParameter class method) (galaxy.datatypes.metadata.PythonObjectParameter class method) (galaxy.datatypes.metadata.RangeParameter class method) (galaxy.datatypes.metadata.SelectParameter class method) (galaxy.model.metadata.FileParameter class method) (galaxy.model.metadata.MetadataParameter class method) (galaxy.model.metadata.PythonObjectParameter class method) (galaxy.model.metadata.RangeParameter class method) (galaxy.model.metadata.SelectParameter class method) MascotDat (class in galaxy.datatypes.proteomics) MascotXML (class in galaxy.datatypes.proteomics) MashSketch (class in galaxy.datatypes.binary) mask_password_from_url() (in module galaxy.util) MassHunterTar (class in galaxy.datatypes.binary) MassLynxTar (class in galaxy.datatypes.binary) match (galaxy.model.store.discover.DiscoveredDeferredFile attribute) (galaxy.model.store.discover.DiscoveredFile attribute) (galaxy.model.store.discover.DiscoveredFileError attribute) match() (galaxy.job_execution.output_collect.DatasetCollector method) match_access_token_to_user() (galaxy.authnz.managers.AuthnzManager method) match_collections() (galaxy.managers.collections.DatasetCollectionManager method) (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.DataCollectionToolParameter method) match_content_type (galaxy.webapps.galaxy.api.APIContentTypeRoute attribute) (galaxy.webapps.galaxy.api.tools.FormDataApiRoute attribute) (galaxy.webapps.galaxy.api.tools.JsonApiRoute attribute) match_multirun_collections() (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.DataCollectionToolParameter method) match_url() (galaxy.workflow.trs_proxy.TrsProxy method) matched_repository_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) MatchedRepositoryGrid (class in tool_shed.grids.repository_grids) MatchedRepositoryGrid.DescriptionColumn (class in tool_shed.grids.repository_grids) MatchedRepositoryGrid.NameColumn (class in tool_shed.grids.repository_grids) MatchedRepositoryGrid.RevisionColumn (class in tool_shed.grids.repository_grids) MatchedRepositoryGrid.UserColumn (class in tool_shed.grids.repository_grids) matches() (galaxy.webapps.galaxy.api.APIContentTypeRoute method) matches_any() (galaxy.datatypes.binary.DynamicCompressedArchive method) (galaxy.datatypes.data.Data method) matches_requirement() (galaxy.tool_util.deps.resolvers.RequirementMapping method) matches_selector() (galaxy.datatypes.dataproviders.hierarchy.XMLDataProvider method) matches_type() (galaxy.managers.base.ModelValidator static method) MatchingCollections (class in galaxy.model.dataset_collections.matching) materialize() (galaxy.managers.hdas.HDAManager method) materialize_collection_input() (in module galaxy.model.deferred) materialize_collection_instance() (in module galaxy.model.deferred) materialize_dataset_instance() (galaxy_test.base.populators.BaseDatasetPopulator method) materialize_datasets (galaxy.tools.evaluation.PartialToolEvaluator attribute) (galaxy.tools.evaluation.RemoteToolEvaluator attribute) (galaxy.tools.evaluation.ToolEvaluator attribute) MaterializeDatasetInstanceAPIRequest (class in galaxy.schema.schema) MaterializeDatasetInstanceRequest (class in galaxy.schema.schema) MaterializeDatasetInstanceTaskRequest (class in galaxy.schema.tasks) materializer_factory() (in module galaxy.model.deferred) MatrixMarket (class in galaxy.datatypes.tabular) MauveXmfa (class in galaxy.datatypes.msa) MAX (galaxy.tool_util.parser.stdio.StdioErrorLevel attribute) MAX_CHUNK_SIZE (galaxy.datatypes.dataproviders.chunk.ChunkDataProvider attribute) max_discovered_files (galaxy.model.store.discover.ModelPersistenceContext attribute) max_edit_dist (in module galaxy.jobs.dynamic_tool_destination) MAX_LINES_RETURNED (galaxy.visualization.data_providers.basic.ColumnDataProvider attribute) MAX_NUMERIC (galaxy.model.JobLike attribute) max_optional_metadata_filesize (galaxy.datatypes.data.Data property) max_peek_columns (galaxy.datatypes.tabular.TabularData attribute) max_peek_size (galaxy.datatypes.binary.H5MLM attribute) max_preview_size (galaxy.datatypes.binary.H5MLM attribute) max_seq_len (galaxy.tools.recommendations.ToolRecommendations attribute) MAX_SEQUENCE_SIZE (galaxy.datatypes.util.maf_utilities.RegionAlignment attribute) (galaxy.tools.util.maf_utilities.RegionAlignment attribute) MaxDiscoveredFilesExceededError maxseconds (galaxy.tool_util.parser.interface.ToolSourceTest attribute) (galaxy.tool_util.verify.interactor.InvalidToolTestDict attribute) (galaxy.tool_util.verify.interactor.ValidToolTestDict attribute) MCool (class in galaxy.datatypes.binary) MD5 (galaxy.schema.fetch_data.BaseDataElement attribute) md5 (galaxy.schema.schema.HashFunctionNames attribute) md5() (in module galaxy.util.hash_util) mem_optimize() (galaxy.tool_util.parser.xml.XmlToolSource method) MEM_SELF (galaxy.web_stack.handlers.HANDLER_ASSIGNMENT_METHODS attribute) MemePsp (class in galaxy.datatypes.sequence) MEMEXml (class in galaxy.datatypes.xml) MemInfoPlugin (class in galaxy.job_metrics.instrumenters.meminfo) merge (galaxy.tool_util.cwl.cwltool_deps.CommentedMap property) merge() (galaxy.datatypes.binary.BamNative static method) (galaxy.datatypes.blast.BlastXml static method) (galaxy.datatypes.data.Data static method) (galaxy.datatypes.graph.Sif static method) (galaxy.datatypes.graph.Xgmml static method) (galaxy.datatypes.molecules.CML static method) (galaxy.datatypes.molecules.FPS static method) (galaxy.datatypes.molecules.OBFS static method) (galaxy.datatypes.tabular.BaseVcf static method) (galaxy.datatypes.tabular.Sam static method) (galaxy.datatypes.xml.GenericXml static method) merge_history_metadata (galaxy.model.store.BcoExportOptions attribute) merge_sorted_iterables() (in module galaxy.util) merge_tool_data_table() (galaxy.tools.data.TabularToolDataTable method) (galaxy.tools.data.ToolDataTable method) merge_type (galaxy.model.WorkflowStepInput attribute) MergeCollectionTool (class in galaxy.tools) merged (galaxy.tool_util.toolbox.views.edam.EdamPanelMode attribute) merged_environment_name() (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method) Meryldb (class in galaxy.datatypes.binary) message (galaxy.managers.display_applications.ReloadFeedback attribute) (galaxy.model.CleanupEvent attribute) (galaxy.model.Event attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.schema.schema.CheckForUpdatesResponse attribute) (galaxy.schema.schema.DeletedCustomBuild attribute) (galaxy.schema.schema.FileLibraryFolderItem attribute) (galaxy.schema.schema.JobImportHistoryResponse attribute) (galaxy.tools.actions.upload_common.LibraryParams attribute) (galaxy.webapps.galaxy.controllers.admin.DatatypesEntryT attribute) (galaxy.workflow.refactor.schema.RefactorActionExecutionMessage attribute) message_list (galaxy.tool_util.lint.LintContext attribute) message_type (galaxy.workflow.refactor.schema.RefactorActionExecutionMessage attribute) MessageException messages (galaxy.model.WorkflowInvocation attribute) (galaxy.workflow.refactor.schema.RefactorActionExecution attribute) meta_error (galaxy.datatypes.molecules.AtomicStructFile attribute) meta_files (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) META_PARAMETERS (galaxy.model.WorkflowRequestInputParameter.types attribute) Metadata (class in tool_shed.repository_types.metadata) metadata (galaxy.model.Base attribute) (galaxy.model.DatasetInstance property) (galaxy.model.tool_shed_install.Base attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) (galaxy.schema.schema.LibraryFolderContentsIndexResult attribute) (galaxy.tool_util.cwl.util.GalaxyOutput attribute) (galaxy.tools.parameters.grouping.Dataset attribute) MetaData (in module galaxy.tool_util.deps.conda_compat) metadata (tool_shed.webapp.model.Base attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) metadata() (tool_shed.webapp.api.repositories.RepositoriesController method) metadata_ (galaxy.model.tool_shed_install.ToolShedRepository attribute) metadata_deferred (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) metadata_dict (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator attribute) (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager attribute) metadata_file_id (galaxy.model.CleanupEventMetadataFileAssociation attribute) metadata_file_types (galaxy.model.DatasetInstance property) metadata_files_dir (galaxy.model.deferred.TransientDatasetPaths attribute) metadata_revisions (tool_shed.webapp.model.Repository attribute) metadata_safe (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) metadata_source_provider (galaxy.job_execution.output_collect.JobContext property) (galaxy.model.store.discover.ModelPersistenceContext property) (galaxy.model.store.discover.SessionlessModelPersistenceContext property) metadata_spec (galaxy.datatypes.annotation.Augustus attribute) (galaxy.datatypes.annotation.SnapHmm attribute) (galaxy.datatypes.anvio.AnvioComposite attribute) (galaxy.datatypes.anvio.AnvioContigsDB attribute) (galaxy.datatypes.anvio.AnvioDB attribute) (galaxy.datatypes.anvio.AnvioGenomesDB attribute) (galaxy.datatypes.anvio.AnvioPanDB attribute) (galaxy.datatypes.anvio.AnvioProfileDB attribute) (galaxy.datatypes.anvio.AnvioSamplesDB attribute) (galaxy.datatypes.anvio.AnvioStructureDB attribute) (galaxy.datatypes.assembly.Amos attribute) (galaxy.datatypes.assembly.Roadmaps attribute) (galaxy.datatypes.assembly.Sequences attribute) (galaxy.datatypes.assembly.Velvet attribute) (galaxy.datatypes.binary.Ab1 attribute) (galaxy.datatypes.binary.Anndata attribute) (galaxy.datatypes.binary.BafTar attribute) (galaxy.datatypes.binary.Bam attribute) (galaxy.datatypes.binary.BamInputSorted attribute) (galaxy.datatypes.binary.BamNative attribute) (galaxy.datatypes.binary.BamQuerynameSorted attribute) (galaxy.datatypes.binary.BaseBcf attribute) (galaxy.datatypes.binary.Bcf attribute) (galaxy.datatypes.binary.BcfUncompressed attribute) (galaxy.datatypes.binary.BigBed attribute) (galaxy.datatypes.binary.BigWig attribute) (galaxy.datatypes.binary.Binary attribute) (galaxy.datatypes.binary.Biom2 attribute) (galaxy.datatypes.binary.BlibSQlite attribute) (galaxy.datatypes.binary.Bref3 attribute) (galaxy.datatypes.binary.Bz2DynamicCompressedArchive attribute) (galaxy.datatypes.binary.Cel attribute) (galaxy.datatypes.binary.ChiraSQLite attribute) (galaxy.datatypes.binary.CompressedArchive attribute) (galaxy.datatypes.binary.CompressedZipArchive attribute) (galaxy.datatypes.binary.Cool attribute) (galaxy.datatypes.binary.Cpt attribute) (galaxy.datatypes.binary.CRAM attribute) (galaxy.datatypes.binary.CuffDiffSQlite attribute) (galaxy.datatypes.binary.DAA attribute) (galaxy.datatypes.binary.Dcd attribute) (galaxy.datatypes.binary.DlibSQlite attribute) (galaxy.datatypes.binary.DMND attribute) (galaxy.datatypes.binary.DynamicCompressedArchive attribute) (galaxy.datatypes.binary.Edr attribute) (galaxy.datatypes.binary.ElibSQlite attribute) (galaxy.datatypes.binary.ExcelXls attribute) (galaxy.datatypes.binary.Fast5Archive attribute) (galaxy.datatypes.binary.Fast5ArchiveBz2 attribute) (galaxy.datatypes.binary.Fast5ArchiveGz attribute) (galaxy.datatypes.binary.Fast5ArchiveXz attribute) (galaxy.datatypes.binary.FITS attribute) (galaxy.datatypes.binary.GAFASQLite attribute) (galaxy.datatypes.binary.GeminiSQLite attribute) (galaxy.datatypes.binary.GeneNoteBook attribute) (galaxy.datatypes.binary.GenericAsn1Binary attribute) (galaxy.datatypes.binary.GmxBinary attribute) (galaxy.datatypes.binary.Grib attribute) (galaxy.datatypes.binary.GzDynamicCompressedArchive attribute) (galaxy.datatypes.binary.H5 attribute) (galaxy.datatypes.binary.H5MLM attribute) (galaxy.datatypes.binary.HexrdEtaOmeNpz attribute) (galaxy.datatypes.binary.HexrdImagesNpz attribute) (galaxy.datatypes.binary.HexrdMaterials attribute) (galaxy.datatypes.binary.ICM attribute) (galaxy.datatypes.binary.Idat attribute) (galaxy.datatypes.binary.IdpDB attribute) (galaxy.datatypes.binary.JP2 attribute) (galaxy.datatypes.binary.Loom attribute) (galaxy.datatypes.binary.LudwigModel attribute) (galaxy.datatypes.binary.MashSketch attribute) (galaxy.datatypes.binary.MassHunterTar attribute) (galaxy.datatypes.binary.MassLynxTar attribute) (galaxy.datatypes.binary.MCool attribute) (galaxy.datatypes.binary.Meryldb attribute) (galaxy.datatypes.binary.MongoDBArchive attribute) (galaxy.datatypes.binary.MzSQlite attribute) (galaxy.datatypes.binary.NcbiTaxonomySQlite attribute) (galaxy.datatypes.binary.NetCDF attribute) (galaxy.datatypes.binary.Npz attribute) (galaxy.datatypes.binary.Numpy attribute) (galaxy.datatypes.binary.OSW attribute) (galaxy.datatypes.binary.OxliBinary attribute) (galaxy.datatypes.binary.OxliCountGraph attribute) (galaxy.datatypes.binary.OxliGraphLabels attribute) (galaxy.datatypes.binary.OxliNodeGraph attribute) (galaxy.datatypes.binary.OxliStopTags attribute) (galaxy.datatypes.binary.OxliSubset attribute) (galaxy.datatypes.binary.OxliTagSet attribute) (galaxy.datatypes.binary.Parquet attribute) (galaxy.datatypes.binary.PostgresqlArchive attribute) (galaxy.datatypes.binary.PQP attribute) (galaxy.datatypes.binary.Pretext attribute) (galaxy.datatypes.binary.ProBam attribute) (galaxy.datatypes.binary.RData attribute) (galaxy.datatypes.binary.RDS attribute) (galaxy.datatypes.binary.RMA6 attribute) (galaxy.datatypes.binary.Scf attribute) (galaxy.datatypes.binary.SearchGuiArchive attribute) (galaxy.datatypes.binary.Sff attribute) (galaxy.datatypes.binary.SQlite attribute) (galaxy.datatypes.binary.SQmass attribute) (galaxy.datatypes.binary.Sra attribute) (galaxy.datatypes.binary.TdfTar attribute) (galaxy.datatypes.binary.Trr attribute) (galaxy.datatypes.binary.TwoBit attribute) (galaxy.datatypes.binary.Vel attribute) (galaxy.datatypes.binary.Visium attribute) (galaxy.datatypes.binary.Wiff2Tar attribute) (galaxy.datatypes.binary.WiffTar attribute) (galaxy.datatypes.binary.Xlsx attribute) (galaxy.datatypes.binary.Xtc attribute) (galaxy.datatypes.binary.YepTar attribute) (galaxy.datatypes.blast.BlastDomainDb attribute) (galaxy.datatypes.blast.BlastDomainDb5 attribute) (galaxy.datatypes.blast.BlastNucDb attribute) (galaxy.datatypes.blast.BlastNucDb5 attribute) (galaxy.datatypes.blast.BlastProtDb attribute) (galaxy.datatypes.blast.BlastProtDb5 attribute) (galaxy.datatypes.blast.BlastXml attribute) (galaxy.datatypes.blast.LastDb attribute) (galaxy.datatypes.chrominfo.ChromInfo attribute) (galaxy.datatypes.constructive_solid_geometry.GmshGeo attribute) (galaxy.datatypes.constructive_solid_geometry.GmshMsh attribute) (galaxy.datatypes.constructive_solid_geometry.NeperMultiScaleCell attribute) (galaxy.datatypes.constructive_solid_geometry.NeperPoints attribute) (galaxy.datatypes.constructive_solid_geometry.NeperPointsTabular attribute) (galaxy.datatypes.constructive_solid_geometry.NeperTesr attribute) (galaxy.datatypes.constructive_solid_geometry.NeperTess attribute) (galaxy.datatypes.constructive_solid_geometry.PlyAscii attribute) (galaxy.datatypes.constructive_solid_geometry.PlyBinary attribute) (galaxy.datatypes.constructive_solid_geometry.STL attribute) (galaxy.datatypes.constructive_solid_geometry.VtkAscii attribute) (galaxy.datatypes.constructive_solid_geometry.VtkBinary attribute) (galaxy.datatypes.constructive_solid_geometry.ZsetGeof attribute) (galaxy.datatypes.coverage.LastzCoverage attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.data.Directory attribute) (galaxy.datatypes.data.GenericAsn1 attribute) (galaxy.datatypes.data.LineCount attribute) (galaxy.datatypes.data.Newick attribute) (galaxy.datatypes.data.Nexus attribute) (galaxy.datatypes.data.Text attribute) (galaxy.datatypes.flow.FCS attribute) (galaxy.datatypes.genetics.Affybatch attribute) (galaxy.datatypes.genetics.AllegroLOD attribute) (galaxy.datatypes.genetics.DataIn attribute) (galaxy.datatypes.genetics.Eigenstratgeno attribute) (galaxy.datatypes.genetics.Eigenstratpca attribute) (galaxy.datatypes.genetics.Eset attribute) (galaxy.datatypes.genetics.Fped attribute) (galaxy.datatypes.genetics.Fphe attribute) (galaxy.datatypes.genetics.GenomeGraphs attribute) (galaxy.datatypes.genetics.GenotypeMatrix attribute) (galaxy.datatypes.genetics.IdeasPre attribute) (galaxy.datatypes.genetics.ldIndep attribute) (galaxy.datatypes.genetics.LinkageStudies attribute) (galaxy.datatypes.genetics.Lped attribute) (galaxy.datatypes.genetics.MAlist attribute) (galaxy.datatypes.genetics.MarkerMap attribute) (galaxy.datatypes.genetics.Pbed attribute) (galaxy.datatypes.genetics.Phe attribute) (galaxy.datatypes.genetics.Pheno attribute) (galaxy.datatypes.genetics.Pphe attribute) (galaxy.datatypes.genetics.RexpBase attribute) (galaxy.datatypes.genetics.Rgenetics attribute) (galaxy.datatypes.genetics.rgFeatureList attribute) (galaxy.datatypes.genetics.rgSampleList attribute) (galaxy.datatypes.genetics.rgTabList attribute) (galaxy.datatypes.genetics.SNPMatrix attribute) (galaxy.datatypes.genetics.Snptest attribute) (galaxy.datatypes.gis.Shapefile attribute) (galaxy.datatypes.goldenpath.GoldenPath attribute) (galaxy.datatypes.graph.Sif attribute) (galaxy.datatypes.graph.Xgmml attribute) (galaxy.datatypes.hdf5.HDF5SummarizedExperiment attribute) (galaxy.datatypes.images.Analyze75 attribute) (galaxy.datatypes.images.Bmp attribute) (galaxy.datatypes.images.Eps attribute) (galaxy.datatypes.images.Gif attribute) (galaxy.datatypes.images.Gifti attribute) (galaxy.datatypes.images.Gmaj attribute) (galaxy.datatypes.images.Hamamatsu attribute) (galaxy.datatypes.images.Html attribute) (galaxy.datatypes.images.Im attribute) (galaxy.datatypes.images.Image attribute) (galaxy.datatypes.images.Jpg attribute) (galaxy.datatypes.images.Laj attribute) (galaxy.datatypes.images.Mirax attribute) (galaxy.datatypes.images.Mrc2014 attribute) (galaxy.datatypes.images.Nifti1 attribute) (galaxy.datatypes.images.Nifti2 attribute) (galaxy.datatypes.images.Nrrd attribute) (galaxy.datatypes.images.OMETiff attribute) (galaxy.datatypes.images.Pbm attribute) (galaxy.datatypes.images.Pcd attribute) (galaxy.datatypes.images.Pcx attribute) (galaxy.datatypes.images.Pdf attribute) (galaxy.datatypes.images.Pgm attribute) (galaxy.datatypes.images.Png attribute) (galaxy.datatypes.images.Ppm attribute) (galaxy.datatypes.images.Psd attribute) (galaxy.datatypes.images.Rast attribute) (galaxy.datatypes.images.Rgb attribute) (galaxy.datatypes.images.Sakura attribute) (galaxy.datatypes.images.Star attribute) (galaxy.datatypes.images.Tck attribute) (galaxy.datatypes.images.Tiff attribute) (galaxy.datatypes.images.Trk attribute) (galaxy.datatypes.images.Xbm attribute) (galaxy.datatypes.images.Xpm attribute) (galaxy.datatypes.interval.Bed attribute) (galaxy.datatypes.interval.Bed12 attribute) (galaxy.datatypes.interval.Bed6 attribute) (galaxy.datatypes.interval.BedGraph attribute) (galaxy.datatypes.interval.BedStrict attribute) (galaxy.datatypes.interval.BedTabix attribute) (galaxy.datatypes.interval.ChromatinInteractions attribute) (galaxy.datatypes.interval.CustomTrack attribute) (galaxy.datatypes.interval.ENCODEPeak attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Gff3 attribute) (galaxy.datatypes.interval.GffTabix attribute) (galaxy.datatypes.interval.Gtf attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.interval.IntervalTabix attribute) (galaxy.datatypes.interval.JuicerMediumTabix attribute) (galaxy.datatypes.interval.ProBed attribute) (galaxy.datatypes.interval.ScIdx attribute) (galaxy.datatypes.interval.Wiggle attribute) (galaxy.datatypes.isa.IsaJson attribute) (galaxy.datatypes.isa.IsaTab attribute) (galaxy.datatypes.media.Audio attribute) (galaxy.datatypes.media.Flv attribute) (galaxy.datatypes.media.Mkv attribute) (galaxy.datatypes.media.Mp3 attribute) (galaxy.datatypes.media.Mp4 attribute) (galaxy.datatypes.media.Mpg attribute) (galaxy.datatypes.media.Video attribute) (galaxy.datatypes.media.Wav attribute) (galaxy.datatypes.metacyto.mStats attribute) (galaxy.datatypes.metacyto.mSummary attribute) (galaxy.datatypes.microarrays.Gal attribute) (galaxy.datatypes.microarrays.GenericMicroarrayFile attribute) (galaxy.datatypes.microarrays.Gpr attribute) (galaxy.datatypes.molecules.AtomicStructFile attribute) (galaxy.datatypes.molecules.Cell attribute) (galaxy.datatypes.molecules.CIF attribute) (galaxy.datatypes.molecules.CML attribute) (galaxy.datatypes.molecules.DRF attribute) (galaxy.datatypes.molecules.ExtendedXYZ attribute) (galaxy.datatypes.molecules.FPS attribute) (galaxy.datatypes.molecules.GenericMolFile attribute) (galaxy.datatypes.molecules.grd attribute) (galaxy.datatypes.molecules.grdtgz attribute) (galaxy.datatypes.molecules.GRO attribute) (galaxy.datatypes.molecules.InChI attribute) (galaxy.datatypes.molecules.Magres attribute) (galaxy.datatypes.molecules.MOL attribute) (galaxy.datatypes.molecules.MOL2 attribute) (galaxy.datatypes.molecules.OBFS attribute) (galaxy.datatypes.molecules.PDB attribute) (galaxy.datatypes.molecules.PDBQT attribute) (galaxy.datatypes.molecules.PHAR attribute) (galaxy.datatypes.molecules.PQR attribute) (galaxy.datatypes.molecules.SDF attribute) (galaxy.datatypes.molecules.SMILES attribute) (galaxy.datatypes.molecules.XYZ attribute) (galaxy.datatypes.mothur.AccNos attribute) (galaxy.datatypes.mothur.AlignCheck attribute) (galaxy.datatypes.mothur.AlignReport attribute) (galaxy.datatypes.mothur.Axes attribute) (galaxy.datatypes.mothur.ConsensusTaxonomy attribute) (galaxy.datatypes.mothur.CountTable attribute) (galaxy.datatypes.mothur.DistanceMatrix attribute) (galaxy.datatypes.mothur.Frequency attribute) (galaxy.datatypes.mothur.Group attribute) (galaxy.datatypes.mothur.GroupAbund attribute) (galaxy.datatypes.mothur.LaneMask attribute) (galaxy.datatypes.mothur.LowerTriangleDistanceMatrix attribute) (galaxy.datatypes.mothur.Names attribute) (galaxy.datatypes.mothur.Oligos attribute) (galaxy.datatypes.mothur.Otu attribute) (galaxy.datatypes.mothur.PairwiseDistanceMatrix attribute) (galaxy.datatypes.mothur.Quantile attribute) (galaxy.datatypes.mothur.RefTaxonomy attribute) (galaxy.datatypes.mothur.Sabund attribute) (galaxy.datatypes.mothur.SecondaryStructureMap attribute) (galaxy.datatypes.mothur.SffFlow attribute) (galaxy.datatypes.mothur.SquareDistanceMatrix attribute) (galaxy.datatypes.mothur.Summary attribute) (galaxy.datatypes.mothur.TaxonomySummary attribute) (galaxy.datatypes.msa.Hmmer attribute) (galaxy.datatypes.msa.Hmmer2 attribute) (galaxy.datatypes.msa.Hmmer3 attribute) (galaxy.datatypes.msa.HmmerPress attribute) (galaxy.datatypes.msa.InfernalCM attribute) (galaxy.datatypes.msa.MauveXmfa attribute) (galaxy.datatypes.msa.Msf attribute) (galaxy.datatypes.msa.Stockholm_1_0 attribute) (galaxy.datatypes.neo4j.Neo4j attribute) (galaxy.datatypes.neo4j.Neo4jDB attribute) (galaxy.datatypes.neo4j.Neo4jDBzip attribute) (galaxy.datatypes.ngsindex.BowtieBaseIndex attribute) (galaxy.datatypes.ngsindex.BowtieColorIndex attribute) (galaxy.datatypes.ngsindex.BowtieIndex attribute) (galaxy.datatypes.phylip.Phylip attribute) (galaxy.datatypes.plant_tribes.PlantTribesKsComponents attribute) (galaxy.datatypes.plant_tribes.Smat attribute) (galaxy.datatypes.proteomics.ConsensusXML attribute) (galaxy.datatypes.proteomics.Dta attribute) (galaxy.datatypes.proteomics.Dta2d attribute) (galaxy.datatypes.proteomics.Edta attribute) (galaxy.datatypes.proteomics.FeatureXML attribute) (galaxy.datatypes.proteomics.IdXML attribute) (galaxy.datatypes.proteomics.ImzML attribute) (galaxy.datatypes.proteomics.Kroenik attribute) (galaxy.datatypes.proteomics.MascotDat attribute) (galaxy.datatypes.proteomics.MascotXML attribute) (galaxy.datatypes.proteomics.Mgf attribute) (galaxy.datatypes.proteomics.Ms2 attribute) (galaxy.datatypes.proteomics.Msp attribute) (galaxy.datatypes.proteomics.MzData attribute) (galaxy.datatypes.proteomics.MzIdentML attribute) (galaxy.datatypes.proteomics.MzML attribute) (galaxy.datatypes.proteomics.MzQuantML attribute) (galaxy.datatypes.proteomics.MzTab attribute) (galaxy.datatypes.proteomics.MzTab2 attribute) (galaxy.datatypes.proteomics.MzXML attribute) (galaxy.datatypes.proteomics.NmrML attribute) (galaxy.datatypes.proteomics.ParamXml attribute) (galaxy.datatypes.proteomics.PEFF attribute) (galaxy.datatypes.proteomics.PepList attribute) (galaxy.datatypes.proteomics.PepXml attribute) (galaxy.datatypes.proteomics.PepXmlReport attribute) (galaxy.datatypes.proteomics.ProteomicsXml attribute) (galaxy.datatypes.proteomics.ProtXML attribute) (galaxy.datatypes.proteomics.ProtXmlReport attribute) (galaxy.datatypes.proteomics.PSMS attribute) (galaxy.datatypes.proteomics.QCML attribute) (galaxy.datatypes.proteomics.Sf3 attribute) (galaxy.datatypes.proteomics.SPLib attribute) (galaxy.datatypes.proteomics.SPLibNoIndex attribute) (galaxy.datatypes.proteomics.TandemXML attribute) (galaxy.datatypes.proteomics.ThermoRAW attribute) (galaxy.datatypes.proteomics.TrafoXML attribute) (galaxy.datatypes.proteomics.TraML attribute) (galaxy.datatypes.proteomics.UniProtXML attribute) (galaxy.datatypes.proteomics.Wiff attribute) (galaxy.datatypes.proteomics.Wiff2 attribute) (galaxy.datatypes.proteomics.XHunterAslFormat attribute) (galaxy.datatypes.proteomics.XquestSpecXML attribute) (galaxy.datatypes.proteomics.XquestXML attribute) (galaxy.datatypes.qiime2.QIIME2Artifact attribute) (galaxy.datatypes.qiime2.QIIME2Metadata attribute) (galaxy.datatypes.qiime2.QIIME2Visualization attribute) (galaxy.datatypes.qualityscore.QualityScore attribute) (galaxy.datatypes.qualityscore.QualityScore454 attribute) (galaxy.datatypes.qualityscore.QualityScoreIllumina attribute) (galaxy.datatypes.qualityscore.QualityScoreSolexa attribute) (galaxy.datatypes.qualityscore.QualityScoreSOLiD attribute) (galaxy.datatypes.sequence.Alignment attribute) (galaxy.datatypes.sequence.Axt attribute) (galaxy.datatypes.sequence.BaseFastq attribute) (galaxy.datatypes.sequence.csFasta attribute) (galaxy.datatypes.sequence.DotBracket attribute) (galaxy.datatypes.sequence.Fasta attribute) (galaxy.datatypes.sequence.Fastg attribute) (galaxy.datatypes.sequence.Fastq attribute) (galaxy.datatypes.sequence.FastqCSSanger attribute) (galaxy.datatypes.sequence.FastqIllumina attribute) (galaxy.datatypes.sequence.FastqSanger attribute) (galaxy.datatypes.sequence.FastqSolexa attribute) (galaxy.datatypes.sequence.Genbank attribute) (galaxy.datatypes.sequence.Lav attribute) (galaxy.datatypes.sequence.Maf attribute) (galaxy.datatypes.sequence.MafCustomTrack attribute) (galaxy.datatypes.sequence.MemePsp attribute) (galaxy.datatypes.sequence.RNADotPlotMatrix attribute) (galaxy.datatypes.sequence.Sequence attribute) (galaxy.datatypes.sequence.SequenceSplitLocations attribute) (galaxy.datatypes.spaln.SpalnNuclDb attribute) (galaxy.datatypes.spaln.SpalnProtDb attribute) (galaxy.datatypes.speech.BPF attribute) (galaxy.datatypes.speech.TextGrid attribute) (galaxy.datatypes.tabular.BaseCSV attribute) (galaxy.datatypes.tabular.BaseVcf attribute) (galaxy.datatypes.tabular.CMAP attribute) (galaxy.datatypes.tabular.ConnectivityTable attribute) (galaxy.datatypes.tabular.CSV attribute) (galaxy.datatypes.tabular.Eland attribute) (galaxy.datatypes.tabular.ElandMulti attribute) (galaxy.datatypes.tabular.FeatureLocationIndex attribute) (galaxy.datatypes.tabular.MatrixMarket attribute) (galaxy.datatypes.tabular.Pileup attribute) (galaxy.datatypes.tabular.Psl attribute) (galaxy.datatypes.tabular.Sam attribute) (galaxy.datatypes.tabular.SraManifest attribute) (galaxy.datatypes.tabular.Tabular attribute) (galaxy.datatypes.tabular.TabularData attribute) (galaxy.datatypes.tabular.Taxonomy attribute) (galaxy.datatypes.tabular.TSV attribute) (galaxy.datatypes.tabular.Vcf attribute) (galaxy.datatypes.tabular.VcfGz attribute) (galaxy.datatypes.text.Arff attribute) (galaxy.datatypes.text.BCSLmodel attribute) (galaxy.datatypes.text.BCSLts attribute) (galaxy.datatypes.text.Biom1 attribute) (galaxy.datatypes.text.Castep attribute) (galaxy.datatypes.text.CTLresult attribute) (galaxy.datatypes.text.DataManagerJson attribute) (galaxy.datatypes.text.ExpressionJson attribute) (galaxy.datatypes.text.FormattedDensity attribute) (galaxy.datatypes.text.GeoJson attribute) (galaxy.datatypes.text.Gfa1 attribute) (galaxy.datatypes.text.Gfa2 attribute) (galaxy.datatypes.text.Html attribute) (galaxy.datatypes.text.ImgtJson attribute) (galaxy.datatypes.text.Ipynb attribute) (galaxy.datatypes.text.IQTree attribute) (galaxy.datatypes.text.Json attribute) (galaxy.datatypes.text.Obo attribute) (galaxy.datatypes.text.Paf attribute) (galaxy.datatypes.text.Param attribute) (galaxy.datatypes.text.PithyaModel attribute) (galaxy.datatypes.text.PithyaProperty attribute) (galaxy.datatypes.text.PithyaResult attribute) (galaxy.datatypes.text.SnpEffDb attribute) (galaxy.datatypes.text.SnpSiftDbNSFP attribute) (galaxy.datatypes.text.StormCheck attribute) (galaxy.datatypes.text.StormSample attribute) (galaxy.datatypes.text.Yaml attribute) (galaxy.datatypes.tracks.GeneTrack attribute) (galaxy.datatypes.tracks.UCSCTrackHub attribute) (galaxy.datatypes.triples.HDT attribute) (galaxy.datatypes.triples.Jsonld attribute) (galaxy.datatypes.triples.N3 attribute) (galaxy.datatypes.triples.NTriples attribute) (galaxy.datatypes.triples.Rdf attribute) (galaxy.datatypes.triples.Sbol attribute) (galaxy.datatypes.triples.Triples attribute) (galaxy.datatypes.triples.Turtle attribute) (galaxy.datatypes.xml.CisML attribute) (galaxy.datatypes.xml.Dzi attribute) (galaxy.datatypes.xml.GenericXml attribute) (galaxy.datatypes.xml.MEMEXml attribute) (galaxy.datatypes.xml.Owl attribute) (galaxy.datatypes.xml.Phyloxml attribute) (galaxy.datatypes.xml.Sbml attribute) MetadataCollection (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) MetadataCollectionStrategy (class in galaxy.metadata) MetadataElement (in module galaxy.model.metadata) MetadataElementSpec (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) MetadataEqualValidator (class in galaxy.tools.parameters.validation) MetadataFile (class in galaxy.model) (class in galaxy.schema.schema) MetadataInDataTableColumnValidator (class in galaxy.tools.parameters.validation) MetadataInFileColumnValidator (class in galaxy.tools.parameters.validation) MetadataInRangeValidator (class in galaxy.tools.parameters.validation) MetadataNotInDataTableColumnValidator (class in galaxy.tools.parameters.validation) MetadataParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) MetadataSourceProvider (class in galaxy.job_execution.output_collect) (class in galaxy.model.store.discover) MetadataSpecCollection (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) MetadataTempFile (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) MetadataToolOutputAction (class in galaxy.tool_util.parser.output_actions) MetadataType (class in galaxy.model.custom_types) MetadataValidator (class in galaxy.tools.parameters.validation) MetadataValueFilter (class in galaxy.tool_util.parser.output_actions) methods (galaxy.webapps.galaxy.api.tools.FormDataApiRoute attribute) (galaxy.webapps.galaxy.api.tools.JsonApiRoute attribute) Metric (class in galaxy.managers.metrics) metric_name (galaxy.model.JobMetricNumeric attribute) (galaxy.model.JobMetricText attribute) (galaxy.model.TaskMetricNumeric attribute) (galaxy.model.TaskMetricText attribute) metric_query() (galaxy.jobs.rule_helper.RuleHelper method) metric_value (galaxy.model.JobMetricNumeric attribute) (galaxy.model.JobMetricText attribute) (galaxy.model.TaskMetricNumeric attribute) (galaxy.model.TaskMetricText attribute) metrics (galaxy.managers.metrics.CreateMetricsPayload attribute) (galaxy.model.JobLike property) MetricsManager (class in galaxy.managers.metrics) Mgf (class in galaxy.datatypes.proteomics) MiddlewareWrapUnsupported mime_type() (galaxy.datatypes.display_applications.parameters.DisplayDataValueWrapper method) (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper method) min_version (galaxy.tools.safe_update attribute) MinimalApp (class in galaxy.structured_app) MinimalGalaxyApplication (class in galaxy.app) MinimalManagerApp (class in galaxy.structured_app) MinimalToolApp (class in galaxy.structured_app) Mirax (class in galaxy.datatypes.images) misc_blurb (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) misc_info (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) missing_meta() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) (galaxy.model.none_like.NoneDataset method) missing_repository_dependencies (galaxy.model.tool_shed_install.ToolShedRepository property) missing_test_components (tool_shed.webapp.model.RepositoryMetadata attribute) missing_tool_data_table_name (galaxy.tools.parameters.dynamic_options.DynamicOptions property) missing_tool_dependencies (galaxy.model.tool_shed_install.ToolShedRepository property) missing_tools (galaxy.managers.workflows.CreatedWorkflow attribute) MissingTestComponent (class in tool_shed.utility_containers) MissingToolsException mkdtemp() (galaxy_test.driver.driver_util.TestDriver method) mkstemp_ln() (in module galaxy.util) Mkv (class in galaxy.datatypes.media) mlget() (galaxy.tool_util.cwl.cwltool_deps.CommentedMap method) mock_trans() (in module galaxy.tool_util.unittest_utils) mock_url_builder() (in module galaxy.app_unittest_utils.galaxy_mock) MockApp (class in galaxy.app_unittest_utils.galaxy_mock) MockAppConfig (class in galaxy.app_unittest_utils.galaxy_mock) MockAppConfig.MockSchema (class in galaxy.app_unittest_utils.galaxy_mock) MockConfig (class in galaxy.objectstore.unittest_utils) MockDir (class in galaxy.app_unittest_utils.galaxy_mock) MockLock (class in galaxy.app_unittest_utils.galaxy_mock) MockSetExternalTool (class in galaxy.model.unittest_utils.data_app) MockTemplateHelpers (class in galaxy.app_unittest_utils.galaxy_mock) MockTrans (class in galaxy.app_unittest_utils.galaxy_mock) MockVisualizationsRegistry (class in galaxy.app_unittest_utils.galaxy_mock) MockWebapp (class in galaxy.app_unittest_utils.galaxy_mock) modal_body_selector() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) mode_is_valid (galaxy.tool_util.deps.container_volumes.ContainerVolume property) Model (class in galaxy.schema.schema) model (galaxy.app.GalaxyManagerApplication attribute) (galaxy.app.MinimalGalaxyApplication attribute) (galaxy.app.UniverseApplication attribute) (galaxy.managers.context.ProvidesAppContext property) (galaxy.model.store.StoreAppProtocol attribute) (galaxy.model.unittest_utils.data_app.GalaxyDataTestApp attribute) (galaxy.model.unittest_utils.GalaxyDataTestApp attribute) (galaxy.schema.schema.ImplicitCollectionJobsStateSummary attribute) (galaxy.schema.schema.JobStateSummary attribute) (galaxy.schema.schema.WorkflowInvocationStateSummary attribute) (galaxy.security.Action attribute) (galaxy.structured_app.BasicSharedApp attribute) (galaxy.structured_app.MinimalApp attribute) (galaxy.webapps.reports.app.UniverseApplication attribute) (tool_shed.webapp.app.UniverseApplication attribute) model_class (galaxy.managers.base.ModelFilterParser attribute) (galaxy.managers.base.ModelManager attribute) (galaxy.managers.cloud.CloudManager attribute) (galaxy.managers.cloudauthzs.CloudAuthzManager attribute) (galaxy.managers.datasets.DatasetAssociationFilterParser attribute) (galaxy.managers.datasets.DatasetManager attribute) (galaxy.managers.hdas.HDAFilterParser attribute) (galaxy.managers.hdas.HDAManager attribute) (galaxy.managers.hdcas.HDCAManager attribute) (galaxy.managers.histories.HistoryFilters attribute) (galaxy.managers.histories.HistoryManager attribute) (galaxy.managers.history_contents.HistoryContentsFilters attribute) (galaxy.managers.lddas.LDDAManager attribute) (galaxy.managers.library_datasets.LibraryDatasetsManager attribute) (galaxy.managers.pages.PageManager attribute) (galaxy.managers.roles.RoleManager attribute) (galaxy.managers.secured.AccessibleManagerMixin attribute) (galaxy.managers.secured.OwnableManagerMixin attribute) (galaxy.managers.sharable.SharableModelFilters attribute) (galaxy.managers.tools.DynamicToolManager attribute) (galaxy.managers.users.AdminUserFilterParser attribute) (galaxy.managers.users.UserManager attribute) (galaxy.managers.visualizations.VisualizationManager attribute) (galaxy.managers.workflows.WorkflowsManager attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.ArchivedHistorySummary attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.DatasetHash attribute) (galaxy.schema.schema.DCESummary attribute) (galaxy.schema.schema.DCObject attribute) (galaxy.schema.schema.DCSummary attribute) (galaxy.schema.schema.GroupModel attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) (galaxy.schema.schema.HDAObject attribute) (galaxy.schema.schema.HDCASummary attribute) (galaxy.schema.schema.HistorySummary attribute) (galaxy.schema.schema.InstalledToolShedRepository attribute) (galaxy.schema.schema.JobBaseModel attribute) (galaxy.schema.schema.LibraryFolderDetails attribute) (galaxy.schema.schema.LibraryLegacySummary attribute) (galaxy.schema.schema.PageSummary attribute) (galaxy.schema.schema.RoleModelResponse attribute) (galaxy.schema.schema.StoredWorkflowSummary attribute) (galaxy.schema.schema.UserModel attribute) (galaxy.schema.schema.WithModelClass attribute) (galaxy.tool_util.toolbox.views.interface.ToolPanelViewModel attribute) (galaxy.web.framework.helpers.grids.GridData attribute) (galaxy.web.legacy_framework.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) model_config (galaxy.managers.datatypes.DatatypeConverterList attribute) (galaxy.managers.datatypes.DatatypeDetails attribute) (galaxy.managers.datatypes.DatatypesCombinedMap attribute) (galaxy.managers.datatypes.DatatypesEDAMDetailsDict attribute) (galaxy.managers.datatypes.DatatypesMap attribute) (galaxy.managers.display_applications.DisplayApplication attribute) (galaxy.managers.display_applications.Link attribute) (galaxy.managers.display_applications.ReloadFeedback attribute) (galaxy.managers.jobs.JobLock attribute) (galaxy.managers.licenses.LicenseMetadataModel attribute) (galaxy.managers.metrics.CreateMetricsPayload attribute) (galaxy.managers.metrics.Metric attribute) (galaxy.managers.sharable.ShareWithExtra attribute) (galaxy.managers.tags.ItemTagsPayload attribute) (galaxy.managers.workflows.RefactorRequest attribute) (galaxy.managers.workflows.RefactorResponse attribute) (galaxy.managers.workflows.WorkflowCreateOptions attribute) (galaxy.managers.workflows.WorkflowStateResolutionOptions attribute) (galaxy.managers.workflows.WorkflowUpdateOptions attribute) (galaxy.model.store.DatasetAttributeImportModel attribute) (galaxy.model.UserQuotaBasicUsage attribute) (galaxy.model.UserQuotaUsage attribute) (galaxy.objectstore.ConcreteObjectStoreModel attribute) (galaxy.objectstore.QuotaModel attribute) (galaxy.schema.APIKeyModel attribute) (galaxy.schema.BootstrapAdminUser attribute) (galaxy.schema.fetch_data.BaseCollectionTarget attribute) (galaxy.schema.fetch_data.BaseDataElement attribute) (galaxy.schema.fetch_data.BaseDataPayload attribute) (galaxy.schema.fetch_data.BaseDataTarget attribute) (galaxy.schema.fetch_data.BaseFetchDataTarget attribute) (galaxy.schema.fetch_data.CompositeDataElement attribute) (galaxy.schema.fetch_data.CompositeItems attribute) (galaxy.schema.fetch_data.DataElementsFromTarget attribute) (galaxy.schema.fetch_data.DataElementsTarget attribute) (galaxy.schema.fetch_data.ExtraFiles attribute) (galaxy.schema.fetch_data.FetchBaseModel attribute) (galaxy.schema.fetch_data.FetchDataFormPayload attribute) (galaxy.schema.fetch_data.FetchDataPayload attribute) (galaxy.schema.fetch_data.FileDataElement attribute) (galaxy.schema.fetch_data.FilesPayload attribute) (galaxy.schema.fetch_data.FtpImportElement attribute) (galaxy.schema.fetch_data.FtpImportTarget attribute) (galaxy.schema.fetch_data.HdaDestination attribute) (galaxy.schema.fetch_data.HdcaDataItemsFromTarget attribute) (galaxy.schema.fetch_data.HdcaDataItemsTarget attribute) (galaxy.schema.fetch_data.HdcaDestination attribute) (galaxy.schema.fetch_data.ItemsFromModel attribute) (galaxy.schema.fetch_data.LibraryDestination attribute) (galaxy.schema.fetch_data.LibraryFolderDestination attribute) (galaxy.schema.fetch_data.NestedElement attribute) (galaxy.schema.fetch_data.PastedDataElement attribute) (galaxy.schema.fetch_data.PathDataElement attribute) (galaxy.schema.fetch_data.ServerDirElement attribute) (galaxy.schema.fetch_data.UrlDataElement attribute) (galaxy.schema.FilterQueryParams attribute) (galaxy.schema.PaginationQueryParams attribute) (galaxy.schema.remote_files.BrowsableFilesSourcePlugin attribute) (galaxy.schema.remote_files.CreatedEntryResponse attribute) (galaxy.schema.remote_files.CreateEntryPayload attribute) (galaxy.schema.remote_files.FilesSourcePlugin attribute) (galaxy.schema.remote_files.FilesSourcePluginList attribute) (galaxy.schema.remote_files.ListJstreeResponse attribute) (galaxy.schema.remote_files.ListUriResponse attribute) (galaxy.schema.remote_files.RemoteDirectory attribute) (galaxy.schema.remote_files.RemoteEntry attribute) (galaxy.schema.remote_files.RemoteFile attribute) (galaxy.schema.schema.AnonUserModel attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.ArchivedHistorySummary attribute) (galaxy.schema.schema.ArchiveHistoryRequestPayload attribute) (galaxy.schema.schema.AsyncFile attribute) (galaxy.schema.schema.AsyncTaskResultSummary attribute) (galaxy.schema.schema.BaseUserModel attribute) (galaxy.schema.schema.BasicRoleModel attribute) (galaxy.schema.schema.BcoGenerationParametersMixin attribute) (galaxy.schema.schema.BulkOperationItemError attribute) (galaxy.schema.schema.BulkOperationParams attribute) (galaxy.schema.schema.ChangeDatatypeOperationParams attribute) (galaxy.schema.schema.ChangeDbkeyOperationParams attribute) (galaxy.schema.schema.CheckForUpdatesResponse attribute) (galaxy.schema.schema.CollectionElementIdentifier attribute) (galaxy.schema.schema.CreatedCustomBuild attribute) (galaxy.schema.schema.CreatedUserModel attribute) (galaxy.schema.schema.CreateHistoryFromStore attribute) (galaxy.schema.schema.CreateHistoryPayload attribute) (galaxy.schema.schema.CreateLibrariesFromStore attribute) (galaxy.schema.schema.CreateLibraryFilePayload attribute) (galaxy.schema.schema.CreateLibraryFolderPayload attribute) (galaxy.schema.schema.CreateLibraryPayload attribute) (galaxy.schema.schema.CreateNewCollectionPayload attribute) (galaxy.schema.schema.CreatePagePayload attribute) (galaxy.schema.schema.Creator attribute) (galaxy.schema.schema.CustomBuildBaseModel attribute) (galaxy.schema.schema.CustomBuildCreationPayload attribute) (galaxy.schema.schema.CustomBuildModel attribute) (galaxy.schema.schema.CustomBuildsCollection attribute) (galaxy.schema.schema.CustomBuildsMetadataResponse attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.DatasetAssociationRoles attribute) (galaxy.schema.schema.DatasetHash attribute) (galaxy.schema.schema.DatasetJobInfo attribute) (galaxy.schema.schema.DatasetPermissions attribute) (galaxy.schema.schema.DatasetSource attribute) (galaxy.schema.schema.DatasetSourceId attribute) (galaxy.schema.schema.DatasetSourceIdBase attribute) (galaxy.schema.schema.DatasetSummary attribute) (galaxy.schema.schema.DCDetailed attribute) (galaxy.schema.schema.DCESummary attribute) (galaxy.schema.schema.DCObject attribute) (galaxy.schema.schema.DCSummary attribute) (galaxy.schema.schema.DeletedCustomBuild attribute) (galaxy.schema.schema.DeleteHistoryContentPayload attribute) (galaxy.schema.schema.DeleteHistoryContentResult attribute) (galaxy.schema.schema.DeleteLibraryPayload attribute) (galaxy.schema.schema.DetailedUserModel attribute) (galaxy.schema.schema.DiskUsageUserModel attribute) (galaxy.schema.schema.DisplayApp attribute) (galaxy.schema.schema.EncodedDataItemSourceId attribute) (galaxy.schema.schema.EncodedDatasetSourceId attribute) (galaxy.schema.schema.EncodedHistoryContentItem attribute) (galaxy.schema.schema.EncodedJobParameterHistoryItem attribute) (galaxy.schema.schema.ExportAssociationData attribute) (galaxy.schema.schema.ExportHistoryArchivePayload attribute) (galaxy.schema.schema.ExportObjectMetadata attribute) (galaxy.schema.schema.ExportObjectRequestMetadata attribute) (galaxy.schema.schema.ExportObjectResultMetadata attribute) (galaxy.schema.schema.ExportRecordData attribute) (galaxy.schema.schema.ExportTaskListResponse attribute) (galaxy.schema.schema.FavoriteObject attribute) (galaxy.schema.schema.FavoriteObjectsSummary attribute) (galaxy.schema.schema.FileLibraryFolderItem attribute) (galaxy.schema.schema.FolderLibraryFolderItem attribute) (galaxy.schema.schema.GroupModel attribute) (galaxy.schema.schema.GroupRoleListResponse attribute) (galaxy.schema.schema.GroupRoleResponse attribute) (galaxy.schema.schema.GroupUserListResponse attribute) (galaxy.schema.schema.GroupUserResponse attribute) (galaxy.schema.schema.HDABasicInfo attribute) (galaxy.schema.schema.HDACommon attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) (galaxy.schema.schema.HDAExtended attribute) (galaxy.schema.schema.HDAInaccessible attribute) (galaxy.schema.schema.HDAObject attribute) (galaxy.schema.schema.HDASummary attribute) (galaxy.schema.schema.HDCACommon attribute) (galaxy.schema.schema.HDCADetailed attribute) (galaxy.schema.schema.HDCASummary attribute) (galaxy.schema.schema.HDCJobStateSummary attribute) (galaxy.schema.schema.HistoryActiveContentCounts attribute) (galaxy.schema.schema.HistoryContentBulkOperationPayload attribute) (galaxy.schema.schema.HistoryContentBulkOperationResult attribute) (galaxy.schema.schema.HistoryContentItem attribute) (galaxy.schema.schema.HistoryContentItemBase attribute) (galaxy.schema.schema.HistoryContentsArchiveDryRunResult attribute) (galaxy.schema.schema.HistoryContentsResult attribute) (galaxy.schema.schema.HistoryContentStats attribute) (galaxy.schema.schema.HistoryContentsWithStatsResult attribute) (galaxy.schema.schema.HistoryDetailed attribute) (galaxy.schema.schema.HistoryItemBase attribute) (galaxy.schema.schema.HistoryItemCommon attribute) (galaxy.schema.schema.HistorySummary attribute) (galaxy.schema.schema.Hyperlink attribute) (galaxy.schema.schema.ImplicitCollectionJobsStateSummary attribute) (galaxy.schema.schema.ImportToolDataBundleDatasetSource attribute) (galaxy.schema.schema.ImportToolDataBundleUriSource attribute) (galaxy.schema.schema.Input attribute) (galaxy.schema.schema.InputConnection attribute) (galaxy.schema.schema.InputDataCollectionStep attribute) (galaxy.schema.schema.InputDataStep attribute) (galaxy.schema.schema.InputParameterStep attribute) (galaxy.schema.schema.InputStep attribute) (galaxy.schema.schema.InstalledRepositoryToolShedStatus attribute) (galaxy.schema.schema.InstalledToolShedRepositories attribute) (galaxy.schema.schema.InstalledToolShedRepository attribute) (galaxy.schema.schema.InvocationIndexQueryPayload attribute) (galaxy.schema.schema.ItemStateSummary attribute) (galaxy.schema.schema.JobBaseModel attribute) (galaxy.schema.schema.JobDetails attribute) (galaxy.schema.schema.JobExportHistoryArchiveListResponse attribute) (galaxy.schema.schema.JobExportHistoryArchiveModel attribute) (galaxy.schema.schema.JobFullDetails attribute) (galaxy.schema.schema.JobIdResponse attribute) (galaxy.schema.schema.JobImportHistoryResponse attribute) (galaxy.schema.schema.JobIndexQueryPayload attribute) (galaxy.schema.schema.JobMetric attribute) (galaxy.schema.schema.JobMetricCollection attribute) (galaxy.schema.schema.JobStateSummary attribute) (galaxy.schema.schema.JobSummary attribute) (galaxy.schema.schema.LabelValuePair attribute) (galaxy.schema.schema.LegacyLibraryPermissionsPayload attribute) (galaxy.schema.schema.LibraryAvailablePermissions attribute) (galaxy.schema.schema.LibraryCurrentPermissions attribute) (galaxy.schema.schema.LibraryFolderContentsIndexQueryPayload attribute) (galaxy.schema.schema.LibraryFolderContentsIndexResult attribute) (galaxy.schema.schema.LibraryFolderCurrentPermissions attribute) (galaxy.schema.schema.LibraryFolderDetails attribute) (galaxy.schema.schema.LibraryFolderItemBase attribute) (galaxy.schema.schema.LibraryFolderMetadata attribute) (galaxy.schema.schema.LibraryFolderPermissionsPayload attribute) (galaxy.schema.schema.LibraryLegacySummary attribute) (galaxy.schema.schema.LibraryPermissionsPayload attribute) (galaxy.schema.schema.LibraryPermissionsPayloadBase attribute) (galaxy.schema.schema.LibrarySummary attribute) (galaxy.schema.schema.LibrarySummaryList attribute) (galaxy.schema.schema.LimitedUserModel attribute) (galaxy.schema.schema.MaterializeDatasetInstanceAPIRequest attribute) (galaxy.schema.schema.MaterializeDatasetInstanceRequest attribute) (galaxy.schema.schema.MetadataFile attribute) (galaxy.schema.schema.Model attribute) (galaxy.schema.schema.ObjectExportResponseBase attribute) (galaxy.schema.schema.ObjectExportTaskResponse attribute) (galaxy.schema.schema.Organization attribute) (galaxy.schema.schema.Output attribute) (galaxy.schema.schema.PageDetails attribute) (galaxy.schema.schema.PageIndexQueryPayload attribute) (galaxy.schema.schema.PageSummary attribute) (galaxy.schema.schema.PageSummaryBase attribute) (galaxy.schema.schema.PageSummaryList attribute) (galaxy.schema.schema.PauseStep attribute) (galaxy.schema.schema.Person attribute) (galaxy.schema.schema.PostJobAction attribute) (galaxy.schema.schema.RemoteUserCreationPayload attribute) (galaxy.schema.schema.RequireOneSetOption attribute) (galaxy.schema.schema.RoleDefinitionModel attribute) (galaxy.schema.schema.RoleListResponse attribute) (galaxy.schema.schema.RoleModelResponse attribute) (galaxy.schema.schema.SetSlugPayload attribute) (galaxy.schema.schema.ShareHistoryExtra attribute) (galaxy.schema.schema.ShareHistoryWithStatus attribute) (galaxy.schema.schema.ShareWithExtra attribute) (galaxy.schema.schema.ShareWithPayload attribute) (galaxy.schema.schema.ShareWithStatus attribute) (galaxy.schema.schema.SharingStatus attribute) (galaxy.schema.schema.ShortTermStoreExportPayload attribute) (galaxy.schema.schema.StoreContentSource attribute) (galaxy.schema.schema.StoredWorkflowSummary attribute) (galaxy.schema.schema.StoreExportPayload attribute) (galaxy.schema.schema.SubworkflowStep attribute) (galaxy.schema.schema.SubworkflowStepToExport attribute) (galaxy.schema.schema.TagCollection attribute) (galaxy.schema.schema.TagOperationParams attribute) (galaxy.schema.schema.ToolShedRepository attribute) (galaxy.schema.schema.ToolShedRepositoryChangeset attribute) (galaxy.schema.schema.ToolShedRepositorySummary attribute) (galaxy.schema.schema.ToolStep attribute) (galaxy.schema.schema.UpdateContentItem attribute) (galaxy.schema.schema.UpdateDatasetPermissionsPayload attribute) (galaxy.schema.schema.UpdateHistoryContentsBatchPayload attribute) (galaxy.schema.schema.UpdateHistoryContentsPayload attribute) (galaxy.schema.schema.UpdateLibraryFolderPayload attribute) (galaxy.schema.schema.UpdateLibraryPayload attribute) (galaxy.schema.schema.UserBeaconSetting attribute) (galaxy.schema.schema.UserCreationPayload attribute) (galaxy.schema.schema.UserDeletionPayload attribute) (galaxy.schema.schema.UserEmail attribute) (galaxy.schema.schema.UserModel attribute) (galaxy.schema.schema.Visualization attribute) (galaxy.schema.schema.WorkflowIndexQueryPayload attribute) (galaxy.schema.schema.WorkflowInput attribute) (galaxy.schema.schema.WorkflowInvocationStateSummary attribute) (galaxy.schema.schema.WorkflowOutput attribute) (galaxy.schema.schema.WorkflowStepBase attribute) (galaxy.schema.schema.WorkflowStepLayoutPosition attribute) (galaxy.schema.schema.WorkflowStepToExport attribute) (galaxy.schema.schema.WorkflowStepToExportBase attribute) (galaxy.schema.schema.WorkflowToExport attribute) (galaxy.schema.schema.WorkflowToolStepToExport attribute) (galaxy.schema.schema.WriteStoreToPayload attribute) (galaxy.schema.SerializationParams attribute) (galaxy.schema.tasks.BcoGenerationTaskParametersMixin attribute) (galaxy.schema.tasks.ComputeDatasetHashTaskRequest attribute) (galaxy.schema.tasks.GenerateHistoryContentDownload attribute) (galaxy.schema.tasks.GenerateHistoryDownload attribute) (galaxy.schema.tasks.GenerateInvocationDownload attribute) (galaxy.schema.tasks.GeneratePdfDownload attribute) (galaxy.schema.tasks.ImportModelStoreTaskRequest attribute) (galaxy.schema.tasks.MaterializeDatasetInstanceTaskRequest attribute) (galaxy.schema.tasks.PrepareDatasetCollectionDownload attribute) (galaxy.schema.tasks.PurgeDatasetsTaskRequest attribute) (galaxy.schema.tasks.RequestUser attribute) (galaxy.schema.tasks.SetupHistoryExportJob attribute) (galaxy.schema.tasks.WriteHistoryContentTo attribute) (galaxy.schema.tasks.WriteHistoryTo attribute) (galaxy.schema.tasks.WriteInvocationTo attribute) (galaxy.schema.ValueFilterQueryParams attribute) (galaxy.tool_util.toolbox.views.definitions.ExcludeTool attribute) (galaxy.tool_util.toolbox.views.definitions.ExcludeToolRegex attribute) (galaxy.tool_util.toolbox.views.definitions.ExcludeTypes attribute) (galaxy.tool_util.toolbox.views.definitions.ItemsFrom attribute) (galaxy.tool_util.toolbox.views.definitions.Label attribute) (galaxy.tool_util.toolbox.views.definitions.LabelShortcut attribute) (galaxy.tool_util.toolbox.views.definitions.Section attribute) (galaxy.tool_util.toolbox.views.definitions.SectionAlias attribute) (galaxy.tool_util.toolbox.views.definitions.SectionAliases attribute) (galaxy.tool_util.toolbox.views.definitions.StaticToolBoxView attribute) (galaxy.tool_util.toolbox.views.definitions.Tool attribute) (galaxy.tool_util.toolbox.views.definitions.Workflow attribute) (galaxy.tool_util.toolbox.views.interface.ToolPanelViewModel attribute) (galaxy.tours.Tour attribute) (galaxy.tours.TourCore attribute) (galaxy.tours.TourDetails attribute) (galaxy.tours.TourList attribute) (galaxy.tours.TourStep attribute) (galaxy.webapps.galaxy.api.tool_data.ImportToolDataBundle attribute) (galaxy.webapps.galaxy.services.authenticate.APIKeyResponse attribute) (galaxy.workflow.refactor.schema.Action attribute) (galaxy.workflow.refactor.schema.AddInputAction attribute) (galaxy.workflow.refactor.schema.AddStepAction attribute) (galaxy.workflow.refactor.schema.BaseAction attribute) (galaxy.workflow.refactor.schema.ConnectAction attribute) (galaxy.workflow.refactor.schema.DisconnectAction attribute) (galaxy.workflow.refactor.schema.ExtractInputAction attribute) (galaxy.workflow.refactor.schema.ExtractUntypedParameter attribute) (galaxy.workflow.refactor.schema.FileDefaultsAction attribute) (galaxy.workflow.refactor.schema.FillStepDefaultsAction attribute) (galaxy.workflow.refactor.schema.InputReferenceByLabel attribute) (galaxy.workflow.refactor.schema.InputReferenceByOrderIndex attribute) (galaxy.workflow.refactor.schema.OutputReferenceByLabel attribute) (galaxy.workflow.refactor.schema.OutputReferenceByOrderIndex attribute) (galaxy.workflow.refactor.schema.Position attribute) (galaxy.workflow.refactor.schema.RefactorActionExecution attribute) (galaxy.workflow.refactor.schema.RefactorActionExecutionMessage attribute) (galaxy.workflow.refactor.schema.RefactorActions attribute) (galaxy.workflow.refactor.schema.RemoveUnlabeledWorkflowOutputs attribute) (galaxy.workflow.refactor.schema.Report attribute) (galaxy.workflow.refactor.schema.StepReferenceByLabel attribute) (galaxy.workflow.refactor.schema.StepReferenceByOrderIndex attribute) (galaxy.workflow.refactor.schema.UpdateAnnotationAction attribute) (galaxy.workflow.refactor.schema.UpdateCreatorAction attribute) (galaxy.workflow.refactor.schema.UpdateLicenseAction attribute) (galaxy.workflow.refactor.schema.UpdateNameAction attribute) (galaxy.workflow.refactor.schema.UpdateOutputLabelAction attribute) (galaxy.workflow.refactor.schema.UpdateReportAction attribute) (galaxy.workflow.refactor.schema.UpdateStepLabelAction attribute) (galaxy.workflow.refactor.schema.UpdateStepPositionAction attribute) (galaxy.workflow.refactor.schema.UpgradeAllStepsAction attribute) (galaxy.workflow.refactor.schema.UpgradeSubworkflowAction attribute) (galaxy.workflow.refactor.schema.UpgradeToolAction attribute) (tool_shed.managers.repositories.UpdatesRequest attribute) model_fields (galaxy.managers.datatypes.DatatypeConverterList attribute) (galaxy.managers.datatypes.DatatypeDetails attribute) (galaxy.managers.datatypes.DatatypesCombinedMap attribute) (galaxy.managers.datatypes.DatatypesEDAMDetailsDict attribute) (galaxy.managers.datatypes.DatatypesMap attribute) (galaxy.managers.display_applications.DisplayApplication attribute) (galaxy.managers.display_applications.Link attribute) (galaxy.managers.display_applications.ReloadFeedback attribute) (galaxy.managers.jobs.JobLock attribute) (galaxy.managers.licenses.LicenseMetadataModel attribute) (galaxy.managers.metrics.CreateMetricsPayload attribute) (galaxy.managers.metrics.Metric attribute) (galaxy.managers.sharable.ShareWithExtra attribute) (galaxy.managers.tags.ItemTagsPayload attribute) (galaxy.managers.workflows.RefactorRequest attribute) (galaxy.managers.workflows.RefactorResponse attribute) (galaxy.managers.workflows.WorkflowCreateOptions attribute) (galaxy.managers.workflows.WorkflowStateResolutionOptions attribute) (galaxy.managers.workflows.WorkflowUpdateOptions attribute) (galaxy.model.store.DatasetAttributeImportModel attribute) (galaxy.model.UserQuotaBasicUsage attribute) (galaxy.model.UserQuotaUsage attribute) (galaxy.objectstore.ConcreteObjectStoreModel attribute) (galaxy.objectstore.QuotaModel attribute) (galaxy.schema.APIKeyModel attribute) (galaxy.schema.BootstrapAdminUser attribute) (galaxy.schema.fetch_data.BaseCollectionTarget attribute) (galaxy.schema.fetch_data.BaseDataElement attribute) (galaxy.schema.fetch_data.BaseDataPayload attribute) (galaxy.schema.fetch_data.BaseDataTarget attribute) (galaxy.schema.fetch_data.BaseFetchDataTarget attribute) (galaxy.schema.fetch_data.CompositeDataElement attribute) (galaxy.schema.fetch_data.CompositeItems attribute) (galaxy.schema.fetch_data.DataElementsFromTarget attribute) (galaxy.schema.fetch_data.DataElementsTarget attribute) (galaxy.schema.fetch_data.ExtraFiles attribute) (galaxy.schema.fetch_data.FetchBaseModel attribute) (galaxy.schema.fetch_data.FetchDataFormPayload attribute) (galaxy.schema.fetch_data.FetchDataPayload attribute) (galaxy.schema.fetch_data.FileDataElement attribute) (galaxy.schema.fetch_data.FilesPayload attribute) (galaxy.schema.fetch_data.FtpImportElement attribute) (galaxy.schema.fetch_data.FtpImportTarget attribute) (galaxy.schema.fetch_data.HdaDestination attribute) (galaxy.schema.fetch_data.HdcaDataItemsFromTarget attribute) (galaxy.schema.fetch_data.HdcaDataItemsTarget attribute) (galaxy.schema.fetch_data.HdcaDestination attribute) (galaxy.schema.fetch_data.ItemsFromModel attribute) (galaxy.schema.fetch_data.LibraryDestination attribute) (galaxy.schema.fetch_data.LibraryFolderDestination attribute) (galaxy.schema.fetch_data.NestedElement attribute) (galaxy.schema.fetch_data.PastedDataElement attribute) (galaxy.schema.fetch_data.PathDataElement attribute) (galaxy.schema.fetch_data.ServerDirElement attribute) (galaxy.schema.fetch_data.UrlDataElement attribute) (galaxy.schema.FilterQueryParams attribute) (galaxy.schema.PaginationQueryParams attribute) (galaxy.schema.remote_files.BrowsableFilesSourcePlugin attribute) (galaxy.schema.remote_files.CreatedEntryResponse attribute) (galaxy.schema.remote_files.CreateEntryPayload attribute) (galaxy.schema.remote_files.FilesSourcePlugin attribute) (galaxy.schema.remote_files.FilesSourcePluginList attribute) (galaxy.schema.remote_files.ListJstreeResponse attribute) (galaxy.schema.remote_files.ListUriResponse attribute) (galaxy.schema.remote_files.RemoteDirectory attribute) (galaxy.schema.remote_files.RemoteEntry attribute) (galaxy.schema.remote_files.RemoteFile attribute) (galaxy.schema.schema.AnonUserModel attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.ArchivedHistorySummary attribute) (galaxy.schema.schema.ArchiveHistoryRequestPayload attribute) (galaxy.schema.schema.AsyncFile attribute) (galaxy.schema.schema.AsyncTaskResultSummary attribute) (galaxy.schema.schema.BaseUserModel attribute) (galaxy.schema.schema.BasicRoleModel attribute) (galaxy.schema.schema.BcoGenerationParametersMixin attribute) (galaxy.schema.schema.BulkOperationItemError attribute) (galaxy.schema.schema.BulkOperationParams attribute) (galaxy.schema.schema.ChangeDatatypeOperationParams attribute) (galaxy.schema.schema.ChangeDbkeyOperationParams attribute) (galaxy.schema.schema.CheckForUpdatesResponse attribute) (galaxy.schema.schema.CollectionElementIdentifier attribute) (galaxy.schema.schema.CreatedCustomBuild attribute) (galaxy.schema.schema.CreatedUserModel attribute) (galaxy.schema.schema.CreateHistoryFromStore attribute) (galaxy.schema.schema.CreateHistoryPayload attribute) (galaxy.schema.schema.CreateLibrariesFromStore attribute) (galaxy.schema.schema.CreateLibraryFilePayload attribute) (galaxy.schema.schema.CreateLibraryFolderPayload attribute) (galaxy.schema.schema.CreateLibraryPayload attribute) (galaxy.schema.schema.CreateNewCollectionPayload attribute) (galaxy.schema.schema.CreatePagePayload attribute) (galaxy.schema.schema.Creator attribute) (galaxy.schema.schema.CustomBuildBaseModel attribute) (galaxy.schema.schema.CustomBuildCreationPayload attribute) (galaxy.schema.schema.CustomBuildModel attribute) (galaxy.schema.schema.CustomBuildsCollection attribute) (galaxy.schema.schema.CustomBuildsMetadataResponse attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.DatasetAssociationRoles attribute) (galaxy.schema.schema.DatasetHash attribute) (galaxy.schema.schema.DatasetJobInfo attribute) (galaxy.schema.schema.DatasetPermissions attribute) (galaxy.schema.schema.DatasetSource attribute) (galaxy.schema.schema.DatasetSourceId attribute) (galaxy.schema.schema.DatasetSourceIdBase attribute) (galaxy.schema.schema.DatasetSummary attribute) (galaxy.schema.schema.DCDetailed attribute) (galaxy.schema.schema.DCESummary attribute) (galaxy.schema.schema.DCObject attribute) (galaxy.schema.schema.DCSummary attribute) (galaxy.schema.schema.DeletedCustomBuild attribute) (galaxy.schema.schema.DeleteHistoryContentPayload attribute) (galaxy.schema.schema.DeleteHistoryContentResult attribute) (galaxy.schema.schema.DeleteLibraryPayload attribute) (galaxy.schema.schema.DetailedUserModel attribute) (galaxy.schema.schema.DiskUsageUserModel attribute) (galaxy.schema.schema.DisplayApp attribute) (galaxy.schema.schema.EncodedDataItemSourceId attribute) (galaxy.schema.schema.EncodedDatasetSourceId attribute) (galaxy.schema.schema.EncodedHistoryContentItem attribute) (galaxy.schema.schema.EncodedJobParameterHistoryItem attribute) (galaxy.schema.schema.ExportAssociationData attribute) (galaxy.schema.schema.ExportHistoryArchivePayload attribute) (galaxy.schema.schema.ExportObjectMetadata attribute) (galaxy.schema.schema.ExportObjectRequestMetadata attribute) (galaxy.schema.schema.ExportObjectResultMetadata attribute) (galaxy.schema.schema.ExportRecordData attribute) (galaxy.schema.schema.ExportTaskListResponse attribute) (galaxy.schema.schema.FavoriteObject attribute) (galaxy.schema.schema.FavoriteObjectsSummary attribute) (galaxy.schema.schema.FileLibraryFolderItem attribute) (galaxy.schema.schema.FolderLibraryFolderItem attribute) (galaxy.schema.schema.GroupModel attribute) (galaxy.schema.schema.GroupRoleListResponse attribute) (galaxy.schema.schema.GroupRoleResponse attribute) (galaxy.schema.schema.GroupUserListResponse attribute) (galaxy.schema.schema.GroupUserResponse attribute) (galaxy.schema.schema.HDABasicInfo attribute) (galaxy.schema.schema.HDACommon attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) (galaxy.schema.schema.HDAExtended attribute) (galaxy.schema.schema.HDAInaccessible attribute) (galaxy.schema.schema.HDAObject attribute) (galaxy.schema.schema.HDASummary attribute) (galaxy.schema.schema.HDCACommon attribute) (galaxy.schema.schema.HDCADetailed attribute) (galaxy.schema.schema.HDCASummary attribute) (galaxy.schema.schema.HDCJobStateSummary attribute) (galaxy.schema.schema.HistoryActiveContentCounts attribute) (galaxy.schema.schema.HistoryContentBulkOperationPayload attribute) (galaxy.schema.schema.HistoryContentBulkOperationResult attribute) (galaxy.schema.schema.HistoryContentItem attribute) (galaxy.schema.schema.HistoryContentItemBase attribute) (galaxy.schema.schema.HistoryContentsArchiveDryRunResult attribute) (galaxy.schema.schema.HistoryContentsResult attribute) (galaxy.schema.schema.HistoryContentStats attribute) (galaxy.schema.schema.HistoryContentsWithStatsResult attribute) (galaxy.schema.schema.HistoryDetailed attribute) (galaxy.schema.schema.HistoryItemBase attribute) (galaxy.schema.schema.HistoryItemCommon attribute) (galaxy.schema.schema.HistorySummary attribute) (galaxy.schema.schema.Hyperlink attribute) (galaxy.schema.schema.ImplicitCollectionJobsStateSummary attribute) (galaxy.schema.schema.ImportToolDataBundleDatasetSource attribute) (galaxy.schema.schema.ImportToolDataBundleUriSource attribute) (galaxy.schema.schema.Input attribute) (galaxy.schema.schema.InputConnection attribute) (galaxy.schema.schema.InputDataCollectionStep attribute) (galaxy.schema.schema.InputDataStep attribute) (galaxy.schema.schema.InputParameterStep attribute) (galaxy.schema.schema.InputStep attribute) (galaxy.schema.schema.InstalledRepositoryToolShedStatus attribute) (galaxy.schema.schema.InstalledToolShedRepositories attribute) (galaxy.schema.schema.InstalledToolShedRepository attribute) (galaxy.schema.schema.InvocationIndexQueryPayload attribute) (galaxy.schema.schema.ItemStateSummary attribute) (galaxy.schema.schema.JobBaseModel attribute) (galaxy.schema.schema.JobDetails attribute) (galaxy.schema.schema.JobExportHistoryArchiveListResponse attribute) (galaxy.schema.schema.JobExportHistoryArchiveModel attribute) (galaxy.schema.schema.JobFullDetails attribute) (galaxy.schema.schema.JobIdResponse attribute) (galaxy.schema.schema.JobImportHistoryResponse attribute) (galaxy.schema.schema.JobIndexQueryPayload attribute) (galaxy.schema.schema.JobMetric attribute) (galaxy.schema.schema.JobMetricCollection attribute) (galaxy.schema.schema.JobStateSummary attribute) (galaxy.schema.schema.JobSummary attribute) (galaxy.schema.schema.LabelValuePair attribute) (galaxy.schema.schema.LegacyLibraryPermissionsPayload attribute) (galaxy.schema.schema.LibraryAvailablePermissions attribute) (galaxy.schema.schema.LibraryCurrentPermissions attribute) (galaxy.schema.schema.LibraryFolderContentsIndexQueryPayload attribute) (galaxy.schema.schema.LibraryFolderContentsIndexResult attribute) (galaxy.schema.schema.LibraryFolderCurrentPermissions attribute) (galaxy.schema.schema.LibraryFolderDetails attribute) (galaxy.schema.schema.LibraryFolderItemBase attribute) (galaxy.schema.schema.LibraryFolderMetadata attribute) (galaxy.schema.schema.LibraryFolderPermissionsPayload attribute) (galaxy.schema.schema.LibraryLegacySummary attribute) (galaxy.schema.schema.LibraryPermissionsPayload attribute) (galaxy.schema.schema.LibraryPermissionsPayloadBase attribute) (galaxy.schema.schema.LibrarySummary attribute) (galaxy.schema.schema.LibrarySummaryList attribute) (galaxy.schema.schema.LimitedUserModel attribute) (galaxy.schema.schema.MaterializeDatasetInstanceAPIRequest attribute) (galaxy.schema.schema.MaterializeDatasetInstanceRequest attribute) (galaxy.schema.schema.MetadataFile attribute) (galaxy.schema.schema.Model attribute) (galaxy.schema.schema.ObjectExportResponseBase attribute) (galaxy.schema.schema.ObjectExportTaskResponse attribute) (galaxy.schema.schema.Organization attribute) (galaxy.schema.schema.Output attribute) (galaxy.schema.schema.PageDetails attribute) (galaxy.schema.schema.PageIndexQueryPayload attribute) (galaxy.schema.schema.PageSummary attribute) (galaxy.schema.schema.PageSummaryBase attribute) (galaxy.schema.schema.PageSummaryList attribute) (galaxy.schema.schema.PauseStep attribute) (galaxy.schema.schema.Person attribute) (galaxy.schema.schema.PostJobAction attribute) (galaxy.schema.schema.RemoteUserCreationPayload attribute) (galaxy.schema.schema.RequireOneSetOption attribute) (galaxy.schema.schema.RoleDefinitionModel attribute) (galaxy.schema.schema.RoleListResponse attribute) (galaxy.schema.schema.RoleModelResponse attribute) (galaxy.schema.schema.SetSlugPayload attribute) (galaxy.schema.schema.ShareHistoryExtra attribute) (galaxy.schema.schema.ShareHistoryWithStatus attribute) (galaxy.schema.schema.ShareWithExtra attribute) (galaxy.schema.schema.ShareWithPayload attribute) (galaxy.schema.schema.ShareWithStatus attribute) (galaxy.schema.schema.SharingStatus attribute) (galaxy.schema.schema.ShortTermStoreExportPayload attribute) (galaxy.schema.schema.StoreContentSource attribute) (galaxy.schema.schema.StoredWorkflowSummary attribute) (galaxy.schema.schema.StoreExportPayload attribute) (galaxy.schema.schema.SubworkflowStep attribute) (galaxy.schema.schema.SubworkflowStepToExport attribute) (galaxy.schema.schema.TagCollection attribute) (galaxy.schema.schema.TagOperationParams attribute) (galaxy.schema.schema.ToolShedRepository attribute) (galaxy.schema.schema.ToolShedRepositoryChangeset attribute) (galaxy.schema.schema.ToolShedRepositorySummary attribute) (galaxy.schema.schema.ToolStep attribute) (galaxy.schema.schema.UpdateContentItem attribute) (galaxy.schema.schema.UpdateDatasetPermissionsPayload attribute) (galaxy.schema.schema.UpdateHistoryContentsBatchPayload attribute) (galaxy.schema.schema.UpdateHistoryContentsPayload attribute) (galaxy.schema.schema.UpdateLibraryFolderPayload attribute) (galaxy.schema.schema.UpdateLibraryPayload attribute) (galaxy.schema.schema.UserBeaconSetting attribute) (galaxy.schema.schema.UserCreationPayload attribute) (galaxy.schema.schema.UserDeletionPayload attribute) (galaxy.schema.schema.UserEmail attribute) (galaxy.schema.schema.UserModel attribute) (galaxy.schema.schema.Visualization attribute) (galaxy.schema.schema.WorkflowIndexQueryPayload attribute) (galaxy.schema.schema.WorkflowInput attribute) (galaxy.schema.schema.WorkflowInvocationStateSummary attribute) (galaxy.schema.schema.WorkflowOutput attribute) (galaxy.schema.schema.WorkflowStepBase attribute) (galaxy.schema.schema.WorkflowStepLayoutPosition attribute) (galaxy.schema.schema.WorkflowStepToExport attribute) (galaxy.schema.schema.WorkflowStepToExportBase attribute) (galaxy.schema.schema.WorkflowToExport attribute) (galaxy.schema.schema.WorkflowToolStepToExport attribute) (galaxy.schema.schema.WriteStoreToPayload attribute) (galaxy.schema.SerializationParams attribute) (galaxy.schema.tasks.BcoGenerationTaskParametersMixin attribute) (galaxy.schema.tasks.ComputeDatasetHashTaskRequest attribute) (galaxy.schema.tasks.GenerateHistoryContentDownload attribute) (galaxy.schema.tasks.GenerateHistoryDownload attribute) (galaxy.schema.tasks.GenerateInvocationDownload attribute) (galaxy.schema.tasks.GeneratePdfDownload attribute) (galaxy.schema.tasks.ImportModelStoreTaskRequest attribute) (galaxy.schema.tasks.MaterializeDatasetInstanceTaskRequest attribute) (galaxy.schema.tasks.PrepareDatasetCollectionDownload attribute) (galaxy.schema.tasks.PurgeDatasetsTaskRequest attribute) (galaxy.schema.tasks.RequestUser attribute) (galaxy.schema.tasks.SetupHistoryExportJob attribute) (galaxy.schema.tasks.WriteHistoryContentTo attribute) (galaxy.schema.tasks.WriteHistoryTo attribute) (galaxy.schema.tasks.WriteInvocationTo attribute) (galaxy.schema.ValueFilterQueryParams attribute) (galaxy.tool_util.toolbox.views.definitions.ExcludeTool attribute) (galaxy.tool_util.toolbox.views.definitions.ExcludeToolRegex attribute) (galaxy.tool_util.toolbox.views.definitions.ExcludeTypes attribute) (galaxy.tool_util.toolbox.views.definitions.ItemsFrom attribute) (galaxy.tool_util.toolbox.views.definitions.Label attribute) (galaxy.tool_util.toolbox.views.definitions.LabelShortcut attribute) (galaxy.tool_util.toolbox.views.definitions.Section attribute) (galaxy.tool_util.toolbox.views.definitions.SectionAlias attribute) (galaxy.tool_util.toolbox.views.definitions.SectionAliases attribute) (galaxy.tool_util.toolbox.views.definitions.StaticToolBoxView attribute) (galaxy.tool_util.toolbox.views.definitions.Tool attribute) (galaxy.tool_util.toolbox.views.definitions.Workflow attribute) (galaxy.tool_util.toolbox.views.interface.ToolPanelViewModel attribute) (galaxy.tours.Tour attribute) (galaxy.tours.TourCore attribute) (galaxy.tours.TourDetails attribute) (galaxy.tours.TourList attribute) (galaxy.tours.TourStep attribute) (galaxy.webapps.galaxy.api.tool_data.ImportToolDataBundle attribute) (galaxy.webapps.galaxy.services.authenticate.APIKeyResponse attribute) (galaxy.workflow.refactor.schema.Action attribute) (galaxy.workflow.refactor.schema.AddInputAction attribute) (galaxy.workflow.refactor.schema.AddStepAction attribute) (galaxy.workflow.refactor.schema.BaseAction attribute) (galaxy.workflow.refactor.schema.ConnectAction attribute) (galaxy.workflow.refactor.schema.DisconnectAction attribute) (galaxy.workflow.refactor.schema.ExtractInputAction attribute) (galaxy.workflow.refactor.schema.ExtractUntypedParameter attribute) (galaxy.workflow.refactor.schema.FileDefaultsAction attribute) (galaxy.workflow.refactor.schema.FillStepDefaultsAction attribute) (galaxy.workflow.refactor.schema.InputReferenceByLabel attribute) (galaxy.workflow.refactor.schema.InputReferenceByOrderIndex attribute) (galaxy.workflow.refactor.schema.OutputReferenceByLabel attribute) (galaxy.workflow.refactor.schema.OutputReferenceByOrderIndex attribute) (galaxy.workflow.refactor.schema.Position attribute) (galaxy.workflow.refactor.schema.RefactorActionExecution attribute) (galaxy.workflow.refactor.schema.RefactorActionExecutionMessage attribute) (galaxy.workflow.refactor.schema.RefactorActions attribute) (galaxy.workflow.refactor.schema.RemoveUnlabeledWorkflowOutputs attribute) (galaxy.workflow.refactor.schema.Report attribute) (galaxy.workflow.refactor.schema.StepReferenceByLabel attribute) (galaxy.workflow.refactor.schema.StepReferenceByOrderIndex attribute) (galaxy.workflow.refactor.schema.UpdateAnnotationAction attribute) (galaxy.workflow.refactor.schema.UpdateCreatorAction attribute) (galaxy.workflow.refactor.schema.UpdateLicenseAction attribute) (galaxy.workflow.refactor.schema.UpdateNameAction attribute) (galaxy.workflow.refactor.schema.UpdateOutputLabelAction attribute) (galaxy.workflow.refactor.schema.UpdateReportAction attribute) (galaxy.workflow.refactor.schema.UpdateStepLabelAction attribute) (galaxy.workflow.refactor.schema.UpdateStepPositionAction attribute) (galaxy.workflow.refactor.schema.UpgradeAllStepsAction attribute) (galaxy.workflow.refactor.schema.UpgradeSubworkflowAction attribute) (galaxy.workflow.refactor.schema.UpgradeToolAction attribute) (tool_shed.managers.repositories.UpdatesRequest attribute)

model_manager_class (galaxy.managers.base.HasAModelManager attribute) (galaxy.managers.cloudauthzs.CloudAuthzsDeserializer attribute) (galaxy.managers.cloudauthzs.CloudAuthzsSerializer attribute) (galaxy.managers.configuration.AdminConfigSerializer attribute) (galaxy.managers.configuration.ConfigSerializer attribute) (galaxy.managers.datasets.DatasetAssociationDeserializer attribute) (galaxy.managers.datasets.DatasetAssociationFilterParser attribute) (galaxy.managers.datasets.DatasetAssociationSerializer attribute) (galaxy.managers.datasets.DatasetSerializer attribute) (galaxy.managers.hdas.HDADeserializer attribute) (galaxy.managers.hdas.HDAFilterParser attribute) (galaxy.managers.hdas.HDASerializer attribute) (galaxy.managers.hdcas.DCESerializer attribute) (galaxy.managers.hdcas.DCSerializer attribute) (galaxy.managers.hdcas.HDCASerializer attribute) (galaxy.managers.histories.HistoryDeserializer attribute) (galaxy.managers.histories.HistoryFilters attribute) (galaxy.managers.histories.HistorySerializer attribute) (galaxy.managers.history_contents.HistoryContentsFilters attribute) (galaxy.managers.history_contents.HistoryContentsSerializer attribute) (galaxy.managers.pages.PageDeserializer attribute) (galaxy.managers.pages.PageSerializer attribute) (galaxy.managers.sharable.SharableModelDeserializer attribute) (galaxy.managers.sharable.SharableModelFilters attribute) (galaxy.managers.users.AdminUserFilterParser attribute) (galaxy.managers.users.CurrentUserSerializer attribute) (galaxy.managers.users.UserDeserializer attribute) (galaxy.managers.users.UserSerializer attribute) (galaxy.managers.visualizations.VisualizationDeserializer attribute) (galaxy.managers.visualizations.VisualizationSerializer attribute) (galaxy.managers.workflows.WorkflowSerializer attribute) model_post_init() (galaxy.model.store.DatasetAttributeImportModel method) model_store_format (galaxy.schema.schema.CreateHistoryFromStore attribute) (galaxy.schema.schema.CreateLibrariesFromStore attribute) (galaxy.schema.schema.ExportRecordData attribute) (galaxy.schema.schema.StoreContentSource attribute) (galaxy.schema.schema.StoreExportPayload attribute) (galaxy.schema.tasks.ImportModelStoreTaskRequest attribute) model_store_storage_target() (in module galaxy.webapps.galaxy.services.base) ModelClassField() (in module galaxy.schema.fields) ModelDeserializer (class in galaxy.managers.base) ModelDeserializingError ModelExportStore (class in galaxy.model.store) ModelFilterParser (class in galaxy.managers.base) ModelImportStore (class in galaxy.model.store) ModelManager (class in galaxy.managers.base) ModelMapping (class in galaxy.model.base) ModelOperationToolAction (class in galaxy.tools.actions.model_operations) ModelPersistenceContext (class in galaxy.model.store.discover) ModelSerializer (class in galaxy.managers.base) ModelSerializingError ModelStoreFormat (class in galaxy.schema.schema) ModelStoreManager (class in galaxy.managers.model_stores) ModelStoreUserContext (class in galaxy.managers.model_stores) ModelValidator (class in galaxy.managers.base) modified_time (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.JobContainerAssociation attribute) modify (galaxy.webapps.galaxy.services.library_folder_contents.UserFolderPermissions attribute) modify_environ() (galaxy.tool_util.deps.brew_exts.EnvAction method) modify_folder_role_list (galaxy.schema.schema.LibraryFolderCurrentPermissions attribute) modify_ids (galaxy.schema.schema.LibraryPermissionsPayloadBase attribute) (galaxy.schema.schema.UpdateDatasetPermissionsPayload attribute) modify_item_roles (galaxy.schema.schema.DatasetAssociationRoles attribute) modify_library_role_list (galaxy.schema.schema.LibraryCurrentPermissions attribute) modtime (galaxy.tools.cache.ToolHash property) modtime_less_than() (galaxy.tools.cache.ToolHash method) module galaxy galaxy.actions galaxy.actions.library galaxy.app galaxy.app_unittest_utils galaxy.app_unittest_utils.galaxy_mock galaxy.app_unittest_utils.tools_support galaxy.auth galaxy.auth.providers galaxy.auth.providers.alwaysreject galaxy.auth.providers.ldap_ad galaxy.auth.providers.localdb galaxy.auth.providers.pam_auth galaxy.auth.util galaxy.authnz galaxy.authnz.custos_authnz galaxy.authnz.managers galaxy.authnz.psa_authnz galaxy.celery galaxy.celery.tasks galaxy.config galaxy.config.config_manage galaxy.config.schema galaxy.config.script galaxy.config_watchers galaxy.datatypes galaxy.datatypes.annotation galaxy.datatypes.anvio galaxy.datatypes.assembly galaxy.datatypes.binary galaxy.datatypes.blast galaxy.datatypes.checkers galaxy.datatypes.chrominfo galaxy.datatypes.constructive_solid_geometry galaxy.datatypes.converters galaxy.datatypes.converters.bed_to_gff_converter galaxy.datatypes.converters.fasta_to_len galaxy.datatypes.converters.fasta_to_tabular_converter galaxy.datatypes.converters.fastq_to_fqtoc galaxy.datatypes.converters.fastqsolexa_to_fasta_converter galaxy.datatypes.converters.fastqsolexa_to_qual_converter galaxy.datatypes.converters.gff_to_bed_converter galaxy.datatypes.converters.gff_to_interval_index_converter galaxy.datatypes.converters.interval_to_bed_converter galaxy.datatypes.converters.interval_to_bedstrict_converter galaxy.datatypes.converters.interval_to_fli galaxy.datatypes.converters.interval_to_interval_index_converter galaxy.datatypes.converters.lped_to_fped_converter galaxy.datatypes.converters.lped_to_pbed_converter galaxy.datatypes.converters.maf_to_fasta_converter galaxy.datatypes.converters.maf_to_interval_converter galaxy.datatypes.converters.parquet_to_csv_converter galaxy.datatypes.converters.pbed_ldreduced_converter galaxy.datatypes.converters.pbed_to_lped_converter galaxy.datatypes.converters.picard_interval_list_to_bed6_converter galaxy.datatypes.converters.pileup_to_interval_index_converter galaxy.datatypes.converters.ref_to_seq_taxonomy_converter galaxy.datatypes.converters.tabular_csv galaxy.datatypes.converters.vcf_to_interval_index_converter galaxy.datatypes.converters.wiggle_to_simple_converter galaxy.datatypes.coverage galaxy.datatypes.data galaxy.datatypes.dataproviders galaxy.datatypes.dataproviders.base galaxy.datatypes.dataproviders.chunk galaxy.datatypes.dataproviders.column galaxy.datatypes.dataproviders.dataset galaxy.datatypes.dataproviders.decorators galaxy.datatypes.dataproviders.exceptions galaxy.datatypes.dataproviders.external galaxy.datatypes.dataproviders.hierarchy galaxy.datatypes.dataproviders.line galaxy.datatypes.display_applications galaxy.datatypes.display_applications.application galaxy.datatypes.display_applications.parameters galaxy.datatypes.display_applications.util galaxy.datatypes.flow galaxy.datatypes.genetics galaxy.datatypes.gis galaxy.datatypes.goldenpath galaxy.datatypes.graph galaxy.datatypes.hdf5 galaxy.datatypes.images galaxy.datatypes.interval galaxy.datatypes.isa galaxy.datatypes.media galaxy.datatypes.metacyto galaxy.datatypes.metadata galaxy.datatypes.microarrays galaxy.datatypes.molecules galaxy.datatypes.mothur galaxy.datatypes.msa galaxy.datatypes.neo4j galaxy.datatypes.ngsindex galaxy.datatypes.phylip galaxy.datatypes.plant_tribes galaxy.datatypes.proteomics galaxy.datatypes.qiime2 galaxy.datatypes.qualityscore galaxy.datatypes.registry galaxy.datatypes.sequence galaxy.datatypes.sniff galaxy.datatypes.spaln galaxy.datatypes.speech galaxy.datatypes.tabular galaxy.datatypes.text galaxy.datatypes.tracks galaxy.datatypes.triples galaxy.datatypes.upload_util galaxy.datatypes.util galaxy.datatypes.util.generic_util galaxy.datatypes.util.gff_util galaxy.datatypes.util.maf_utilities galaxy.datatypes.xml galaxy.dependencies galaxy.di galaxy.exceptions galaxy.exceptions.error_codes galaxy.files galaxy.files.sources galaxy.files.sources.anvil galaxy.files.sources.basespace galaxy.files.sources.dropbox galaxy.files.sources.ftp galaxy.files.sources.galaxy galaxy.files.sources.googlecloudstorage galaxy.files.sources.googledrive galaxy.files.sources.onedata galaxy.files.sources.posix galaxy.files.sources.s3fs galaxy.files.sources.ssh galaxy.files.sources.webdav galaxy.files.unittest_utils galaxy.files.uris galaxy.forms galaxy.forms.forms galaxy.job_execution galaxy.job_execution.actions galaxy.job_execution.actions.post galaxy.job_execution.compute_environment galaxy.job_execution.datasets galaxy.job_execution.output_collect galaxy.job_execution.ports galaxy.job_execution.ports.view galaxy.job_execution.setup galaxy.job_metrics galaxy.job_metrics.formatting galaxy.job_metrics.instrumenters galaxy.job_metrics.instrumenters.cgroup galaxy.job_metrics.instrumenters.core galaxy.job_metrics.instrumenters.cpuinfo galaxy.job_metrics.instrumenters.env galaxy.job_metrics.instrumenters.hostname galaxy.job_metrics.instrumenters.meminfo galaxy.job_metrics.instrumenters.uname galaxy.job_metrics.safety galaxy.jobs galaxy.jobs.command_factory galaxy.jobs.dynamic_tool_destination galaxy.jobs.handler galaxy.jobs.manager galaxy.jobs.mapper galaxy.jobs.rule_helper galaxy.jobs.rules galaxy.jobs.runners galaxy.jobs.runners.chronos galaxy.jobs.runners.cli galaxy.jobs.runners.condor galaxy.jobs.runners.drmaa galaxy.jobs.runners.godocker galaxy.jobs.runners.kubernetes galaxy.jobs.runners.local galaxy.jobs.runners.pbs galaxy.jobs.runners.pulsar galaxy.jobs.runners.slurm galaxy.jobs.runners.state_handler_factory galaxy.jobs.runners.state_handlers galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners.tasks galaxy.jobs.runners.univa galaxy.jobs.runners.util galaxy.jobs.runners.util.cli galaxy.jobs.runners.util.cli.factory galaxy.jobs.runners.util.cli.job galaxy.jobs.runners.util.cli.job.lsf galaxy.jobs.runners.util.cli.job.pbs galaxy.jobs.runners.util.cli.job.slurm galaxy.jobs.runners.util.cli.job.slurm_torque galaxy.jobs.runners.util.cli.job.torque galaxy.jobs.runners.util.cli.shell galaxy.jobs.runners.util.cli.shell.local galaxy.jobs.runners.util.cli.shell.rsh galaxy.jobs.runners.util.condor galaxy.jobs.runners.util.env galaxy.jobs.runners.util.external galaxy.jobs.runners.util.job_script galaxy.jobs.runners.util.kill galaxy.jobs.runners.util.process_groups galaxy.jobs.runners.util.pykube_util galaxy.jobs.runners.util.sudo galaxy.jobs.splitters galaxy.jobs.splitters.basic galaxy.jobs.splitters.multi galaxy.jobs.stock_rules galaxy.main galaxy.main_config galaxy.managers galaxy.managers.annotatable galaxy.managers.api_keys galaxy.managers.base galaxy.managers.citations galaxy.managers.cloud galaxy.managers.cloudauthzs galaxy.managers.collections galaxy.managers.collections_util galaxy.managers.configuration galaxy.managers.context galaxy.managers.datasets galaxy.managers.datatypes galaxy.managers.deletable galaxy.managers.display_applications galaxy.managers.executables galaxy.managers.folders galaxy.managers.genomes galaxy.managers.group_roles galaxy.managers.group_users galaxy.managers.groups galaxy.managers.hdas galaxy.managers.hdcas galaxy.managers.histories galaxy.managers.history_contents galaxy.managers.interactivetool galaxy.managers.jobs galaxy.managers.lddas galaxy.managers.libraries galaxy.managers.library_datasets galaxy.managers.licenses galaxy.managers.markdown_parse galaxy.managers.markdown_util galaxy.managers.metrics galaxy.managers.model_stores galaxy.managers.pages galaxy.managers.quotas galaxy.managers.ratable galaxy.managers.rbac_secured galaxy.managers.remote_files galaxy.managers.roles galaxy.managers.secured galaxy.managers.session galaxy.managers.sharable galaxy.managers.taggable galaxy.managers.tags galaxy.managers.tool_data galaxy.managers.tools galaxy.managers.users galaxy.managers.visualizations galaxy.managers.workflows galaxy.metadata galaxy.metadata.set_metadata galaxy.model galaxy.model.base galaxy.model.custom_types galaxy.model.database_heartbeat galaxy.model.database_utils galaxy.model.dataset_collections galaxy.model.dataset_collections.builder galaxy.model.dataset_collections.matching galaxy.model.dataset_collections.registry galaxy.model.dataset_collections.structure galaxy.model.dataset_collections.subcollections galaxy.model.dataset_collections.type_description galaxy.model.dataset_collections.types galaxy.model.dataset_collections.types.list galaxy.model.dataset_collections.types.paired galaxy.model.deferred galaxy.model.index_filter_util galaxy.model.item_attrs galaxy.model.mapping galaxy.model.metadata galaxy.model.migrations galaxy.model.migrations.scripts galaxy.model.migrations.util galaxy.model.none_like galaxy.model.orm galaxy.model.orm.engine_factory galaxy.model.orm.now galaxy.model.orm.scripts galaxy.model.orm.util galaxy.model.scoped_session galaxy.model.security galaxy.model.store galaxy.model.store.build_objects galaxy.model.store.discover galaxy.model.store.load_objects galaxy.model.tags galaxy.model.tool_shed_install galaxy.model.tool_shed_install.mapping galaxy.model.triggers galaxy.model.triggers.history_update_time_field galaxy.model.triggers.update_audit_table galaxy.model.triggers.utils galaxy.model.unittest_utils galaxy.model.unittest_utils.data_app galaxy.model.unittest_utils.store_fixtures galaxy.objectstore galaxy.objectstore.azure_blob galaxy.objectstore.cloud galaxy.objectstore.irods galaxy.objectstore.pithos galaxy.objectstore.pulsar galaxy.objectstore.s3 galaxy.objectstore.s3_multipart_upload galaxy.objectstore.unittest_utils galaxy.queue_worker galaxy.queues galaxy.quota galaxy.schema galaxy.schema.fetch_data galaxy.schema.fields galaxy.schema.remote_files galaxy.schema.schema galaxy.schema.tasks galaxy.schema.types galaxy.security galaxy.security.idencoding galaxy.security.object_wrapper galaxy.security.passwords galaxy.security.ssh_util galaxy.security.validate_user_input galaxy.security.vault galaxy.selenium galaxy.selenium.cli galaxy.selenium.context galaxy.selenium.driver_factory galaxy.selenium.has_driver galaxy.selenium.jupyter_context galaxy.selenium.navigates_galaxy galaxy.selenium.scripts galaxy.selenium.scripts.dump_tour galaxy.selenium.sizzle galaxy.selenium.smart_components galaxy.selenium.toolbox galaxy.selenium.toolbox.filters galaxy.structured_app galaxy.tool_shed galaxy.tool_shed.galaxy_install galaxy.tool_shed.galaxy_install.install_manager galaxy.tool_shed.galaxy_install.installed_repository_manager galaxy.tool_shed.galaxy_install.metadata galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager galaxy.tool_shed.galaxy_install.repository_dependencies galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager galaxy.tool_shed.galaxy_install.tools galaxy.tool_shed.galaxy_install.tools.data_manager galaxy.tool_shed.galaxy_install.tools.tool_panel_manager galaxy.tool_shed.galaxy_install.update_repository_manager galaxy.tool_shed.metadata galaxy.tool_shed.metadata.metadata_generator galaxy.tool_shed.repository_type galaxy.tool_shed.tools galaxy.tool_shed.tools.data_table_manager galaxy.tool_shed.tools.tool_validator galaxy.tool_shed.util galaxy.tool_shed.util.basic_util galaxy.tool_shed.util.container_util galaxy.tool_shed.util.hg_util galaxy.tool_shed.util.metadata_util galaxy.tool_shed.util.repository_util galaxy.tool_shed.util.shed_util_common galaxy.tool_shed.util.tool_dependency_util galaxy.tool_shed.util.tool_util galaxy.tool_util galaxy.tool_util.biotools galaxy.tool_util.biotools.interface galaxy.tool_util.biotools.source galaxy.tool_util.client galaxy.tool_util.client.staging galaxy.tool_util.cwl galaxy.tool_util.cwl.cwltool_deps galaxy.tool_util.cwl.parser galaxy.tool_util.cwl.representation galaxy.tool_util.cwl.runnable galaxy.tool_util.cwl.runtime_actions galaxy.tool_util.cwl.schema galaxy.tool_util.cwl.util galaxy.tool_util.deps galaxy.tool_util.deps.brew_exts galaxy.tool_util.deps.brew_util galaxy.tool_util.deps.commands galaxy.tool_util.deps.conda_compat galaxy.tool_util.deps.conda_util galaxy.tool_util.deps.container_classes galaxy.tool_util.deps.container_resolvers galaxy.tool_util.deps.container_resolvers.explicit galaxy.tool_util.deps.container_resolvers.mulled galaxy.tool_util.deps.container_volumes galaxy.tool_util.deps.containers galaxy.tool_util.deps.dependencies galaxy.tool_util.deps.docker_util galaxy.tool_util.deps.dockerfiles galaxy.tool_util.deps.installable galaxy.tool_util.deps.mulled galaxy.tool_util.deps.mulled.get_tests galaxy.tool_util.deps.mulled.mulled_build galaxy.tool_util.deps.mulled.mulled_build_channel galaxy.tool_util.deps.mulled.mulled_build_files galaxy.tool_util.deps.mulled.mulled_build_tool galaxy.tool_util.deps.mulled.mulled_hash galaxy.tool_util.deps.mulled.mulled_list galaxy.tool_util.deps.mulled.mulled_search galaxy.tool_util.deps.mulled.mulled_update_singularity_containers galaxy.tool_util.deps.mulled.util galaxy.tool_util.deps.requirements galaxy.tool_util.deps.resolvers galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages galaxy.tool_util.deps.resolvers.conda galaxy.tool_util.deps.resolvers.galaxy_packages galaxy.tool_util.deps.resolvers.homebrew galaxy.tool_util.deps.resolvers.lmod galaxy.tool_util.deps.resolvers.modules galaxy.tool_util.deps.resolvers.resolver_mixins galaxy.tool_util.deps.resolvers.tool_shed_packages galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages galaxy.tool_util.deps.singularity_util galaxy.tool_util.deps.views galaxy.tool_util.edam_util galaxy.tool_util.fetcher galaxy.tool_util.lint galaxy.tool_util.linters galaxy.tool_util.linters.citations galaxy.tool_util.linters.command galaxy.tool_util.linters.cwl galaxy.tool_util.linters.general galaxy.tool_util.linters.help galaxy.tool_util.linters.inputs galaxy.tool_util.linters.stdio galaxy.tool_util.linters.tests galaxy.tool_util.linters.xml_order galaxy.tool_util.loader galaxy.tool_util.loader_directory galaxy.tool_util.locations galaxy.tool_util.locations.dockstore galaxy.tool_util.locations.file galaxy.tool_util.locations.http galaxy.tool_util.ontologies galaxy.tool_util.ontologies.ontology_data galaxy.tool_util.output_checker galaxy.tool_util.parser galaxy.tool_util.parser.cwl galaxy.tool_util.parser.factory galaxy.tool_util.parser.interface galaxy.tool_util.parser.output_actions galaxy.tool_util.parser.output_collection_def galaxy.tool_util.parser.output_objects galaxy.tool_util.parser.stdio galaxy.tool_util.parser.util galaxy.tool_util.parser.xml galaxy.tool_util.parser.yaml galaxy.tool_util.provided_metadata galaxy.tool_util.toolbox galaxy.tool_util.toolbox.base galaxy.tool_util.toolbox.filters galaxy.tool_util.toolbox.integrated_panel galaxy.tool_util.toolbox.lineages galaxy.tool_util.toolbox.lineages.factory galaxy.tool_util.toolbox.lineages.interface galaxy.tool_util.toolbox.panel galaxy.tool_util.toolbox.parser galaxy.tool_util.toolbox.views galaxy.tool_util.toolbox.views.definitions galaxy.tool_util.toolbox.views.edam galaxy.tool_util.toolbox.views.interface galaxy.tool_util.toolbox.views.sources galaxy.tool_util.toolbox.views.static galaxy.tool_util.toolbox.watcher galaxy.tool_util.unittest_utils galaxy.tool_util.unittest_utils.sample_data galaxy.tool_util.verify galaxy.tool_util.verify.asserts galaxy.tool_util.verify.asserts.archive galaxy.tool_util.verify.asserts.hdf5 galaxy.tool_util.verify.asserts.size galaxy.tool_util.verify.asserts.tabular galaxy.tool_util.verify.asserts.text galaxy.tool_util.verify.asserts.xml galaxy.tool_util.verify.interactor galaxy.tool_util.verify.script galaxy.tool_util.verify.test_data galaxy.tool_util.verify.wait galaxy.tools galaxy.tools.actions galaxy.tools.actions.data_manager galaxy.tools.actions.data_source galaxy.tools.actions.history_imp_exp galaxy.tools.actions.metadata galaxy.tools.actions.model_operations galaxy.tools.actions.upload galaxy.tools.actions.upload_common galaxy.tools.biotools galaxy.tools.cache galaxy.tools.data galaxy.tools.data_fetch galaxy.tools.data_manager galaxy.tools.data_manager.manager galaxy.tools.error_reports galaxy.tools.error_reports.plugins galaxy.tools.error_reports.plugins.base_git galaxy.tools.error_reports.plugins.email galaxy.tools.error_reports.plugins.github galaxy.tools.error_reports.plugins.gitlab galaxy.tools.error_reports.plugins.influxdb galaxy.tools.error_reports.plugins.json galaxy.tools.error_reports.plugins.sentry galaxy.tools.errors galaxy.tools.evaluation galaxy.tools.exception_handling galaxy.tools.execute galaxy.tools.expressions galaxy.tools.expressions.evaluation galaxy.tools.expressions.script galaxy.tools.expressions.util galaxy.tools.filters galaxy.tools.imp_exp galaxy.tools.imp_exp.export_history galaxy.tools.imp_exp.unpack_tar_gz_archive galaxy.tools.parameters galaxy.tools.parameters.basic galaxy.tools.parameters.dataset_matcher galaxy.tools.parameters.dynamic_options galaxy.tools.parameters.grouping galaxy.tools.parameters.history_query galaxy.tools.parameters.input_translation galaxy.tools.parameters.meta galaxy.tools.parameters.sanitize galaxy.tools.parameters.validation galaxy.tools.parameters.wrapped galaxy.tools.parameters.wrapped_json galaxy.tools.recommendations galaxy.tools.remote_tool_eval galaxy.tools.repositories galaxy.tools.search galaxy.tools.special_tools galaxy.tools.test galaxy.tools.util galaxy.tools.util.galaxyops galaxy.tools.util.maf_utilities galaxy.tools.wrappers galaxy.tours galaxy.tours.validate galaxy.util galaxy.util.aliaspickler galaxy.util.bool_expressions galaxy.util.bunch galaxy.util.bytesize galaxy.util.checkers galaxy.util.commands galaxy.util.compression_utils galaxy.util.custom_logging galaxy.util.custom_logging.fluent_log galaxy.util.dictifiable galaxy.util.dynamic galaxy.util.expressions galaxy.util.facts galaxy.util.filelock galaxy.util.form_builder galaxy.util.hash_util galaxy.util.heartbeat galaxy.util.image_util galaxy.util.inflection galaxy.util.json galaxy.util.jstree 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galaxy.visualization.data_providers.genome galaxy.visualization.data_providers.phyloviz galaxy.visualization.data_providers.phyloviz.baseparser galaxy.visualization.data_providers.phyloviz.newickparser galaxy.visualization.data_providers.phyloviz.nexusparser galaxy.visualization.data_providers.phyloviz.phyloxmlparser galaxy.visualization.data_providers.registry galaxy.visualization.genome galaxy.visualization.genomes galaxy.visualization.plugins galaxy.visualization.plugins.config_parser galaxy.visualization.plugins.plugin galaxy.visualization.plugins.registry galaxy.visualization.plugins.resource_parser galaxy.visualization.plugins.utils galaxy.visualization.tracks galaxy.web galaxy.web.form_builder galaxy.web.framework galaxy.web.framework.base galaxy.web.framework.decorators galaxy.web.framework.helpers galaxy.web.framework.helpers.grids galaxy.web.framework.helpers.tags galaxy.web.framework.middleware galaxy.web.framework.middleware.error galaxy.web.framework.middleware.profile galaxy.web.framework.middleware.remoteuser galaxy.web.framework.middleware.request_id galaxy.web.framework.middleware.sqldebug galaxy.web.framework.middleware.static galaxy.web.framework.middleware.statsd galaxy.web.framework.middleware.translogger galaxy.web.framework.middleware.xforwardedhost galaxy.web.legacy_framework galaxy.web.legacy_framework.grids galaxy.web.proxy galaxy.web.statsd_client galaxy.web_stack galaxy.web_stack.gunicorn_config galaxy.web_stack.handlers galaxy.web_stack.message galaxy.web_stack.transport galaxy.webapps galaxy.webapps.base galaxy.webapps.base.api galaxy.webapps.base.controller galaxy.webapps.base.webapp galaxy.webapps.galaxy galaxy.webapps.galaxy.api galaxy.webapps.galaxy.api.annotations galaxy.webapps.galaxy.api.authenticate galaxy.webapps.galaxy.api.cloudauthz galaxy.webapps.galaxy.api.common galaxy.webapps.galaxy.api.configuration galaxy.webapps.galaxy.api.container_resolution galaxy.webapps.galaxy.api.datatypes galaxy.webapps.galaxy.api.display_applications galaxy.webapps.galaxy.api.dynamic_tools galaxy.webapps.galaxy.api.extended_metadata galaxy.webapps.galaxy.api.folder_contents galaxy.webapps.galaxy.api.folders galaxy.webapps.galaxy.api.forms galaxy.webapps.galaxy.api.genomes galaxy.webapps.galaxy.api.group_roles galaxy.webapps.galaxy.api.group_users galaxy.webapps.galaxy.api.groups galaxy.webapps.galaxy.api.job_files galaxy.webapps.galaxy.api.job_lock galaxy.webapps.galaxy.api.job_ports galaxy.webapps.galaxy.api.libraries galaxy.webapps.galaxy.api.library_contents galaxy.webapps.galaxy.api.library_datasets galaxy.webapps.galaxy.api.licenses galaxy.webapps.galaxy.api.metrics galaxy.webapps.galaxy.api.page_revisions galaxy.webapps.galaxy.api.pages galaxy.webapps.galaxy.api.plugins galaxy.webapps.galaxy.api.provenance galaxy.webapps.galaxy.api.quotas galaxy.webapps.galaxy.api.remote_files galaxy.webapps.galaxy.api.roles galaxy.webapps.galaxy.api.sanitize_allow galaxy.webapps.galaxy.api.short_term_storage galaxy.webapps.galaxy.api.tags galaxy.webapps.galaxy.api.tasks galaxy.webapps.galaxy.api.tool_data galaxy.webapps.galaxy.api.tool_dependencies galaxy.webapps.galaxy.api.tool_entry_points galaxy.webapps.galaxy.api.tool_shed_repositories galaxy.webapps.galaxy.api.tools galaxy.webapps.galaxy.api.toolshed galaxy.webapps.galaxy.api.tours galaxy.webapps.galaxy.api.trs_consumer galaxy.webapps.galaxy.api.trs_search galaxy.webapps.galaxy.api.uploads galaxy.webapps.galaxy.api.users galaxy.webapps.galaxy.api.visualizations galaxy.webapps.galaxy.api.webhooks galaxy.webapps.galaxy.buildapp galaxy.webapps.galaxy.controllers galaxy.webapps.galaxy.controllers.admin galaxy.webapps.galaxy.controllers.admin_toolshed galaxy.webapps.galaxy.controllers.async galaxy.webapps.galaxy.controllers.authnz galaxy.webapps.galaxy.controllers.data_manager galaxy.webapps.galaxy.controllers.error galaxy.webapps.galaxy.controllers.forms galaxy.webapps.galaxy.controllers.history galaxy.webapps.galaxy.controllers.page galaxy.webapps.galaxy.controllers.root galaxy.webapps.galaxy.controllers.shed_tool_static galaxy.webapps.galaxy.controllers.tag galaxy.webapps.galaxy.controllers.tool_runner galaxy.webapps.galaxy.controllers.user galaxy.webapps.galaxy.controllers.visualization galaxy.webapps.galaxy.controllers.workflow galaxy.webapps.galaxy.fast_app galaxy.webapps.galaxy.fast_factory galaxy.webapps.galaxy.services galaxy.webapps.galaxy.services.authenticate galaxy.webapps.galaxy.services.base galaxy.webapps.galaxy.services.histories galaxy.webapps.galaxy.services.libraries galaxy.webapps.galaxy.services.library_folder_contents galaxy.webapps.galaxy.services.library_folders galaxy.webapps.galaxy.services.pages galaxy.webapps.galaxy.services.quotas galaxy.webapps.galaxy.services.sharable galaxy.webapps.galaxy.services.tools galaxy.webapps.galaxy.services.users galaxy.webapps.galaxy.services.visualizations galaxy.webapps.galaxy.workers galaxy.webapps.openapi galaxy.webapps.openapi.utils galaxy.webapps.reports galaxy.webapps.reports.api galaxy.webapps.reports.app galaxy.webapps.reports.buildapp galaxy.webapps.reports.config galaxy.webapps.reports.controllers galaxy.webapps.reports.controllers.history galaxy.webapps.reports.controllers.home galaxy.webapps.reports.controllers.jobs galaxy.webapps.reports.controllers.query galaxy.webapps.reports.controllers.root galaxy.webapps.reports.controllers.system galaxy.webapps.reports.controllers.tools galaxy.webapps.reports.controllers.users galaxy.webapps.reports.controllers.workflows galaxy.webapps.reports.fast_app galaxy.webapps.reports.fast_factory galaxy.webapps.util galaxy.webhooks galaxy.work galaxy.work.context galaxy.workflow galaxy.workflow.extract galaxy.workflow.modules galaxy.workflow.refactor galaxy.workflow.refactor.execute galaxy.workflow.refactor.schema galaxy.workflow.render galaxy.workflow.reports galaxy.workflow.reports.generators galaxy.workflow.reports.generators.markdown galaxy.workflow.resources galaxy.workflow.run galaxy.workflow.run_request galaxy.workflow.schedulers galaxy.workflow.schedulers.core galaxy.workflow.scheduling_manager galaxy.workflow.steps galaxy.workflow.trs_proxy galaxy_ext galaxy_ext.container_monitor galaxy_ext.container_monitor.monitor galaxy_ext.expressions galaxy_ext.expressions.handle_job galaxy_ext.metadata galaxy_ext.metadata.set_metadata galaxy_test galaxy_test.api galaxy_test.api.cwl galaxy_test.api.sharable galaxy_test.api.test_authenticate galaxy_test.api.test_configuration galaxy_test.api.test_dataset_collections galaxy_test.api.test_datasets galaxy_test.api.test_datatypes galaxy_test.api.test_display_applications galaxy_test.api.test_folder_contents galaxy_test.api.test_folders galaxy_test.api.test_framework galaxy_test.api.test_group_roles galaxy_test.api.test_group_users galaxy_test.api.test_groups galaxy_test.api.test_histories galaxy_test.api.test_history_contents galaxy_test.api.test_history_contents_provenance galaxy_test.api.test_jobs galaxy_test.api.test_libraries galaxy_test.api.test_licenses galaxy_test.api.test_page_revisions galaxy_test.api.test_pages galaxy_test.api.test_roles galaxy_test.api.test_tool_data galaxy_test.api.test_tools galaxy_test.api.test_tools_upload galaxy_test.api.test_tours galaxy_test.api.test_users galaxy_test.api.test_visualizations galaxy_test.api.test_webhooks galaxy_test.api.test_workflow_extraction galaxy_test.api.test_workflows galaxy_test.api.test_workflows_cwl galaxy_test.api.test_workflows_from_yaml galaxy_test.base galaxy_test.base.api galaxy_test.base.api_asserts galaxy_test.base.api_util galaxy_test.base.constants galaxy_test.base.env galaxy_test.base.interactor galaxy_test.base.populators galaxy_test.base.rules_test_data galaxy_test.base.testcase galaxy_test.base.workflow_fixtures galaxy_test.conftest galaxy_test.driver galaxy_test.driver.driver_util galaxy_test.driver.integration_setup galaxy_test.driver.integration_util galaxy_test.driver.test_logging galaxy_test.driver.testcase galaxy_test.performance galaxy_test.performance.test_workflow_framework_performance galaxy_test.selenium galaxy_test.selenium.conftest galaxy_test.selenium.framework galaxy_test.selenium.jupyter galaxy_test.selenium.jupyter_context galaxy_test.selenium.test_admin_app galaxy_test.selenium.test_anon_history galaxy_test.selenium.test_change_password galaxy_test.selenium.test_collection_builders galaxy_test.selenium.test_collection_edit galaxy_test.selenium.test_custom_builds galaxy_test.selenium.test_data_source_tools galaxy_test.selenium.test_dataset_metadata_download galaxy_test.selenium.test_histories_list galaxy_test.selenium.test_history_copy_elements galaxy_test.selenium.test_history_dataset_state galaxy_test.selenium.test_history_multi_view galaxy_test.selenium.test_history_options galaxy_test.selenium.test_history_panel galaxy_test.selenium.test_history_panel_collections galaxy_test.selenium.test_history_sharing galaxy_test.selenium.test_invocation_grid galaxy_test.selenium.test_library_contents galaxy_test.selenium.test_library_landing galaxy_test.selenium.test_library_to_collections galaxy_test.selenium.test_login galaxy_test.selenium.test_navigates_galaxy galaxy_test.selenium.test_pages galaxy_test.selenium.test_personal_information galaxy_test.selenium.test_registration galaxy_test.selenium.test_sign_out galaxy_test.selenium.test_sizzle_loading galaxy_test.selenium.test_stock_tours galaxy_test.selenium.test_tool_describing_tours galaxy_test.selenium.test_tool_form galaxy_test.selenium.test_uploads galaxy_test.selenium.test_workflow_editor galaxy_test.selenium.test_workflow_invocation_details galaxy_test.selenium.test_workflow_management galaxy_test.selenium.test_workflow_run galaxy_test.selenium.test_workflow_sharing tool_shed tool_shed.dependencies tool_shed.dependencies.attribute_handlers tool_shed.dependencies.repository tool_shed.dependencies.repository.relation_builder tool_shed.dependencies.tool tool_shed.dependencies.tool.tag_attribute_handler tool_shed.galaxy_install tool_shed.grids tool_shed.grids.admin_grids tool_shed.grids.repository_grid_filter_manager tool_shed.grids.repository_grids tool_shed.grids.util tool_shed.managers tool_shed.managers.groups tool_shed.managers.repositories tool_shed.metadata tool_shed.metadata.repository_metadata_manager tool_shed.repository_registry tool_shed.repository_types tool_shed.repository_types.metadata tool_shed.repository_types.registry tool_shed.repository_types.repository_suite_definition tool_shed.repository_types.tool_dependency_definition tool_shed.repository_types.unrestricted tool_shed.repository_types.util tool_shed.test tool_shed.test.base tool_shed.test.base.common tool_shed.test.base.test_db_util tool_shed.test.base.twilltestcase tool_shed.test.functional tool_shed.test.functional.test_0000_basic_repository_features tool_shed.test.functional.test_0010_repository_with_tool_dependencies tool_shed.test.functional.test_0020_basic_repository_dependencies tool_shed.test.functional.test_0030_repository_dependency_revisions tool_shed.test.functional.test_0040_repository_circular_dependencies tool_shed.test.functional.test_0050_circular_dependencies_4_levels tool_shed.test.functional.test_0070_invalid_tool tool_shed.test.functional.test_0080_advanced_circular_dependencies tool_shed.test.functional.test_0090_tool_search tool_shed.test.functional.test_0100_complex_repository_dependencies tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners tool_shed.test.functional.test_0140_tool_help_images tool_shed.test.functional.test_0150_prior_installation_required tool_shed.test.functional.test_0160_circular_prior_installation_required tool_shed.test.functional.test_0170_complex_prior_installation_required tool_shed.test.functional.test_0300_reset_all_metadata tool_shed.test.functional.test_0310_hg_api_features tool_shed.test.functional.test_0420_citable_urls_for_repositories tool_shed.test.functional.test_0430_browse_utilities tool_shed.test.functional.test_0440_deleting_dependency_definitions tool_shed.test.functional.test_0460_upload_to_repository tool_shed.test.functional.test_0470_tool_dependency_repository_type tool_shed.test.functional.test_0480_tool_dependency_xml_verification tool_shed.test.functional.test_0530_repository_admin_feature tool_shed.test.functional.test_0550_metadata_updated_dependencies tool_shed.test.functional.test_1000_install_basic_repository tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies tool_shed.test.functional.test_1050_circular_dependencies_4_levels tool_shed.test.functional.test_1070_invalid_tool tool_shed.test.functional.test_1080_advanced_circular_dependency_installation tool_shed.test.functional.test_1090_repository_dependency_handling tool_shed.test.functional.test_1100_install_updated_repository_dependencies tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners tool_shed.test.functional.test_1160_tool_help_images tool_shed.test.functional.test_1170_prior_installation_required tool_shed.test.functional.test_1180_circular_prior_installation_required tool_shed.test.functional.test_1190_complex_prior_installation_required tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions tool_shed.test.functional.test_1300_reset_all_metadata tool_shed.test.functional.test_1410_update_manager tool_shed.test.functional.test_1430_repair_installed_repository tool_shed.test.functional.test_1460_data_managers tool_shed.test.functional.test_1470_updating_installed_repositories tool_shed.tools tool_shed.tools.data_table_manager tool_shed.tools.tool_validator tool_shed.tools.tool_version_manager tool_shed.util tool_shed.util.admin_util tool_shed.util.basic_util tool_shed.util.commit_util tool_shed.util.common_util tool_shed.util.container_util tool_shed.util.encoding_util tool_shed.util.hg_util tool_shed.util.hgweb_config tool_shed.util.metadata_util tool_shed.util.readme_util tool_shed.util.repository_content_util tool_shed.util.repository_util tool_shed.util.search_util tool_shed.util.shed_index tool_shed.util.shed_util_common tool_shed.util.tool_dependency_util tool_shed.util.tool_util tool_shed.util.web_util tool_shed.util.xml_util tool_shed.utility_containers tool_shed.utility_containers.utility_container_manager tool_shed.webapp tool_shed.webapp.api tool_shed.webapp.api.authenticate tool_shed.webapp.api.categories tool_shed.webapp.api.configuration tool_shed.webapp.api.groups tool_shed.webapp.api.repositories tool_shed.webapp.api.repository_revisions tool_shed.webapp.api.tools tool_shed.webapp.api.users tool_shed.webapp.app tool_shed.webapp.buildapp tool_shed.webapp.config tool_shed.webapp.controllers tool_shed.webapp.controllers.admin tool_shed.webapp.controllers.groups tool_shed.webapp.controllers.hg tool_shed.webapp.controllers.repository tool_shed.webapp.controllers.user tool_shed.webapp.fast_app tool_shed.webapp.fast_factory tool_shed.webapp.framework tool_shed.webapp.framework.decorators tool_shed.webapp.framework.middleware tool_shed.webapp.framework.middleware.remoteuser tool_shed.webapp.model tool_shed.webapp.model.mapping tool_shed.webapp.search tool_shed.webapp.search.repo_search tool_shed.webapp.search.tool_search tool_shed.webapp.security tool_shed.webapp.util tool_shed.webapp.util.ratings_util tool_shed.webapp.util.shed_statistics module (galaxy.model.WorkflowStep attribute) module_code (galaxy.util.template.FixedModuleCodeCompiler attribute) ModuleDependencyResolver (class in galaxy.tool_util.deps.resolvers.modules) MOL (class in galaxy.datatypes.molecules) MOL2 (class in galaxy.datatypes.molecules) MongoDBArchive (class in galaxy.datatypes.binary) monitor() (galaxy.jobs.runners.AsynchronousJobRunner method) (galaxy.tool_util.toolbox.watcher.ToolConfWatcher method) (galaxy.util.watcher.BaseWatcher method) monitor_job() (galaxy.jobs.runners.AsynchronousJobRunner method) monitor_thread_join_timeout (galaxy.config.GalaxyAppConfiguration attribute) Monitors (class in galaxy.util.monitors) most_recent() (galaxy.managers.histories.HistoryManager method) mouse_drag() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) move_center_of_canvas() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) move_file() (in module galaxy.tool_shed.util.basic_util) (in module tool_shed.util.basic_util) move_merge() (in module galaxy.util) Mp3 (class in galaxy.datatypes.media) Mp4 (class in galaxy.datatypes.media) mp_from_ids() (in module galaxy.objectstore.s3_multipart_upload) Mpg (class in galaxy.datatypes.media) Mrc2014 (class in galaxy.datatypes.images) Ms2 (class in galaxy.datatypes.proteomics) Msf (class in galaxy.datatypes.msa) Msp (class in galaxy.datatypes.proteomics) mStats (class in galaxy.datatypes.metacyto) mSummary (class in galaxy.datatypes.metacyto) mulled_channels (galaxy.config.GalaxyAppConfiguration attribute) mulled_resolution_cache (galaxy.tool_util.deps.container_resolvers.ResolutionCache attribute) mulled_tags_for() (in module galaxy.tool_util.deps.mulled.util) MulledDockerContainerResolver (class in galaxy.tool_util.deps.container_resolvers.mulled) MulledSingularityContainerResolver (class in galaxy.tool_util.deps.container_resolvers.mulled) multi_select_email_alerts() (tool_shed.webapp.controllers.repository.RepositoryController method) MulticolFilterColumn (class in galaxy.web.legacy_framework.grids) multipart_upload() (in module galaxy.objectstore.s3_multipart_upload) multiple (galaxy.tools.parameters.basic.BaseDataToolParameter attribute) (galaxy.tools.parameters.basic.DataCollectionToolParameter attribute) (galaxy.tools.parameters.basic.DataToolParameter attribute) (galaxy.tools.parameters.basic.HiddenDataToolParameter attribute) (galaxy.tools.parameters.DataCollectionToolParameter attribute) (galaxy.tools.parameters.DataToolParameter attribute) MultipleDependencyResolver (class in galaxy.tool_util.deps.resolvers) MultipleSplitterFilter (class in galaxy.tool_util.parser.output_actions) (class in galaxy.tools.parameters.dynamic_options) multiply() (galaxy.model.dataset_collections.structure.Leaf method) (galaxy.model.dataset_collections.structure.Tree method) (galaxy.model.dataset_collections.structure.UninitializedTree method) (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) MultiSourceDataProvider (class in galaxy.datatypes.dataproviders.base) MutableJSONType (class in galaxy.model.custom_types) MutationDict (class in galaxy.model.custom_types) MutationList (class in galaxy.model.custom_types) MutationObj (class in galaxy.model.custom_types) my_writable_repositories_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) my_writable_repositories_missing_tool_test_components_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) my_writable_repositories_with_invalid_tools_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) MySQLDatabaseManager (class in galaxy.model.database_utils) MyWritableRepositoriesGrid (class in tool_shed.grids.repository_grids) MyWritableRepositoriesMissingToolTestComponentsGrid (class in tool_shed.grids.repository_grids) MyWritableRepositoriesWithInvalidToolsGrid (class in tool_shed.grids.repository_grids) MzData (class in galaxy.datatypes.proteomics) MzIdentML (class in galaxy.datatypes.proteomics) MzML (class in galaxy.datatypes.proteomics) MzQuantML (class in galaxy.datatypes.proteomics) MzSQlite (class in galaxy.datatypes.binary) MzTab (class in galaxy.datatypes.proteomics) MzTab2 (class in galaxy.datatypes.proteomics) MzXML (class in galaxy.datatypes.proteomics)

N

N3 (class in galaxy.datatypes.triples) name (galaxy.config.config_manage.OptionValue attribute) (galaxy.datatypes.display_applications.parameters.DatasetLikeObject attribute) (galaxy.files.sources.Entry attribute) (galaxy.files.sources.EntryData attribute) (galaxy.files.sources.RemoteDirectory attribute) (galaxy.files.sources.RemoteEntry attribute) (galaxy.files.sources.RemoteFile attribute) (galaxy.job_execution.actions.post.ChangeDatatypeAction attribute) (galaxy.job_execution.actions.post.ColumnSetAction attribute) (galaxy.job_execution.actions.post.DefaultJobAction attribute) (galaxy.job_execution.actions.post.DeleteDatasetAction attribute) (galaxy.job_execution.actions.post.DeleteIntermediatesAction attribute) (galaxy.job_execution.actions.post.EmailAction attribute) (galaxy.job_execution.actions.post.HideDatasetAction attribute) (galaxy.job_execution.actions.post.RemoveTagDatasetAction attribute) (galaxy.job_execution.actions.post.RenameDatasetAction attribute) (galaxy.job_execution.actions.post.SetMetadataAction attribute) (galaxy.job_execution.actions.post.TagDatasetAction attribute) (galaxy.job_execution.actions.post.ValidateOutputsAction attribute) (galaxy.managers.display_applications.DisplayApplication attribute) (galaxy.managers.display_applications.Link attribute) (galaxy.managers.licenses.LicenseMetadataModel attribute) (galaxy.model.FormDefinition attribute) (galaxy.model.Group attribute) (galaxy.model.History attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetAssociationHistory attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.ImplicitlyCreatedDatasetCollectionInput attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.JobParameter attribute) (galaxy.model.JobToImplicitOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetAssociation attribute) (galaxy.model.JobToInputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetCollectionElementAssociation attribute) (galaxy.model.JobToInputLibraryDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToOutputLibraryDatasetAssociation attribute) (galaxy.model.Library attribute) (galaxy.model.LibraryDataset property) (galaxy.model.LibraryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryFolder attribute) (galaxy.model.MetadataFile attribute) (galaxy.model.Quota attribute) (galaxy.model.Role attribute) (galaxy.model.store.discover.JsonCollectedDatasetMatch property) (galaxy.model.StoredWorkflow attribute) (galaxy.model.Tag attribute) (galaxy.model.tool_shed_install.HasToolBox attribute) (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.model.UserAddress attribute) (galaxy.model.UserPreference attribute) (galaxy.model.Workflow attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowStepInput attribute) (galaxy.objectstore.ConcreteObjectStoreModel attribute) (galaxy.schema.fetch_data.BaseCollectionTarget attribute) (galaxy.schema.fetch_data.BaseDataElement attribute) (galaxy.schema.fetch_data.LibraryDestination attribute) (galaxy.schema.remote_files.CreatedEntryResponse attribute) (galaxy.schema.remote_files.CreateEntryPayload attribute) (galaxy.schema.remote_files.RemoteEntry attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.ArchivedHistorySummary attribute) (galaxy.schema.schema.AsyncTaskResultSummary attribute) (galaxy.schema.schema.BasicRoleModel attribute) (galaxy.schema.schema.CollectionElementIdentifier attribute) (galaxy.schema.schema.CreateHistoryPayload attribute) (galaxy.schema.schema.CreateLibraryFolderPayload attribute) (galaxy.schema.schema.CreateLibraryPayload attribute) (galaxy.schema.schema.CreateNewCollectionPayload attribute) (galaxy.schema.schema.Creator attribute) (galaxy.schema.schema.CustomBuildBaseModel attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.EncodedJobParameterHistoryItem attribute) (galaxy.schema.schema.GroupModel attribute) (galaxy.schema.schema.GroupRoleResponse attribute) (galaxy.schema.schema.HDABasicInfo attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HistoryItemBase attribute) (galaxy.schema.schema.HistorySummary attribute) (galaxy.schema.schema.Input attribute) (galaxy.schema.schema.InstalledToolShedRepository attribute) (galaxy.schema.schema.JobMetric attribute) (galaxy.schema.schema.LibraryFolderDetails attribute) (galaxy.schema.schema.LibraryFolderItemBase attribute) (galaxy.schema.schema.LibraryLegacySummary attribute) (galaxy.schema.schema.Output attribute) (galaxy.schema.schema.RoleDefinitionModel attribute) (galaxy.schema.schema.StoredWorkflowSummary attribute) (galaxy.schema.schema.ToolShedRepository attribute) (galaxy.schema.schema.ToolShedRepositorySummary attribute) (galaxy.schema.schema.UpdateHistoryContentsPayload attribute) (galaxy.schema.schema.UpdateLibraryFolderPayload attribute) (galaxy.schema.schema.UpdateLibraryPayload attribute) (galaxy.schema.schema.WorkflowStepToExportBase attribute) (galaxy.schema.schema.WorkflowToExport attribute) (galaxy.selenium.navigates_galaxy.WaitType attribute) (galaxy.structured_app.BasicSharedApp attribute) (galaxy.structured_app.MinimalToolApp attribute) (galaxy.tool_shed.metadata.metadata_generator.RepositoryProtocol attribute) (galaxy.tool_util.cwl.representation.TypeRepresentation attribute) (galaxy.tool_util.deps.resolvers.ContainerDependency property) (galaxy.tool_util.toolbox.views.definitions.Section attribute) (galaxy.tool_util.toolbox.views.definitions.StaticToolBoxView attribute) (galaxy.tool_util.toolbox.views.interface.ToolPanelViewModel attribute) (galaxy.tool_util.verify.interactor.ToolTestDescription attribute) (galaxy.tool_util.verify.interactor.ToolTestDescriptionDict attribute) (galaxy.tools.data_manager.manager.Tool attribute) (galaxy.tools.parameters.grouping.Dataset attribute) (galaxy.tools.remote_tool_eval.ToolApp attribute) (galaxy.tools.remote_tool_eval.ToolAppConfig attribute) (galaxy.tools.wrappers.DatasetCollectionWrapper attribute) (galaxy.tours.TourCore attribute) (galaxy.util.resources.Traversable property) (galaxy.web_stack.ApplicationStack attribute) (galaxy.web_stack.GunicornApplicationStack attribute) (galaxy.web_stack.WebApplicationStack attribute) (galaxy.web_stack.WeblessApplicationStack attribute) (galaxy.webapps.reports.app.UniverseApplication attribute) (galaxy.workflow.modules.InputDataCollectionModule attribute) (galaxy.workflow.modules.InputDataModule attribute) (galaxy.workflow.modules.InputModule attribute) (galaxy.workflow.modules.InputParameterModule attribute) (galaxy.workflow.modules.InputProxy property) (galaxy.workflow.modules.PauseModule attribute) (galaxy.workflow.modules.SubWorkflowModule attribute) (galaxy.workflow.modules.ToolModule attribute) (galaxy.workflow.modules.WorkflowModule attribute) (galaxy.workflow.refactor.schema.ExtractUntypedParameter attribute) (galaxy.workflow.refactor.schema.UpdateNameAction attribute) (tool_shed.managers.repositories.UpdatesRequest attribute) (tool_shed.webapp.model.Category attribute) (tool_shed.webapp.model.Group attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.Role attribute) (tool_shed.webapp.model.Tag attribute) name() (galaxy.datatypes.util.gff_util.GFFFeature method) (galaxy.tool_util.lint.Linter class method) name_and_ext (galaxy.tools.wrappers.DatasetFilenameWrapper property) name_autocomplete_data() (tool_shed.util.admin_util.Admin method) nameext (galaxy.tool_util.cwl.util.OutputPropertiesType attribute) nameroot (galaxy.tool_util.cwl.util.OutputPropertiesType attribute) Names (class in galaxy.datatypes.mothur) namespace (galaxy.managers.metrics.Metric attribute) navigate_to_custom_builds_page() (galaxy_test.selenium.test_custom_builds.TestCustomBuilds method) navigate_to_database_tab() (galaxy_test.selenium.test_collection_edit.TestCollectionEdit method) navigate_to_datatype_tab() (galaxy_test.selenium.test_collection_edit.TestCollectionEdit method) navigate_to_histories_page() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) navigate_to_histories_shared_with_me_page() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) navigate_to_invocations() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) navigate_to_manage_information() (galaxy_test.selenium.test_personal_information.TestManageInformation method) navigate_to_new_library() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) navigate_to_pages() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) navigate_to_published_histories() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) navigate_to_published_pages() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) navigate_to_published_workflows() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) navigate_to_user_preferences() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) NavigatesGalaxy (class in galaxy.selenium.navigates_galaxy) navigation (galaxy.selenium.navigates_galaxy.NavigatesGalaxy property) NcbiTaxonomySQlite (class in galaxy.datatypes.binary) needs_shell_quoting() (in module galaxy.tool_util.cwl) (in module galaxy.tool_util.cwl.cwltool_deps) Neo4j (class in galaxy.datatypes.neo4j) Neo4jDB (class in galaxy.datatypes.neo4j) Neo4jDBzip (class in galaxy.datatypes.neo4j) NeperMultiScaleCell (class in galaxy.datatypes.constructive_solid_geometry) NeperPoints (class in galaxy.datatypes.constructive_solid_geometry) NeperPointsTabular (class in galaxy.datatypes.constructive_solid_geometry) NeperTesr (class in galaxy.datatypes.constructive_solid_geometry) NeperTess (class in galaxy.datatypes.constructive_solid_geometry) nested_collection_identifiers() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method) NestedElement (class in galaxy.schema.fetch_data) NestedObjectStore (class in galaxy.objectstore) NetCDF (class in galaxy.datatypes.binary)

NEVER_SANITIZE (galaxy.util.Params attribute) NEW (galaxy.model.ImplicitCollectionJobs.populated_states attribute) new (galaxy.model.JobStateSummary attribute) NEW (galaxy.model.Task.states attribute) (galaxy.model.tool_shed_install.ToolShedRepository.installation_status attribute) (galaxy.schema.schema.DatasetCollectionPopulatedState attribute) (galaxy.schema.schema.DatasetState attribute) new (galaxy.schema.schema.HDCJobStateSummary attribute) NEW (galaxy.schema.schema.JobState attribute) new() (galaxy.forms.forms.FormDefinitionAddressFieldFactory method) (galaxy.forms.forms.FormDefinitionFactory method) (galaxy.forms.forms.FormDefinitionFieldFactory method) (galaxy.forms.forms.FormDefinitionHistoryFieldFactory method) (galaxy.forms.forms.FormDefinitionPasswordFieldFactory method) (galaxy.forms.forms.FormDefinitionSelectFieldFactory method) (galaxy.forms.forms.FormDefinitionTextFieldFactory method) (galaxy.forms.forms.FormDefinitionWorkflowFieldFactory method) (galaxy.forms.forms.FormDefinitionWorkflowMappingFieldFactory method) new_bam_dataset() (galaxy_test.base.populators.BaseDatasetPopulator method) new_clean_env() (in module galaxy.util.commands) new_collection (galaxy.schema.schema.ColletionSourceType attribute) (galaxy.schema.schema.HistoryContentSource attribute) new_data_manager_required() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) new_dataset() (galaxy_test.base.populators.BaseDatasetPopulator method) new_dataset_request() (galaxy_test.base.populators.BaseDatasetPopulator method) new_error_dataset() (galaxy_test.base.populators.BaseDatasetPopulator method) new_file() (galaxy.datatypes.metadata.FileParameter method) (galaxy.model.metadata.FileParameter method) new_file_path (galaxy.config.GalaxyAppConfiguration attribute) new_file_path() (galaxy.job_execution.compute_environment.ComputeEnvironment method) (galaxy.job_execution.compute_environment.SharedComputeEnvironment method) new_history() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) (galaxy.webapps.base.webapp.GalaxyWebTransaction method) (galaxy_test.base.populators.BaseDatasetPopulator method) new_history_properties() (galaxy.model.store.BaseDirectoryImportModelStore method) (galaxy.model.store.DictImportModelStore method) (galaxy.model.store.ModelImportStore method) new_insecure_hash() (in module galaxy.util.hash_util) new_library() (galaxy_test.base.populators.LibraryPopulator method) new_library_dataset() (galaxy_test.base.populators.LibraryPopulator method) new_library_dataset_in_private_library() (galaxy_test.base.populators.LibraryPopulator method) new_metadata_required_for_utilities() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) new_page() (galaxy_test.base.populators.BaseDatasetPopulator method) new_page_payload() (galaxy_test.base.populators.BaseDatasetPopulator method) new_page_raw() (galaxy_test.base.populators.BaseDatasetPopulator method) new_private_library() (galaxy_test.base.populators.LibraryPopulator method) new_repo_alert (tool_shed.webapp.model.User attribute) new_repository_dependency_metadata_required() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) new_secure_hash_v2() (in module galaxy.util.hash_util) new_session() (galaxy.model.base.ModelMapping method) new_slug (galaxy.schema.schema.SetSlugPayload attribute) new_state() (galaxy.tools.Tool method) (in module tool_shed.util.tool_util) new_tool_dependency_metadata_required() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) new_tool_metadata_required() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) new_tool_panel_section_label (galaxy.managers.workflows.WorkflowCreateOptions attribute) new_upload() (in module galaxy.tools.actions.upload_common) Newick (class in galaxy.datatypes.data) Newick_Parser (class in galaxy.visualization.data_providers.phyloviz.newickparser) next() (galaxy.tools.exception_handling.UCSCOutWrapper method) (galaxy.util.ucsc.UCSCOutWrapper method) next_installable_changeset_revision() (tool_shed.webapp.controllers.repository.RepositoryController method) next_line_starts_with() (galaxy.datatypes.proteomics.Msp static method) next_step (galaxy.model.PSAPartial attribute) Nexus (class in galaxy.datatypes.data) Nexus_Parser (class in galaxy.visualization.data_providers.phyloviz.nexusparser) nginx_upload_path (galaxy.tools.remote_tool_eval.ToolAppConfig attribute) nginx_upload_store (galaxy.config.GalaxyAppConfiguration attribute) nginx_x_accel_redirect_base (galaxy.webapps.base.api.GalaxyFileResponse attribute) nice_size (galaxy.schema.schema.CustomHistoryView attribute) nice_size() (in module galaxy.util) (in module galaxy.webapps.reports.controllers.system) nice_total_disk_usage (galaxy.model.User property) (galaxy.schema.schema.DiskUsageUserModel attribute) (tool_shed.webapp.model.User property) NicerConfigParser (class in galaxy.util.properties) Nifti1 (class in galaxy.datatypes.images) Nifti2 (class in galaxy.datatypes.images) NmrML (class in galaxy.datatypes.proteomics) no_changes (galaxy.managers.sharable.SharingOptions attribute) (galaxy.schema.schema.SharingOptions attribute) NO_CHROMOSOME (galaxy.model.Dataset.conversion_messages attribute) (galaxy.model.DatasetInstance.conversion_messages attribute) NO_CONVERTER (galaxy.model.Dataset.conversion_messages attribute) (galaxy.model.DatasetInstance.conversion_messages attribute) NO_DATA (galaxy.model.Dataset.conversion_messages attribute) (galaxy.model.DatasetInstance.conversion_messages attribute) no_data_states (galaxy.model.Dataset attribute) NO_ERROR (galaxy.tool_util.parser.stdio.StdioErrorLevel attribute) NO_TOOL (galaxy.model.Dataset.conversion_messages attribute) (galaxy.model.DatasetInstance.conversion_messages attribute) NoContentException NoConverterException Node (class in galaxy.util.jstree) (class in galaxy.visualization.data_providers.phyloviz.baseparser) node_edge_dataprovider() (galaxy.datatypes.graph.Sif method) (galaxy.datatypes.graph.Xgmml method) NodeProxyLauncher (class in galaxy.web.proxy) NoMatchingFileSource non_batch_execute() (galaxy.model.migrations.util.AlterColumn method) (galaxy.model.migrations.util.CreateForeignKey method) (galaxy.model.migrations.util.CreateUniqueConstraint method) (galaxy.model.migrations.util.DDLAlterOperation method) (galaxy.model.migrations.util.DropColumn method) (galaxy.model.migrations.util.DropConstraint method) NON_DATA_CONNECTION (galaxy.model.WorkflowStepConnection attribute) non_data_connection (galaxy.model.WorkflowStepConnection property) non_merged_items() (galaxy.tool_util.cwl.cwltool_deps.CommentedMap method) non_private_roles (galaxy.model.User attribute) (tool_shed.webapp.model.User attribute) non_ready_jobs() (galaxy.managers.histories.HistoryManager method) non_ready_states (galaxy.model.Dataset attribute) (galaxy.model.Job attribute) non_terminal_states (galaxy.model.WorkflowInvocation attribute) nonce (galaxy.authnz.psa_authnz.Storage attribute) NONCHANGING_WORDS (galaxy.util.inflection.Inflector attribute) none (galaxy.schema.schema.InvocationSortByEnum attribute) NoneDataset (class in galaxy.model.none_like) NoopHandler (class in galaxy.jobs.manager) NoOpLazyProcess (class in galaxy.util.lazy_process) NoopManager (class in galaxy.jobs.manager) NoopQueue (class in galaxy.jobs) NoOptionsValidator (class in galaxy.tools.parameters.validation) NoProviderAvailable NoQuotaAgent (class in galaxy.quota) NoReplacement (class in galaxy.workflow.modules) normalize_input_connections_to_list() (galaxy.workflow.refactor.execute.WorkflowRefactorExecutor static method) normalize_key() (galaxy.security.vault.VaultKeyValidationWrapper method) normalize_workflow_format() (galaxy.managers.workflows.WorkflowContentsManager method) normalizeFilesDirs() (in module galaxy.tool_util.cwl.cwltool_deps) Notification (class in galaxy.model) notification (galaxy.model.UserNotificationAssociation attribute) notification_id (galaxy.model.UserNotificationAssociation attribute) notification_manager (galaxy.structured_app.MinimalManagerApp attribute) NotImplemented NotLoggedInException NotTested (class in tool_shed.utility_containers) now() (in module galaxy.model) (in module galaxy.model.database_heartbeat) (in module galaxy.model.orm.now) (in module galaxy.model.tool_shed_install) (in module galaxy.model.unittest_utils.store_fixtures) (in module tool_shed.webapp.model) Npz (class in galaxy.datatypes.binary) Nrrd (class in galaxy.datatypes.images) NTriples (class in galaxy.datatypes.triples) nullable_basestring() (galaxy.managers.base.ModelValidator static method) NullClientTestConfig (class in galaxy.tool_util.verify.interactor) NullConfiguredFileSources (class in galaxy.files) NullContainerFinder (class in galaxy.tool_util.deps.containers) NullDatasetPathRewriter (class in galaxy.job_execution.datasets) NullDependency (class in galaxy.tool_util.deps.resolvers) NullDependencyManager (class in galaxy.tool_util.deps) NullErrorPlugin (class in galaxy.tools.error_reports) NullToolOutputActionOption (class in galaxy.tool_util.parser.output_actions) NullToolProvidedMetadata (class in galaxy.tool_util.provided_metadata) NullToolTagManager (class in galaxy.tool_util.toolbox.base) (class in galaxy.tools) NullTourCallback (class in galaxy.selenium.navigates_galaxy) NullVault (class in galaxy.security.vault) NullWatcher (class in galaxy.util.watcher) num_heads (galaxy.tools.recommendations.ToolRecommendations attribute) num_lines (galaxy.datatypes.goldenpath.AGPFile property) (galaxy.datatypes.goldenpath.AGPObject property) num_outputs (galaxy.tool_util.verify.interactor.ToolTestDescription attribute) (galaxy.tool_util.verify.interactor.ToolTestDescriptionDict attribute) (galaxy.tool_util.verify.interactor.ValidToolTestDict attribute) num_page_links (galaxy.web.legacy_framework.grids.Grid attribute) num_rows_per_page (galaxy.web.legacy_framework.grids.Grid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) number_of_steps (galaxy.schema.schema.StoredWorkflowSummary attribute) numeric_metrics (galaxy.model.Job attribute) (galaxy.model.Task attribute) numeric_revision (tool_shed.webapp.model.RepositoryMetadata attribute) Numpy (class in galaxy.datatypes.binary) nworkers_changed() (in module galaxy.web_stack.gunicorn_config)

O

OBFS (class in galaxy.datatypes.molecules) obj (galaxy.datatypes.goldenpath.AGPObject property) obj_len (galaxy.datatypes.goldenpath.AGPObject property) object (galaxy.schema.schema.DCESummary attribute) object_id (galaxy.model.store.discover.JsonCollectedDatasetMatch property) (galaxy.model.StoreExportAssociation attribute) (galaxy.schema.schema.ExportObjectRequestMetadata attribute) (galaxy.schema.schema.FavoriteObject attribute) object_key (galaxy.model.store.DictImportModelStore attribute) (galaxy.model.store.DirectoryImportModelStore1901 attribute) (galaxy.model.store.DirectoryImportModelStoreLatest attribute) (galaxy.model.store.ModelImportStore property) object_name (galaxy.tool_util.lint.LintContext attribute) object_store (galaxy.app.MinimalGalaxyApplication attribute) (galaxy.job_execution.output_collect.JobContext property) (galaxy.model.Dataset attribute) (galaxy.model.store.discover.ModelPersistenceContext property) (galaxy.model.store.discover.SessionlessModelPersistenceContext property) (galaxy.model.store.StoreAppProtocol attribute) (galaxy.structured_app.MinimalManagerApp attribute) (galaxy.structured_app.MinimalToolApp attribute) (galaxy.tools.remote_tool_eval.ToolApp attribute) object_store_allows_id_selection() (galaxy.objectstore.DistributedObjectStore method) (galaxy.objectstore.ObjectStore method) object_store_id (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance property) (galaxy.model.Job attribute) (galaxy.model.MetadataFile attribute) (galaxy.model.store.DatasetAttributeImportModel attribute) (galaxy.objectstore.ConcreteObjectStoreModel attribute) object_store_id_overrides (galaxy.model.Job attribute) object_store_ids() (galaxy.objectstore.DistributedObjectStore method) (galaxy.objectstore.ObjectStore method) object_store_ids_allowing_selection() (galaxy.objectstore.DistributedObjectStore method) (galaxy.objectstore.ObjectStore method) object_store_store_by (galaxy.config.BaseAppConfiguration attribute) (tool_shed.webapp.config.ToolShedAppConfiguration attribute) object_stores_parent (galaxy_test.driver.integration_util.ConfiguresObjectStores attribute) object_to_string() (in module galaxy.util) object_type (galaxy.model.StoreExportAssociation attribute) (galaxy.schema.schema.ExportObjectRequestMetadata attribute) ObjectAttributeInvalidException ObjectAttributeMissingException ObjectCreationProblem ObjectCreationProblemSharingDisabled ObjectCreationProblemStoreFull ObjectExportResponseBase (class in galaxy.schema.schema) ObjectExportTaskResponse (class in galaxy.schema.schema) ObjectImportTracker (class in galaxy.model.store) ObjectInvalid ObjectNotFound ObjectStore (class in galaxy.objectstore) ObjectStorePopulator (class in galaxy.objectstore) ObjectUploadTarget (class in galaxy.tool_util.cwl.util) Obo (class in galaxy.datatypes.text) odict (class in galaxy.util.odict) offset (galaxy.schema.PaginationQueryParams attribute) (galaxy.schema.schema.InvocationIndexQueryPayload attribute) (galaxy.schema.schema.JobIndexQueryPayload attribute) (galaxy.schema.schema.LibraryFolderContentsIndexQueryPayload attribute) (galaxy.schema.schema.PageIndexQueryPayload attribute) (galaxy.schema.schema.WorkflowIndexQueryPayload attribute) OIDC (class in galaxy.webapps.galaxy.controllers.authnz) OIDCAuthnzBase (class in galaxy.authnz.custos_authnz) OIDCAuthnzBaseCiLogon (class in galaxy.authnz.custos_authnz) OIDCAuthnzBaseCustos (class in galaxy.authnz.custos_authnz) OIDCAuthnzBaseKeycloak (class in galaxy.authnz.custos_authnz) OK (galaxy.model.Dataset.conversion_messages attribute) (galaxy.model.DatasetInstance.conversion_messages attribute) (galaxy.model.ImplicitCollectionJobs.populated_states attribute) ok (galaxy.model.JobStateSummary attribute) OK (galaxy.model.Task.states attribute) (galaxy.model.tool_shed_install.ToolDependency.states attribute) (galaxy.model.tool_shed_install.ToolShedRepository.states attribute) (galaxy.schema.schema.DatasetCollectionPopulatedState attribute) (galaxy.schema.schema.DatasetState attribute) (galaxy.schema.schema.DatasetValidatedState attribute) ok (galaxy.schema.schema.HDCJobStateSummary attribute) OK (galaxy.schema.schema.JobState attribute) (galaxy.tool_util.output_checker.DETECTED_JOB_STATE attribute) ok_to_display() (galaxy.model.security.GalaxyRBACAgent method) ok_to_edit_metadata() (galaxy.model.DatasetInstance method) old_id (galaxy.tools.ApplyRulesTool attribute) (galaxy.tools.AsyncDataSourceTool attribute) (galaxy.tools.BuildListCollectionTool attribute) (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.DataDestinationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.DuplicateFileToCollectionTool attribute) (galaxy.tools.ExportHistoryTool attribute) (galaxy.tools.ExpressionTool attribute) (galaxy.tools.ExtractDatasetCollectionTool attribute) (galaxy.tools.FilterDatasetsTool attribute) (galaxy.tools.FilterEmptyDatasetsTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) (galaxy.tools.FilterFromFileTool attribute) (galaxy.tools.FlattenTool attribute) (galaxy.tools.HarmonizeTool attribute) (galaxy.tools.ImportHistoryTool attribute) (galaxy.tools.InteractiveTool attribute) (galaxy.tools.KeepSuccessDatasetsTool attribute) (galaxy.tools.MergeCollectionTool attribute) (galaxy.tools.OutputParameterJSONTool attribute) (galaxy.tools.RelabelFromFileTool attribute) (galaxy.tools.SortTool attribute) (galaxy.tools.TagFromFileTool attribute) (galaxy.tools.UnzipCollectionTool attribute) (galaxy.tools.ZipCollectionTool attribute) Oligos (class in galaxy.datatypes.mothur) OMETiff (class in galaxy.datatypes.images) on_any_event() (galaxy.tool_util.toolbox.watcher.ToolFileEventHandler method) on_created() (galaxy.util.watcher.EventHandler method) on_deleted() (galaxy.util.watcher.EventHandler method) on_modified() (galaxy.util.watcher.EventHandler method) on_moved() (galaxy.util.watcher.EventHandler method) on_reload() (in module galaxy.web_stack.gunicorn_config) on_response() (galaxy.queue_worker.ControlTask method) on_starting() (in module galaxy.web_stack.gunicorn_config) on_text_for_names() (in module galaxy.tools.actions) on_the_fly_config() (in module galaxy.authnz.psa_authnz) one() (galaxy.managers.base.ModelManager method) one_hda_model_store_dict() (in module galaxy.model.unittest_utils.store_fixtures) one_ld_library_deferred_model_store_dict() (in module galaxy.model.unittest_utils.store_fixtures) one_ld_library_model_store_dict() (in module galaxy.model.unittest_utils.store_fixtures) OnedataFilesSource (class in galaxy.files.sources.onedata) only_invocation (galaxy.model.store.WorkflowInvocationOnlyExportStore property) ontology (galaxy.tool_util.toolbox.views.interface.ToolPanelViewModelType attribute) OntologyData (class in galaxy.tool_util.ontologies.ontology_data) open() (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method) (galaxy.util.resources.Traversable method) open_collection_edit_view() (galaxy_test.selenium.test_collection_edit.TestCollectionEdit method) open_data_file() (galaxy.visualization.data_providers.genome.BamDataProvider method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) (galaxy.visualization.data_providers.genome.IntervalIndexDataProvider method) (galaxy.visualization.data_providers.genome.RawVcfDataProvider method) (galaxy.visualization.data_providers.genome.TabixDataProvider method) open_folder() (tool_shed.webapp.controllers.repository.RepositoryController method) open_history_editor() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) open_history_multi_view() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) open_in_workflow_editor() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) open_logs() (galaxy.util.heartbeat.Heartbeat method) open_or_build_maf_index() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) open_recipe_file() (in module galaxy.tool_util.deps.mulled.get_tests) open_repository_files_folder() (in module tool_shed.util.shed_util_common) open_tags() (galaxy_test.selenium.test_history_panel.TestHistoryPanel method) open_tar() (galaxy.util.compression_utils.CompressedFile method) open_zip() (galaxy.util.compression_utils.CompressedFile method) OpenObject (class in galaxy.visualization.plugins.utils) OpenPBS (class in galaxy.jobs.runners.util.cli.job.pbs) operation (galaxy.model.Quota attribute) (galaxy.schema.schema.HistoryContentBulkOperationPayload attribute) operations (galaxy.tool_util.toolbox.views.edam.EdamPanelMode attribute) (galaxy.web.legacy_framework.grids.Grid attribute) (tool_shed.grids.admin_grids.AdminRepositoryGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.DockerImageGrid attribute) (tool_shed.grids.repository_grids.EmailAlertsRepositoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) operator_function (galaxy.model.InnerCollectionFilter attribute) option (galaxy.config.config_manage.OptionValue attribute) option_type (in module galaxy.tool_util.parser.output_actions) optional (galaxy.workflow.modules.InputModuleState attribute) (galaxy.workflow.modules.InputParameterModule attribute) (galaxy.workflow.refactor.schema.AddInputAction attribute) optional() (in module galaxy.dependencies) optional_headers (galaxy.datatypes.speech.BPF attribute)

optional_param() (in module galaxy.workflow.modules) options (galaxy.auth.util.Authenticator attribute) (galaxy.util.jstree.Path attribute) (galaxy.webapps.galaxy.api.RestVerb attribute) options() (galaxy.webapps.galaxy.api.authenticate.AuthenticationController method) (galaxy.webapps.galaxy.api.FrameworkRouter method) OptionValue (class in galaxy.config.config_manage) optionxform() (galaxy.util.properties.NicerConfigParser method) order (galaxy.schema.FilterQueryParams attribute) order_by (galaxy.schema.schema.JobIndexQueryPayload attribute) (galaxy.schema.schema.LibraryFolderContentsIndexQueryPayload attribute) order_components_for_installation() (galaxy.tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) order_id (galaxy.model.LibraryDataset attribute) (galaxy.model.LibraryFolder attribute) order_index (galaxy.model.ImplicitCollectionJobsJobAssociation attribute) (galaxy.model.StoredWorkflowMenuEntry attribute) (galaxy.model.WorkflowComment attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowStep attribute) (galaxy.workflow.refactor.schema.RefactorActionExecutionMessage attribute) (galaxy.workflow.refactor.schema.StepReferenceByOrderIndex attribute) order_workflow_steps() (in module galaxy.workflow.steps) order_workflow_steps_with_levels() (in module galaxy.workflow.steps) ordered_dump() (in module galaxy.util.yaml_util) ordered_load() (in module galaxy.util.yaml_util) OrderedLoader (class in galaxy.util.yaml_util) OrderedSet (class in galaxy.util.oset) Organization (class in galaxy.schema.schema) orient_block_by_region() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) original_dataset (galaxy.visualization.data_providers.basic.BaseDataProvider attribute) (galaxy.visualization.data_providers.basic.ColumnDataProvider attribute) (galaxy.visualization.data_providers.genome.BamDataProvider attribute) (galaxy.visualization.data_providers.genome.BBIDataProvider attribute) (galaxy.visualization.data_providers.genome.BedDataProvider attribute) (galaxy.visualization.data_providers.genome.BedTabixDataProvider attribute) (galaxy.visualization.data_providers.genome.BigBedDataProvider attribute) (galaxy.visualization.data_providers.genome.BigWigDataProvider attribute) (galaxy.visualization.data_providers.genome.ChromatinInteractionsDataProvider attribute) (galaxy.visualization.data_providers.genome.ChromatinInteractionsTabixDataProvider attribute) (galaxy.visualization.data_providers.genome.ENCODEPeakDataProvider attribute) (galaxy.visualization.data_providers.genome.ENCODEPeakTabixDataProvider attribute) (galaxy.visualization.data_providers.genome.FeatureLocationIndexDataProvider attribute) (galaxy.visualization.data_providers.genome.FilterableMixin attribute) (galaxy.visualization.data_providers.genome.GtfTabixDataProvider attribute) (galaxy.visualization.data_providers.genome.IntervalDataProvider attribute) (galaxy.visualization.data_providers.genome.IntervalIndexDataProvider attribute) (galaxy.visualization.data_providers.genome.IntervalTabixDataProvider attribute) (galaxy.visualization.data_providers.genome.RawBedDataProvider attribute) (galaxy.visualization.data_providers.genome.RawGFFDataProvider attribute) (galaxy.visualization.data_providers.genome.RawVcfDataProvider attribute) (galaxy.visualization.data_providers.genome.SamDataProvider attribute) (galaxy.visualization.data_providers.genome.VcfTabixDataProvider attribute) (galaxy.visualization.data_providers.phyloviz.PhylovizDataProvider attribute) orm_filter_parsers (galaxy.managers.base.ModelFilterParser attribute) (galaxy.managers.datasets.DatasetAssociationFilterParser attribute) (galaxy.managers.deletable.DeletableFiltersMixin attribute) (galaxy.managers.deletable.PurgableFiltersMixin attribute) (galaxy.managers.genomes.GenomeFilterMixin attribute) (galaxy.managers.hdas.HDAFilterParser attribute) (galaxy.managers.histories.HistoryFilters attribute) (galaxy.managers.history_contents.HistoryContentsFilters attribute) (galaxy.managers.sharable.SharableModelFilters attribute) (galaxy.managers.tools.ToolFilterMixin attribute) (galaxy.managers.users.AdminUserFilterParser attribute) OSW (class in galaxy.datatypes.binary) Otu (class in galaxy.datatypes.mothur) out_collections (galaxy.model.IoDicts attribute) out_data (galaxy.model.IoDicts attribute) out_file (galaxy.model.store.ROCrateArchiveModelExportStore attribute) (galaxy.model.store.TarModelExportStore attribute) OUT_OF_MEMORY_ERROR (galaxy.tool_util.output_checker.DETECTED_JOB_STATE attribute) outdir (galaxy.tool_util.cwl.cwltool_deps.RuntimeContext attribute) Output (class in galaxy.schema.schema) output (galaxy.workflow.refactor.schema.ConnectAction attribute) (galaxy.workflow.refactor.schema.DisconnectAction attribute) (galaxy.workflow.refactor.schema.UpdateOutputLabelAction attribute) output() (galaxy.managers.pages.PageContentProcessor method) output_associations (galaxy.model.WorkflowInvocation property) output_collection_def() (galaxy.job_execution.output_collect.JobContext method) (galaxy.job_execution.output_collect.SessionlessJobContext method) output_collections (galaxy.tool_util.parser.interface.ToolSourceTest attribute) (galaxy.tool_util.verify.interactor.RunToolResponse attribute) (galaxy.tool_util.verify.interactor.ToolTestDescriptionDict attribute) (galaxy.tool_util.verify.interactor.ValidToolTestDict attribute) output_connections (galaxy.model.WorkflowStep attribute) output_dataset_collection_instances (galaxy.model.Job attribute) output_dataset_collections (galaxy.model.Job attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowInvocationStep attribute) output_datasets (galaxy.model.Job attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowInvocationStep attribute) output_datasets_ids (galaxy.model.InteractiveToolEntryPoint property) output_def() (galaxy.job_execution.output_collect.JobContext method) (galaxy.job_execution.output_collect.SessionlessJobContext method) output_discover_patterns (galaxy.tool_util.parser.output_objects.ToolOutput property) (galaxy.tool_util.parser.output_objects.ToolOutputBase property) (galaxy.tool_util.parser.output_objects.ToolOutputCollection property) (galaxy.tool_util.parser.output_objects.ToolOutputCollectionStructure property) (galaxy.tools.Tool property) output_extra_files_rewrite() (galaxy.job_execution.compute_environment.ComputeEnvironment method) (galaxy.job_execution.compute_environment.SharedComputeEnvironment method) output_hdas_and_paths (galaxy.job_execution.setup.JobIO property) output_hid() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) output_label (galaxy.workflow.refactor.schema.RefactorActionExecutionMessage attribute) (galaxy.workflow.refactor.schema.UpdateOutputLabelAction attribute) output_library_datasets (galaxy.model.Job attribute) output_name (galaxy.job_execution.setup.JobOutput attribute) (galaxy.model.EffectiveOutput attribute) (galaxy.model.PostJobAction attribute) (galaxy.model.WorkflowInvocationMessage attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowOutput attribute) (galaxy.model.WorkflowStepConnection attribute) (galaxy.schema.schema.InputConnection attribute) (galaxy.schema.schema.PostJobAction attribute) (galaxy.schema.schema.WorkflowOutput attribute) (galaxy.workflow.refactor.schema.OutputReferenceByLabel attribute) (galaxy.workflow.refactor.schema.OutputReferenceByOrderIndex attribute) (galaxy.workflow.refactor.schema.RefactorActionExecutionMessage attribute) output_names() (galaxy.job_execution.compute_environment.ComputeEnvironment method) (galaxy.job_execution.compute_environment.SharedComputeEnvironment method) output_path_rewrite() (galaxy.job_execution.compute_environment.ComputeEnvironment method) (galaxy.job_execution.compute_environment.SharedComputeEnvironment method) output_paths (galaxy.job_execution.setup.JobIO property) output_paths() (galaxy.job_execution.compute_environment.SharedComputeEnvironment method) output_properties() (in module galaxy.tool_util.cwl.util) output_step (galaxy.model.WorkflowStepConnection attribute) output_step_id (galaxy.model.WorkflowStepConnection attribute) output_to_cwl_json() (in module galaxy.tool_util.cwl.util) output_value (galaxy.model.WorkflowInvocationStep attribute) output_values (galaxy.model.WorkflowInvocation attribute) OutputCollections (class in galaxy.tools.actions) OutputParameterJSONTool (class in galaxy.tools) OutputPropertiesType (class in galaxy.tool_util.cwl.util) OutputReferenceByLabel (class in galaxy.workflow.refactor.schema) OutputReferenceByOrderIndex (class in galaxy.workflow.refactor.schema) outputs (galaxy.schema.schema.JobDetails attribute) (galaxy.schema.schema.WorkflowStepToExportBase attribute) (galaxy.tool_util.parser.interface.ToolSourceTest attribute) (galaxy.tool_util.verify.interactor.RunToolResponse attribute) (galaxy.tool_util.verify.interactor.ToolTestDescriptionDict attribute) (galaxy.tool_util.verify.interactor.ValidToolTestDict attribute) OutputsDict (class in galaxy.tool_util.verify.interactor) OutputsToWorkingDirectoryPathRewriter (class in galaxy.job_execution.datasets) override_algorithmic_error (galaxy.model.store.BcoExportOptions attribute) override_empirical_error (galaxy.model.store.BcoExportOptions attribute) override_environment_variables (galaxy.model.store.BcoExportOptions attribute) override_object_store_id() (galaxy.model.store.discover.ModelPersistenceContext method) override_xref (galaxy.model.store.BcoExportOptions attribute) overwrite_metadata() (galaxy.managers.datasets.DatasetAssociationManager method) Owl (class in galaxy.datatypes.xml) OwnableManagerMixin (class in galaxy.managers.secured) owner (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.schema.schema.InstalledToolShedRepository attribute) (galaxy.schema.schema.StoredWorkflowSummary attribute) (galaxy.schema.schema.ToolShedRepository attribute) (galaxy.schema.schema.ToolShedRepositorySummary attribute) (tool_shed.managers.repositories.UpdatesRequest attribute) owner_tags (galaxy.model.StoredWorkflow attribute) OwnerAnnotationColumn (class in galaxy.web.legacy_framework.grids) OwnerColumn (class in galaxy.web.legacy_framework.grids) OxliBinary (class in galaxy.datatypes.binary) OxliCountGraph (class in galaxy.datatypes.binary) OxliGraphLabels (class in galaxy.datatypes.binary) OxliNodeGraph (class in galaxy.datatypes.binary) OxliStopTags (class in galaxy.datatypes.binary) OxliSubset (class in galaxy.datatypes.binary) OxliTagSet (class in galaxy.datatypes.binary)

P

package_gff_feature() (in module galaxy.visualization.data_providers.genome) package_specifier (galaxy.tool_util.deps.conda_util.CondaTarget property) package_tool() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) packages (galaxy.tool_util.deps.requirements.ToolRequirements property) Paf (class in galaxy.datatypes.text) Page (class in galaxy.model) (galaxy.managers.tags.TaggableItemClass attribute) page (galaxy.model.PageAnnotationAssociation attribute) (galaxy.model.PageRatingAssociation attribute) (galaxy.model.PageRevision attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.PageUserShareAssociation attribute) (galaxy.schema.PdfDocumentType attribute) (galaxy.schema.schema.LibraryAvailablePermissions attribute) page_exists() (in module galaxy.managers.pages) page_id (galaxy.model.PageAnnotationAssociation attribute) (galaxy.model.PageRatingAssociation attribute) (galaxy.model.PageRevision attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.PageUserShareAssociation attribute) page_limit (galaxy.schema.schema.LibraryAvailablePermissions attribute) page_manager (galaxy.webapps.galaxy.controllers.page.PageController attribute) page_open_and_screenshot() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) PageAnnotationAssociation (class in galaxy.model) PageContentFormat (class in galaxy.schema.schema) PageContentProcessor (class in galaxy.managers.pages) PageController (class in galaxy.webapps.galaxy.controllers.page) PageDeserializer (class in galaxy.managers.pages) PageDetails (class in galaxy.schema.schema) PageIndexQueryPayload (class in galaxy.schema.schema) PageManager (class in galaxy.managers.pages) PageRatingAssociation (class in galaxy.model) PageRevision (class in galaxy.model) PageRevisionsController (class in galaxy.webapps.galaxy.api.page_revisions) pages_index_table_elements() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) PageSerializer (class in galaxy.managers.pages) PageSource (class in galaxy.tool_util.parser.interface) PagesService (class in galaxy.webapps.galaxy.services.pages) PagesSource (class in galaxy.tool_util.parser.interface) PageSummary (class in galaxy.schema.schema) PageSummaryBase (class in galaxy.schema.schema) PageSummaryList (class in galaxy.schema.schema) PageTagAssociation (class in galaxy.model) PageUserShareAssociation (class in galaxy.model) PaginationQueryParams (class in galaxy.schema) pair_identifiers() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method) PairedDatasetCollectionType (class in galaxy.model.dataset_collections.types.paired) PairwiseDistanceMatrix (class in galaxy.datatypes.mothur) PAM (class in galaxy.auth.providers.pam_auth) panel_entry_per_tool() (in module galaxy.tool_shed.util.tool_util) panel_has_tool() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) panel_item_types (class in galaxy.tool_util.toolbox) (class in galaxy.tool_util.toolbox.panel) panel_items() (galaxy.tool_util.toolbox.panel.HasPanelItems method) (galaxy.tool_util.toolbox.panel.ToolPanelElements method) (galaxy.tool_util.toolbox.panel.ToolSection method) (galaxy.tool_util.toolbox.ToolSection method) panel_items_iter() (galaxy.tool_util.toolbox.panel.HasPanelItems method) panel_view() (galaxy.webapps.galaxy.api.tools.ToolsController method) panel_view_dicts() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) panel_views() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) (galaxy.webapps.galaxy.api.tools.ToolsController method) ParallelismInfo (class in galaxy.tool_util.parser.xml) Param (class in galaxy.datatypes.text) param_combinations (galaxy.tools.parameters.meta.WorkflowParameterExpansion attribute) param_dict (galaxy.tools.evaluation.PartialToolEvaluator attribute) (galaxy.tools.evaluation.RemoteToolEvaluator attribute) param_filename (galaxy.model.Job attribute) (galaxy.model.Task attribute) param_keys (galaxy.tools.parameters.meta.WorkflowParameterExpansion attribute) param_names() (galaxy.tools.test.ParamContext method) (galaxy.tools.test.RootParamContext method) ParamContext (class in galaxy.tools.test) parameter_type (galaxy.workflow.modules.InputParameterModule attribute) parameter_value (galaxy.model.WorkflowRequestInputStepParameter attribute) parameters (galaxy.model.Job attribute) ParameterValueError ParamikoShell (class in galaxy.jobs.runners.util.cli.shell.rsh) ParamKey (class in galaxy.tools.parameters.meta) ParamMessage (class in galaxy.web_stack.message) ParamModifierParser (class in galaxy.visualization.plugins.config_parser) ParamParser (class in galaxy.visualization.plugins.config_parser) Params (class in galaxy.util) params (galaxy.model.Job attribute) (galaxy.model.UserAction attribute) (galaxy.schema.schema.HistoryContentBulkOperationPayload attribute) (galaxy.schema.schema.JobDetails attribute) (galaxy.tools.parameters.wrapped.WrappedParameters property) (galaxy.web_stack.message.ParamMessage property) params_from_strings() (galaxy.tools.Tool method) params_to_strings() (galaxy.tools.Tool method) params_with_missing_data_table_entry (galaxy.tools.Tool property) params_with_missing_index_file (galaxy.tools.Tool property) ParamsWithSpecs (class in galaxy.util) ParamValueFilter (class in galaxy.tools.parameters.dynamic_options) ParamValueToolOutputActionOptionFilter (class in galaxy.tool_util.parser.output_actions) ParamXml (class in galaxy.datatypes.proteomics) parent (galaxy.datatypes.metadata.MetadataCollection property) (galaxy.model.LibraryFolder attribute) (galaxy.model.metadata.MetadataCollection property) (galaxy.model.Tag attribute) (galaxy.model.Vault attribute) (tool_shed.webapp.model.Tag attribute) parent_comment (galaxy.model.WorkflowComment attribute) (galaxy.model.WorkflowStep attribute) parent_comment_id (galaxy.model.WorkflowComment attribute) (galaxy.model.WorkflowStep attribute) parent_hda (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) parent_id (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryFolder attribute) (galaxy.model.Tag attribute) (galaxy.model.tool_shed_install.ToolVersionAssociation attribute) (galaxy.schema.schema.HDAExtended attribute) (galaxy.schema.schema.LibraryFolderDetails attribute) (tool_shed.webapp.model.Tag attribute) parent_key (galaxy.model.Vault attribute) parent_ldda (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) parent_library (galaxy.model.LibraryFolder property) parent_library_id (galaxy.schema.schema.LibraryFolderDetails attribute) (galaxy.schema.schema.LibraryFolderMetadata attribute) parent_path (galaxy.tool_util.deps.conda_util.CondaContext property) (galaxy.tool_util.deps.installable.InstallableContext property) parent_tool_association (galaxy.model.tool_shed_install.ToolVersion attribute) parent_workflow_id (galaxy.model.Workflow attribute) parent_workflow_invocation (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute) parent_workflow_steps (galaxy.model.Workflow attribute) Parquet (class in galaxy.datatypes.binary) parse() (galaxy.tools.SetParamAction static method) (galaxy.tools.Tool method) (galaxy.tools.TracksterConfig static method) (galaxy.visualization.plugins.config_parser.DataSourceParser method) (galaxy.visualization.plugins.config_parser.ParamModifierParser method) (galaxy.visualization.plugins.config_parser.ParamParser method) parse_action_module() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_auth_results() (in module galaxy.auth.util) parse_badges_from_config_xml() (galaxy.objectstore.BaseObjectStore class method) parse_bool() (in module galaxy.managers.base) parse_bytesize() (in module galaxy.util.bytesize) parse_cast_attribute() (in module galaxy.tool_util.parser.output_actions) parse_change_format() (in module galaxy.tool_util.parser.xml) parse_checksum_hash() (in module galaxy.util.hash_util) parse_citation() (galaxy.managers.citations.CitationsManager method) (in module galaxy.managers.citations) parse_cols_arg() (in module galaxy.tools.util.galaxyops) parse_column_at_index() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) parse_column_definitions() (galaxy.tools.parameters.dynamic_options.DynamicOptions method) parse_column_spec() (galaxy.tools.data.RefgenieToolDataTable method) (galaxy.tools.data.TabularToolDataTable method) parse_columns_from_line() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) parse_command() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) (galaxy.tools.ExpressionTool method) (galaxy.tools.Tool method) parse_compare_type() (in module galaxy.tool_util.parser.output_actions) parse_config() (galaxy.visualization.plugins.resource_parser.ResourceParser method) parse_config_xml() (in module galaxy.objectstore.azure_blob) (in module galaxy.objectstore.irods) (in module galaxy.objectstore.pithos) (in module galaxy.objectstore.s3) parse_configs() (galaxy.dependencies.ConditionalDependencies method) parse_conversion_tuples() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) parse_creator() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_date() (galaxy.managers.base.ModelFilterParser method) parse_default() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) (galaxy.tool_util.parser.yaml.YamlInputSource method) parse_description() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_destination_params() (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.chronos.ChronosJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.pbs.PBSJobRunner method) parse_display() (galaxy.tool_util.parser.interface.PageSource method) (galaxy.tool_util.parser.xml.XmlPageSource method) parse_display_interface() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_docker_env_pass_through() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) parse_dynamic_options() (in module galaxy.tools.parameters.basic) parse_dynamic_options_elem() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) parse_edam_operations() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_edam_topics() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_entry_point() (galaxy.visualization.plugins.config_parser.VisualizationsConfigParser method) parse_environment_variables() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) (galaxy.tools.ExpressionTool method) (galaxy.tools.Tool method) parse_error_level() (galaxy.tool_util.parser.xml.StdioParser method) parse_expression() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_external_id() (in module galaxy.jobs.runners.util.external) parse_failure_reason() (galaxy.jobs.runners.util.cli.job.BaseJobExec method) (galaxy.jobs.runners.util.cli.job.lsf.LSF method) parse_file() (galaxy.visualization.plugins.config_parser.VisualizationsConfigParser method) parse_file_fields() (galaxy.tools.data.RefgenieToolDataTable method) (galaxy.tools.data.TabularToolDataTable method) (galaxy.tools.parameters.dynamic_options.DynamicOptions method) parse_filter() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) (galaxy.managers.base.ModelFilterParser method) parse_filters() (galaxy.managers.base.ModelFilterParser method) (in module galaxy.util.search) parse_filters_structured() (in module galaxy.util.search) parse_from_url_options() (in module galaxy.tools.parameters.dynamic_options) parse_gff3_attributes() (in module galaxy.datatypes.util.gff_util) parse_gff_attributes() (in module galaxy.datatypes.util.gff_util) parse_help() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_hidden() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_home_target() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_id() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_id_list() (galaxy.managers.base.ModelFilterParser method) parse_input_elem() (galaxy.tools.Tool method) parse_input_pages() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_input_sources() (galaxy.tool_util.parser.interface.PageSource method) (galaxy.tool_util.parser.xml.XmlPageSource method) (galaxy.tool_util.parser.yaml.YamlPageSource method) parse_input_type() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) (galaxy.tool_util.parser.yaml.YamlInputSource method) parse_inputs() (galaxy.tools.DataSourceTool method) (galaxy.tools.Tool method) parse_int() (in module galaxy.util) parse_int_list() (galaxy.managers.base.ModelFilterParser method) parse_interactivetool() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_interpreter() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_label() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) parse_license() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_model_class() (galaxy.visualization.plugins.config_parser.DataSourceParser method) parse_name() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) (galaxy.tools.parameters.basic.ToolParameter static method) parse_nested_inputs_source() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) (galaxy.tool_util.parser.yaml.YamlInputSource method) parse_non_hex_float() (in module galaxy.util) parse_optional() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) parse_order_by() (galaxy.managers.base.SortableManager method) (galaxy.managers.histories.HistoryManager method) (galaxy.managers.history_contents.HistoryContentsManager method) parse_outputs() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) (galaxy.tools.ExpressionTool method) (galaxy.tools.Tool method) parse_package_elem() (in module galaxy.tool_shed.util.tool_dependency_util) parse_parallelism() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_param_elem() (galaxy.tools.Tool method) parse_param_type() (galaxy.visualization.plugins.config_parser.ParamParser method) parse_parameter() (galaxy.visualization.plugins.resource_parser.ResourceParser method) parse_parameter_default() (galaxy.visualization.plugins.resource_parser.ResourceParser method) parse_parameter_dictionary() (galaxy.visualization.plugins.resource_parser.ResourceParser method) parse_parameter_modifiers() (galaxy.visualization.plugins.resource_parser.ResourceParser method) parse_port_text() (in module galaxy.tool_util.deps.docker_util) parse_private_from_config_xml() (galaxy.objectstore.BaseObjectStore class method) parse_profile() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_provided_metadata_file() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_provided_metadata_style() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_pvc_param_line() (in module galaxy.jobs.runners.util.pykube_util) parse_python_template_version() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_query_filters() (galaxy.managers.base.ModelFilterParser method) parse_query_filters_with_relations() (galaxy.managers.history_contents.HistoryContentsFilters method) parse_redirect_url() (galaxy.tools.Tool method) parse_redirect_url_params_elem() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_refresh() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_repository_dependency_tuple() (in module galaxy.util.tool_shed.common_util) (in module tool_shed.util.common_util) parse_request_param_translation_elem() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_require_login() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_required_files() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_requirements_and_containers() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_requirements_from_lists() (in module galaxy.tool_util.deps.requirements) parse_requirements_from_xml() (in module galaxy.tool_util.deps.requirements) parse_resource_parameters() (in module galaxy.util) parse_row() (galaxy.datatypes.util.gff_util.GFFIntervalToBEDReaderWrapper method) (galaxy.datatypes.util.gff_util.GFFReaderWrapper method) parse_sanitize() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_sanitizer_elem() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) parse_search_kwds() (in module galaxy.workflow.trs_proxy) parse_serialization_params() (in module galaxy.webapps.galaxy.api.common) parse_single_status() (galaxy.jobs.runners.util.cli.job.BaseJobExec method) (galaxy.jobs.runners.util.cli.job.lsf.LSF method) (galaxy.jobs.runners.util.cli.job.slurm.Slurm method) (galaxy.jobs.runners.util.cli.job.torque.Torque method) parse_species_option() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) parse_static_options() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) (galaxy.tool_util.parser.yaml.YamlInputSource method) parse_status() (galaxy.jobs.runners.util.cli.job.BaseJobExec method) (galaxy.jobs.runners.util.cli.job.lsf.LSF method) (galaxy.jobs.runners.util.cli.job.pbs.OpenPBS method) (galaxy.jobs.runners.util.cli.job.slurm.Slurm method) (galaxy.jobs.runners.util.cli.job.slurm_torque.SlurmTorque method) (galaxy.jobs.runners.util.cli.job.torque.Torque method) parse_stdio() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) (galaxy.tools.Tool method) parse_stdio_exit_codes() (galaxy.tool_util.parser.xml.StdioParser method) parse_stdio_regexes() (galaxy.tool_util.parser.xml.StdioParser method) parse_strict_shell() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_tags() (galaxy.model.tags.TagHandler method) parse_tags_list() (galaxy.model.tags.TagHandler method) parse_test_input_source() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) (galaxy.tool_util.parser.yaml.YamlInputSource method) parse_tests() (galaxy.tools.Tool method) (galaxy.visualization.plugins.config_parser.DataSourceParser method) (in module galaxy.tools.test) parse_tests_to_dict() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_tmp_directory_vars() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) parse_tmp_target() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_to_params() (galaxy.visualization.plugins.config_parser.DataSourceParser method) parse_tool_module() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_tool_provided_metadata() (in module galaxy.tool_util.provided_metadata) parse_tool_type() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_type_id_list() (galaxy.managers.history_contents.HistoryContentsFilters method) parse_validator_elems() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) parse_value() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) parse_version() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_version_command() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_version_command_interpreter() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_visualization() (galaxy.visualization.plugins.config_parser.VisualizationsConfigParser method) parse_volume_str() (galaxy.tool_util.deps.container_classes.Volume static method) parse_when_input_sources() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) (galaxy.tool_util.parser.yaml.YamlInputSource method) parse_xml() (galaxy.objectstore.azure_blob.AzureBlobObjectStore class method) (galaxy.objectstore.BaseObjectStore class method) (galaxy.objectstore.cloud.Cloud class method) (galaxy.objectstore.DiskObjectStore class method) (galaxy.objectstore.DistributedObjectStore class method) (galaxy.objectstore.HierarchicalObjectStore class method) (galaxy.objectstore.irods.IRODSObjectStore class method) (galaxy.objectstore.pithos.PithosObjectStore class method) (galaxy.objectstore.s3.S3ObjectStore class method) (in module galaxy.util) (in module galaxy.util.tool_shed.xml_util) (in module tool_shed.util.xml_util) parse_xml_string() (in module galaxy.util) parse_xml_string_to_etree() (in module galaxy.util) parse_xrefs() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_yaml() (in module galaxy.jobs.dynamic_tool_destination) parsed_filter (galaxy.managers.base.ModelFilterParser attribute) (in module galaxy.managers.base) parseData() (galaxy.visualization.data_providers.phyloviz.newickparser.Newick_Parser method) ParsedBiotoolsEntry (class in galaxy.tool_util.biotools) (class in galaxy.tool_util.biotools.interface) ParsedFilter (class in galaxy.managers.base) parseFile() (galaxy.visualization.data_providers.phyloviz.baseparser.Base_Parser method) (galaxy.visualization.data_providers.phyloviz.newickparser.Newick_Parser method) (galaxy.visualization.data_providers.phyloviz.nexusparser.Nexus_Parser method) (galaxy.visualization.data_providers.phyloviz.phyloxmlparser.Phyloxml_Parser method) parseNexus() (galaxy.visualization.data_providers.phyloviz.nexusparser.Nexus_Parser method) parseNode() (galaxy.visualization.data_providers.phyloviz.newickparser.Newick_Parser method) (galaxy.visualization.data_providers.phyloviz.phyloxmlparser.Phyloxml_Parser method) ParsingException partial (galaxy.authnz.psa_authnz.Storage attribute) partial_model() (in module galaxy.schema) PartialToolEvaluator (class in galaxy.tools.evaluation) PassedTest (class in tool_shed.utility_containers) passes_filters() (galaxy.managers.history_contents.HistoryContentsManager static method) password (galaxy.model.User attribute) (galaxy.schema.schema.UserCreationPayload attribute) (tool_shed.webapp.model.User attribute) password_expiration_period (galaxy.config.GalaxyAppConfiguration attribute) PasswordField (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) PasswordResetToken (class in galaxy.model) (class in tool_shed.webapp.model) (galaxy.model.base.SharedModelMapping attribute) paste_content (galaxy.schema.fetch_data.PastedDataElement attribute) pasted (galaxy.schema.fetch_data.Src attribute) PastedDataElement (class in galaxy.schema.fetch_data) patch (galaxy.webapps.galaxy.api.RestVerb attribute) patch() (galaxy.webapps.galaxy.api.FrameworkRouter method) (galaxy_test.base.api.ApiTestInteractor method) Path (class in galaxy.util.jstree) path (galaxy.files.FileSourcePath attribute) (galaxy.files.sources.RemoteDirectory attribute) (galaxy.files.sources.RemoteEntry attribute) (galaxy.files.sources.RemoteFile attribute) (galaxy.model.ExtendedMetadataIndex attribute) (galaxy.model.store.discover.DiscoveredDeferredFile property) (galaxy.model.store.discover.DiscoveredFile attribute) (galaxy.model.store.discover.DiscoveredFileError attribute) (galaxy.schema.fetch_data.ItemsFromModel attribute) (galaxy.schema.fetch_data.ItemsFromSrc attribute) (galaxy.schema.fetch_data.PathDataElement attribute) (galaxy.schema.fetch_data.Src attribute) (galaxy.schema.remote_files.RemoteEntry attribute) (galaxy.tool_util.cwl.util.OutputPropertiesType attribute) (galaxy.util.jstree.Path attribute) (galaxy.visualization.plugins.plugin.ChartVisualizationPlugin attribute) (galaxy.visualization.plugins.plugin.ScriptVisualizationPlugin attribute) (galaxy.visualization.plugins.plugin.ServesTemplatesPluginMixin attribute) (galaxy.visualization.plugins.plugin.StaticFileVisualizationPlugin attribute) (galaxy.visualization.plugins.plugin.VisualizationPlugin attribute) path() (galaxy.tool_util.verify.test_data.FileDataResolver method) path_or_uri_to_uri() (in module galaxy.tool_util.cwl.util) PathDataElement (class in galaxy.schema.fetch_data) paths_and_modtimes() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) paths_as_file() (galaxy.tools.wrappers.HasDatasets method) paths_to_check_against_root (galaxy.config.BaseAppConfiguration attribute) (galaxy.config.GalaxyAppConfiguration attribute) paths_to_resolve (galaxy.config.schema.AppSchema property) paused (galaxy.model.JobStateSummary attribute) PAUSED (galaxy.schema.schema.DatasetState attribute) paused (galaxy.schema.schema.HDCJobStateSummary attribute) PAUSED (galaxy.schema.schema.JobState attribute) paused_jobs (galaxy.model.History property) PauseModule (class in galaxy.workflow.modules) PauseStep (class in galaxy.schema.schema) payload (galaxy.schema.schema.ExportObjectRequestMetadata attribute) payload_to_source_uri() (in module galaxy.model.store) Pbed (class in galaxy.datatypes.genetics) pbkdf2_bin() (in module galaxy.security.passwords) Pbm (class in galaxy.datatypes.images) PBSJobRunner (class in galaxy.jobs.runners.pbs) Pcd (class in galaxy.datatypes.images) Pcx (class in galaxy.datatypes.images) PDB (class in galaxy.datatypes.molecules) PDBQT (class in galaxy.datatypes.molecules) Pdf (class in galaxy.datatypes.images) PdfDocumentType (class in galaxy.schema) peek (galaxy.model.DatasetInstance property) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) peek_size (galaxy.datatypes.tabular.BaseCSV attribute) PEFF (class in galaxy.datatypes.proteomics) PENDING (galaxy.model.Dataset.conversion_messages attribute) (galaxy.model.DatasetInstance.conversion_messages attribute) PepList (class in galaxy.datatypes.proteomics) PepXml (class in galaxy.datatypes.proteomics) PepXmlReport (class in galaxy.datatypes.proteomics) per_host_options (galaxy.config.schema.AppSchema property) per_month_all() (galaxy.webapps.reports.controllers.jobs.Jobs method) (galaxy.webapps.reports.controllers.workflows.Workflows method) per_month_in_error() (galaxy.webapps.reports.controllers.jobs.Jobs method) per_tool() (galaxy.webapps.reports.controllers.jobs.Jobs method) per_user() (galaxy.webapps.reports.controllers.jobs.Jobs method) (galaxy.webapps.reports.controllers.workflows.Workflows method) per_workflow() (galaxy.webapps.reports.controllers.workflows.Workflows method) perform_import() (galaxy.model.store.ModelImportStore method) perform_single_upload() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) perform_upload() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) perform_upload_of_composite_dataset_pasted_data() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) perform_upload_of_pasted_content() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) permission_failed_error_class (galaxy.managers.rbac_secured.AccessDatasetRBACPermission attribute) (galaxy.managers.rbac_secured.ManageDatasetRBACPermission attribute) (galaxy.managers.rbac_secured.RBACPermission attribute) permission_provider (galaxy.job_execution.output_collect.JobContext property) (galaxy.model.store.discover.ModelPersistenceContext property) (galaxy.model.store.discover.SessionlessModelPersistenceContext property) PermissionProvider (class in galaxy.job_execution.output_collect) (class in galaxy.model.store.discover) permissions (galaxy.job_execution.output_collect.PermissionProvider property) (galaxy.model.store.discover.PermissionProvider property) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) permissions() (galaxy.webapps.galaxy.controllers.history.HistoryController method) permissions_class (galaxy.managers.rbac_secured.DatasetRBACPermission attribute) (galaxy.managers.rbac_secured.RBACPermission attribute) permitted_actions (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance attribute) (galaxy.model.Library attribute) (galaxy.security.RBACAgent attribute) (tool_shed.webapp.security.RBACAgent attribute) persist (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator attribute) (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager attribute) persist() (galaxy.tools.cache.ToolDocumentCache method) persist_cache() (galaxy.tools.ToolBox method) persist_elements_to_folder() (in module galaxy.model.store.discover) persist_elements_to_hdca() (in module galaxy.model.store.discover) persist_extra_files() (in module galaxy.objectstore) persist_hdas() (in module galaxy.model.store.discover) persist_library_folder() (galaxy.model.store.discover.ModelPersistenceContext method) (galaxy.model.store.discover.SessionlessModelPersistenceContext method) persist_object() (galaxy.job_execution.output_collect.JobContext method) (galaxy.model.store.discover.ModelPersistenceContext method) (galaxy.model.store.discover.SessionlessModelPersistenceContext method) persist_target_to_export_store() (in module galaxy.model.store.discover) persist_uploads() (in module galaxy.tools.actions.upload_common) PersistentToolTagManager (class in galaxy.tools)

Person (class in galaxy.schema.schema) Pgm (class in galaxy.datatypes.images) PHAR (class in galaxy.datatypes.molecules) Phe (class in galaxy.datatypes.genetics) Pheno (class in galaxy.datatypes.genetics) phone (galaxy.model.UserAddress attribute) Phylip (class in galaxy.datatypes.phylip) PhyloTree (class in galaxy.visualization.data_providers.phyloviz.baseparser) PhylovizDataProvider (class in galaxy.visualization.data_providers.phyloviz) Phyloxml (class in galaxy.datatypes.xml) Phyloxml_Parser (class in galaxy.visualization.data_providers.phyloviz.phyloxmlparser) pick_a_cycle() (galaxy.util.topsort.CycleError method) pickle_SafeStringWrapper() (in module galaxy.security.object_wrapper) pid (galaxy.model.WorkerProcess attribute) Pileup (class in galaxy.datatypes.tabular) PithosObjectStore (class in galaxy.objectstore.pithos) PithyaModel (class in galaxy.datatypes.text) PithyaProperty (class in galaxy.datatypes.text) PithyaResult (class in galaxy.datatypes.text) pkce_support (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute) placeholderRenderForEdit() (in module galaxy.managers.pages) placeholderRenderForSave() (in module galaxy.managers.pages) placement (galaxy.tours.TourStep attribute) PlantTribesKsComponents (class in galaxy.datatypes.plant_tribes) plugin (galaxy.auth.util.Authenticator attribute) (galaxy.model.JobMetricNumeric attribute) (galaxy.model.JobMetricText attribute) (galaxy.model.TaskMetricNumeric attribute) (galaxy.model.TaskMetricText attribute) (galaxy.schema.schema.JobMetric attribute) plugin_kind (galaxy.files.sources.BaseFilesSource attribute) (galaxy.files.sources.galaxy.LibraryImportFilesSource attribute) (galaxy.files.sources.galaxy.UserFtpFilesSource attribute) (galaxy.files.sources.galaxy.UserLibraryImportFilesSource attribute) plugin_source_from_dict() (in module galaxy.util.plugin_config) plugin_source_from_path() (in module galaxy.util.plugin_config) plugin_type (galaxy.auth.providers.alwaysreject.AlwaysReject attribute) (galaxy.auth.providers.AuthProvider property) (galaxy.auth.providers.ldap_ad.ActiveDirectory attribute) (galaxy.auth.providers.ldap_ad.LDAP attribute) (galaxy.auth.providers.ldap_ad.LDAP3 attribute) (galaxy.auth.providers.localdb.LocalDB attribute) (galaxy.auth.providers.pam_auth.PAM attribute) (galaxy.files.sources.anvil.AnVILFilesSource attribute) (galaxy.files.sources.BaseFilesSource attribute) (galaxy.files.sources.basespace.BaseSpaceFilesSource attribute) (galaxy.files.sources.dropbox.DropboxFilesSource attribute) (galaxy.files.sources.ftp.FtpFilesSource attribute) (galaxy.files.sources.galaxy.LibraryImportFilesSource attribute) (galaxy.files.sources.galaxy.UserFtpFilesSource attribute) (galaxy.files.sources.galaxy.UserLibraryImportFilesSource attribute) (galaxy.files.sources.googlecloudstorage.GoogleCloudStorageFilesSource attribute) (galaxy.files.sources.googledrive.GoogleDriveFilesSource attribute) (galaxy.files.sources.onedata.OnedataFilesSource attribute) (galaxy.files.sources.posix.PosixFilesSource attribute) (galaxy.files.sources.s3fs.S3FsFilesSource attribute) (galaxy.files.sources.ssh.SshFilesSource attribute) (galaxy.files.sources.webdav.WebDavFilesSource attribute) (galaxy.job_metrics.instrumenters.cgroup.CgroupPlugin attribute) (galaxy.job_metrics.instrumenters.core.CorePlugin attribute) (galaxy.job_metrics.instrumenters.cpuinfo.CpuInfoPlugin attribute) (galaxy.job_metrics.instrumenters.env.EnvPlugin attribute) (galaxy.job_metrics.instrumenters.hostname.HostnamePlugin attribute) (galaxy.job_metrics.instrumenters.InstrumentPlugin property) (galaxy.job_metrics.instrumenters.meminfo.MemInfoPlugin attribute) (galaxy.job_metrics.instrumenters.uname.UnamePlugin attribute) (galaxy.tools.error_reports.plugins.email.EmailPlugin attribute) (galaxy.tools.error_reports.plugins.ErrorPlugin property) (galaxy.tools.error_reports.plugins.github.GithubPlugin attribute) (galaxy.tools.error_reports.plugins.gitlab.GitLabPlugin attribute) (galaxy.tools.error_reports.plugins.influxdb.InfluxDBPlugin attribute) (galaxy.tools.error_reports.plugins.json.JsonPlugin attribute) (galaxy.tools.error_reports.plugins.sentry.SentryPlugin attribute) (galaxy.workflow.reports.generators.markdown.MarkdownWorkflowMarkdownReportGeneratorPlugin attribute) (galaxy.workflow.reports.generators.WorkflowReportGeneratorPlugin property) (galaxy.workflow.schedulers.core.CoreWorkflowSchedulingPlugin attribute) (galaxy.workflow.schedulers.WorkflowSchedulingPlugin property) PluginConfigSource (class in galaxy.util.plugin_config) PluginKind (class in galaxy.files.sources) plugins() (galaxy.webapps.galaxy.api.remote_files.FastAPIRemoteFiles method) plugins_dict() (in module galaxy.util.plugin_config) plugins_to_dict() (galaxy.files.ConfiguredFileSources method) PluginsController (class in galaxy.webapps.galaxy.api.plugins) pluralize() (galaxy.util.inflection.Inflector method) PLURALIZE_RULES (galaxy.util.inflection.Inflector attribute) Ply (class in galaxy.datatypes.constructive_solid_geometry) PlyAscii (class in galaxy.datatypes.constructive_solid_geometry) PlyBinary (class in galaxy.datatypes.constructive_solid_geometry) Png (class in galaxy.datatypes.images) poll (galaxy.jobs.runners.pulsar.PulsarMQJobRunner attribute) poll_active_workflow_ids() (galaxy.model.WorkflowInvocation static method) poll_unhandled_workflow_ids() (galaxy.model.WorkflowInvocation static method) pool_members() (galaxy.web_stack.ApplicationStack method) (galaxy.web_stack.WeblessApplicationStack method) pool_name (galaxy.web_stack.ApplicationStack property) pop() (galaxy.model.custom_types.MutationDict method) (galaxy.model.custom_types.MutationList method) (galaxy.tool_util.cwl.cwltool_deps.CommentedMap method) (galaxy.util.oset.OrderedSet method) pop_tool_ids() (in module galaxy.tool_util.deps.views) popitem() (galaxy.util.odict.odict method) populate() (galaxy.model.dataset_collections.builder.BoundCollectionBuilder method) (galaxy.model.FormDefinition method) populate_api_routes() (in module galaxy.webapps.galaxy.buildapp) populate_collection_elements() (galaxy.model.store.discover.ModelPersistenceContext method) populate_config_args() (in module galaxy.util.script) populate_data_for_step() (galaxy.workflow.render.WorkflowCanvas method) populate_library_folder_from_import_dir() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) populate_model() (galaxy.tools.Tool method) populate_module_and_state() (in module galaxy.workflow.modules) populate_options() (galaxy.main.GalaxyConfigBuilder class method) populate_partial() (galaxy.model.dataset_collections.builder.BoundCollectionBuilder method) populate_repository_dependency_objects_for_processing() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) populate_resource_parameters() (galaxy.tools.Tool method) populate_tool_shed_info() (galaxy.tools.Tool method) populated (galaxy.job_execution.setup.JobOutputs property) (galaxy.model.DatasetCollection property) (galaxy.model.DatasetCollectionInstance property) (galaxy.schema.schema.DCDetailed attribute) (galaxy.schema.schema.DCObject attribute) (galaxy.schema.schema.HDCADetailed attribute) populated_optimized (galaxy.model.DatasetCollection property) populated_state (galaxy.model.DatasetCollection attribute) (galaxy.model.ImplicitCollectionJobs attribute) (galaxy.schema.schema.DCSummary attribute) (galaxy.schema.schema.HDCASummary attribute) (galaxy.schema.schema.ItemStateSummary attribute) populated_state_message (galaxy.model.DatasetCollection attribute) (galaxy.schema.schema.DCSummary attribute) (galaxy.schema.schema.HDCASummary attribute) populated_states (galaxy.model.DatasetCollection attribute) PopulatedDisplayApplicationLink (class in galaxy.datatypes.display_applications.application) port (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.web.proxy.ProxyMapping attribute) (galaxy_test.api.test_pages.TestPagesApi attribute) (galaxy_test.api.test_workflows.TestAdminWorkflowsApi attribute) (galaxy_test.api.test_workflows_cwl.BaseCwlWorkflowsApiTestCase attribute) (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi attribute) (galaxy_test.base.testcase.FunctionalTestCase attribute) (galaxy_test.driver.testcase.DrivenFunctionalTestCase attribute) (galaxy_test.selenium.test_admin_app.TestAdminApp attribute) (galaxy_test.selenium.test_anon_history.TestAnonymousHistories attribute) (galaxy_test.selenium.test_change_password.TestChangePassword attribute) (galaxy_test.selenium.test_collection_builders.TestCollectionBuilders attribute) (galaxy_test.selenium.test_collection_edit.TestCollectionEdit attribute) (galaxy_test.selenium.test_data_source_tools.TestDataSource attribute) (galaxy_test.selenium.test_dataset_metadata_download.TestHistoryDatasetState attribute) (galaxy_test.selenium.test_histories_list.TestSavedHistories attribute) (galaxy_test.selenium.test_history_copy_elements.TestHistoryCopyElements attribute) (galaxy_test.selenium.test_history_dataset_state.TestHistoryDatasetState attribute) (galaxy_test.selenium.test_history_multi_view.TestHistoryMultiView attribute) (galaxy_test.selenium.test_history_options.TestHistoryOptions attribute) (galaxy_test.selenium.test_history_panel.TestHistoryPanel attribute) (galaxy_test.selenium.test_history_panel_collections.TestHistoryPanelCollections attribute) (galaxy_test.selenium.test_history_sharing.TestHistoryRequiresLoginSelenium attribute) (galaxy_test.selenium.test_history_sharing.TestHistorySharing attribute) (galaxy_test.selenium.test_invocation_grid.TestInvocationGridSelenium attribute) (galaxy_test.selenium.test_library_contents.TestLibraryContents attribute) (galaxy_test.selenium.test_library_landing.TestLibraryLanding attribute) (galaxy_test.selenium.test_library_to_collections.TestLibraryToCollections attribute) (galaxy_test.selenium.test_login.TestLogin attribute) (galaxy_test.selenium.test_navigates_galaxy.TestNavigatesGalaxySelenium attribute) (galaxy_test.selenium.test_pages.TestPages attribute) (galaxy_test.selenium.test_personal_information.TestDeleteCurrentAccount attribute) (galaxy_test.selenium.test_personal_information.TestManageInformation attribute) (galaxy_test.selenium.test_registration.TestRegistration attribute) (galaxy_test.selenium.test_sign_out.TestSignOut attribute) (galaxy_test.selenium.test_sizzle_loading.TestSizzleLoading attribute) (galaxy_test.selenium.test_stock_tours.TestStockToursTestCase attribute) (galaxy_test.selenium.test_tool_describing_tours.TestToolDescribingTours attribute) (galaxy_test.selenium.test_tool_form.TestLoggedInToolForm attribute) (galaxy_test.selenium.test_tool_form.TestToolForm attribute) (galaxy_test.selenium.test_uploads.TestUploads attribute) (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor attribute) (galaxy_test.selenium.test_workflow_invocation_details.TestWorkflowInvocationDetails attribute) (galaxy_test.selenium.test_workflow_management.TestWorkflowManagement attribute) (galaxy_test.selenium.test_workflow_run.TestWorkflowRun attribute) (galaxy_test.selenium.test_workflow_sharing.TestWorkflowSharing attribute) (galaxy_test.selenium.test_workflow_sharing.TestWorkflowSharingRedirect attribute) (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures attribute) (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository attribute) (tool_shed.test.functional.test_0020_basic_repository_dependencies.TestBasicRepositoryDependencies attribute) (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions attribute) (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies attribute) (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels attribute) (tool_shed.test.functional.test_0070_invalid_tool.TestBismarkRepository attribute) (tool_shed.test.functional.test_0080_advanced_circular_dependencies.TestRepositoryCircularDependencies attribute) (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain attribute) (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies attribute) (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies attribute) (tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners.TestRepositoryMultipleOwners attribute) (tool_shed.test.functional.test_0140_tool_help_images.TestToolHelpImages attribute) (tool_shed.test.functional.test_0150_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_0160_circular_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_0170_complex_prior_installation_required.TestComplexPriorInstallation attribute) (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata attribute) (tool_shed.test.functional.test_0310_hg_api_features.TestHgWebFeatures attribute) (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs attribute) (tool_shed.test.functional.test_0430_browse_utilities.TestToolShedBrowseUtilities attribute) (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies attribute) (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision attribute) (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance attribute) (tool_shed.test.functional.test_0480_tool_dependency_xml_verification.TestDependencyDefinitionValidation attribute) (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole attribute) (tool_shed.test.functional.test_0550_metadata_updated_dependencies.TestGetUpdatedMetadata attribute) (tool_shed.test.functional.test_1000_install_basic_repository.TestBasicToolShedFeatures attribute) (tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies.TestToolWithToolDependencies attribute) (tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies.TestToolWithRepositoryDependencies attribute) (tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions.TestRepositoryWithDependencyRevisions attribute) (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies attribute) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies attribute) (tool_shed.test.functional.test_1070_invalid_tool.TestFreebayesRepository attribute) (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies attribute) (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies attribute) (tool_shed.test.functional.test_1100_install_updated_repository_dependencies.TestRepositoryDependencies attribute) (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies attribute) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies attribute) (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners attribute) (tool_shed.test.functional.test_1160_tool_help_images.TestToolHelpImages attribute) (tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_1190_complex_prior_installation_required.TestComplexPriorInstallation attribute) (tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository.TestUninstallingAndReinstallingRepositories attribute) (tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies.TestUninstallingAndReinstallingRepositories attribute) (tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions.TestUninstallingAndReinstallingRepositories attribute) (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata attribute) (tool_shed.test.functional.test_1410_update_manager.TestUpdateManager attribute) (tool_shed.test.functional.test_1430_repair_installed_repository.TestRepairRepository attribute) (tool_shed.test.functional.test_1460_data_managers.TestDataManagers attribute) (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository attribute) portable (galaxy.metadata.PortableDirectoryMetadataGenerator attribute) PortableDirectoryMetadataGenerator (class in galaxy.metadata) PortAsStringMiddleware (class in tool_shed.webapp.controllers.hg) PosgresDatabaseManager (class in galaxy.model.database_utils) Position (class in galaxy.workflow.refactor.schema) position (galaxy.model.WorkflowComment attribute) (galaxy.model.WorkflowStep attribute) (galaxy.schema.schema.WorkflowStepToExportBase attribute) (galaxy.workflow.refactor.schema.AddInputAction attribute) (galaxy.workflow.refactor.schema.AddStepAction attribute) (galaxy.workflow.refactor.schema.ExtractInputAction attribute) (galaxy.workflow.refactor.schema.ExtractUntypedParameter attribute) position_shift (galaxy.workflow.refactor.schema.UpdateStepPositionAction attribute) PosixFileSourceSetup (class in galaxy_test.driver.integration_setup) PosixFilesSource (class in galaxy.files.sources.posix) POSSIBLE_PARAMETER_TYPES (galaxy.workflow.modules.InputParameterModule attribute) post (galaxy.webapps.galaxy.api.RestVerb attribute) post() (galaxy.webapps.galaxy.api.FrameworkRouter method) (galaxy_test.base.api.ApiTestInteractor method) post_execute_commands() (galaxy.job_metrics.JobInstrumenter method) post_execute_instrument() (galaxy.job_metrics.instrumenters.cgroup.CgroupPlugin method) (galaxy.job_metrics.instrumenters.core.CorePlugin method) (galaxy.job_metrics.instrumenters.env.EnvPlugin method) (galaxy.job_metrics.instrumenters.InstrumentPlugin method) post_fork() (in module galaxy.web_stack.gunicorn_config) post_job_action (galaxy.model.PostJobActionAssociation attribute) post_job_action_id (galaxy.model.PostJobActionAssociation attribute) post_job_actions (galaxy.model.Job attribute) (galaxy.model.WorkflowStep attribute) (galaxy.schema.schema.WorkflowToolStepToExport attribute) post_task() (galaxy.jobs.runners.godocker.GodockerJobRunner method) postal_code (galaxy.model.UserAddress attribute) postclick (galaxy.tours.TourStep attribute) postfork_functions (galaxy.web_stack.GunicornApplicationStack attribute) postfork_setup() (in module galaxy.webapps.galaxy.buildapp) PostgresqlArchive (class in galaxy.datatypes.binary) PostJobAction (class in galaxy.model) (class in galaxy.schema.schema) PostJobActionAssociation (class in galaxy.model) postprocess_expression (galaxy.tools.parameters.dynamic_options.FromUrlOptions attribute) POTENTIALLY_SENSITVE (galaxy.job_metrics.Safety attribute) (galaxy.job_metrics.safety.Safety attribute) Pphe (class in galaxy.datatypes.genetics) Ppm (class in galaxy.datatypes.images) PQP (class in galaxy.datatypes.binary) PQR (class in galaxy.datatypes.molecules) pre_execute_check() (galaxy.model.migrations.util.AddColumn method) (galaxy.model.migrations.util.AlterColumn method) (galaxy.model.migrations.util.CreateForeignKey method) (galaxy.model.migrations.util.CreateIndex method) (galaxy.model.migrations.util.CreateTable method) (galaxy.model.migrations.util.CreateUniqueConstraint method) (galaxy.model.migrations.util.DDLOperation method) (galaxy.model.migrations.util.DropColumn method) (galaxy.model.migrations.util.DropConstraint method) (galaxy.model.migrations.util.DropIndex method) (galaxy.model.migrations.util.DropTable method) pre_execute_commands() (galaxy.job_metrics.JobInstrumenter method) pre_execute_instrument() (galaxy.job_metrics.instrumenters.core.CorePlugin method) (galaxy.job_metrics.instrumenters.cpuinfo.CpuInfoPlugin method) (galaxy.job_metrics.instrumenters.env.EnvPlugin method) (galaxy.job_metrics.instrumenters.hostname.HostnamePlugin method) (galaxy.job_metrics.instrumenters.InstrumentPlugin method) (galaxy.job_metrics.instrumenters.meminfo.MemInfoPlugin method) (galaxy.job_metrics.instrumenters.uname.UnamePlugin method) pre_fork() (in module galaxy.web_stack.gunicorn_config) precache (galaxy.tool_util.deps.DependencyManager property) preclick (galaxy.tours.TourStep attribute) precreate_dataset_collection() (galaxy.managers.collections.DatasetCollectionManager method) precreate_dataset_collection_instance() (galaxy.managers.collections.DatasetCollectionManager method) prefer_template_database (galaxy_test.driver.integration_util.IntegrationInstance attribute) preferences (galaxy.files.DictFileSourcesUserContext property) (galaxy.files.ProvidesUserFileSourcesUserContext property) (galaxy.model.User attribute) (galaxy.schema.BootstrapAdminUser attribute) (galaxy.schema.schema.DetailedUserModel attribute) preferences() (galaxy.managers.users.UserManager method) preferred_intermediate_object_store_id (galaxy.model.WorkflowInvocationStepObjectStores attribute) preferred_object_store_id (galaxy.model.History attribute) (galaxy.model.Job attribute) (galaxy.model.User attribute) (galaxy.model.WorkflowInvocationStepObjectStores attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.ArchivedHistorySummary attribute) (galaxy.schema.schema.CreatedUserModel attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.DetailedUserModel attribute) (galaxy.schema.schema.HistorySummary attribute) preferred_object_stores (galaxy.model.WorkflowInvocationStep property) preferred_outputs_object_store_id (galaxy.model.WorkflowInvocationStepObjectStores attribute) prefix (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver property) prepare() (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter method) (galaxy.jobs.TaskWrapper method) prepare_display() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) prepare_download() (galaxy.webapps.galaxy.services.histories.HistoriesService method) prepare_export() (galaxy_test.base.populators.BaseDatasetPopulator method) prepare_history_content_download() (galaxy.managers.model_stores.ModelStoreManager method) prepare_history_download() (galaxy.managers.model_stores.ModelStoreManager method) prepare_input_files_cmd (galaxy.model.Task attribute) prepare_invocation_download() (galaxy.managers.model_stores.ModelStoreManager method) prepare_job() (galaxy.jobs.runners.BaseJobRunner method) prepare_library_for_data_export() (galaxy_test.selenium.test_library_to_collections.TestLibraryToCollections method) prepare_multi_history_view() (galaxy_test.selenium.test_history_multi_view.TestHistoryMultiView method) prepare_pdf() (galaxy.webapps.galaxy.api.pages.FastAPIPages method) (galaxy.webapps.galaxy.services.pages.PagesService method) prepare_request_params() (in module galaxy.tool_util.verify.interactor) PrepareDatasetCollectionDownload (class in galaxy.schema.tasks) preparing (galaxy.model.JobExportHistoryArchive property) (galaxy.schema.schema.ObjectExportResponseBase attribute) preparing_display() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) prepend_anaconda_url() (in module galaxy.tool_util.deps.mulled.get_tests) prepend_timeout_message() (galaxy.selenium.has_driver.HasDriver method) preprocess_volumes() (in module galaxy.tool_util.deps.container_classes) preserve_python_environment (galaxy.config.GalaxyAppConfiguration attribute) Pretext (class in galaxy.datatypes.binary) pretty() (galaxy.util.jstree.JSTree method) pretty_datetime_format (galaxy.config.GalaxyAppConfiguration attribute) pretty_print_json() (in module galaxy.util) pretty_print_time_interval() (in module galaxy.util) pretty_print_xml() (in module galaxy.util) pretty_stack() (in module galaxy.model.orm.engine_factory) prev_session_id (galaxy.model.GalaxySession attribute) (tool_shed.webapp.model.GalaxySession attribute) preview_repository_in_tool_shed() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) preview_tools_in_changeset() (tool_shed.webapp.controllers.repository.RepositoryController method) previous_changeset_revisions() (tool_shed.webapp.controllers.repository.RepositoryController method) primary_file (galaxy.tools.parameters.grouping.Dataset attribute) primary_file_name (galaxy.datatypes.data.Data attribute) primitive_parsers (galaxy.visualization.plugins.resource_parser.ResourceParser attribute) print_nonsleeping() (galaxy.util.heartbeat.Heartbeat method) print_versioned_deps() (in module galaxy.tool_util.deps.brew_exts) priority (galaxy.celery.GalaxyTask attribute) priority_list (in module galaxy.jobs.dynamic_tool_destination) PRIVATE (galaxy.model.Role.types attribute) private (galaxy.objectstore.ConcreteObjectStoreModel attribute) (tool_shed.webapp.model.Repository attribute) private_id (galaxy.model.Role attribute) (tool_shed.webapp.model.Role attribute) private_key (galaxy.security.ssh_util.SSHKeys attribute) private_key_file (galaxy.security.ssh_util.SSHKeys attribute) private_role() (galaxy.managers.users.UserManager method) privately_share_dataset() (galaxy.model.security.GalaxyRBACAgent method) ProBam (class in galaxy.datatypes.binary) ProBed (class in galaxy.datatypes.interval) process() (galaxy.datatypes.metadata.Statement class method) (galaxy.model.metadata.Statement class method) process_action_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_actions_group_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_actions_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_bind_param() (galaxy.model.custom_types.JSONType method) (galaxy.model.custom_types.MetadataType method) (galaxy.model.custom_types.TrimmedString method) (galaxy.model.custom_types.UUIDType method) process_config() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_data() (galaxy.visualization.data_providers.basic.BaseDataProvider method) (galaxy.visualization.data_providers.genome.BamDataProvider method) (galaxy.visualization.data_providers.genome.BedDataProvider method) (galaxy.visualization.data_providers.genome.ChromatinInteractionsDataProvider method) (galaxy.visualization.data_providers.genome.ENCODEPeakDataProvider method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) (galaxy.visualization.data_providers.genome.GtfTabixDataProvider method) (galaxy.visualization.data_providers.genome.IntervalDataProvider method) (galaxy.visualization.data_providers.genome.IntervalIndexDataProvider method) (galaxy.visualization.data_providers.genome.RawGFFDataProvider method) (galaxy.visualization.data_providers.genome.VcfDataProvider method) process_definition() (galaxy.tool_util.cwl.schema.SchemaLoader method) process_install_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_key() (in module galaxy.tools.parameters.wrapped) process_object (galaxy.tool_util.cwl.schema.RawProcessReference attribute) process_package_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_repository_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_request() (galaxy.webapps.base.api.AccessLoggingMiddleware method) process_result() (galaxy.tools.data_manager.manager.DataManager method) process_result_value() (galaxy.model.custom_types.DoubleEncodedJsonType method) (galaxy.model.custom_types.JSONType method) (galaxy.model.custom_types.MetadataType method) (galaxy.model.custom_types.UUIDType method) process_split_file() (galaxy.datatypes.sequence.BaseFastq static method) process_task() (galaxy.queue_worker.GalaxyQueueWorker method) produce_filter() (galaxy.model.InnerCollectionFilter method) produce_k8s_job_prefix() (in module galaxy.jobs.runners.util.pykube_util) produce_outputs() (galaxy.tools.ApplyRulesTool method) (galaxy.tools.BuildListCollectionTool method) (galaxy.tools.DatabaseOperationTool method) (galaxy.tools.DuplicateFileToCollectionTool method) (galaxy.tools.ExtractDatasetCollectionTool method) (galaxy.tools.FilterDatasetsTool method) (galaxy.tools.FilterFromFileTool method) (galaxy.tools.FlattenTool method) (galaxy.tools.HarmonizeTool method) (galaxy.tools.MergeCollectionTool method) (galaxy.tools.RelabelFromFileTool method) (galaxy.tools.SortTool method) (galaxy.tools.TagFromFileTool method) (galaxy.tools.UnzipCollectionTool method) (galaxy.tools.ZipCollectionTool method) produces_collections_with_unknown_structure (galaxy.tools.Tool property) produces_entry_points (galaxy.tools.InteractiveTool attribute) (galaxy.tools.Tool attribute) produces_real_jobs (galaxy.tools.actions.DefaultToolAction attribute) (galaxy.tools.actions.history_imp_exp.ExportHistoryToolAction attribute) (galaxy.tools.actions.history_imp_exp.ImportHistoryToolAction attribute) (galaxy.tools.actions.metadata.SetMetadataToolAction attribute) (galaxy.tools.actions.model_operations.ModelOperationToolAction attribute) (galaxy.tools.actions.upload.BaseUploadToolAction attribute) ProfileMiddleware (class in galaxy.web.framework.middleware.profile) prohibited_middleware (galaxy.web_stack.ApplicationStack attribute) prop() (galaxy.tool_util.deps.container_classes.Container method) ProteomicsXml (class in galaxy.datatypes.proteomics) protocol (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.tool_util.deps.container_resolvers.mulled.MulledDockerContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.MulledSingularityContainerResolver attribute) prototype() (galaxy.model.dataset_collections.registry.DatasetCollectionTypesRegistry method) prototype_elements() (galaxy.model.dataset_collections.types.paired.PairedDatasetCollectionType method) ProtXML (class in galaxy.datatypes.proteomics) ProtXmlReport (class in galaxy.datatypes.proteomics) provenance_item_class (galaxy.webapps.galaxy.api.provenance.HDAProvenanceController attribute) (galaxy.webapps.galaxy.api.provenance.LDDAProvenanceController attribute) provenance_item_id (galaxy.webapps.galaxy.api.provenance.HDAProvenanceController attribute) (galaxy.webapps.galaxy.api.provenance.LDDAProvenanceController attribute) provider (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute) (galaxy.model.CloudAuthz attribute) (galaxy.model.CustosAuthnzToken attribute) (galaxy.model.UserAuthnzToken attribute) ProvidesAppContext (class in galaxy.managers.context) ProvidesHistoryContext (class in galaxy.managers.context) ProvidesUserContext (class in galaxy.managers.context) ProvidesUserFileSourcesUserContext (class in galaxy.files) proxy_ipc() (in module galaxy.web.proxy) proxy_launcher() (galaxy.web.proxy.ProxyManager method) proxy_work_context_for_history() (in module galaxy.work.context) ProxyIpc (class in galaxy.web.proxy) ProxyLauncher (class in galaxy.web.proxy) ProxyManager (class in galaxy.web.proxy) ProxyMapping (class in galaxy.web.proxy) ProxyRequests (class in galaxy.web.proxy) prune() (galaxy.model.HistoryAudit class method) prune_invalid_repository_dependencies() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) pruneLD() (in module galaxy.datatypes.converters.pbed_ldreduced_converter) PSAAssociation (class in galaxy.model) PSAAuthnz (class in galaxy.authnz.psa_authnz) PSACode (class in galaxy.model) PSANonce (class in galaxy.model) PSAPartial (class in galaxy.model) Psd (class in galaxy.datatypes.images) Psl (class in galaxy.datatypes.tabular) PSMS (class in galaxy.datatypes.proteomics) pstats_as_html() (in module galaxy.web.framework.middleware.profile) public (galaxy.schema.schema.LibrarySummary attribute) public_actions (galaxy.job_execution.actions.post.ActionBox attribute) public_key (galaxy.security.ssh_util.SSHKeys attribute) public_key_file (galaxy.security.ssh_util.SSHKeys attribute) publication (galaxy.tool_util.toolbox.views.definitions.StaticToolBoxViewTypeEnum attribute) (galaxy.tool_util.toolbox.views.interface.ToolPanelViewModelType attribute) publication_time (galaxy.model.Notification attribute) PublicURLColumn (class in galaxy.web.legacy_framework.grids) publish (galaxy.managers.workflows.WorkflowCreateOptions attribute) publish() (galaxy.managers.sharable.SharableModelManager method) (galaxy.webapps.galaxy.api.pages.FastAPIPages method) (galaxy.webapps.galaxy.api.visualizations.FastAPIVisualizations method) (galaxy.webapps.galaxy.services.sharable.ShareableService method) publish_history() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) published (galaxy.model.History attribute) (galaxy.model.Page attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.Visualization attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.ArchivedHistorySummary attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.HistorySummary attribute) (galaxy.schema.schema.PageSummary attribute) (galaxy.schema.schema.SharingStatus attribute) (galaxy.schema.schema.StoredWorkflowSummary attribute) published() (galaxy.webapps.galaxy.services.histories.HistoriesService method) published_grid_search_for() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) pull() (galaxy.tool_util.deps.container_resolvers.mulled.MulledDockerContainerResolver method) (galaxy.tool_util.deps.container_resolvers.mulled.MulledSingularityContainerResolver method) pull_mulled_singularity_command() (in module galaxy.tool_util.deps.singularity_util) pull_policy() (in module galaxy.jobs.runners.util.pykube_util) pull_repository() (in module galaxy.tool_shed.util.hg_util) (in module tool_shed.util.hg_util) pull_singularity_command() (in module galaxy.tool_util.deps.singularity_util) PulsarEmbeddedJobRunner (class in galaxy.jobs.runners.pulsar) PulsarEmbeddedMQJobRunner (class in galaxy.jobs.runners.pulsar) PulsarLegacyJobRunner (class in galaxy.jobs.runners.pulsar) PulsarMQJobRunner (class in galaxy.jobs.runners.pulsar) PulsarObjectStore (class in galaxy.objectstore.pulsar) PulsarRESTJobRunner (class in galaxy.jobs.runners.pulsar) purgable (galaxy.model.Dataset attribute) (galaxy.schema.schema.DatasetSummary attribute) PurgableDeserializerMixin (class in galaxy.managers.deletable) PurgableFiltersMixin (class in galaxy.managers.deletable) PurgableManagerMixin (class in galaxy.managers.deletable) PurgableSerializerMixin (class in galaxy.managers.deletable) purge (galaxy.schema.schema.DeleteHistoryContentPayload attribute) (galaxy.schema.schema.HistoryContentItemOperation attribute) (galaxy.schema.schema.UserDeletionPayload attribute) purge() (galaxy.managers.datasets.DatasetAssociationManager method) (galaxy.managers.datasets.DatasetManager method) (galaxy.managers.deletable.PurgableManagerMixin method) (galaxy.managers.groups.GroupsManager method) (galaxy.managers.hdas.HDAManager method) (galaxy.managers.histories.HistoryManager method) (galaxy.managers.roles.RoleManager method) (galaxy.managers.users.UserManager method) (galaxy.webapps.galaxy.api.groups.FastAPIGroups method) (galaxy.webapps.galaxy.api.quotas.FastAPIQuota method) (galaxy.webapps.galaxy.api.roles.FastAPIRoles method) (galaxy.webapps.galaxy.services.quotas.QuotasService method) purge_category() (tool_shed.webapp.controllers.admin.AdminController method) purge_datasets() (galaxy.managers.datasets.DatasetManager method) purge_deleted_datasets() (galaxy.webapps.galaxy.controllers.history.HistoryController method) purge_group() (tool_shed.util.admin_util.Admin method) purge_history (galaxy.schema.schema.ArchiveHistoryRequestPayload attribute) purge_operation (tool_shed.util.admin_util.Admin attribute) (tool_shed.webapp.controllers.admin.AdminController attribute) purge_quota() (galaxy.managers.quotas.QuotaManager method) purge_role() (tool_shed.util.admin_util.Admin method) purge_usage_from_quota() (galaxy.model.HistoryDatasetAssociation method) purge_user() (tool_shed.util.admin_util.Admin method) purged (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance attribute) (galaxy.model.History attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.Library attribute) (galaxy.model.LibraryDataset attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryFolder attribute) (galaxy.model.MetadataFile attribute) (galaxy.model.User attribute) (galaxy.model.UserAddress attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.ArchivedHistorySummary attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.DatasetSummary attribute) (galaxy.schema.schema.DeleteHistoryContentResult attribute) (galaxy.schema.schema.DetailedUserModel attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDAObject attribute) (galaxy.schema.schema.HDASummary attribute) (galaxy.schema.schema.HistorySummary attribute) (tool_shed.webapp.model.User attribute) purged_history_associations (galaxy.model.Dataset attribute) PurgeDatasetsTaskRequest (class in galaxy.schema.tasks) push_if_necessary() (in module galaxy.metadata.set_metadata) push_metadata_files() (galaxy.model.store.DirectoryModelExportStore method) put (galaxy.webapps.galaxy.api.RestVerb attribute) put() (galaxy.jobs.handler.DefaultJobDispatcher method) (galaxy.jobs.handler.JobHandlerQueue method) (galaxy.jobs.handler.JobHandlerStopQueue method) (galaxy.jobs.NoopQueue method) (galaxy.jobs.runners.BaseJobRunner method) (galaxy.webapps.galaxy.api.FrameworkRouter method) (galaxy_test.base.api.ApiTestInteractor method) put_stop() (galaxy.jobs.NoopQueue method) pykube_client_from_dict() (in module galaxy.jobs.runners.util.pykube_util) pytest_configure() (in module galaxy_test.conftest) pytest_json_modifyreport() (galaxy_test.conftest.JsonReportHooks method) pytest_json_runtest_metadata() (galaxy_test.conftest.JsonReportHooks method) pytestmark (galaxy_test.base.testcase.FunctionalTestCase attribute) (tool_shed.test.base.twilltestcase.ShedTwillTestCase attribute) python_template_version (galaxy.tools.ApplyRulesTool attribute) (galaxy.tools.AsyncDataSourceTool attribute) (galaxy.tools.BuildListCollectionTool attribute) (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.DataDestinationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.DuplicateFileToCollectionTool attribute) (galaxy.tools.ExportHistoryTool attribute) (galaxy.tools.ExpressionTool attribute) (galaxy.tools.ExtractDatasetCollectionTool attribute) (galaxy.tools.FilterDatasetsTool attribute) (galaxy.tools.FilterEmptyDatasetsTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) (galaxy.tools.FilterFromFileTool attribute) (galaxy.tools.FlattenTool attribute) (galaxy.tools.HarmonizeTool attribute) (galaxy.tools.ImportHistoryTool attribute) (galaxy.tools.InteractiveTool attribute) (galaxy.tools.KeepSuccessDatasetsTool attribute) (galaxy.tools.MergeCollectionTool attribute) (galaxy.tools.OutputParameterJSONTool attribute) (galaxy.tools.RelabelFromFileTool attribute) (galaxy.tools.SortTool attribute) (galaxy.tools.TagFromFileTool attribute) (galaxy.tools.UnzipCollectionTool attribute) (galaxy.tools.ZipCollectionTool attribute) PythonObjectParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata)

Q

q (galaxy.schema.ValueFilterQueryParams attribute) QC (galaxy.tool_util.parser.stdio.StdioErrorLevel attribute) QCML (class in galaxy.datatypes.proteomics) QIIME2Artifact (class in galaxy.datatypes.qiime2) QIIME2Metadata (class in galaxy.datatypes.qiime2) QIIME2Visualization (class in galaxy.datatypes.qiime2) qp (galaxy.datatypes.display_applications.parameters.DisplayDataValueWrapper property) (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper property) qualified_url_for_path() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) quality_check() (galaxy.datatypes.sequence.BaseFastq static method) (galaxy.datatypes.sequence.FastqIllumina static method) (galaxy.datatypes.sequence.FastqSanger static method) (galaxy.datatypes.sequence.FastqSolexa static method) QualityScore (class in galaxy.datatypes.qualityscore) QualityScore454 (class in galaxy.datatypes.qualityscore) QualityScoreIllumina (class in galaxy.datatypes.qualityscore) QualityScoreSolexa (class in galaxy.datatypes.qualityscore) QualityScoreSOLiD (class in galaxy.datatypes.qualityscore) Quantile (class in galaxy.datatypes.mothur) quay_versions() (in module galaxy.tool_util.deps.mulled.util) query() (galaxy.jobs.rule_helper.RuleHelper method) (galaxy.managers.base.ModelManager method) (galaxy.model.store.SessionlessContext method) query_associated() (galaxy.managers.base.ModelManager method) query_parameter_as_list() (in module galaxy.webapps.galaxy.api.common) query_proxy() (galaxy.web.proxy.ProxyManager method) query_serialization_params() (in module galaxy.webapps.galaxy.api.common) queue (galaxy.jobs.handler.JobHandlerQueue attribute) (galaxy.jobs.handler.JobHandlerStopQueue attribute) (galaxy.schema.schema.AsyncTaskResultSummary attribute) queue() (galaxy.workflow.scheduling_manager.WorkflowSchedulingManager method) queue_history_export() (galaxy.managers.histories.HistoryManager method) queue_history_import() (galaxy.managers.histories.HistoryManager method) queue_invoke() (in module galaxy.workflow.run) queue_job() (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.chronos.ChronosJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.condor.CondorJobRunner method) (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) (galaxy.jobs.runners.godocker.GodockerJobRunner method) (galaxy.jobs.runners.kubernetes.KubernetesJobRunner method) (galaxy.jobs.runners.local.LocalJobRunner method) (galaxy.jobs.runners.pbs.PBSJobRunner method) (galaxy.jobs.runners.tasks.TaskedJobRunner method) queue_worker (galaxy.structured_app.StructuredApp attribute) queued (galaxy.model.JobStateSummary attribute) QUEUED (galaxy.model.Task.states attribute) (galaxy.schema.schema.DatasetState attribute)

queued (galaxy.schema.schema.HDCJobStateSummary attribute) QUEUED (galaxy.schema.schema.JobState attribute) Quota (class in galaxy.model) quota (galaxy.model.DefaultQuotaAssociation attribute) (galaxy.model.GroupQuotaAssociation attribute) (galaxy.model.UserQuotaAssociation attribute) (galaxy.model.UserQuotaUsage attribute) (galaxy.objectstore.ConcreteObjectStoreModel attribute) (galaxy.schema.schema.DetailedUserModel attribute) quota() (galaxy.managers.users.UserManager method) quota_agent (galaxy.managers.quotas.QuotaManager property) (galaxy.structured_app.BasicSharedApp attribute) (galaxy.webapps.reports.app.UniverseApplication attribute) quota_amount() (galaxy.model.HistoryDatasetAssociation method) quota_bytes (galaxy.model.UserQuotaUsage attribute) (galaxy.schema.schema.DetailedUserModel attribute) quota_bytes() (galaxy.managers.users.UserManager method) quota_id (galaxy.model.DefaultQuotaAssociation attribute) (galaxy.model.GroupQuotaAssociation attribute) (galaxy.model.UserQuotaAssociation attribute) quota_list_grid (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) quota_manager (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed attribute) quota_percent (galaxy.model.UserQuotaUsage attribute) (galaxy.schema.schema.AnonUserModel attribute) quota_source_info (galaxy.model.Dataset property) quota_source_label (galaxy.model.Dataset property) (galaxy.model.DatasetInstance property) (galaxy.model.Quota attribute) (galaxy.model.UserQuotaBasicUsage attribute) (galaxy.model.UserQuotaSourceUsage attribute) quota_source_usage_for() (galaxy.model.User method) quota_source_usages (galaxy.model.User attribute) QuotaListGrid (class in galaxy.webapps.galaxy.controllers.admin) QuotaListGrid.AmountColumn (class in galaxy.webapps.galaxy.controllers.admin) QuotaListGrid.DefaultTypeColumn (class in galaxy.webapps.galaxy.controllers.admin) QuotaListGrid.GroupsColumn (class in galaxy.webapps.galaxy.controllers.admin) QuotaListGrid.UsersColumn (class in galaxy.webapps.galaxy.controllers.admin) QuotaManager (class in galaxy.managers.quotas) QuotaModel (class in galaxy.objectstore) quotas (galaxy.model.Group attribute) (galaxy.model.User attribute) quotas_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) QuotaSourceInfo (class in galaxy.objectstore) QuotaSourceMap (class in galaxy.objectstore) QuotasService (class in galaxy.webapps.galaxy.services.quotas) quote_plus_string() (in module galaxy.datatypes.display_applications.application) qv (galaxy.schema.ValueFilterQueryParams attribute)

R

raise_filter_err() (in module galaxy.managers.base) random_name() (in module galaxy_test.base.api_util) RangeParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) rank_collection_type() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) rank_type_plugin() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) Rast (class in galaxy.datatypes.images) RatableDeserializerMixin (class in galaxy.managers.ratable) RatableFilterMixin (class in galaxy.managers.ratable) RatableManagerMixin (class in galaxy.managers.ratable) RatableSerializerMixin (class in galaxy.managers.ratable) rate() (galaxy.managers.ratable.RatableManagerMixin method) rate_item() (galaxy.model.item_attrs.UsesItemRatings method) (tool_shed.webapp.util.ratings_util.ItemRatings method) rate_limit (galaxy.celery.GalaxyTask attribute) rate_repository() (tool_shed.webapp.controllers.repository.RepositoryController method) rating (galaxy.model.HistoryDatasetAssociationRatingAssociation attribute) (galaxy.model.HistoryDatasetCollectionRatingAssociation attribute) (galaxy.model.HistoryRatingAssociation attribute) (galaxy.model.LibraryDatasetCollectionRatingAssociation attribute) (galaxy.model.PageRatingAssociation attribute) (galaxy.model.StoredWorkflowRatingAssociation attribute) (galaxy.model.VisualizationRatingAssociation attribute) (tool_shed.webapp.model.RepositoryRatingAssociation attribute) rating() (galaxy.managers.ratable.RatableManagerMixin method) rating_assoc (galaxy.managers.histories.HistoryManager attribute) (galaxy.managers.pages.PageManager attribute) (galaxy.managers.ratable.RatableManagerMixin attribute) (galaxy.managers.visualizations.VisualizationManager attribute) (galaxy.managers.workflows.WorkflowsManager attribute) ratings (galaxy.model.History attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetCollectionAssociation attribute) (galaxy.model.Page attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.Visualization attribute) (tool_shed.webapp.model.Repository attribute) ratings() (galaxy.managers.ratable.RatableManagerMixin method) ratings_avg() (galaxy.managers.ratable.RatableManagerMixin method) ratings_count() (galaxy.managers.ratable.RatableManagerMixin method) raw_document_loader (galaxy.tool_util.cwl.schema.SchemaLoader property) raw_element_identifiers (galaxy.model.store.discover.JsonCollectedDatasetMatch property) raw_library_contents_create() (galaxy_test.base.populators.LibraryPopulator method) raw_metadata() (in module galaxy.tool_util.deps.conda_compat) raw_param_dict() (galaxy.model.Job method) raw_process_reference (galaxy.tool_util.cwl.schema.ResolvedProcessDefinition attribute) raw_process_reference() (galaxy.tool_util.cwl.schema.SchemaLoader method) raw_process_reference_for_object() (galaxy.tool_util.cwl.schema.SchemaLoader method) raw_size (galaxy.schema.schema.FileLibraryFolderItem attribute) raw_text_column_filter() (in module galaxy.model.index_filter_util) raw_to_galaxy() (in module galaxy.tools.parameters.basic) raw_tool_source() (galaxy.webapps.galaxy.api.tools.ToolsController method) raw_tool_xml_tree() (in module galaxy.tool_util.loader) raw_value (galaxy.schema.schema.JobMetric attribute) raw_xml_tree() (in module galaxy.util.xml_macros) RawBedDataProvider (class in galaxy.visualization.data_providers.genome) RawGFFDataProvider (class in galaxy.visualization.data_providers.genome) RawObjectWrapper (class in galaxy.tools.wrappers) RawProcessReference (class in galaxy.tool_util.cwl.schema) RawVcfDataProvider (class in galaxy.visualization.data_providers.genome) RawWorkflowDescription (class in galaxy.managers.workflows) RBACAgent (class in galaxy.security) (class in tool_shed.webapp.security) RBACPermission (class in galaxy.managers.rbac_secured) RBACPermissionFailedException RData (class in galaxy.datatypes.binary) Rdf (class in galaxy.datatypes.triples) rdm (galaxy.files.sources.PluginKind attribute) RDS (class in galaxy.datatypes.binary) re_get_with_query_params() (galaxy.selenium.has_driver.HasDriver method) reactivate_repository() (tool_shed.test.base.twilltestcase.GalaxyInteractorToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) (tool_shed.test.base.twilltestcase.StandaloneToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ToolShedInstallationClient method) read_blocks() (galaxy.datatypes.molecules.ExtendedXYZ method) (galaxy.datatypes.molecules.XYZ method) read_build_sites() (in module galaxy.util) read_bytes() (galaxy.util.resources.Traversable method) READ_CHUNK_SIZE (galaxy.webapps.galaxy.api.uploads.UploadsAPIController attribute) read_config() (tool_shed.util.hgweb_config.HgWebConfigManager method) read_exit_code() (galaxy.jobs.runners.JobState method) read_exit_code_from() (in module galaxy.job_execution.output_collect) read_only (galaxy.tool_util.deps.container_resolvers.ContainerResolver attribute) (galaxy.tool_util.deps.resolvers.DependencyResolver attribute) read_secret() (galaxy.security.vault.CustosVault method) (galaxy.security.vault.DatabaseVault method) (galaxy.security.vault.HashicorpVault method) (galaxy.security.vault.NullVault method) (galaxy.security.vault.UserVaultWrapper method) (galaxy.security.vault.Vault method) (galaxy.security.vault.VaultKeyPrefixWrapper method) (galaxy.security.vault.VaultKeyValidationWrapper method) read_text() (galaxy.util.resources.Traversable method) read_unordered_gtf() (in module galaxy.datatypes.util.gff_util) read_workflow_from_path() (galaxy.managers.workflows.WorkflowContentsManager method) readline() (galaxy.tools.exception_handling.UCSCOutWrapper method) (galaxy.util.ucsc.UCSCOutWrapper method) readlines() (galaxy.datatypes.dataproviders.base.DataProvider method) readmes() (in module tool_shed.managers.repositories) ready (galaxy.model.JobExportHistoryArchive property) (galaxy.schema.schema.ObjectExportResponseBase attribute) ready() (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter method) ready_galaxy_markdown_for_export() (in module galaxy.managers.markdown_util) ready_galaxy_markdown_for_import() (in module galaxy.managers.markdown_util) ready_name_for_url() (in module galaxy.util) ready_states (galaxy.model.Dataset attribute) real_driver() (in module galaxy_test.conftest) (in module galaxy_test.selenium.conftest) realize_to() (galaxy.files.sources.BaseFilesSource method) (galaxy.files.sources.SingleFileSource method) realpath() (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method) RealUserRequiredException reason (galaxy.model.WorkflowInvocationMessage attribute) rebuild_toolbox_search_index() (in module galaxy.queue_worker) recalculate_disk_usage() (galaxy.webapps.galaxy.api.users.FastAPIUsers method) (galaxy.webapps.galaxy.services.users.UsersService method) recalculate_disk_usage_by_user_id() (galaxy.webapps.galaxy.api.users.FastAPIUsers method) recalculate_user_disk_usage() (in module galaxy.queue_worker) receive_init() (in module galaxy.model) recipe_cellar_path() (in module galaxy.tool_util.deps.brew_exts) RecipeContext (class in galaxy.tool_util.deps.brew_exts) recommended (galaxy.managers.licenses.LicenseMetadataModel attribute) reconfigure_watcher() (in module galaxy.queue_worker) record_section_for_tool_id() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) recover() (galaxy.jobs.handler.DefaultJobDispatcher method) (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.chronos.ChronosJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.condor.CondorJobRunner method) (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) (galaxy.jobs.runners.godocker.GodockerJobRunner method) (galaxy.jobs.runners.kubernetes.KubernetesJobRunner method) (galaxy.jobs.runners.local.LocalJobRunner method) (galaxy.jobs.runners.pbs.PBSJobRunner method) (galaxy.jobs.runners.tasks.TaskedJobRunner method) recover_mapping() (galaxy.workflow.modules.InputModule method) (galaxy.workflow.modules.PauseModule method) (galaxy.workflow.modules.WorkflowModule method) recover_state() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) recursive (galaxy.schema.schema.DeleteHistoryContentPayload attribute) RecursiveNone (class in galaxy.model.none_like) redirect() (galaxy.authnz.psa_authnz.Strategy method) redirect_aware_commmunicate() (in module galaxy.util.commands) redirect_uri (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute) redirecting_io() (in module galaxy.util.commands) reduce_block_by_primary_genome() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) refactor() (galaxy.managers.workflows.WorkflowContentsManager method) (galaxy.workflow.refactor.execute.WorkflowRefactorExecutor method) refactor_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method) RefactorActionExecution (class in galaxy.workflow.refactor.schema) RefactorActionExecutionMessage (class in galaxy.workflow.refactor.schema) RefactorActionExecutionMessageTypeEnum (class in galaxy.workflow.refactor.schema) RefactorActions (class in galaxy.workflow.refactor.schema) RefactorRequest (class in galaxy.managers.workflows) RefactorResponse (class in galaxy.managers.workflows) reference (galaxy.managers.licenses.LicenseMetadataModel attribute) reference() (galaxy.visualization.genomes.Genomes method) ReferenceDataError referenceNumber (galaxy.managers.licenses.LicenseMetadataModel attribute) referer (galaxy.model.GalaxySession attribute) (tool_shed.webapp.model.GalaxySession attribute) RefgenieToolDataTable (class in galaxy.tools.data) refresh() (galaxy.authnz.custos_authnz.OIDCAuthnzBase method) (galaxy.authnz.IdentityProvider method) (galaxy.authnz.psa_authnz.PSAAuthnz method) (in module tool_shed.test.base.test_db_util) refresh_azure() (galaxy.authnz.psa_authnz.PSAAuthnz method) refresh_expiration_time (galaxy.model.CustosAuthnzToken attribute) refresh_expiring_oidc_tokens() (galaxy.authnz.managers.AuthnzManager method) refresh_expiring_oidc_tokens_for_provider() (galaxy.authnz.managers.AuthnzManager method) refresh_token (galaxy.model.CustosAuthnzToken attribute) refresh_tool_shed_repository() (tool_shed.test.base.twilltestcase.GalaxyInteractorToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.StandaloneToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ToolShedInstallationClient method) RefTaxonomy (class in galaxy.datatypes.mothur) regenerate_imported_metadata_if_needed() (galaxy.model.unittest_utils.data_app.MockSetExternalTool method) (galaxy.tools.SetMetadataTool method) regenerate_primary_file() (galaxy.datatypes.assembly.Velvet method) (galaxy.datatypes.genetics.IdeasPre method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.genetics.Rgenetics method) (galaxy.datatypes.ngsindex.BowtieIndex method) (galaxy.datatypes.text.SnpSiftDbNSFP method) regenerate_statistics() (tool_shed.webapp.controllers.admin.AdminController method) regex_line_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.data.Text method) (galaxy.datatypes.tabular.Sam method) RegexCollectedDatasetMatch (class in galaxy.model.store.discover) RegexLineDataProvider (class in galaxy.datatypes.dataproviders.line) RegexpFilter (class in galaxy.tools.parameters.dynamic_options) RegexSubprocessDataProvider (class in galaxy.datatypes.dataproviders.external) RegexValidator (class in galaxy.tools.parameters.validation) RegionAlignment (class in galaxy.datatypes.util.maf_utilities) (class in galaxy.tools.util.maf_utilities) register() (galaxy.managers.users.UserManager method) (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) (galaxy.tool_util.toolbox.lineages.factory.LineageMap method) (galaxy.tool_util.toolbox.lineages.LineageMap method) register_and_change_password() (galaxy_test.selenium.test_change_password.TestChangePassword method) register_cleanup_file_attribute() (galaxy.jobs.runners.AsynchronousJobState method) register_container_information() (galaxy.job_execution.ports.JobPortsView method) (galaxy.job_execution.ports.view.JobPortsView method) register_exception() (galaxy.tool_util.verify.script.Results method) register_func() (galaxy.web_stack.message.ApplicationStackMessageDispatcher method) register_postfork_function() (galaxy.web_stack.ApplicationStack class method) (galaxy.web_stack.GunicornApplicationStack class method) (in module galaxy.web_stack) register_result() (galaxy.tool_util.verify.script.Results method) register_signals() (in module galaxy.main) register_sniffable_binary_format() (galaxy.datatypes.binary.Binary static method) register_tool() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) register_unsniffable_binary_ext() (galaxy.datatypes.binary.Binary static method) register_version() (galaxy.tool_util.toolbox.lineages.interface.ToolLineage method) (galaxy.tool_util.toolbox.lineages.ToolLineage method) REGISTERED (galaxy.model.DefaultQuotaAssociation.types attribute) registered_users() (galaxy.webapps.reports.controllers.users.Users method) registered_users_per_month() (galaxy.webapps.reports.controllers.users.Users method) Registry (class in galaxy.datatypes.registry) (class in tool_shed.repository_registry) (class in tool_shed.repository_types.registry) registry (galaxy.model.Base attribute) (galaxy.model.tool_shed_install.Base attribute) (galaxy.webapps.galaxy.api.tours.FastAPITours attribute) (tool_shed.webapp.model.Base attribute) reimport_history() (galaxy_test.base.populators.BaseDatasetPopulator method) reindex_tool_search() (galaxy.app.MinimalGalaxyApplication method) (galaxy.app_unittest_utils.galaxy_mock.MockApp method) reinstall_repository_api() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) reject_on_worker_lost (galaxy.celery.GalaxyTask attribute) relabel_quota_for_dataset() (galaxy.quota.NoQuotaAgent method) RelabelFromFileTool (class in galaxy.tools) RelationBuilder (class in tool_shed.dependencies.repository.relation_builder) relative_install_dir (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator attribute) (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager attribute) relativize_symlinks() (in module galaxy.util) release() (galaxy.util.filelock.FileLock method) relink_initialworkdir() (in module galaxy.tool_util.cwl.cwltool_deps) reload() (galaxy.datatypes.display_applications.application.DisplayApplication method) (galaxy.managers.display_applications.DisplayApplicationsManager method) (galaxy.managers.tool_data.ToolDataManager method) (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.display_applications.FastAPIDisplay method) (galaxy.webapps.galaxy.api.tool_data.FastAPIToolData method) (galaxy.webapps.galaxy.api.tools.ToolsController method) reload_config_options() (in module galaxy.config) reload_core_config() (in module galaxy.queue_worker) reload_data_managers() (in module galaxy.queue_worker) reload_dependency_manager() (galaxy.tools.ToolBox method) reload_display_application() (in module galaxy.queue_worker) reload_display_applications() (galaxy.datatypes.registry.Registry method) reload_from_files() (galaxy.tools.data.ToolDataTable method) reload_genomes() (galaxy.visualization.genomes.Genomes method) reload_job_rules() (in module galaxy.queue_worker) reload_sanitize_allowlist() (galaxy.config.GalaxyAppConfiguration method) (in module galaxy.queue_worker) reload_tool() (in module galaxy.queue_worker) reload_tool_by_id() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) reload_tool_data_table() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) reload_tool_data_tables() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) (in module galaxy.queue_worker) reload_toolbox() (galaxy.managers.configuration.ConfigurationManager method) (galaxy.webapps.galaxy.api.configuration.FastAPIConfiguration method) (in module galaxy.queue_worker) reload_tour() (in module galaxy.queue_worker) reloadable_options (galaxy.config.schema.AppSchema property) reloaded (galaxy.managers.display_applications.ReloadFeedback attribute) ReloadFeedback (class in galaxy.managers.display_applications) remappable() (galaxy.model.Job method) remote_addr (galaxy.model.GalaxySession attribute) (galaxy.webapps.galaxy.api.GalaxyASGIRequest property) (tool_shed.webapp.model.GalaxySession attribute) remote_host (galaxy.model.GalaxySession attribute) (galaxy.webapps.galaxy.api.GalaxyASGIRequest property) (tool_shed.webapp.model.GalaxySession attribute) remote_repository_url (tool_shed.webapp.model.Repository attribute) remote_user_email (galaxy.schema.schema.RemoteUserCreationPayload attribute) RemoteDirectory (class in galaxy.files.sources) (class in galaxy.schema.remote_files) RemoteEntry (class in galaxy.files.sources) (class in galaxy.schema.remote_files) RemoteFile (class in galaxy.files.sources) (class in galaxy.schema.remote_files) RemoteFilesDisableMode (class in galaxy.schema.remote_files) RemoteFilesFormat (class in galaxy.schema.remote_files) RemoteFilesManager (class in galaxy.managers.remote_files) RemoteFilesTarget (class in galaxy.schema.remote_files) RemoteShell (class in galaxy.jobs.runners.util.cli.shell.rsh) RemoteToolEvaluator (class in galaxy.tools.evaluation) RemoteUser (class in galaxy.web.framework.middleware.remoteuser) (class in tool_shed.webapp.framework.middleware.remoteuser) RemoteUserCreationPayload (class in galaxy.schema.schema) remove() (galaxy.app_unittest_utils.galaxy_mock.MockDir method) (galaxy.managers.interactivetool.InteractiveToolSqlite method) (galaxy.model.custom_types.MutationList method) (galaxy.model.PSAAssociation class method) (in module galaxy.model.triggers.update_audit_table) remove_category_entry() (tool_shed.repository_registry.Registry method) remove_dir() (in module galaxy.tool_shed.util.basic_util) (in module tool_shed.util.basic_util) remove_display_app() (galaxy.datatypes.data.Data method) remove_entry() (galaxy.tools.data.ToolDataTable method) (tool_shed.repository_registry.Registry method) remove_entry_from_installed_repository_dependencies_of_installed_repositories() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) remove_entry_from_repository_dependencies_of_installed_repositories() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) remove_entry_point() (galaxy.managers.interactivetool.InteractiveToolManager method) (galaxy.managers.interactivetool.InteractiveToolSqlite method) remove_entry_points() (galaxy.managers.interactivetool.InteractiveToolManager method) remove_favorite() (galaxy.webapps.galaxy.api.users.FastAPIUsers method) remove_from_cache() (galaxy.tools.Tool method) remove_from_data_manager() (galaxy.tool_shed.galaxy_install.tools.data_manager.DataManagerHandler method) remove_from_key_rd_dicts() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) remove_from_shed_tool_config() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) remove_item_tag() (galaxy.model.tags.TagHandler method) remove_key() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataCollection method) remove_manager() (galaxy.tools.data_manager.manager.DataManagers method) remove_path() (in module tool_shed.util.hg_util) remove_port_from_tool_shed_url() (in module galaxy.util.tool_shed.common_util) (in module tool_shed.util.common_util) remove_protocol_and_port_from_tool_shed_url() (in module galaxy.util.tool_shed.common_util) (in module tool_shed.util.common_util) remove_protocol_and_user_from_clone_url() (in module galaxy.util.tool_shed.common_util) (in module tool_shed.util.common_util) remove_protocol_from_tool_shed_url() (in module galaxy.util.tool_shed.common_util) (in module tool_shed.util.common_util) remove_protocol_from_url() (in module galaxy.util) remove_repository_contents() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) remove_repository_dependency_reference_to_self() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) remove_repository_registry_entry() (tool_shed.webapp.api.repositories.RepositoriesController method) remove_restrictions (galaxy.schema.schema.DatasetPermissionAction attribute) (galaxy.schema.schema.LibraryPermissionAction attribute) remove_tag_async() (galaxy.webapps.galaxy.controllers.tag.TagsController method) remove_tags (galaxy.schema.schema.HistoryContentItemOperation attribute) remove_tags_from_list() (galaxy.model.tags.TagHandler method) remove_temp_index_file() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) remove_tool() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) remove_tool_by_id() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) remove_tool_dependency() (in module galaxy.tool_shed.util.tool_dependency_util) remove_tool_dependency_installation_directory() (in module galaxy.tool_shed.util.tool_dependency_util) remove_unused_dependency_paths() (galaxy.tool_util.deps.views.DependencyResolversView method) remove_version_from_guid() (in module galaxy.util.tool_version) RemoveColumnsRuleDefinition (class in galaxy.util.rules_dsl) RemoveTagDatasetAction (class in galaxy.job_execution.actions.post) RemoveUnlabeledWorkflowOutputs (class in galaxy.workflow.refactor.schema) RemoveValueFilter (class in galaxy.tools.parameters.dynamic_options) rename() (galaxy.webapps.galaxy.controllers.history.HistoryController method) rename_async() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) rename_config_argument() (galaxy.model.migrations.scripts.LegacyManageDb method) rename_group() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (tool_shed.util.admin_util.Admin method) rename_history() (galaxy_test.base.populators.BaseDatasetPopulator method) rename_quota() (galaxy.managers.quotas.QuotaManager method) (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) rename_role() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (tool_shed.util.admin_util.Admin method) renamed_options (galaxy.config.BaseAppConfiguration attribute) (galaxy.config.GalaxyAppConfiguration attribute) RenameDatasetAction (class in galaxy.job_execution.actions.post) RenamedTemporaryFile (class in galaxy.util.renamed_temporary_file) render() (galaxy.visualization.plugins.plugin.VisualizationPlugin method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) render_html() (galaxy.authnz.psa_authnz.Strategy method) render_saved() (galaxy.visualization.plugins.plugin.VisualizationPlugin method) reopen_ro() (galaxy.tools.cache.ToolDocumentCache method) Repeat (class in galaxy.tools.parameters.grouping) replace_dataset (galaxy.tools.actions.upload_common.LibraryParams attribute) replace_elements_in_collection() (galaxy.model.dataset_collections.builder.CollectionBuilder method) replace_failed_elements() (galaxy.model.DatasetCollection method) replace_metadata_file() (in module galaxy.model.store) replace_request_syntax_sugar() (in module galaxy.model.store.discover) replace_tool() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) replace_tool_for_id() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) REPLACEMENT_PARAMETERS (galaxy.model.WorkflowRequestInputParameter.types attribute) repo_files_directory() (galaxy.model.tool_shed_install.ToolShedRepository method) repo_info (galaxy.tools.data_manager.manager.DataManager property) REPO_INSTALL (galaxy.selenium.navigates_galaxy.WAIT_TYPES attribute) repo_path() (galaxy.model.tool_shed_install.ToolShedRepository method) (galaxy.tool_shed.metadata.metadata_generator.RepositoryProtocol method) (tool_shed.webapp.model.Repository method) Report (class in galaxy.webapps.reports.controllers.root) (class in galaxy.workflow.refactor.schema) report (galaxy.workflow.refactor.schema.UpdateReportAction attribute) ReportQueryBuilder (class in galaxy.webapps.reports.controllers.query) reports_config (galaxy.model.Workflow attribute) ReportsWebApplication (class in galaxy.webapps.reports.buildapp) RepoSearch (class in tool_shed.webapp.search.repo_search) repositories (tool_shed.webapp.model.Category attribute) (tool_shed.webapp.model.Role attribute) repositories_by_category() (in module tool_shed.managers.repositories) repositories_by_user_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) repositories_hostname (tool_shed.webapp.buildapp.ToolShedGalaxyWebTransaction property) repositories_i_can_administer_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) repositories_i_own_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) repositories_in_category_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) repositories_missing_tool_test_components_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) repositories_with_invalid_tools_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) RepositoriesByUserGrid (class in tool_shed.grids.repository_grids) RepositoriesController (class in tool_shed.webapp.api.repositories) RepositoriesICanAdministerGrid (class in tool_shed.grids.repository_grids) RepositoriesInCategoryGrid (class in tool_shed.grids.repository_grids) RepositoriesInstalledException RepositoriesIOwnGrid (class in tool_shed.grids.repository_grids) RepositoriesMissingToolTestComponentsGrid (class in tool_shed.grids.repository_grids) RepositoriesWithInvalidToolsGrid (class in tool_shed.grids.repository_grids) RepositoriesWithInvalidToolsGrid.InvalidToolConfigColumn (class in tool_shed.grids.repository_grids) Repository (class in tool_shed.webapp.model) repository (galaxy.model.tool_shed_install.RepositoryDependency attribute) (galaxy.model.tool_shed_install.RepositoryRepositoryDependencyAssociation attribute) (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator attribute) (galaxy.tool_shed.metadata.metadata_generator.GalaxyMetadataGenerator attribute) (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager attribute) (tool_shed.metadata.repository_metadata_manager.ToolShedMetadataGenerator attribute) (tool_shed.webapp.model.RepositoryCategoryAssociation attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) (tool_shed.webapp.model.RepositoryRatingAssociation attribute) (tool_shed.webapp.model.RepositoryRoleAssociation attribute) repository_clone_url (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator attribute) (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager attribute) (tool_shed.metadata.repository_metadata_manager.ToolShedMetadataGenerator attribute) repository_dependencies (galaxy.model.tool_shed_install.ToolShedRepository property) (tool_shed.webapp.model.RepositoryMetadata property) repository_dependencies() (tool_shed.webapp.api.repository_revisions.RepositoryRevisionsController method) repository_dependencies_being_installed (galaxy.model.tool_shed_install.ToolShedRepository property) repository_dependencies_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) repository_dependencies_missing_or_being_installed (galaxy.model.tool_shed_install.ToolShedRepository property) repository_dependencies_of_installed_repositories (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager attribute) repository_dependencies_with_installation_errors (galaxy.model.tool_shed_install.ToolShedRepository property) repository_dependency (galaxy.model.tool_shed_install.RepositoryRepositoryDependencyAssociation attribute) repository_dependency_id (galaxy.model.tool_shed_install.RepositoryRepositoryDependencyAssociation attribute) repository_dependency_needed_only_for_compiling_tool_dependency() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) repository_deprecated (galaxy.schema.schema.InstalledRepositoryToolShedStatus attribute) repository_files_dir (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator attribute) (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager attribute) repository_grid (tool_shed.webapp.controllers.admin.AdminController attribute) (tool_shed.webapp.controllers.repository.RepositoryController attribute) repository_id (tool_shed.webapp.model.RepositoryCategoryAssociation attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) (tool_shed.webapp.model.RepositoryRatingAssociation attribute) (tool_shed.webapp.model.RepositoryRoleAssociation attribute) repository_is_new() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) repository_long_description (in module tool_shed.test.functional.test_0010_repository_with_tool_dependencies) (in module tool_shed.test.functional.test_0480_tool_dependency_xml_verification) repository_metadata_by_changeset_revision() (in module tool_shed.util.metadata_util) repository_metadata_grid (tool_shed.webapp.controllers.admin.AdminController attribute) (tool_shed.webapp.controllers.repository.RepositoryController attribute) repository_registry (tool_shed.webapp.app.UniverseApplication attribute) repository_types_registry (tool_shed.webapp.app.UniverseApplication attribute) repository_was_previously_installed() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) RepositoryCategoryAssociation (class in tool_shed.webapp.model) RepositoryController (class in tool_shed.webapp.controllers.repository) RepositoryDependenciesGrid (class in tool_shed.grids.repository_grids) RepositoryDependenciesGrid.RequiredRepositoryColumn (class in tool_shed.grids.repository_grids) RepositoryDependency (class in galaxy.model.tool_shed_install) RepositoryDependencyAttributeHandler (class in tool_shed.dependencies.attribute_handlers) RepositoryDependencyInstallManager (class in galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager) RepositoryGrid (class in tool_shed.grids.repository_grids) RepositoryGrid.CategoryColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.DeprecatedColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.DescriptionColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.EmailAlertsColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.EmailColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.HeadsColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.LatestInstallableRevisionColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.MetadataRevisionColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.NameColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.RepositoryCategoryColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.TipRevisionColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.TypeColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.UserColumn (class in tool_shed.grids.repository_grids) RepositoryGridFilterManager (class in tool_shed.grids.repository_grid_filter_manager) RepositoryInstallationError (class in tool_shed.utility_containers) RepositoryMetadata (class in tool_shed.webapp.model) RepositoryMetadataGrid (class in tool_shed.grids.admin_grids) (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.ChangesetRevisionColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.DatatypesColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.DeletedColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.DeprecatedColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.DownloadableColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.HasRepositoryDependenciesColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.IdColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.IncludesDatatypesColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.IncludesToolDependenciesColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.IncludesToolsColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.IncludesWorkflowsColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.MaliciousColumn (class in tool_shed.grids.admin_grids) (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.NameColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.OwnerColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.RepositoryNameColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.RepositoryOwnerColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.RepositoryTypeColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.RevisionColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.ToolsColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.WorkflowsColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataManager (class in tool_shed.metadata.repository_metadata_manager) RepositoryProtocol (class in galaxy.tool_shed.metadata.metadata_generator) RepositoryRatingAssociation (class in tool_shed.webapp.model) RepositoryRepositoryDependencyAssociation (class in galaxy.model.tool_shed_install) RepositoryRevisionsController (class in tool_shed.webapp.api.repository_revisions) RepositoryRoleAssociation (class in tool_shed.webapp.model) RepositorySuccessfulInstallation (class in tool_shed.utility_containers) RepositorySuiteDefinition (class in tool_shed.repository_types.repository_suite_definition) RepoWeighting (class in tool_shed.webapp.search.repo_search) REPR (galaxy.datatypes.binary.H5MLM attribute) RepresentById (class in galaxy.model) reprsymbol (galaxy.util.bool_expressions.BoolAnd attribute) (galaxy.util.bool_expressions.BoolBinaryOperation attribute) (galaxy.util.bool_expressions.BoolOr attribute) request (galaxy.work.context.SessionRequestContext property) request() (galaxy.webapps.galaxy.api.toolshed.ToolShedController method) request_body (galaxy.tools.parameters.dynamic_options.FromUrlOptions attribute) request_data (galaxy.schema.schema.ExportObjectMetadata attribute) request_data() (galaxy.authnz.psa_authnz.Strategy method) request_headers (galaxy.tools.parameters.dynamic_options.FromUrlOptions attribute) request_host() (galaxy.authnz.psa_authnz.Strategy method) request_invocation_cancellation() (galaxy.managers.workflows.WorkflowsManager method) request_method (galaxy.tools.parameters.dynamic_options.FromUrlOptions attribute) request_scopefunc() (galaxy.model.base.ModelMapping method) request_stack (galaxy.celery.GalaxyTask attribute) RequestIDMiddleware (class in galaxy.web.framework.middleware.request_id) RequestParameterInvalidException RequestParameterMissingException RequestUser (class in galaxy.schema.tasks) require_admin() (in module galaxy.web) (in module galaxy.web.framework.decorators) require_admin_message() (in module galaxy.web.framework.decorators) require_admin_user (galaxy_test.api.test_workflows.TestAdminWorkflowsApi attribute) (galaxy_test.api.test_workflows_cwl.BaseCwlWorkflowsApiTestCase attribute) require_create_confirmation (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute) require_dataset_ok (galaxy.tools.BuildListCollectionTool attribute) (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.DuplicateFileToCollectionTool attribute) (galaxy.tools.ExtractDatasetCollectionTool attribute) (galaxy.tools.FilterDatasetsTool attribute) (galaxy.tools.FilterEmptyDatasetsTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) (galaxy.tools.FlattenTool attribute) (galaxy.tools.HarmonizeTool attribute) (galaxy.tools.KeepSuccessDatasetsTool attribute) (galaxy.tools.MergeCollectionTool attribute) (galaxy.tools.SortTool attribute) (galaxy.tools.UnzipCollectionTool attribute) (galaxy.tools.ZipCollectionTool attribute)

require_file() (in module galaxy.tools.test) require_login() (in module galaxy.web) (in module galaxy.web.framework.decorators) (in module tool_shed.webapp.framework.decorators) require_terminal_or_paused_states (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.KeepSuccessDatasetsTool attribute) require_terminal_states (galaxy.tools.BuildListCollectionTool attribute) (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.DuplicateFileToCollectionTool attribute) (galaxy.tools.ExtractDatasetCollectionTool attribute) (galaxy.tools.FilterDatasetsTool attribute) (galaxy.tools.FlattenTool attribute) (galaxy.tools.HarmonizeTool attribute) (galaxy.tools.KeepSuccessDatasetsTool attribute) (galaxy.tools.MergeCollectionTool attribute) (galaxy.tools.SortTool attribute) (galaxy.tools.UnzipCollectionTool attribute) (galaxy.tools.ZipCollectionTool attribute) required_data_tables (galaxy.tool_util.verify.interactor.ToolTestDescription attribute) (galaxy.tool_util.verify.interactor.ToolTestDescriptionDict attribute) (galaxy.tool_util.verify.interactor.ValidToolTestDict attribute) required_files (galaxy.tool_util.verify.interactor.ToolTestDescription attribute) (galaxy.tool_util.verify.interactor.ToolTestDescriptionDict attribute) (galaxy.tool_util.verify.interactor.ValidToolTestDict attribute) required_loc_files (galaxy.tool_util.verify.interactor.ToolTestDescription attribute) (galaxy.tool_util.verify.interactor.ToolTestDescriptionDict attribute) (galaxy.tool_util.verify.interactor.ValidToolTestDict attribute) required_module (galaxy.files.sources.anvil.AnVILFilesSource attribute) (galaxy.files.sources.basespace.BaseSpaceFilesSource attribute) (galaxy.files.sources.dropbox.DropboxFilesSource attribute) (galaxy.files.sources.ftp.FtpFilesSource attribute) (galaxy.files.sources.googlecloudstorage.GoogleCloudStorageFilesSource attribute) (galaxy.files.sources.googledrive.GoogleDriveFilesSource attribute) (galaxy.files.sources.onedata.OnedataFilesSource attribute) (galaxy.files.sources.ssh.SshFilesSource attribute) (galaxy.files.sources.webdav.WebDavFilesSource attribute) required_package (galaxy.files.sources.anvil.AnVILFilesSource attribute) (galaxy.files.sources.basespace.BaseSpaceFilesSource attribute) (galaxy.files.sources.dropbox.DropboxFilesSource attribute) (galaxy.files.sources.ftp.FtpFilesSource attribute) (galaxy.files.sources.googlecloudstorage.GoogleCloudStorageFilesSource attribute) (galaxy.files.sources.googledrive.GoogleDriveFilesSource attribute) (galaxy.files.sources.onedata.OnedataFilesSource attribute) (galaxy.files.sources.ssh.SshFilesSource attribute) (galaxy.files.sources.webdav.WebDavFilesSource attribute) required_repositories (galaxy.model.tool_shed_install.ToolShedRepository attribute) RequiredFiles (class in galaxy.tool_util.parser) (class in galaxy.tool_util.parser.interface) requirement_to_recipe() (in module galaxy.tool_util.deps.brew_util) RequirementMapping (class in galaxy.tool_util.deps.resolvers) RequirementNameMissing (class in galaxy.tool_util.linters.general) requirements (galaxy.tours.TourCore attribute) requirements() (galaxy.webapps.galaxy.api.tools.ToolsController method) requirements_to_conda_targets() (in module galaxy.tool_util.deps.conda_util) requirements_to_dependencies() (galaxy.tool_util.deps.DependencyManager method) requirements_to_mulled_targets() (in module galaxy.tool_util.deps.mulled.mulled_build_tool) requirements_to_recipe_contexts() (in module galaxy.tool_util.deps.brew_util) requirements_to_recipes() (in module galaxy.tool_util.deps.brew_util) RequirementSpecification (class in galaxy.tool_util.deps.requirements) RequirementVersionMissing (class in galaxy.tool_util.linters.general) RequirementVersionWhitespace (class in galaxy.tool_util.linters.general) RequireOneSetOption (class in galaxy.schema.schema) requires_admin (galaxy_test.selenium.test_library_to_collections.TestLibraryToCollections attribute) requires_dataset_id (galaxy.datatypes.metadata.MetadataCollection property) (galaxy.model.metadata.MetadataCollection property) requires_dataset_metadata (galaxy.tools.parameters.validation.MetadataEqualValidator attribute) (galaxy.tools.parameters.validation.MetadataInDataTableColumnValidator attribute) (galaxy.tools.parameters.validation.MetadataInFileColumnValidator attribute) (galaxy.tools.parameters.validation.MetadataInRangeValidator attribute) (galaxy.tools.parameters.validation.MetadataNotInDataTableColumnValidator attribute) (galaxy.tools.parameters.validation.MetadataValidator attribute) (galaxy.tools.parameters.validation.UnspecifiedBuildValidator attribute) (galaxy.tools.parameters.validation.Validator attribute) requires_domain (galaxy.model.InteractiveToolEntryPoint attribute) requires_galaxy (tool_shed.test.base.twilltestcase.ShedTwillTestCase attribute) (tool_shed.test.functional.test_1000_install_basic_repository.TestBasicToolShedFeatures attribute) (tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies.TestToolWithToolDependencies attribute) (tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies.TestToolWithRepositoryDependencies attribute) (tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions.TestRepositoryWithDependencyRevisions attribute) (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies attribute) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies attribute) (tool_shed.test.functional.test_1070_invalid_tool.TestFreebayesRepository attribute) (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies attribute) (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies attribute) (tool_shed.test.functional.test_1100_install_updated_repository_dependencies.TestRepositoryDependencies attribute) (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies attribute) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies attribute) (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners attribute) (tool_shed.test.functional.test_1160_tool_help_images.TestToolHelpImages attribute) (tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_1190_complex_prior_installation_required.TestComplexPriorInstallation attribute) (tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository.TestUninstallingAndReinstallingRepositories attribute) (tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies.TestUninstallingAndReinstallingRepositories attribute) (tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions.TestUninstallingAndReinstallingRepositories attribute) (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata attribute) (tool_shed.test.functional.test_1410_update_manager.TestUpdateManager attribute) (tool_shed.test.functional.test_1430_repair_installed_repository.TestRepairRepository attribute) (tool_shed.test.functional.test_1460_data_managers.TestDataManagers attribute) (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository attribute) requires_galaxy_python_environment (galaxy.tools.Tool property) requires_groups (galaxy.files.sources.FilesSourceProperties attribute) (galaxy.schema.remote_files.FilesSourcePlugin attribute) requires_hid (galaxy.model.store.ObjectImportTracker attribute) requires_js_runtime (galaxy.tools.ExpressionTool attribute) requires_path_in_header_named (galaxy.model.InteractiveToolEntryPoint attribute) requires_path_in_url (galaxy.model.InteractiveToolEntryPoint attribute) requires_prior_installation_of (galaxy.model.tool_shed_install.ToolShedRepository property) requires_roles (galaxy.files.sources.FilesSourceProperties attribute) (galaxy.schema.remote_files.FilesSourcePlugin attribute) requires_setting_metadata (galaxy.tools.SetMetadataTool attribute) (galaxy.tools.Tool attribute) requires_shareable_storage() (galaxy.model.Job method) RequiresGalaxyEnvironmentContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit) RequiresGalaxyEnvironmentSingularityContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit) rerun() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) rerunnable (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) resend_activation_email() (galaxy.webapps.galaxy.controllers.user.User method) resend_verification() (galaxy.webapps.galaxy.controllers.user.User method) reset() (galaxy.managers.pages.PageContentProcessor method) reset_all_metadata() (tool_shed.webapp.controllers.repository.RepositoryController method) reset_all_metadata_on_installed_repository() (galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) reset_all_metadata_on_repository_in_tool_shed() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) reset_external_filename() (in module galaxy.metadata.set_metadata) reset_installed_repository_metadata() (tool_shed.test.base.twilltestcase.GalaxyInteractorToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.StandaloneToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ToolShedInstallationClient method) reset_metadata_on_installed_repositories() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) (tool_shed.test.base.twilltestcase.GalaxyInteractorToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) (tool_shed.test.base.twilltestcase.StandaloneToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ToolShedInstallationClient method) reset_metadata_on_my_writable_repositories_in_tool_shed() (tool_shed.webapp.controllers.repository.RepositoryController method) reset_metadata_on_repositories() (tool_shed.webapp.api.repositories.RepositoriesController method) reset_metadata_on_repository() (in module tool_shed.managers.repositories) (tool_shed.webapp.api.repositories.RepositoriesController method) reset_metadata_on_selected_installed_repositories() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) reset_metadata_on_selected_repositories() (galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) reset_metadata_on_selected_repositories_in_tool_shed() (tool_shed.webapp.controllers.admin.AdminController method) reset_password() (galaxy.webapps.galaxy.controllers.user.User method) (tool_shed.webapp.controllers.user.User method) reset_previously_installed_repository() (galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) reset_repository_metadata() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) reset_request_query_counts() (in module galaxy.model.orm.engine_factory) reset_status() (galaxy.tools.cache.ToolCache method) reset_tags() (galaxy.tool_util.toolbox.AbstractToolTagManager method) (galaxy.tool_util.toolbox.base.AbstractToolTagManager method) (galaxy.tool_util.toolbox.base.NullToolTagManager method) (galaxy.tools.NullToolTagManager method) (galaxy.tools.PersistentToolTagManager method) reset_tokens (tool_shed.webapp.model.User attribute) reset_tool_data_tables() (galaxy.tool_shed.tools.data_table_manager.ShedToolDataTableManager method) (tool_shed.tools.data_table_manager.ShedToolDataTableManager method) reset_user_password() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (tool_shed.util.admin_util.Admin method) resolution_cache() (galaxy.tool_util.deps.containers.ContainerFinder method) ResolutionCache (class in galaxy.tool_util.deps.container_resolvers) resolvable (galaxy.tool_util.deps.requirements.ToolRequirements property) resolve() (galaxy.tool_util.deps.container_resolvers.ContainerResolver method) (galaxy.tool_util.deps.container_resolvers.explicit.CachedExplicitSingularityContainerResolver method) (galaxy.tool_util.deps.container_resolvers.explicit.ExplicitContainerResolver method) (galaxy.tool_util.deps.container_resolvers.explicit.ExplicitSingularityContainerResolver method) (galaxy.tool_util.deps.container_resolvers.explicit.FallbackContainerResolver method) (galaxy.tool_util.deps.container_resolvers.explicit.MappingContainerResolver method) (galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledDockerContainerResolver method) (galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledSingularityContainerResolver method) (galaxy.tool_util.deps.container_resolvers.mulled.CachedMulledDockerContainerResolver method) (galaxy.tool_util.deps.container_resolvers.mulled.CachedMulledSingularityContainerResolver method) (galaxy.tool_util.deps.container_resolvers.mulled.MulledDockerContainerResolver method) (galaxy.tool_util.deps.containers.ContainerFinder method) (galaxy.tool_util.deps.containers.ContainerRegistry method) (galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages.HomebrewToolShedDependencyResolver method) (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method) (galaxy.tool_util.deps.resolvers.DependencyResolver method) (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependencyResolver method) (galaxy.tool_util.deps.resolvers.homebrew.HomebrewDependencyResolver method) (galaxy.tool_util.deps.resolvers.lmod.LmodDependencyResolver method) (galaxy.tool_util.deps.resolvers.modules.ModuleDependencyResolver method) (galaxy.tool_util.deps.views.ContainerResolutionView method) (galaxy.webapps.galaxy.api.container_resolution.ContainerResolutionAPIController method) resolve_all() (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method) (galaxy.tool_util.deps.resolvers.MultipleDependencyResolver method) resolve_and_validate_document() (in module galaxy.tool_util.cwl.cwltool_deps) resolve_config() (galaxy.main_config.WebappConfigResolver method) resolve_dependencies (galaxy.tool_util.deps.container_classes.Container property) resolve_invocation_markdown() (in module galaxy.managers.markdown_util) resolve_or_none() (galaxy.di.Container method) resolve_path() (galaxy.config.BaseAppConfiguration method) (in module galaxy.webapps.reports.config) resolve_toolbox() (galaxy.tool_util.deps.views.ContainerResolutionView method) (galaxy.webapps.galaxy.api.container_resolution.ContainerResolutionAPIController method) resolve_toolbox_with_install() (galaxy.webapps.galaxy.api.container_resolution.ContainerResolutionAPIController method) resolve_with_install() (galaxy.webapps.galaxy.api.container_resolution.ContainerResolutionAPIController method) ResolvedContainerDescription (class in galaxy.tool_util.deps.containers) ResolvedProcessDefinition (class in galaxy.tool_util.cwl.schema) resolver_dependency() (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) resolver_msg (galaxy.tool_util.deps.resolvers.Dependency property) (galaxy.tool_util.deps.resolvers.NullDependency property) resolver_requirements() (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) resolver_type (galaxy.tool_util.deps.container_resolvers.ContainerResolver property) (galaxy.tool_util.deps.container_resolvers.explicit.CachedExplicitSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.ExplicitContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.ExplicitSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.FallbackContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.FallbackNoRequirementsContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.FallbackNoRequirementsSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.FallbackSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.MappingContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.RequiresGalaxyEnvironmentContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.RequiresGalaxyEnvironmentSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledDockerContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.CachedMulledDockerContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.CachedMulledSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.MulledDockerContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.MulledSingularityContainerResolver attribute) (galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages.HomebrewToolShedDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.homebrew.HomebrewDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.lmod.LmodDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.modules.ModuleDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.tool_shed_packages.ToolShedPackageDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages.UnlinkedToolShedPackageDependencyResolver attribute) resolves_simple_dependencies (galaxy.tool_util.deps.resolvers.DependencyResolver attribute) (galaxy.tool_util.deps.resolvers.tool_shed_packages.ToolShedPackageDependencyResolver attribute) resource_from_element() (in module galaxy.tool_util.deps.requirements) resource_groups (galaxy.jobs.JobConfiguration attribute) resource_parameters (galaxy.jobs.JobConfiguration attribute) (galaxy.model.WorkflowInvocation property) RESOURCE_PARAMETERS (galaxy.model.WorkflowRequestInputParameter.types attribute) resource_path() (in module galaxy.util.resources) resource_requirements_from_list() (in module galaxy.tool_util.deps.requirements) resource_string() (in module galaxy.util.resources) ResourceParser (class in galaxy.visualization.plugins.resource_parser) ResourceRequirement (class in galaxy.tool_util.deps.requirements) ResourceRequirementExpression (class in galaxy.tool_util.linters.general) response (galaxy.work.context.SessionRequestContext property) response() (galaxy.util.zipstream.ZipstreamWrapper method) response_fields (galaxy.webapps.galaxy.api.tools.FormDataApiRoute attribute) (galaxy.webapps.galaxy.api.tools.JsonApiRoute attribute) restart() (galaxy_test.driver.integration_util.IntegrationInstance method) RestGolangProxyIpc (class in galaxy.web.proxy) restore_archived_history() (galaxy.managers.histories.HistoryManager method) (galaxy.webapps.galaxy.services.histories.HistoriesService method) (galaxy_test.base.populators.BaseDatasetPopulator method) restore_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) restore_text() (galaxy.tools.parameters.sanitize.ToolParameterSanitizer method) (in module galaxy.util) restore_times() (in module galaxy.model.store) restrict_job_name_length (galaxy.jobs.runners.drmaa.DRMAAJobRunner attribute) (galaxy.jobs.runners.slurm.SlurmJobRunner attribute) restrict_on_connections (galaxy.workflow.refactor.schema.AddInputAction attribute) restrict_options() (galaxy.workflow.modules.InputParameterModule method) restrict_test() (in module galaxy.selenium.toolbox.filters) restrictions (galaxy.workflow.refactor.schema.AddInputAction attribute) RestVerb (class in galaxy.webapps.galaxy.api) resubmitted (galaxy.model.JobStateSummary attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) (galaxy.schema.schema.HDCJobStateSummary attribute) RESUBMITTED (galaxy.schema.schema.JobState attribute) result_data (galaxy.schema.schema.ExportObjectMetadata attribute) result_processor() (galaxy.model.custom_types.GalaxyLargeBinary method) Results (class in galaxy.tool_util.verify.script) resume() (galaxy.model.Job method) resume_paused_jobs() (galaxy.model.History method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) resume_watching() (galaxy.util.watcher.BaseWatcher method) retry_after (galaxy.exceptions.AcceptedRetryLater attribute) retry_call_during_transitions() (in module galaxy.selenium.navigates_galaxy) retry_during_transitions() (in module galaxy.selenium.navigates_galaxy) (in module galaxy_test.selenium.framework) return_action() (galaxy.workflow.refactor.schema.Action class method) reupload_contents() (galaxy_test.base.populators.BaseDatasetPopulator method) reverse() (galaxy.util.odict.odict method) reversed_lower_upper_bounded_changelog() (in module galaxy.tool_shed.util.hg_util) (in module tool_shed.util.hg_util) reversed_upper_bounded_changelog() (in module galaxy.tool_shed.util.hg_util) (in module tool_shed.util.hg_util) ReverseSortColumn (class in galaxy.web.legacy_framework.grids) revision() (tool_shed.webapp.model.Repository method) revision_ids (galaxy.schema.schema.PageSummary attribute) revision_update (galaxy.schema.schema.InstalledRepositoryToolShedStatus attribute) revision_update_available (galaxy.model.tool_shed_install.ToolShedRepository property) revision_upgrade (galaxy.schema.schema.InstalledRepositoryToolShedStatus attribute) revisions (galaxy.model.Page attribute) (galaxy.model.Visualization attribute) revoke() (galaxy.managers.rbac_secured.AccessDatasetRBACPermission method) (galaxy.managers.rbac_secured.ManageDatasetRBACPermission method) (galaxy.managers.rbac_secured.RBACPermission method) revoke_write_access() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) rewrite() (galaxy.tool_util.provided_metadata.BaseToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.LegacyToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.ToolProvidedMetadata method) rewrite_content_for_export() (galaxy.managers.pages.PageManager method) rewrite_content_for_import() (galaxy.managers.pages.PageManager method) rewrite_dataset_path() (galaxy.job_execution.datasets.DatasetPathRewriter method) (galaxy.job_execution.datasets.NullDatasetPathRewriter method) (galaxy.job_execution.datasets.OutputsToWorkingDirectoryPathRewriter method) (galaxy.job_execution.datasets.TaskPathRewriter method) RexpBase (class in galaxy.datatypes.genetics) rfs (galaxy.files.sources.PluginKind attribute) Rgb (class in galaxy.datatypes.images) rgConv() (in module galaxy.datatypes.converters.lped_to_fped_converter) (in module galaxy.datatypes.converters.lped_to_pbed_converter) (in module galaxy.datatypes.converters.pbed_to_lped_converter) Rgenetics (class in galaxy.datatypes.genetics) rgFeatureList (class in galaxy.datatypes.genetics) rgSampleList (class in galaxy.datatypes.genetics) rgTabList (class in galaxy.datatypes.genetics) right (galaxy.schema.schema.WorkflowStepLayoutPosition attribute) RMA6 (class in galaxy.datatypes.binary) RNADotPlotMatrix (class in galaxy.datatypes.sequence) Roadmaps (class in galaxy.datatypes.assembly) ROCRATE_ZIP (galaxy.schema.schema.ModelStoreFormat attribute) ROCrateArchiveModelExportStore (class in galaxy.model.store) ROCrateModelExportStore (class in galaxy.model.store) Role (class in galaxy.model) (class in tool_shed.webapp.model) role (galaxy.model.DatasetPermissions attribute) (galaxy.model.DefaultHistoryPermissions attribute) (galaxy.model.DefaultUserPermissions attribute) (galaxy.model.GroupRoleAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationPermissions attribute) (galaxy.model.LibraryDatasetPermissions attribute) (galaxy.model.LibraryFolderPermissions attribute) (galaxy.model.LibraryPermissions attribute) (galaxy.model.UserRoleAssociation attribute) (tool_shed.webapp.model.GroupRoleAssociation attribute) (tool_shed.webapp.model.RepositoryRoleAssociation attribute) (tool_shed.webapp.model.UserRoleAssociation attribute) Role.types (class in galaxy.model) role_id (galaxy.model.DatasetPermissions attribute) (galaxy.model.DefaultHistoryPermissions attribute) (galaxy.model.DefaultUserPermissions attribute) (galaxy.model.GroupRoleAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationPermissions attribute) (galaxy.model.LibraryDatasetPermissions attribute) (galaxy.model.LibraryFolderPermissions attribute) (galaxy.model.LibraryPermissions attribute) (galaxy.model.UserRoleAssociation attribute) (tool_shed.webapp.model.GroupRoleAssociation attribute) (tool_shed.webapp.model.RepositoryRoleAssociation attribute) (tool_shed.webapp.model.UserRoleAssociation attribute) role_list_grid (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) (tool_shed.util.admin_util.Admin attribute) (tool_shed.webapp.controllers.admin.AdminController attribute) role_manager (galaxy.structured_app.MinimalManagerApp attribute) (galaxy.webapps.galaxy.api.roles.FastAPIRoles attribute) role_names (galaxy.files.DictFileSourcesUserContext property) (galaxy.files.FileSourceDictifiable property) (galaxy.files.ProvidesUserFileSourcesUserContext property) role_search_option (galaxy.auth.providers.ldap_ad.LDAP attribute) role_to_model() (in module galaxy.webapps.galaxy.api.roles) RoleDefinitionModel (class in galaxy.schema.schema) RoleGrid (class in tool_shed.grids.admin_grids) RoleGrid.DescriptionColumn (class in tool_shed.grids.admin_grids) RoleGrid.GroupsColumn (class in tool_shed.grids.admin_grids) RoleGrid.NameColumn (class in tool_shed.grids.admin_grids) RoleGrid.RepositoriesColumn (class in tool_shed.grids.admin_grids) RoleGrid.StatusColumn (class in tool_shed.grids.admin_grids) RoleGrid.TypeColumn (class in tool_shed.grids.admin_grids) RoleGrid.UsersColumn (class in tool_shed.grids.admin_grids) RoleListGrid (class in galaxy.webapps.galaxy.controllers.admin) RoleListGrid.GroupsColumn (class in galaxy.webapps.galaxy.controllers.admin) RoleListGrid.UsersColumn (class in galaxy.webapps.galaxy.controllers.admin) RoleListResponse (class in galaxy.schema.schema) RoleManager (class in galaxy.managers.roles) RoleModelResponse (class in galaxy.schema.schema) roles (galaxy.model.Group attribute) (galaxy.model.User attribute) (galaxy.schema.schema.LibraryAvailablePermissions attribute) (galaxy.tools.actions.upload_common.LibraryParams attribute) (tool_shed.webapp.model.Group attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.User attribute) roles() (tool_shed.util.admin_util.Admin method) roles_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) root (galaxy.app_unittest_utils.galaxy_mock.MockAppConfig attribute) (galaxy.datatypes.proteomics.ConsensusXML attribute) (galaxy.datatypes.proteomics.FeatureXML attribute) (galaxy.datatypes.proteomics.IdXML attribute) (galaxy.datatypes.proteomics.MascotXML attribute) (galaxy.datatypes.proteomics.MzData attribute) (galaxy.datatypes.proteomics.MzIdentML attribute) (galaxy.datatypes.proteomics.MzML attribute) (galaxy.datatypes.proteomics.MzQuantML attribute) (galaxy.datatypes.proteomics.MzXML attribute) (galaxy.datatypes.proteomics.NmrML attribute) (galaxy.datatypes.proteomics.ParamXml attribute) (galaxy.datatypes.proteomics.PepXml attribute) (galaxy.datatypes.proteomics.ProteomicsXml attribute) (galaxy.datatypes.proteomics.ProtXML attribute) (galaxy.datatypes.proteomics.QCML attribute) (galaxy.datatypes.proteomics.TandemXML attribute) (galaxy.datatypes.proteomics.TrafoXML attribute) (galaxy.datatypes.proteomics.TraML attribute) (galaxy.datatypes.proteomics.UniProtXML attribute) (galaxy.datatypes.proteomics.XquestSpecXML attribute) (galaxy.datatypes.proteomics.XquestXML attribute) (galaxy.managers.datatypes.DatatypeConverterList attribute) (galaxy.managers.datatypes.DatatypesEDAMDetailsDict attribute) (galaxy.model.unittest_utils.data_app.GalaxyDataTestConfig attribute) (galaxy.model.unittest_utils.GalaxyDataTestConfig attribute) (galaxy.schema.remote_files.FilesSourcePluginList attribute) (galaxy.schema.remote_files.ListJstreeResponse attribute) (galaxy.schema.remote_files.ListUriResponse attribute) (galaxy.schema.schema.CustomBuildsCollection attribute) (galaxy.schema.schema.ExportTaskListResponse attribute) (galaxy.schema.schema.GroupRoleListResponse attribute) (galaxy.schema.schema.GroupUserListResponse attribute) (galaxy.schema.schema.HistoryContentsArchiveDryRunResult attribute) (galaxy.schema.schema.HistoryContentsResult attribute) (galaxy.schema.schema.InstalledToolShedRepositories attribute) (galaxy.schema.schema.JobExportHistoryArchiveListResponse attribute) (galaxy.schema.schema.JobMetricCollection attribute) (galaxy.schema.schema.LibrarySummaryList attribute) (galaxy.schema.schema.PageSummaryList attribute) (galaxy.schema.schema.RoleListResponse attribute) (galaxy.schema.schema.TagCollection attribute) (galaxy.tool_shed.galaxy_install.tools.data_manager.DataManagerHandler attribute) (galaxy.tools.remote_tool_eval.ToolAppConfig attribute) (galaxy.tours.TourList attribute) root_container_class (galaxy.managers.history_contents.HistoryContentsManager attribute) root_dir (galaxy_test.driver.integration_setup.PosixFileSourceSetup attribute) root_folder (galaxy.model.Library attribute) root_folder_id (galaxy.model.Library attribute) (galaxy.schema.schema.LibraryLegacySummary attribute) RootController (class in galaxy.webapps.galaxy.controllers.root) RootParamContext (class in galaxy.tools.test) roundify() (in module galaxy.util) Router (class in galaxy.webapps.galaxy.api) rst_invalid() (in module galaxy.tool_util.linters.help) rule_builder_add_regex_groups() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_add_regex_replacement() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_add_value() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_concatenate_columns() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_enter_source_text() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_filter_count() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_remove_columns() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_rule_editor() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_set_collection_name() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_set_extension() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_set_mapping() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_set_source() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_sort() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_split_columns() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_swap_columns() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_class (in module galaxy.util.rules_dsl) rule_type (galaxy.util.rules_dsl.AddColumnBasenameRuleDefinition attribute) (galaxy.util.rules_dsl.AddColumnConcatenateRuleDefinition attribute) (galaxy.util.rules_dsl.AddColumnGroupTagValueRuleDefinition attribute) (galaxy.util.rules_dsl.AddColumnMetadataRuleDefinition attribute) (galaxy.util.rules_dsl.AddColumnRegexRuleDefinition attribute) (galaxy.util.rules_dsl.AddColumnRownumRuleDefinition attribute) (galaxy.util.rules_dsl.AddColumnSubstrRuleDefinition attribute) (galaxy.util.rules_dsl.AddColumnValueRuleDefinition attribute) (galaxy.util.rules_dsl.AddFilterCompareRuleDefinition attribute) (galaxy.util.rules_dsl.AddFilterCountRuleDefinition attribute) (galaxy.util.rules_dsl.AddFilterEmptyRuleDefinition attribute) (galaxy.util.rules_dsl.AddFilterMatchesRuleDefinition attribute) (galaxy.util.rules_dsl.AddFilterRegexRuleDefinition attribute) (galaxy.util.rules_dsl.BaseRuleDefinition property) (galaxy.util.rules_dsl.RemoveColumnsRuleDefinition attribute) (galaxy.util.rules_dsl.SortRuleDefinition attribute) (galaxy.util.rules_dsl.SplitColumnsRuleDefinition attribute) (galaxy.util.rules_dsl.SwapColumnsRuleDefinition attribute) RuleHelper (class in galaxy.jobs.rule_helper) rules (galaxy.util.rules_dsl.RuleSet property) rules_module (galaxy.jobs.mapper.JobRunnerMapper attribute) RuleSet (class in galaxy.util.rules_dsl) RulesListToolParameter (class in galaxy.tools.parameters.basic) RuleValidator (class in galaxy.jobs.dynamic_tool_destination) run() (galaxy.model.migrations.DatabaseStateVerifier method) (galaxy.model.migrations.util.DDLAlterOperation method) (galaxy.model.migrations.util.DDLOperation method) (galaxy.util.heartbeat.Heartbeat method) (galaxy.util.task.IntervalTask method) (in module galaxy_ext.expressions.handle_job) run_as_admin (galaxy_test.selenium.test_admin_app.TestAdminApp attribute) (galaxy_test.selenium.test_library_contents.TestLibraryContents attribute) (galaxy_test.selenium.test_library_landing.TestLibraryLanding attribute) run_collection_creates_list() (galaxy_test.base.populators.BaseDatasetPopulator method) run_conformance_test() (galaxy_test.base.populators.CwlPopulator method) run_cwl_job() (galaxy_test.base.populators.CwlPopulator method) run_environment_test_tool() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) run_exit_code_from_file() (galaxy_test.base.populators.BaseDatasetPopulator method) run_next() (galaxy.jobs.runners.BaseJobRunner method) run_postfork() (galaxy.web_stack.GunicornApplicationStack class method) run_sniffers_raw() (in module galaxy.datatypes.sniff) run_stats() (galaxy.webapps.reports.controllers.home.HomePage method) run_tests() (in module galaxy.tool_util.verify.script) run_tool() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) (galaxy_test.base.populators.BaseDatasetPopulator method) run_tool_payload() (galaxy_test.base.populators.BaseDatasetPopulator method) run_tool_raw() (galaxy_test.base.populators.BaseDatasetPopulator method) run_tour() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) run_tour_step() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) run_upgrade() (galaxy.model.migrations.scripts.LegacyManageDb method) run_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method) RunJobsSummary (class in galaxy_test.api.test_workflow_extraction) (class in galaxy_test.base.populators) runner_name (galaxy.jobs.runners.BaseJobRunner attribute) (galaxy.jobs.runners.chronos.ChronosJobRunner attribute) (galaxy.jobs.runners.cli.ShellJobRunner attribute) (galaxy.jobs.runners.condor.CondorJobRunner attribute) (galaxy.jobs.runners.drmaa.DRMAAJobRunner attribute) (galaxy.jobs.runners.godocker.GodockerJobRunner attribute) (galaxy.jobs.runners.kubernetes.KubernetesJobRunner attribute) (galaxy.jobs.runners.local.LocalJobRunner attribute) (galaxy.jobs.runners.pbs.PBSJobRunner attribute) (galaxy.jobs.runners.slurm.SlurmJobRunner attribute) (galaxy.jobs.runners.tasks.TaskedJobRunner attribute) (galaxy.jobs.runners.univa.UnivaJobRunner attribute) (galaxy.model.Job attribute) (galaxy.model.Task attribute) RUNNER_PARAM_SPEC (galaxy.jobs.runners.chronos.ChronosJobRunner attribute) RUNNER_PARAM_SPEC_KEY (galaxy.jobs.runners.chronos.ChronosJobRunner attribute) runner_plugins (galaxy.jobs.JobConfiguration attribute) runner_states (galaxy.jobs.runners.JobState attribute) RunnerParams (class in galaxy.jobs.runners) running (galaxy.jobs.runners.AsynchronousJobState property) (galaxy.model.Job property) (galaxy.model.JobStateSummary attribute) RUNNING (galaxy.model.Task.states attribute) (galaxy.schema.schema.DatasetState attribute) running (galaxy.schema.schema.HDCJobStateSummary attribute) RUNNING (galaxy.schema.schema.JobState attribute) running (galaxy.util.lazy_process.LazyProcess property) (galaxy.util.lazy_process.NoOpLazyProcess property) RunsWorkflowFixtures (class in galaxy_test.api.test_workflows) runtime_value (galaxy.model.WorkflowStepInput attribute) RuntimeContext (class in galaxy.tool_util.cwl.cwltool_deps) RunToolException RunToolResponse (class in galaxy.tool_util.verify.interactor)

S

S3FsFilesSource (class in galaxy.files.sources.s3fs) S3ObjectStore (class in galaxy.objectstore.s3) sa_session (galaxy.job_execution.output_collect.JobContext property) (galaxy.managers.context.ProvidesAppContext property) (galaxy.managers.quotas.QuotaManager property) (galaxy.model.database_heartbeat.DatabaseHeartbeat property) (galaxy.model.PSAAssociation attribute) (galaxy.model.PSACode attribute) (galaxy.model.PSANonce attribute) (galaxy.model.PSAPartial attribute) (galaxy.model.security.GalaxyRBACAgent property) (galaxy.model.security.HostAgent property) (galaxy.model.store.discover.ModelPersistenceContext property) (galaxy.model.store.discover.SessionlessModelPersistenceContext property) (galaxy.model.UserAuthnzToken attribute) (galaxy.tools.Tool property) (galaxy.tools.ToolBox property) (tool_shed.repository_registry.Registry property) (tool_shed.webapp.security.CommunityRBACAgent property) (tool_shed.webapp.util.shed_statistics.ShedCounter property) sa_session() (in module tool_shed.test.base.test_db_util) Sabund (class in galaxy.datatypes.mothur) SAFE (galaxy.job_metrics.Safety attribute) (galaxy.job_metrics.safety.Safety attribute) safe_contains() (in module galaxy.util.path) safe_dumps() (in module galaxy.util.json) safe_makedirs() (in module galaxy.util.path) safe_relpath() (in module galaxy.util.path) safe_str_cmp() (in module galaxy.util) safe_update (class in galaxy.tools) safe_walk() (in module galaxy.util.path) safe_wraps() (in module galaxy.managers.workflows) SafeJsonEncoder (class in galaxy.model.custom_types) safemembers() (galaxy.util.compression_utils.CompressedFile method) SafeStringWrapper (class in galaxy.security.object_wrapper) Safety (class in galaxy.job_metrics) (class in galaxy.job_metrics.safety) safety() (galaxy.job_metrics.instrumenters.InstrumentPlugin method) Sakura (class in galaxy.datatypes.images) salt (galaxy.model.PSANonce attribute) Sam (class in galaxy.datatypes.tabular) SamDataProvider (class in galaxy.visualization.data_providers.genome) sample_destination (galaxy.config.config_manage.App property) samtools_dataprovider() (galaxy.datatypes.binary.Bam method) SamtoolsDataProvider (class in galaxy.datatypes.dataproviders.dataset) sanitize_allowlist_file (galaxy.config.GalaxyAppConfiguration attribute) sanitize_for_filename() (in module galaxy.util) sanitize_html() (in module galaxy.util.sanitize_html) sanitize_lists_to_string() (in module galaxy.security.object_wrapper) (in module galaxy.util) sanitize_param() (galaxy.tools.parameters.sanitize.ToolParameterSanitizer method) (in module galaxy.util) sanitize_text() (galaxy.tools.parameters.sanitize.ToolParameterSanitizer method) (in module galaxy.util) SanitizeAllowController (class in galaxy.webapps.galaxy.api.sanitize_allow) save() (galaxy.managers.interactivetool.InteractiveToolSqlite method) (galaxy.model.PSAAssociation method) (galaxy.model.PSACode method) (galaxy.model.PSANonce method) (galaxy.model.PSAPartial method) (galaxy.model.UserAuthnzToken method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) save_entry_point() (galaxy.managers.interactivetool.InteractiveToolManager method) (galaxy.managers.interactivetool.InteractiveToolSqlite method) save_form_definition() (galaxy.webapps.galaxy.controllers.forms.Forms method) save_new_revision() (galaxy.managers.pages.PageManager method) save_to_step() (galaxy.workflow.modules.InputModule method) (galaxy.workflow.modules.InputParameterModule method) (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) save_widget_field() (galaxy.webapps.base.controller.UsesFormDefinitionsMixin method) save_workflow_as() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) saved() (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) Sbml (class in galaxy.datatypes.xml) Sbol (class in galaxy.datatypes.triples) scaling_workflow_yaml() (galaxy_test.base.populators.WorkflowPopulator method) ScannerError scatter_type (galaxy.model.WorkflowStepInput attribute) Scf (class in galaxy.datatypes.binary) schedule() (galaxy.workflow.schedulers.ActiveWorkflowSchedulingPlugin method) (galaxy.workflow.schedulers.core.CoreWorkflowSchedulingPlugin method) scheduler (galaxy.model.WorkflowInvocation attribute) Schema (class in galaxy.config.schema) schema (galaxy.config.config_manage.App property) schema_path (galaxy.config.config_manage.App attribute) SchemaLoader (class in galaxy.tool_util.cwl.schema) scheme (galaxy.files.sources.FilesSourceProperties attribute) (galaxy.tool_util.locations.dockstore.DockStoreResolver attribute) (galaxy.tool_util.locations.file.HttpToolResolver attribute) (galaxy.tool_util.locations.http.HttpsToolResolver attribute) (galaxy.tool_util.locations.http.HttpToolResolver attribute) (galaxy.tool_util.locations.ToolLocationResolver property) ScIdx (class in galaxy.datatypes.interval) score (galaxy.files.FileSourceScore attribute) score_url_match() (galaxy.files.sources.BaseFilesSource method) (galaxy.files.sources.ftp.FtpFilesSource method) (galaxy.files.sources.posix.PosixFilesSource method) (galaxy.files.sources.s3fs.S3FsFilesSource method) (galaxy.files.sources.SingleFileSource method) screenshot() (galaxy.selenium.cli.DriverWrapper method) (galaxy.selenium.context.GalaxySeleniumContext method) (galaxy.selenium.jupyter_context.JupyterContextImpl method) (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) screenshot_if() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) ScriptVisualizationPlugin (class in galaxy.visualization.plugins.plugin) SDF (class in galaxy.datatypes.molecules) search (galaxy.schema.schema.JobIndexQueryPayload attribute) (galaxy.schema.schema.PageIndexQueryPayload attribute) (galaxy.schema.schema.WorkflowIndexQueryPayload attribute) search() (galaxy.datatypes.sniff.FilePrefix method) (galaxy.tools.search.ToolBoxSearch method) (galaxy.tools.search.ToolPanelViewSearch method) (in module tool_shed.managers.repositories) (tool_shed.webapp.search.repo_search.RepoSearch method) (tool_shed.webapp.search.tool_search.ToolSearch method) search_for_valid_tools() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) search_ids_names() (in module tool_shed.util.search_util) search_ids_versions() (in module tool_shed.util.search_util) search_names_versions() (in module tool_shed.util.search_util) search_query_param() (in module galaxy.webapps.galaxy.api) search_repository_metadata() (in module tool_shed.util.search_util) search_str() (galaxy.datatypes.sniff.FilePrefix method) search_text (galaxy.schema.schema.LibraryFolderContentsIndexQueryPayload attribute) searchable (galaxy.tool_util.toolbox.views.interface.ToolPanelViewModel attribute) SearchGuiArchive (class in galaxy.datatypes.binary) secondaryFiles (galaxy.tool_util.cwl.util.OutputPropertiesType attribute) SecondaryStructureMap (class in galaxy.datatypes.mothur) seconds_since_created (galaxy.model.UsesCreateAndUpdateTime property) seconds_since_updated (galaxy.model.UsesCreateAndUpdateTime property) seconds_to_str() (in module galaxy.job_metrics.formatting) secret (galaxy.model.PSAAssociation attribute) Section (class in galaxy.tool_util.toolbox.views.definitions) (class in galaxy.tools.parameters.grouping) SECTION (galaxy.tool_util.toolbox.panel.panel_item_types attribute) (galaxy.tool_util.toolbox.panel_item_types attribute) section (galaxy.tool_util.toolbox.views.definitions.SectionAlias attribute) SectionAlias (class in galaxy.tool_util.toolbox.views.definitions) SectionAliases (class in galaxy.tool_util.toolbox.views.definitions) sections (galaxy.tool_util.toolbox.views.definitions.SectionAliases attribute) secure() (galaxy.managers.folders.FolderManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.managers.library_datasets.LibraryDatasetsManager method) secure_cloned_response_field (galaxy.webapps.galaxy.api.tools.FormDataApiRoute attribute) (galaxy.webapps.galaxy.api.tools.JsonApiRoute attribute) SecureShell (class in galaxy.jobs.runners.util.cli.shell.rsh) Security (class in galaxy.schema.fields) security (galaxy.app_unittest_utils.galaxy_mock.MockAppConfig attribute) (galaxy.managers.context.ProvidesAppContext property) (galaxy.model.store.StoreAppProtocol attribute) (galaxy.model.unittest_utils.data_app.GalaxyDataTestApp attribute) (galaxy.model.unittest_utils.data_app.GalaxyDataTestConfig attribute) (galaxy.model.unittest_utils.GalaxyDataTestApp attribute) (galaxy.model.unittest_utils.GalaxyDataTestConfig attribute) (galaxy.schema.fields.Security attribute) (galaxy.structured_app.BasicSharedApp attribute) (galaxy.structured_app.MinimalToolApp attribute) (galaxy.tools.remote_tool_eval.ToolApp attribute) (galaxy.webapps.galaxy.services.base.ServiceBase property) (galaxy.webapps.reports.app.UniverseApplication attribute) security_agent (galaxy.managers.folders.SecurityParams attribute) (galaxy.model.mapping.GalaxyModelMapping attribute) (galaxy.model.unittest_utils.data_app.GalaxyDataTestApp attribute) (galaxy.model.unittest_utils.GalaxyDataTestApp attribute) (galaxy.structured_app.BasicSharedApp attribute) (galaxy.structured_app.MinimalApp attribute) (galaxy.webapps.reports.app.UniverseApplication attribute) (tool_shed.webapp.app.UniverseApplication attribute) (tool_shed.webapp.model.mapping.ToolShedModelMapping attribute) security_check() (in module galaxy.managers.base) SecurityNotProvidedError SecurityParams (class in galaxy.managers.folders) seeAlso (galaxy.managers.licenses.LicenseMetadataModel attribute) seen_time (galaxy.model.UserNotificationAssociation attribute) SELECT (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute) select2_set_value() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) select_dataset_from_lib_import_modal() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) select_day() (galaxy.webapps.reports.controllers.query.ReportQueryBuilder method) select_dropdown_item() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) select_grid_cell() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) select_grid_operation() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) select_month() (galaxy.webapps.reports.controllers.query.ReportQueryBuilder method) select_set_value() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) select_storage() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) selectable_object_store_ids() (galaxy_test.base.populators.BaseDatasetPopulator method) selectable_object_stores() (galaxy_test.base.populators.BaseDatasetPopulator method) SelectField (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) selector_is_displayed() (galaxy.selenium.has_driver.HasDriver method) SelectParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) SelectTagParameter (class in galaxy.tools.parameters.basic) SelectToolParameter (class in galaxy.tools.parameters) (class in galaxy.tools.parameters.basic) SelectToolParameterWrapper (class in galaxy.tools.wrappers) SelectToolParameterWrapper.SelectToolParameterFieldWrapper (class in galaxy.tools.wrappers) selenium_to_requests_cookies() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) SeleniumTimeoutException (in module galaxy.selenium.has_driver) self_handler_tags (galaxy.web_stack.handlers.ConfiguresHandlers property) send() (galaxy.managers.cloud.CloudManager method) send_activation_email() (galaxy.managers.users.UserManager method) (galaxy.webapps.galaxy.api.users.FastAPIUsers method) send_backspace() (galaxy.selenium.has_driver.HasDriver method) send_control_task() (galaxy.queue_worker.GalaxyQueueWorker method) (in module galaxy.queue_worker) send_database_heartbeat() (galaxy.model.database_heartbeat.DatabaseHeartbeat method) send_enter() (galaxy.selenium.has_driver.HasDriver method) send_escape() (galaxy.selenium.has_driver.HasDriver method) send_local_control_task() (galaxy.queue_worker.GalaxyQueueWorker method) (in module galaxy.queue_worker) send_mail() (in module galaxy.util) send_message() (galaxy.web_stack.transport.ApplicationStackTransport method) send_report() (galaxy.tools.errors.ErrorReporter method) send_reset_email() (galaxy.managers.users.UserManager method) send_subscription_email() (galaxy.managers.users.UserManager method) send_task() (galaxy.queue_worker.ControlTask method) sentry_dsn (galaxy.config.CommonConfigurationMixin attribute) sentry_dsn_public (galaxy.config.CommonConfigurationMixin property) (galaxy.webapps.reports.config.Configuration property) SentryClientMixin (class in galaxy.app) SentryPlugin (class in galaxy.tools.error_reports.plugins.sentry) sep() (galaxy.job_execution.compute_environment.ComputeEnvironment method) (galaxy.job_execution.compute_environment.SimpleComputeEnvironment method) Sequence (class in galaxy.datatypes.sequence) sequence_regexp (galaxy.datatypes.sequence.DotBracket attribute) Sequences (class in galaxy.datatypes.assembly) sequences() (galaxy.webapps.galaxy.api.genomes.FastAPIGenomes method) SequenceSplitLocations (class in galaxy.datatypes.sequence) Serializable (class in galaxy.model) serializable_keyset (galaxy.managers.cloudauthzs.CloudAuthzsSerializer attribute) (galaxy.managers.configuration.AdminConfigSerializer attribute) (galaxy.managers.configuration.ConfigSerializer attribute) (galaxy.managers.datasets.DatasetAssociationSerializer attribute) (galaxy.managers.datasets.DatasetSerializer attribute) (galaxy.managers.deletable.DeletableSerializerMixin attribute) (galaxy.managers.deletable.PurgableSerializerMixin attribute) (galaxy.managers.hdcas.DCESerializer attribute) (galaxy.managers.hdcas.DCSerializer attribute) (galaxy.managers.hdcas.HDCASerializer attribute) (galaxy.managers.history_contents.HistoryContentsSerializer attribute) (galaxy.managers.users.CurrentUserSerializer attribute) (galaxy.managers.users.UserSerializer attribute) (galaxy.managers.visualizations.VisualizationSerializer attribute) (galaxy.managers.workflows.WorkflowSerializer attribute) SerializationOptions (class in galaxy.model) SerializationParams (class in galaxy.schema) serialize() (galaxy.managers.base.ModelSerializer method) (galaxy.managers.datasets.DatasetAssociationSerializer method) (galaxy.managers.hdas.HDASerializer method) (galaxy.managers.histories.HistoryExportManager method) (galaxy.managers.library_datasets.LibraryDatasetsManager method) (galaxy.managers.users.CurrentUserSerializer method) (galaxy.model.Serializable method) (galaxy.tools.wrappers.DatasetCollectionWrapper method) (galaxy.tools.wrappers.DatasetFilenameWrapper method) (galaxy.tools.wrappers.DatasetListWrapper method) serialize_annotation() (galaxy.managers.annotatable.AnnotatableSerializerMixin method) serialize_community_rating() (galaxy.managers.ratable.RatableSerializerMixin method) serialize_contents() (galaxy.managers.histories.HistorySerializer method) serialize_contents_active() (galaxy.managers.histories.HistorySerializer method) serialize_contents_states() (galaxy.managers.histories.HistorySerializer method) serialize_copied_from_ldda_id() (galaxy.managers.hdas.HDASerializer method) serialize_current_anonymous_user() (galaxy.managers.users.CurrentUserSerializer method) serialize_dataset_association_roles() (galaxy.managers.datasets.DatasetAssociationManager method) serialize_date() (galaxy.managers.base.ModelSerializer method) serialize_disk_usage() (galaxy.managers.users.UserSerializer method) serialize_disk_usage_for() (galaxy.managers.users.UserSerializer method) serialize_display_apps() (galaxy.managers.hdas.HDASerializer method) serialize_elements() (galaxy.managers.hdcas.DCSerializer method) serialize_elements_datatypes() (galaxy.managers.hdcas.HDCASerializer method) serialize_email_hash() (galaxy.managers.sharable.SharableModelSerializer method) serialize_extra_files_path() (galaxy.managers.datasets.DatasetSerializer method) serialize_file_name() (galaxy.managers.datasets.DatasetSerializer method) serialize_files() (galaxy.model.SerializationOptions method) (galaxy.model.SerializeFilesHandler method) (galaxy.model.store.DirectoryModelExportStore method) serialize_history_state() (galaxy.managers.histories.HistorySerializer method) serialize_id() (galaxy.managers.base.ModelSerializer method) serialize_id_or_skip() (galaxy.managers.history_contents.HistoryContentsSerializer method) serialize_job_state_summary() (galaxy.managers.hdcas.HDCASerializer method) serialize_object() (galaxy.managers.hdcas.DCESerializer method) serialize_old_display_applications() (galaxy.managers.hdas.HDASerializer method) serialize_permissions() (galaxy.managers.datasets.DatasetSerializer method) serialize_state_counts() (galaxy.managers.histories.HistorySerializer method) serialize_state_ids() (galaxy.managers.histories.HistorySerializer method) serialize_tags() (galaxy.managers.taggable.TaggableSerializerMixin method) serialize_title() (galaxy.managers.sharable.SharableModelSerializer method) serialize_to_view() (galaxy.managers.base.ModelSerializer method) serialize_type_id() (galaxy.managers.base.ModelSerializer method) serialize_urls() (galaxy.managers.hdas.HDASerializer method) serialize_user_rating() (galaxy.managers.ratable.RatableSerializerMixin method) serialize_username() (galaxy.managers.sharable.SharableModelSerializer method) serialize_username_and_slug() (galaxy.managers.sharable.SharableModelSerializer method) serialize_users_shared_with() (galaxy.managers.sharable.SharableModelSerializer method) SerializeFilesHandler (class in galaxy.model) Serializer (class in galaxy.managers.base) serializer (galaxy.celery.GalaxyTask attribute) (galaxy.webapps.base.controller.SharableMixin attribute) serializers (galaxy.managers.annotatable.AnnotatableSerializerMixin attribute) (galaxy.managers.cloudauthzs.CloudAuthzsSerializer attribute) (galaxy.managers.configuration.AdminConfigSerializer attribute) (galaxy.managers.configuration.ConfigSerializer attribute) (galaxy.managers.datasets.DatasetAssociationSerializer attribute) (galaxy.managers.datasets.DatasetSerializer attribute) (galaxy.managers.hdcas.DCESerializer attribute) (galaxy.managers.hdcas.DCSerializer attribute) (galaxy.managers.hdcas.HDCASerializer attribute) (galaxy.managers.history_contents.HistoryContentsSerializer attribute) (galaxy.managers.users.CurrentUserSerializer attribute) (galaxy.managers.users.UserSerializer attribute) (galaxy.managers.visualizations.VisualizationSerializer attribute) (galaxy.managers.workflows.WorkflowSerializer attribute) serve() (galaxy.webapps.galaxy.api.short_term_storage.FastAPIShortTermStorage method) serve_export_store() (galaxy.webapps.galaxy.services.base.ServesExportStores method) ServedExportStore (class in galaxy.webapps.galaxy.services.base) server_dir (galaxy.schema.fetch_data.ItemsFromModel attribute) (galaxy.schema.fetch_data.ItemsFromSrc attribute) (galaxy.schema.fetch_data.ServerDirElement attribute) (galaxy.schema.fetch_data.Src attribute) server_from_url() (galaxy.workflow.trs_proxy.TrsProxy method) server_name (galaxy.model.database_heartbeat.DatabaseHeartbeat property) (galaxy.model.WorkerProcess attribute) server_name_template (galaxy.web_stack.ApplicationStack attribute) server_starttime (galaxy.structured_app.MinimalApp attribute) (in module galaxy.web.framework.base) server_url (galaxy.model.PSAAssociation attribute) (galaxy.model.PSANonce attribute) ServerDirElement (class in galaxy.schema.fetch_data) ServerNotConfiguredForRequest ServesExportStores (class in galaxy.webapps.galaxy.services.base) ServesTemplatesPluginMixin (class in galaxy.visualization.plugins.plugin) service (galaxy.webapps.galaxy.api.folder_contents.FastAPILibraryFoldersContents attribute) (galaxy.webapps.galaxy.api.folders.FastAPILibraryFolders attribute) (galaxy.webapps.galaxy.api.libraries.FastAPILibraries attribute) (galaxy.webapps.galaxy.api.pages.FastAPIPages attribute) (galaxy.webapps.galaxy.api.quotas.FastAPIQuota attribute) (galaxy.webapps.galaxy.api.tool_shed_repositories.FastAPIToolShedRepositories attribute) (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController attribute) (galaxy.webapps.galaxy.api.tools.FetchTools attribute) (galaxy.webapps.galaxy.api.tools.ToolsController attribute) (galaxy.webapps.galaxy.api.users.FastAPIUsers attribute) (galaxy.webapps.galaxy.api.users.UserAPIController attribute) (galaxy.webapps.galaxy.api.visualizations.FastAPIVisualizations attribute) (galaxy.webapps.galaxy.api.visualizations.VisualizationsController attribute) service_object_dict() (in module galaxy.jobs.runners.util.pykube_util) ServiceBase (class in galaxy.webapps.galaxy.services.base) Session (galaxy.model.base.ModelMapping property) session (galaxy.web.framework.base.DefaultWebTransaction attribute) session() (galaxy.managers.annotatable.AnnotatableManagerMixin method) (galaxy.managers.base.ModelManager method) (galaxy.managers.rbac_secured.RBACPermission method) session_csrf_token (galaxy.webapps.base.webapp.GalaxyWebTransaction property) session_get() (galaxy.authnz.psa_authnz.Strategy method) session_id (galaxy.model.Event attribute) (galaxy.model.GalaxySessionToHistoryAssociation attribute) (galaxy.model.Job attribute) (galaxy.model.UserAction attribute) session_key (galaxy.model.GalaxySession attribute) (tool_shed.webapp.model.GalaxySession attribute) session_pop() (galaxy.authnz.psa_authnz.Strategy method) session_set() (galaxy.authnz.psa_authnz.Strategy method) SessionlessContext (class in galaxy.model.store) SessionlessJobContext (class in galaxy.job_execution.output_collect) SessionlessModelPersistenceContext (class in galaxy.model.store.discover) SessionRequestContext (class in galaxy.work.context) set() (galaxy.managers.datasets.DatasetRBACPermissions method) (galaxy.managers.rbac_secured.DatasetRBACPermission method) (galaxy.tools.cache.ToolDocumentCache method) set_access_permission() (galaxy_test.base.populators.LibraryPopulator method) set_add_permission() (galaxy_test.base.populators.LibraryPopulator method) set_all_dataset_permissions() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) set_all_library_permissions() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) set_allow_push() (tool_shed.webapp.model.Repository method) set_amount() (galaxy.model.Quota method) set_as_current() (galaxy.webapps.galaxy.controllers.history.HistoryController method) set_attribute_metadata() (galaxy.datatypes.interval.Gff method) set_basename_and_derived_properties() (in module galaxy.tool_util.cwl.util) set_basic_defaults() (in module galaxy.jobs.splitters.basic) set_beacon() (galaxy.webapps.galaxy.api.users.FastAPIUsers method) set_cache_value() (galaxy.work.context.WorkRequestContext method) set_changeset_revision() (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator method) set_collection_attributes() (in module galaxy.managers.hdcas) set_collection_elements() (in module galaxy.model.dataset_collections.builder) set_command_line() (galaxy.model.Job method) (galaxy.model.Task method) set_compute_environment() (galaxy.tools.evaluation.ToolEvaluator method) set_content_type() (galaxy.work.context.GalaxyAbstractResponse method) set_cookie() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) (galaxy.webapps.galaxy.api.GalaxyASGIResponse method) (galaxy.work.context.GalaxyAbstractResponse method) set_copied_from_job_id() (galaxy.model.Job method) set_cors_allow() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) set_cors_headers() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) set_cors_origin() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) set_created_from_basename() (galaxy.model.DatasetInstance method) set_current() (galaxy.managers.histories.HistoryManager method) set_current_by_id() (galaxy.managers.histories.HistoryManager method) set_dataset_matcher_factory() (in module galaxy.tools.parameters.dataset_matcher) set_dataset_object_store_id() (galaxy.objectstore.ObjectStorePopulator method) set_dataset_permission() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) set_dataset_permissions() (galaxy.model.security.HostAgent method) set_datasets_metadata() (galaxy.model.store.discover.ModelPersistenceContext static method) set_datatypes_registry() (in module galaxy.model) set_dbkey() (galaxy.model.DatasetInstance method) set_default() (galaxy.schema.schema.WithModelClass class method) set_default_hda_permissions() (galaxy.job_execution.output_collect.PermissionProvider method) (galaxy.model.store.discover.PermissionProvider method) set_default_values() (galaxy.datatypes.registry.Registry method) set_defaults() (galaxy.jobs.runners.JobState method) set_dependencies() (galaxy.model.Job method) set_disk_usage() (galaxy.model.GalaxySession method) (galaxy.model.User method) (tool_shed.webapp.model.User method) set_email_alerts() (tool_shed.webapp.controllers.repository.RepositoryController method) set_enabled_container_types() (galaxy.tool_util.deps.DependencyManager method) set_entity_group_associations() (galaxy.model.security.GalaxyRBACAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) set_entity_role_associations() (galaxy.model.security.GalaxyRBACAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) set_entity_user_associations() (galaxy.model.security.GalaxyRBACAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) set_extra_data() (galaxy.model.UserAuthnzToken method) set_extra_files_path() (galaxy.model.Dataset method) set_favorite() (galaxy.webapps.galaxy.api.users.FastAPIUsers method) set_file_name() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) set_filter() (tool_shed.grids.repository_grid_filter_manager.RepositoryGridFilterManager method) set_final_state() (galaxy.model.Job method) set_from_dict() (galaxy.model.DatasetCollection method) (galaxy.model.DatasetCollectionInstance method) set_handler() (galaxy.model.Job method) (galaxy.model.WorkflowInvocation method) set_history() (galaxy.app_unittest_utils.galaxy_mock.MockTrans method) (galaxy.webapps.base.webapp.GalaxyWebTransaction method) (galaxy.work.context.SessionRequestContext method) set_history_annotation() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) set_history_export_request_metadata() (galaxy.managers.model_stores.ModelStoreManager method) set_history_export_result_metadata() (galaxy.managers.model_stores.ModelStoreManager method) set_id() (galaxy.model.Task method) set_image_paths() (in module galaxy.tool_shed.util.shed_util_common) set_imported() (galaxy.model.Job method) set_index_file() (galaxy.datatypes.binary.CRAM method) set_info() (galaxy.model.Job method) (galaxy.model.LibraryDataset method) (galaxy.model.Task method) set_information() (galaxy.webapps.galaxy.api.users.UserAPIController method) set_initial_metadata() (galaxy.datatypes.constructive_solid_geometry.Vtk method) set_input_datasets() (galaxy.model.Job method) set_input_library_datasets() (galaxy.model.Job method) set_item() (tool_shed.webapp.model.ItemRatingAssociation method) (tool_shed.webapp.model.RepositoryRatingAssociation method) set_item_extended_metadata_obj() (galaxy.webapps.base.controller.UsesExtendedMetadataMixin method) set_job() (galaxy.model.Task method) set_job_destination() (galaxy.jobs.JobWrapper method) set_job_outputs() (galaxy.job_execution.setup.JobOutputs method) set_job_runner_external_id() (galaxy.model.Task method) set_legacy_alias() (galaxy.tools.parameters.wrapped.LegacyUnprefixedDict method) set_library_item_permission() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) set_log_handler() (in module galaxy.util.script) set_malicious() (tool_shed.webapp.controllers.repository.RepositoryController method) set_manage_permission() (galaxy_test.base.populators.LibraryPopulator method) set_max_optional_metadata_filesize() (galaxy.datatypes.data.Data method) set_message() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) set_meta() (galaxy.datatypes.anvio.AnvioDB method) (galaxy.datatypes.assembly.Velvet method) (galaxy.datatypes.binary.Anndata method) (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.binary.Bcf method) (galaxy.datatypes.binary.Biom2 method) (galaxy.datatypes.binary.BlibSQlite method) (galaxy.datatypes.binary.Cel method) (galaxy.datatypes.binary.ChiraSQLite method) (galaxy.datatypes.binary.CRAM method) (galaxy.datatypes.binary.CuffDiffSQlite method) (galaxy.datatypes.binary.DlibSQlite method) (galaxy.datatypes.binary.ElibSQlite method) (galaxy.datatypes.binary.Fast5Archive method) (galaxy.datatypes.binary.FITS method) (galaxy.datatypes.binary.GAFASQLite method) (galaxy.datatypes.binary.GeminiSQLite method) (galaxy.datatypes.binary.Grib method) (galaxy.datatypes.binary.H5MLM method) (galaxy.datatypes.binary.HexrdEtaOmeNpz method) (galaxy.datatypes.binary.HexrdImagesNpz method) (galaxy.datatypes.binary.HexrdMaterials method) (galaxy.datatypes.binary.IdpDB method) (galaxy.datatypes.binary.Loom method) (galaxy.datatypes.binary.MongoDBArchive method) (galaxy.datatypes.binary.MzSQlite method) (galaxy.datatypes.binary.NcbiTaxonomySQlite method) (galaxy.datatypes.binary.Npz method) (galaxy.datatypes.binary.Numpy method) (galaxy.datatypes.binary.OSW method) (galaxy.datatypes.binary.PostgresqlArchive method) (galaxy.datatypes.binary.PQP method) (galaxy.datatypes.binary.RData method) (galaxy.datatypes.binary.RDS method) (galaxy.datatypes.binary.SearchGuiArchive method) (galaxy.datatypes.binary.SQlite method) (galaxy.datatypes.binary.SQmass method) (galaxy.datatypes.constructive_solid_geometry.GmshMsh method) (galaxy.datatypes.constructive_solid_geometry.NeperPoints method) (galaxy.datatypes.constructive_solid_geometry.NeperPointsTabular method) (galaxy.datatypes.constructive_solid_geometry.NeperTesr method) (galaxy.datatypes.constructive_solid_geometry.NeperTess method) (galaxy.datatypes.constructive_solid_geometry.Ply method) (galaxy.datatypes.constructive_solid_geometry.Vtk method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.data.Text method) (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.genetics.IdeasPre method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.genetics.Rgenetics method) (galaxy.datatypes.goldenpath.GoldenPath method) (galaxy.datatypes.images.Tiff method) (galaxy.datatypes.interval.Bed method) (galaxy.datatypes.interval.BedStrict method) (galaxy.datatypes.interval.CustomTrack method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Gff3 method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.IntervalTabix method) (galaxy.datatypes.interval.Wiggle method) (galaxy.datatypes.media.Audio method) (galaxy.datatypes.media.Video method) (galaxy.datatypes.media.Wav method) (galaxy.datatypes.microarrays.Gal method) (galaxy.datatypes.microarrays.Gpr method) (galaxy.datatypes.molecules.AtomicStructFile method) (galaxy.datatypes.molecules.CML method) (galaxy.datatypes.molecules.DRF method) (galaxy.datatypes.molecules.FPS method) (galaxy.datatypes.molecules.InChI method) (galaxy.datatypes.molecules.MOL method) (galaxy.datatypes.molecules.MOL2 method) (galaxy.datatypes.molecules.PDB method) (galaxy.datatypes.molecules.PQR method) (galaxy.datatypes.molecules.SDF method) (galaxy.datatypes.molecules.SMILES method) (galaxy.datatypes.mothur.AlignCheck method) (galaxy.datatypes.mothur.CountTable method) (galaxy.datatypes.mothur.DistanceMatrix method) (galaxy.datatypes.mothur.Group method) (galaxy.datatypes.mothur.GroupAbund method) (galaxy.datatypes.mothur.Otu method) (galaxy.datatypes.mothur.PairwiseDistanceMatrix method) (galaxy.datatypes.mothur.SffFlow method) (galaxy.datatypes.msa.InfernalCM method) (galaxy.datatypes.msa.MauveXmfa method) (galaxy.datatypes.msa.Stockholm_1_0 method) (galaxy.datatypes.phylip.Phylip method) (galaxy.datatypes.plant_tribes.PlantTribesKsComponents method) (galaxy.datatypes.proteomics.Dta method) (galaxy.datatypes.proteomics.Dta2d method) (galaxy.datatypes.proteomics.Edta method) (galaxy.datatypes.qiime2.QIIME2Metadata method) (galaxy.datatypes.qualityscore.QualityScoreSOLiD method) (galaxy.datatypes.sequence.BaseFastq method) (galaxy.datatypes.sequence.csFasta method) (galaxy.datatypes.sequence.DotBracket method) (galaxy.datatypes.sequence.Fasta method) (galaxy.datatypes.sequence.Fastg method) (galaxy.datatypes.sequence.Maf method) (galaxy.datatypes.sequence.MafCustomTrack method) (galaxy.datatypes.sequence.Sequence method) (galaxy.datatypes.speech.BPF method) (galaxy.datatypes.tabular.BaseCSV method) (galaxy.datatypes.tabular.BaseVcf method) (galaxy.datatypes.tabular.CMAP method) (galaxy.datatypes.tabular.ConnectivityTable method) (galaxy.datatypes.tabular.Eland method) (galaxy.datatypes.tabular.MatrixMarket method) (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.SraManifest method) (galaxy.datatypes.tabular.Tabular method) (galaxy.datatypes.tabular.TabularData method) (galaxy.datatypes.tabular.VcfGz method) (galaxy.datatypes.text.Arff method) (galaxy.datatypes.text.Biom1 method) (galaxy.datatypes.text.DataManagerJson method) (galaxy.datatypes.text.ExpressionJson method) (galaxy.datatypes.text.ImgtJson method) (galaxy.datatypes.text.Ipynb method) (galaxy.datatypes.text.SnpEffDb method) (galaxy.datatypes.text.SnpSiftDbNSFP method) (galaxy.datatypes.triples.Sbol method) (galaxy.datatypes.xml.Dzi method) (galaxy.model.DatasetInstance method) set_meta_with_tool_provided() (in module galaxy.metadata.set_metadata) set_metadata() (galaxy.managers.datasets.DatasetAssociationManager method) (galaxy.model.DatasetInstance method) (in module galaxy.metadata.set_metadata) (in module galaxy_ext.metadata.set_metadata) set_metadata_portable() (in module galaxy.metadata.set_metadata) set_metadata_requires_flush (galaxy.model.DatasetInstance property) set_metadata_success_state() (galaxy.model.DatasetInstance method) set_modify_permission() (galaxy_test.base.populators.LibraryPopulator method) set_name() (galaxy.model.LibraryDataset method) set_object_store_id() (galaxy.objectstore.ObjectStorePopulator method) set_only_if_compiling_contained_td() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) set_output_datasets() (galaxy.model.Job method) set_output_library_datasets() (galaxy.model.Job method) set_param_filename() (galaxy.model.Job method) set_parameters() (galaxy.model.Job method) (galaxy.model.Task method) set_params() (galaxy.model.Job method) set_parent() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataCollection method) set_password() (galaxy.webapps.galaxy.api.users.UserAPIController method) set_password_cleartext() (galaxy.model.User method) (tool_shed.webapp.model.User method) set_peek() (galaxy.datatypes.annotation.Augustus method) (galaxy.datatypes.annotation.SnapHmm method) (galaxy.datatypes.anvio.AnvioComposite method) (galaxy.datatypes.binary.Ab1 method) (galaxy.datatypes.binary.Anndata method) (galaxy.datatypes.binary.BafTar method) (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.binary.BigWig method) (galaxy.datatypes.binary.Binary method) (galaxy.datatypes.binary.Biom2 method) (galaxy.datatypes.binary.Bref3 method) (galaxy.datatypes.binary.Cel method) (galaxy.datatypes.binary.CompressedArchive method) (galaxy.datatypes.binary.CompressedZipArchive method) (galaxy.datatypes.binary.Cool method) (galaxy.datatypes.binary.CRAM method) (galaxy.datatypes.binary.CuffDiffSQlite method) (galaxy.datatypes.binary.Dcd method) (galaxy.datatypes.binary.ExcelXls method) (galaxy.datatypes.binary.Fast5Archive method) (galaxy.datatypes.binary.FITS method) (galaxy.datatypes.binary.GeminiSQLite method) (galaxy.datatypes.binary.GmxBinary method) (galaxy.datatypes.binary.Grib method) (galaxy.datatypes.binary.H5 method) (galaxy.datatypes.binary.H5MLM method) (galaxy.datatypes.binary.HexrdEtaOmeNpz method) (galaxy.datatypes.binary.HexrdImagesNpz method) (galaxy.datatypes.binary.HexrdMaterials method) (galaxy.datatypes.binary.ICM method) (galaxy.datatypes.binary.IdpDB method) (galaxy.datatypes.binary.JP2 method) (galaxy.datatypes.binary.Loom method) (galaxy.datatypes.binary.MCool method) (galaxy.datatypes.binary.MongoDBArchive method) (galaxy.datatypes.binary.NcbiTaxonomySQlite method) (galaxy.datatypes.binary.NetCDF method) (galaxy.datatypes.binary.Npz method) (galaxy.datatypes.binary.Numpy method) (galaxy.datatypes.binary.PostgresqlArchive method) (galaxy.datatypes.binary.Pretext method) (galaxy.datatypes.binary.Scf method) (galaxy.datatypes.binary.SearchGuiArchive method) (galaxy.datatypes.binary.Sff method) (galaxy.datatypes.binary.SQlite method) (galaxy.datatypes.binary.Sra method) (galaxy.datatypes.binary.TwoBit method) (galaxy.datatypes.binary.Vel method) (galaxy.datatypes.blast.BlastXml method) (galaxy.datatypes.blast.LastDb method) (galaxy.datatypes.constructive_solid_geometry.GmshMsh method) (galaxy.datatypes.constructive_solid_geometry.NeperPoints method) (galaxy.datatypes.constructive_solid_geometry.NeperPointsTabular method) (galaxy.datatypes.constructive_solid_geometry.NeperTesr method) (galaxy.datatypes.constructive_solid_geometry.NeperTess method) (galaxy.datatypes.constructive_solid_geometry.Ply method) (galaxy.datatypes.constructive_solid_geometry.Vtk method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.data.Text method) (galaxy.datatypes.flow.FCS method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.genetics.SNPMatrix method) (galaxy.datatypes.gis.Shapefile method) (galaxy.datatypes.graph.Sif method) (galaxy.datatypes.graph.Xgmml method) (galaxy.datatypes.images.Image method) (galaxy.datatypes.images.Star method) (galaxy.datatypes.microarrays.GenericMicroarrayFile method) (galaxy.datatypes.molecules.AtomicStructFile method) (galaxy.datatypes.molecules.CML method) (galaxy.datatypes.molecules.GenericMolFile method) (galaxy.datatypes.molecules.grd method) (galaxy.datatypes.molecules.grdtgz method) (galaxy.datatypes.molecules.GRO method) (galaxy.datatypes.molecules.InChI method) (galaxy.datatypes.molecules.OBFS method) (galaxy.datatypes.molecules.PDB method) (galaxy.datatypes.molecules.PDBQT method) (galaxy.datatypes.molecules.PHAR method) (galaxy.datatypes.molecules.PQR method) (galaxy.datatypes.molecules.SMILES method) (galaxy.datatypes.msa.Hmmer method) (galaxy.datatypes.msa.HmmerPress method) (galaxy.datatypes.msa.InfernalCM method) (galaxy.datatypes.msa.MauveXmfa method) (galaxy.datatypes.msa.Stockholm_1_0 method) (galaxy.datatypes.neo4j.Neo4j method) (galaxy.datatypes.ngsindex.BowtieIndex method) (galaxy.datatypes.phylip.Phylip method) (galaxy.datatypes.plant_tribes.PlantTribesKsComponents method) (galaxy.datatypes.plant_tribes.Smat method) (galaxy.datatypes.proteomics.MascotDat method) (galaxy.datatypes.proteomics.Mgf method) (galaxy.datatypes.proteomics.MzTab method) (galaxy.datatypes.proteomics.MzTab2 method) (galaxy.datatypes.proteomics.ProteomicsXml method) (galaxy.datatypes.proteomics.SPLib method) (galaxy.datatypes.proteomics.SPLibNoIndex method) (galaxy.datatypes.proteomics.ThermoRAW method) (galaxy.datatypes.sequence.Fastg method) (galaxy.datatypes.sequence.Maf method) (galaxy.datatypes.sequence.RNADotPlotMatrix method) (galaxy.datatypes.sequence.Sequence method) (galaxy.datatypes.sequence.SequenceSplitLocations method) (galaxy.datatypes.tabular.TabularData method) (galaxy.datatypes.text.Arff method) (galaxy.datatypes.text.BCSLts method) (galaxy.datatypes.text.Biom1 method) (galaxy.datatypes.text.CTLresult method) (galaxy.datatypes.text.GeoJson method) (galaxy.datatypes.text.Html method) (galaxy.datatypes.text.ImgtJson method) (galaxy.datatypes.text.Ipynb method) (galaxy.datatypes.text.Json method) (galaxy.datatypes.text.Obo method) (galaxy.datatypes.text.SnpSiftDbNSFP method) (galaxy.datatypes.text.StormCheck method) (galaxy.datatypes.text.StormSample method) (galaxy.datatypes.tracks.UCSCTrackHub method) (galaxy.datatypes.triples.HDT method) (galaxy.datatypes.triples.Jsonld method) (galaxy.datatypes.triples.N3 method) (galaxy.datatypes.triples.NTriples method) (galaxy.datatypes.triples.Rdf method) (galaxy.datatypes.triples.Sbol method) (galaxy.datatypes.triples.Triples method) (galaxy.datatypes.triples.Turtle method) (galaxy.datatypes.xml.CisML method) (galaxy.datatypes.xml.Dzi method) (galaxy.datatypes.xml.GenericXml method) (galaxy.datatypes.xml.MEMEXml method) (galaxy.datatypes.xml.Owl method) (galaxy.datatypes.xml.Phyloxml method) (galaxy.datatypes.xml.Sbml method) (galaxy.model.DatasetInstance method) set_permissions (galaxy.schema.schema.DatasetPermissionAction attribute) (galaxy.schema.schema.LibraryFolderPermissionAction attribute) (galaxy.schema.schema.LibraryPermissionAction attribute) set_permissions() (galaxy.webapps.galaxy.api.folders.FastAPILibraryFolders method) (galaxy.webapps.galaxy.api.libraries.FastAPILibraries method) (galaxy.webapps.galaxy.api.users.UserAPIController method) (galaxy.webapps.galaxy.services.libraries.LibrariesService method) (galaxy.webapps.galaxy.services.library_folders.LibraryFoldersService method) (galaxy_test.base.populators.LibraryPopulator method) set_permissions_old() (galaxy.webapps.galaxy.services.libraries.LibrariesService method) set_permissions_with_action() (galaxy_test.base.populators.LibraryPopulator method) set_position() (galaxy.datatypes.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.RegionAlignment method) set_post_job_actions() (galaxy.model.Job method) set_postfork_server_name() (galaxy.web_stack.ApplicationStack method) set_prepare_input_files_cmd() (galaxy.model.Task method) set_prior_installation_required() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) set_private() (galaxy.managers.rbac_secured.AccessDatasetRBACPermission method) set_private_to_one_user() (galaxy.managers.datasets.DatasetRBACPermissions method) set_public_with_single_manager() (galaxy.managers.datasets.DatasetRBACPermissions method) set_quota_default() (galaxy.managers.quotas.QuotaManager method) (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) set_random_password() (galaxy.model.User method) (tool_shed.webapp.model.User method) set_range() (galaxy.datatypes.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.RegionAlignment method) set_relative_install_dir() (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator method) set_repository() (galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) (galaxy.tool_shed.metadata.metadata_generator.GalaxyMetadataGenerator method) (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) (tool_shed.metadata.repository_metadata_manager.ToolShedMetadataGenerator method) set_repository_attributes() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) set_repository_deprecated() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) set_repository_files_dir() (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator method) set_repository_malicious() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) set_repository_metadata() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) set_repository_metadata_due_to_new_tip() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) set_request_id() (galaxy.model.base.ModelMapping static method) set_runner() (galaxy.jobs.TaskWrapper method) set_runner_external_id() (galaxy.model.Job method) set_runner_name() (galaxy.model.Job method) set_session_id() (galaxy.model.Job method) set_size() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) set_slug() (galaxy.managers.sharable.SharableModelManager method) (galaxy.webapps.galaxy.api.pages.FastAPIPages method) (galaxy.webapps.galaxy.api.visualizations.FastAPIVisualizations method) (galaxy.webapps.galaxy.services.sharable.ShareableService method) set_slug_async() (galaxy.webapps.base.controller.SharableMixin method) set_sqlite_connect_args() (in module galaxy.model.orm.engine_factory) set_state() (galaxy.model.Job method) (galaxy.model.Task method) (galaxy.model.WorkflowInvocation method) set_streams() (galaxy.model.JobLike method) set_structure_metadata() (galaxy.datatypes.constructive_solid_geometry.Vtk method) set_tags() (galaxy_test.base.populators.BaseWorkflowPopulator method) set_tags_from_list() (galaxy.model.tags.TagHandler method) (galaxy.webapps.base.controller.UsesTagsMixin method) set_target (galaxy.web_stack.message.ApplicationStackMessage property) set_task_runner_external_id() (galaxy.model.Task method) set_task_runner_name() (galaxy.model.Task method) set_text_element() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor static method) set_theme() (galaxy.webapps.galaxy.api.users.FastAPIUsers method) set_thread_app() (in module galaxy.celery) set_tool_id() (galaxy.model.Job method) set_tool_version() (galaxy.model.Job method) set_toolbox_filters() (galaxy.webapps.galaxy.api.users.UserAPIController method) set_total_size() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) set_transaction_factory() (galaxy.web.framework.base.WebApplication method) set_user() (galaxy.app_unittest_utils.galaxy_mock.MockTrans method) (galaxy.managers.model_stores.ModelStoreUserContext method) (galaxy.webapps.base.webapp.GalaxyWebTransaction method) (galaxy.work.context.WorkRequestContext method) set_user_id() (galaxy.model.Job method) set_validated_state() (in module galaxy.metadata.set_metadata) set_working_directory() (galaxy.model.Task method) setdefault() (galaxy.util.odict.odict method) SetMetadataAction (class in galaxy.job_execution.actions.post) SetMetadataTool (class in galaxy.tools) SetMetadataToolAction (class in galaxy.tools.actions.metadata) SetParamAction (class in galaxy.tools) SetSlugPayload (class in galaxy.schema.schema) SETTING_METADATA (galaxy.schema.schema.DatasetState attribute) SETTING_TOOL_VERSIONS (galaxy.model.tool_shed_install.ToolShedRepository.installation_status attribute) settings (galaxy.datatypes.dataproviders.base.DataProvider attribute) (galaxy.datatypes.dataproviders.base.FilteredDataProvider attribute) (galaxy.datatypes.dataproviders.base.LimitedOffsetDataProvider attribute) (galaxy.datatypes.dataproviders.base.MultiSourceDataProvider attribute) (galaxy.datatypes.dataproviders.chunk.Base64ChunkDataProvider attribute) (galaxy.datatypes.dataproviders.chunk.ChunkDataProvider attribute) (galaxy.datatypes.dataproviders.column.ColumnarDataProvider attribute) (galaxy.datatypes.dataproviders.column.DictDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.BigWigDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.ConvertedDatasetDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.DatasetColumnarDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.DatasetDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.DatasetDictDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.DatasetSubprocessDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.FastaDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.GenomicRegionDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.IntervalDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.SQliteDataDictProvider attribute) (galaxy.datatypes.dataproviders.dataset.SQliteDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.SQliteDataTableProvider attribute) (galaxy.datatypes.dataproviders.dataset.TwoBitFastaDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.WiggleDataProvider attribute) (galaxy.datatypes.dataproviders.external.GzipDataProvider attribute) (galaxy.datatypes.dataproviders.external.RegexSubprocessDataProvider attribute) (galaxy.datatypes.dataproviders.external.SubprocessDataProvider attribute) (galaxy.datatypes.dataproviders.external.TempfileDataProvider attribute) (galaxy.datatypes.dataproviders.external.URLDataProvider attribute) (galaxy.datatypes.dataproviders.hierarchy.HierarchalDataProvider attribute) (galaxy.datatypes.dataproviders.hierarchy.XMLDataProvider attribute) (galaxy.datatypes.dataproviders.line.BlockDataProvider attribute) (galaxy.datatypes.dataproviders.line.FilteredLineDataProvider attribute) (galaxy.datatypes.dataproviders.line.RegexLineDataProvider attribute) (galaxy.datatypes.graph.SIFGraphDataProvider attribute) (galaxy.datatypes.graph.XGMMLGraphDataProvider attribute) setUp() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) (galaxy_test.api.test_datasets.TestDatasetsApi method) (galaxy_test.api.test_folder_contents.TestFolderContentsApi method) (galaxy_test.api.test_folders.TestFoldersApi method) (galaxy_test.api.test_group_roles.TestGroupRolesApi method) (galaxy_test.api.test_group_users.TestGroupUsersApi method) (galaxy_test.api.test_groups.TestGroupsApi method) (galaxy_test.api.test_histories.TestArchivingHistoriesWithoutExportRecord method) (galaxy_test.api.test_histories.TestHistoriesApi method) (galaxy_test.api.test_histories.TestImportExportHistory method) (galaxy_test.api.test_histories.TestSharingHistory method) (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) (galaxy_test.api.test_history_contents.TestHistoryContentsApiBulkOperation method) (galaxy_test.api.test_history_contents_provenance.TestProvenance method) (galaxy_test.api.test_jobs.TestJobsApi method) (galaxy_test.api.test_libraries.TestLibrariesApi method) (galaxy_test.api.test_pages.BasePagesApiTestCase method) (galaxy_test.api.test_roles.TestRolesApi method) (galaxy_test.api.test_tools.TestToolsApi method) (galaxy_test.api.test_tools_upload.TestToolsUpload method) (galaxy_test.api.test_webhooks.TestWebhooksApi method) (galaxy_test.api.test_workflows.BaseWorkflowsApiTestCase method) (galaxy_test.api.test_workflows.TestWorkflowSharingApi method) (galaxy_test.api.test_workflows_cwl.BaseCwlWorkflowsApiTestCase method) (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi method) (galaxy_test.base.testcase.FunctionalTestCase method) setup() (galaxy_test.driver.driver_util.TestDriver method) setUp() (galaxy_test.driver.integration_util.IntegrationInstance method) (galaxy_test.performance.test_workflow_framework_performance.TestWorkflowFrameworkPerformance method) (galaxy_test.selenium.test_tool_describing_tours.TestToolDescribingTours method) setup() (tool_shed.test.base.twilltestcase.GalaxyInteractorToolShedInstallationClient method) setUp() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) setup() (tool_shed.test.base.twilltestcase.StandaloneToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ToolShedInstallationClient method) setup_app() (galaxy.app_unittest_utils.tools_support.UsesApp method) setup_base_volumes() (galaxy.jobs.runners.kubernetes.KubernetesJobRunner method) setup_data_table_manager() (in module galaxy.celery.tasks) setup_external_metadata() (galaxy.jobs.TaskWrapper method) (galaxy.metadata.ExtendedDirectoryMetadataGenerator method) (galaxy.metadata.MetadataCollectionStrategy method) (galaxy.metadata.PortableDirectoryMetadataGenerator method) setup_fetch_to_folder() (galaxy_test.base.populators.LibraryPopulator method) setup_freebayes_0010_repo() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) setup_galaxy_config() (in module galaxy_test.driver.driver_util) setup_global_logger() (in module galaxy.tool_util.verify.script) setup_history_export_job() (galaxy.managers.model_stores.ModelStoreManager method) setup_history_for_export_testing() (galaxy_test.base.populators.BaseDatasetPopulator method) setup_input_connections_by_name() (galaxy.model.WorkflowStep method) setup_inputs_by_name() (galaxy.model.WorkflowStep method) setup_job() (galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper method) (galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper method) setup_keep_outdir() (in module galaxy_test.base.env) setup_logging() (galaxy.main.GalaxyConfigBuilder method) setup_periodic_tasks() (in module galaxy.celery) setup_proxy() (galaxy.web.proxy.ProxyManager method) setup_query() (galaxy.jobs.handler.ItemGrabber method) setup_root() (in module galaxy.files.unittest_utils) setup_shared_state() (galaxy_test.selenium.test_custom_builds.TestCustomBuilds method) (galaxy_test.selenium.test_histories_list.TestSavedHistories method) setup_subworkflow() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) setup_two_users_with_one_shared_history() (galaxy_test.selenium.test_history_sharing.TestHistorySharing method) setup_two_users_with_one_shared_workflow() (galaxy_test.selenium.test_workflow_sharing.TestWorkflowSharing method) setup_with_driver() (galaxy_test.selenium.test_library_landing.TestLibraryLanding method) setup_worker_pool() (in module galaxy.celery) setup_workflow_run() (galaxy_test.base.populators.BaseWorkflowPopulator method) setUpClass() (galaxy_test.base.testcase.FunctionalTestCase class method) (galaxy_test.driver.integration_util.IntegrationInstance class method) SetupHistoryExportJob (class in galaxy.schema.tasks) Sf3 (class in galaxy.datatypes.proteomics) Sff (class in galaxy.datatypes.binary) SffFlow (class in galaxy.datatypes.mothur) sha() (in module galaxy.util.hash_util) sha1 (galaxy.schema.schema.HashFunctionNames attribute) sha1() (in module galaxy.util.hash_util) sha256 (galaxy.schema.schema.HashFunctionNames attribute) sha512 (galaxy.schema.schema.HashFunctionNames attribute) Shapefile (class in galaxy.datatypes.gis) sharable_owner() (tool_shed.webapp.controllers.repository.RepositoryController method) sharable_repository() (tool_shed.webapp.controllers.repository.RepositoryController method) sharable_repository_revision() (tool_shed.webapp.controllers.repository.RepositoryController method) SharableMixin (class in galaxy.webapps.base.controller) SharableModelDeserializer (class in galaxy.managers.sharable) SharableModelFilters (class in galaxy.managers.sharable) SharableModelManager (class in galaxy.managers.sharable) SharableModelSerializer (class in galaxy.managers.sharable) share() (galaxy.webapps.base.controller.SharableMixin method) share_ensure_by_user_available() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) share_history_with_user() (galaxy_test.selenium.test_history_sharing.TestHistorySharing method) share_option (galaxy.schema.schema.ShareWithPayload attribute) share_unshare_with_user() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) share_with() (galaxy.managers.sharable.SharableModelManager method) share_with_status_cls (galaxy.webapps.galaxy.services.histories.ShareableHistoryService attribute) (galaxy.webapps.galaxy.services.sharable.ShareableService attribute) share_with_user() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) (galaxy_test.base.populators.BaseWorkflowPopulator method) share_with_users() (galaxy.webapps.galaxy.api.pages.FastAPIPages method) (galaxy.webapps.galaxy.api.visualizations.FastAPIVisualizations method) (galaxy.webapps.galaxy.services.histories.ShareableHistoryService method) (galaxy.webapps.galaxy.services.sharable.ShareableService method) shareable (galaxy.model.Dataset property) ShareableHistoryService (class in galaxy.webapps.galaxy.services.histories) ShareableService (class in galaxy.webapps.galaxy.services.sharable) shared_with_me() (galaxy.webapps.galaxy.services.histories.HistoriesService method) SharedComputeEnvironment (class in galaxy.job_execution.compute_environment) SharedItemNotificationFactory (class in galaxy.webapps.galaxy.services.sharable) SharedModelMapping (class in galaxy.model.base) ShareHistoryExtra (class in galaxy.schema.schema) ShareHistoryWithStatus (class in galaxy.schema.schema) ShareWithExtra (class in galaxy.managers.sharable) (class in galaxy.schema.schema) ShareWithPayload (class in galaxy.schema.schema) ShareWithStatus (class in galaxy.schema.schema) SHARING (galaxy.model.Role.types attribute) sharing() (galaxy.webapps.galaxy.api.pages.FastAPIPages method) (galaxy.webapps.galaxy.api.visualizations.FastAPIVisualizations method) (galaxy.webapps.galaxy.services.sharable.ShareableService method) sharing_roles() (galaxy.managers.users.UserManager method) SharingApiTests (class in galaxy_test.api.sharable) SharingOptions (class in galaxy.managers.sharable) (class in galaxy.schema.schema) SharingStatus (class in galaxy.schema.schema) SharingStatusColumn (class in galaxy.web.legacy_framework.grids) shed_config_dict (galaxy.tool_shed.metadata.metadata_generator.BaseMetadataGenerator attribute) (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager attribute) shed_config_filename (galaxy.model.tool_shed_install.ToolShedRepository property) shed_counter (tool_shed.webapp.model.mapping.ToolShedModelMapping attribute) SHED_SEARCH (galaxy.selenium.navigates_galaxy.WAIT_TYPES attribute) shed_tool_conf (galaxy.managers.workflows.WorkflowCreateOptions attribute) shed_tool_data_path (galaxy.config.GalaxyAppConfiguration attribute) (galaxy.tools.repositories.ValidationContextConfig attribute) (tool_shed.webapp.config.ToolShedAppConfiguration property) shed_tool_data_table_conf (tool_shed.test.base.twilltestcase.GalaxyInteractorToolShedInstallationClient property) (tool_shed.test.base.twilltestcase.ShedTwillTestCase property) (tool_shed.test.base.twilltestcase.StandaloneToolShedInstallationClient property) (tool_shed.test.base.twilltestcase.ToolShedInstallationClient property) shed_tool_data_table_config (galaxy.tools.repositories.ValidationContextConfig attribute) ShedCounter (class in tool_shed.webapp.util.shed_statistics) ShedToolDataTableManager (class in galaxy.tool_shed.tools.data_table_manager) (class in tool_shed.tools.data_table_manager) ShedToolStatic (class in galaxy.webapps.galaxy.controllers.shed_tool_static) ShedTwillTestCase (class in tool_shed.test.base.twilltestcase) shell (galaxy.tool_util.deps.container_classes.Container property) (galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledDockerContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.CachedMulledDockerContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.CachedMulledSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.MulledDockerContainerResolver attribute) shell() (in module galaxy.util.commands) shell_commands (galaxy.tool_util.deps.resolvers.ContainerDependency property) shell_commands() (galaxy.tool_util.deps.resolvers.Dependency method) (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependency method) (galaxy.tool_util.deps.resolvers.NullDependency method) (galaxy.tool_util.deps.resolvers.resolver_mixins.HomebrewDependency method) shell_process() (in module galaxy.util.commands) ShellJobRunner (class in galaxy.jobs.runners.cli) short_name (galaxy.tool_util.deps.requirements.RequirementSpecification property) short_term_storage_monitor (galaxy.webapps.galaxy.api.short_term_storage.FastAPIShortTermStorage attribute) short_term_storage_request_id (galaxy.schema.schema.ShortTermStoreExportPayload attribute) (galaxy.schema.tasks.GeneratePdfDownload attribute) (galaxy.schema.tasks.PrepareDatasetCollectionDownload attribute) ShortTermStoreExportPayload (class in galaxy.schema.schema) should_burst() (galaxy.jobs.rule_helper.RuleHelper method) show() (galaxy.managers.group_roles.GroupRolesManager method) (galaxy.managers.group_users.GroupUsersManager method) (galaxy.managers.groups.GroupsManager method) (galaxy.managers.tool_data.ToolDataManager method) (galaxy.tool_util.deps.views.ContainerResolutionView method) (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.container_resolution.ContainerResolutionAPIController method) (galaxy.webapps.galaxy.api.dynamic_tools.DynamicToolsController method) (galaxy.webapps.galaxy.api.folders.FastAPILibraryFolders method) (galaxy.webapps.galaxy.api.forms.FormDefinitionAPIController method) (galaxy.webapps.galaxy.api.genomes.FastAPIGenomes method) (galaxy.webapps.galaxy.api.group_roles.FastAPIGroupRoles method) (galaxy.webapps.galaxy.api.group_users.FastAPIGroupUsers method) (galaxy.webapps.galaxy.api.groups.FastAPIGroups method) (galaxy.webapps.galaxy.api.libraries.FastAPILibraries method) (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method) (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method) (galaxy.webapps.galaxy.api.pages.FastAPIPages method) (galaxy.webapps.galaxy.api.plugins.PluginsController method) (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method) (galaxy.webapps.galaxy.api.quotas.FastAPIQuota method) (galaxy.webapps.galaxy.api.roles.FastAPIRoles method) (galaxy.webapps.galaxy.api.tool_data.FastAPIToolData method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) (galaxy.webapps.galaxy.api.tool_shed_repositories.FastAPIToolShedRepositories method) (galaxy.webapps.galaxy.api.tools.ToolsController method) (galaxy.webapps.galaxy.api.tours.FastAPITours method) (galaxy.webapps.galaxy.api.users.FastAPIUsers method) (galaxy.webapps.galaxy.api.visualizations.VisualizationsController method) (galaxy.webapps.galaxy.services.histories.HistoriesService method) (galaxy.webapps.galaxy.services.libraries.LibrariesService method) (galaxy.webapps.galaxy.services.library_folders.LibraryFoldersService method) (galaxy.webapps.galaxy.services.pages.PagesService method) (galaxy.webapps.galaxy.services.quotas.QuotasService method) (tool_shed.webapp.api.categories.CategoriesController method) (tool_shed.webapp.api.groups.GroupsController method) (tool_shed.webapp.api.repositories.RepositoriesController method) (tool_shed.webapp.api.repository_revisions.RepositoryRevisionsController method) (tool_shed.webapp.api.users.UsersController method) show_deleted (galaxy.schema.schema.WorkflowIndexQueryPayload attribute) show_deleted() (galaxy.webapps.galaxy.api.quotas.FastAPIQuota method) (galaxy.webapps.galaxy.api.users.FastAPIUsers method) show_dependencies() (galaxy.tool_util.deps.views.DependencyResolversView method) show_dynamic_tool() (galaxy_test.base.populators.BaseDatasetPopulator method) show_error_message() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) show_field() (galaxy.managers.tool_data.ToolDataManager method) (galaxy.webapps.galaxy.api.tool_data.FastAPIToolData method) show_hidden (galaxy.schema.schema.WorkflowIndexQueryPayload attribute) show_in_tool_panel (galaxy.schema.schema.StoredWorkflowSummary attribute) show_in_tool_panel() (galaxy.model.StoredWorkflow method) show_item_checkboxes (galaxy.web.legacy_framework.grids.Grid attribute) (tool_shed.grids.repository_grids.DockerImageGrid attribute) show_ld() (galaxy_test.base.populators.LibraryPopulator method) show_ld_raw() (galaxy_test.base.populators.LibraryPopulator method) show_ldda() (galaxy_test.base.populators.LibraryPopulator method) show_library_item() (galaxy.model.security.GalaxyRBACAgent method) show_message() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) show_ok_message() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) show_own (galaxy.schema.schema.PageIndexQueryPayload attribute) show_pdf() (galaxy.webapps.galaxy.api.pages.FastAPIPages method) (galaxy.webapps.galaxy.services.pages.PagesService method) show_published (galaxy.schema.schema.PageIndexQueryPayload attribute) (galaxy.schema.schema.WorkflowIndexQueryPayload attribute) show_roles() (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method) show_shared (galaxy.schema.schema.PageIndexQueryPayload attribute) (galaxy.schema.schema.WorkflowIndexQueryPayload attribute) show_tools() (tool_shed.webapp.api.repositories.RepositoriesController method) show_user() (galaxy.webapps.galaxy.services.users.UsersService method) show_version() (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method) show_warn_message() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) shrink_and_unicodify() (in module galaxy.util) shrink_stream_by_size() (in module galaxy.util) shrink_string_by_size() (in module galaxy.util) shutdown() (galaxy.app.HaltableContainer method) (galaxy.config_watchers.ConfigWatchers method) (galaxy.jobs.handler.DefaultJobDispatcher method) (galaxy.jobs.handler.JobHandler method) (galaxy.jobs.handler.JobHandlerI method) (galaxy.jobs.handler.JobHandlerQueue method) (galaxy.jobs.handler.JobHandlerStopQueue method) (galaxy.jobs.manager.JobManager method) (galaxy.jobs.manager.NoopHandler method) (galaxy.jobs.NoopQueue method) (galaxy.jobs.runners.AsynchronousJobRunner method) (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.local.LocalJobRunner method) (galaxy.model.database_heartbeat.DatabaseHeartbeat method) (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.cloud.Cloud method) (galaxy.objectstore.DistributedObjectStore method) (galaxy.objectstore.irods.IRODSObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.pulsar.PulsarObjectStore method) (galaxy.objectstore.s3.S3ObjectStore method) (galaxy.queue_worker.GalaxyQueueWorker method) (galaxy.tool_shed.galaxy_install.update_repository_manager.UpdateRepositoryManager method) (galaxy.tool_util.toolbox.watcher.ToolConfWatcher method) (galaxy.util.heartbeat.Heartbeat method) (galaxy.util.lazy_process.LazyProcess method) (galaxy.util.lazy_process.NoOpLazyProcess method) (galaxy.util.task.IntervalTask method) (galaxy.util.watcher.BaseWatcher method) (galaxy.util.watcher.NullWatcher method) (galaxy.web.proxy.ProxyManager method) (galaxy.web_stack.ApplicationStack method) (galaxy.web_stack.transport.ApplicationStackTransport method) (galaxy.webapps.reports.app.UniverseApplication method) (galaxy.workflow.schedulers.core.CoreWorkflowSchedulingPlugin method) (galaxy.workflow.schedulers.WorkflowSchedulingPlugin method) (galaxy.workflow.scheduling_manager.WorkflowRequestMonitor method) (galaxy.workflow.scheduling_manager.WorkflowSchedulingManager method)

shutdown_monitor() (galaxy.util.monitors.Monitors method) SHUTDOWN_MSG (galaxy.web_stack.transport.ApplicationStackTransport attribute) Sif (class in galaxy.datatypes.graph) SIFGraphDataProvider (class in galaxy.datatypes.graph) SILENT (galaxy.tool_util.lint.LintLevel attribute) simple_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method) SimpleComputeEnvironment (class in galaxy.job_execution.compute_environment) SimpleGraph (class in galaxy.util.simplegraph) SimpleGraphEdge (class in galaxy.util.simplegraph) SimpleGraphNode (class in galaxy.util.simplegraph) SimpleTextToolParameter (class in galaxy.tools.parameters.basic) SimpleTransientPathMapper (class in galaxy.model.deferred) simplify_edam_dict() (in module galaxy.tool_util.biotools.interface) simplify_edam_dicts() (in module galaxy.tool_util.biotools.interface) SINGLE_CHAR_ABBR (galaxy.managers.histories.HistorySerializer attribute) (galaxy.managers.pages.PageSerializer attribute) (galaxy.managers.sharable.SharableModelManager attribute) (galaxy.managers.sharable.SharableModelSerializer attribute) (galaxy.managers.visualizations.VisualizationSerializer attribute) (galaxy.managers.workflows.WorkflowSerializer attribute) SingleFileSource (class in galaxy.files.sources) SingleTagContentsParser (class in galaxy.webapps.galaxy.controllers.workflow) singularity_container_test() (in module galaxy.tool_util.deps.mulled.mulled_update_singularity_containers) SingularityContainer (class in galaxy.tool_util.deps.container_classes) singularize() (galaxy.util.inflection.Inflector method) SINGULARIZE_RULES (galaxy.util.inflection.Inflector attribute) site (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization attribute) sites (galaxy.model.security.HostAgent attribute) size (galaxy.files.sources.RemoteFile attribute) (galaxy.model.WorkflowComment attribute) (galaxy.schema.remote_files.RemoteFile attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.HistoryDetailed attribute) (galaxy.tool_util.cwl.util.OutputPropertiesType attribute) size() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method) size_string() (in module galaxy.tool_shed.util.basic_util) (in module tool_shed.util.basic_util) size_to_bytes() (in module galaxy.util) sizzle_presence_of_selector() (in module galaxy.selenium.sizzle) sizzle_selector_clickable() (in module galaxy.selenium.sizzle) skip() (galaxy.managers.base.ModelSerializer method) skip_if_github_workflow() (in module galaxy_test.driver.integration_util) skip_if_jenkins() (in module galaxy_test.driver.integration_util) skip_step_counts (galaxy.schema.schema.WorkflowIndexQueryPayload attribute) skip_types (galaxy.tool_util.lint.LintContext attribute) skip_unless_amqp() (in module galaxy_test.driver.integration_util) skip_unless_docker() (in module galaxy_test.driver.integration_util) skip_unless_environ() (in module galaxy_test.driver.integration_util) skip_unless_fixed_port() (in module galaxy_test.driver.integration_util) skip_unless_kubernetes() (in module galaxy_test.driver.integration_util) skip_unless_postgres() (in module galaxy_test.driver.integration_util) skip_without_asgi() (in module galaxy_test.base.populators) skip_without_datatype() (in module galaxy_test.base.populators) skip_without_tool() (in module galaxy_test.base.populators) skip_without_visualization_plugin() (in module galaxy_test.base.populators) SkipAttribute skipped (galaxy.model.JobStateSummary attribute) (galaxy.schema.schema.HDCJobStateSummary attribute) SKIPPED (galaxy.schema.schema.JobState attribute) skipped() (in module galaxy.tools.util.galaxyops) SkipWorkflowStepEvaluation slash_join() (in module galaxy.files.sources) sleep() (galaxy.util.sleeper.Sleeper method) sleep_for() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) sleep_for_seconds() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) Sleeper (class in galaxy.util.sleeper) slice_collections() (galaxy.model.dataset_collections.matching.MatchingCollections method) sliced_collection_type() (galaxy.model.dataset_collections.structure.Leaf method) slug (galaxy.model.History attribute) (galaxy.model.Page attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.Visualization attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.HistoryDetailed attribute) (galaxy.schema.schema.PageSummaryBase attribute) slug_builder (galaxy.webapps.base.controller.SharableMixin attribute) (galaxy.webapps.galaxy.controllers.history.HistoryController attribute) (galaxy.webapps.galaxy.controllers.page.PageController attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController attribute) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController attribute) SlugBuilder (class in galaxy.managers.sharable) Slurm (class in galaxy.jobs.runners.util.cli.job.slurm) SlurmJobRunner (class in galaxy.jobs.runners.slurm) SlurmTorque (class in galaxy.jobs.runners.util.cli.job.slurm_torque) smart_str() (in module galaxy.util) SmartComponent (class in galaxy.selenium.smart_components) SmartTarget (class in galaxy.selenium.smart_components) Smat (class in galaxy.datatypes.plant_tribes) SMILES (class in galaxy.datatypes.molecules) SnapHmm (class in galaxy.datatypes.annotation) snapshot() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) sniff() (galaxy.datatypes.annotation.Augustus method) (galaxy.datatypes.annotation.SnapHmm method) (galaxy.datatypes.assembly.Amos method) (galaxy.datatypes.assembly.Roadmaps method) (galaxy.datatypes.assembly.Sequences method) (galaxy.datatypes.binary.Anndata method) (galaxy.datatypes.binary.BafTar method) (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.binary.BamInputSorted method) (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.binary.BamQuerynameSorted method) (galaxy.datatypes.binary.Bcf method) (galaxy.datatypes.binary.BcfUncompressed method) (galaxy.datatypes.binary.BigWig method) (galaxy.datatypes.binary.Biom2 method) (galaxy.datatypes.binary.BlibSQlite method) (galaxy.datatypes.binary.Cel method) (galaxy.datatypes.binary.ChiraSQLite method) (galaxy.datatypes.binary.CompressedZipArchive method) (galaxy.datatypes.binary.Cool method) (galaxy.datatypes.binary.CRAM method) (galaxy.datatypes.binary.CuffDiffSQlite method) (galaxy.datatypes.binary.DAA method) (galaxy.datatypes.binary.Dcd method) (galaxy.datatypes.binary.DlibSQlite method) (galaxy.datatypes.binary.DMND method) (galaxy.datatypes.binary.ElibSQlite method) (galaxy.datatypes.binary.ExcelXls method) (galaxy.datatypes.binary.Fast5Archive method) (galaxy.datatypes.binary.Fast5ArchiveBz2 method) (galaxy.datatypes.binary.Fast5ArchiveGz method) (galaxy.datatypes.binary.Fast5ArchiveXz method) (galaxy.datatypes.binary.FITS method) (galaxy.datatypes.binary.GAFASQLite method) (galaxy.datatypes.binary.GeminiSQLite method) (galaxy.datatypes.binary.GmxBinary method) (galaxy.datatypes.binary.Grib method) (galaxy.datatypes.binary.H5 method) (galaxy.datatypes.binary.H5MLM method) (galaxy.datatypes.binary.HexrdEtaOmeNpz method) (galaxy.datatypes.binary.HexrdImagesNpz method) (galaxy.datatypes.binary.HexrdMaterials method) (galaxy.datatypes.binary.ICM method) (galaxy.datatypes.binary.Idat method) (galaxy.datatypes.binary.IdpDB method) (galaxy.datatypes.binary.JP2 method) (galaxy.datatypes.binary.Loom method) (galaxy.datatypes.binary.MCool method) (galaxy.datatypes.binary.Meryldb method) (galaxy.datatypes.binary.MongoDBArchive method) (galaxy.datatypes.binary.MzSQlite method) (galaxy.datatypes.binary.NcbiTaxonomySQlite method) (galaxy.datatypes.binary.NetCDF method) (galaxy.datatypes.binary.Npz method) (galaxy.datatypes.binary.Numpy method) (galaxy.datatypes.binary.OSW method) (galaxy.datatypes.binary.OxliCountGraph method) (galaxy.datatypes.binary.OxliGraphLabels method) (galaxy.datatypes.binary.OxliNodeGraph method) (galaxy.datatypes.binary.OxliStopTags method) (galaxy.datatypes.binary.OxliSubset method) (galaxy.datatypes.binary.OxliTagSet method) (galaxy.datatypes.binary.Parquet method) (galaxy.datatypes.binary.PostgresqlArchive method) (galaxy.datatypes.binary.PQP method) (galaxy.datatypes.binary.Pretext method) (galaxy.datatypes.binary.RData method) (galaxy.datatypes.binary.RDS method) (galaxy.datatypes.binary.RMA6 method) (galaxy.datatypes.binary.SearchGuiArchive method) (galaxy.datatypes.binary.Sff method) (galaxy.datatypes.binary.SQlite method) (galaxy.datatypes.binary.SQmass method) (galaxy.datatypes.binary.Sra method) (galaxy.datatypes.binary.TwoBit method) (galaxy.datatypes.binary.Vel method) (galaxy.datatypes.binary.Visium method) (galaxy.datatypes.binary.Wiff2Tar method) (galaxy.datatypes.binary.WiffTar method) (galaxy.datatypes.binary.Xlsx method) (galaxy.datatypes.blast.BlastXml method) (galaxy.datatypes.constructive_solid_geometry.GmshMsh method) (galaxy.datatypes.constructive_solid_geometry.NeperTesr method) (galaxy.datatypes.constructive_solid_geometry.NeperTess method) (galaxy.datatypes.constructive_solid_geometry.Ply method) (galaxy.datatypes.constructive_solid_geometry.Vtk method) (galaxy.datatypes.data.Newick method) (galaxy.datatypes.data.Nexus method) (galaxy.datatypes.flow.FCS method) (galaxy.datatypes.genetics.AllegroLOD method) (galaxy.datatypes.genetics.DataIn method) (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.genetics.GenotypeMatrix method) (galaxy.datatypes.genetics.MarkerMap method) (galaxy.datatypes.genetics.SNPMatrix method) (galaxy.datatypes.goldenpath.GoldenPath method) (galaxy.datatypes.graph.Sif method) (galaxy.datatypes.graph.Xgmml method) (galaxy.datatypes.hdf5.HDF5SummarizedExperiment method) (galaxy.datatypes.images.Gifti method) (galaxy.datatypes.images.Image method) (galaxy.datatypes.images.Mrc2014 method) (galaxy.datatypes.images.Nifti1 method) (galaxy.datatypes.images.Nifti2 method) (galaxy.datatypes.images.OMETiff method) (galaxy.datatypes.images.Pdf method) (galaxy.datatypes.images.Star method) (galaxy.datatypes.images.Tck method) (galaxy.datatypes.images.Trk method) (galaxy.datatypes.interval.BedStrict method) (galaxy.datatypes.interval.ChromatinInteractions method) (galaxy.datatypes.interval.CustomTrack method) (galaxy.datatypes.interval.ENCODEPeak method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.ScIdx method) (galaxy.datatypes.interval.Wiggle method) (galaxy.datatypes.media.Flv method) (galaxy.datatypes.media.Mkv method) (galaxy.datatypes.media.Mp3 method) (galaxy.datatypes.media.Mp4 method) (galaxy.datatypes.media.Mpg method) (galaxy.datatypes.media.Wav method) (galaxy.datatypes.microarrays.Gal method) (galaxy.datatypes.microarrays.Gpr method) (galaxy.datatypes.molecules.Cell method) (galaxy.datatypes.molecules.CIF method) (galaxy.datatypes.molecules.CML method) (galaxy.datatypes.molecules.ExtendedXYZ method) (galaxy.datatypes.molecules.FPS method) (galaxy.datatypes.molecules.InChI method) (galaxy.datatypes.molecules.Magres method) (galaxy.datatypes.molecules.MOL2 method) (galaxy.datatypes.molecules.PDB method) (galaxy.datatypes.molecules.PDBQT method) (galaxy.datatypes.molecules.PQR method) (galaxy.datatypes.molecules.SDF method) (galaxy.datatypes.molecules.XYZ method) (galaxy.datatypes.mothur.Axes method) (galaxy.datatypes.mothur.Frequency method) (galaxy.datatypes.mothur.LaneMask method) (galaxy.datatypes.mothur.LowerTriangleDistanceMatrix method) (galaxy.datatypes.mothur.Oligos method) (galaxy.datatypes.mothur.Otu method) (galaxy.datatypes.mothur.PairwiseDistanceMatrix method) (galaxy.datatypes.mothur.Quantile method) (galaxy.datatypes.mothur.RefTaxonomy method) (galaxy.datatypes.mothur.SecondaryStructureMap method) (galaxy.datatypes.mothur.SquareDistanceMatrix method) (galaxy.datatypes.msa.Hmmer method) (galaxy.datatypes.msa.InfernalCM method) (galaxy.datatypes.msa.MauveXmfa method) (galaxy.datatypes.msa.Stockholm_1_0 method) (galaxy.datatypes.phylip.Phylip method) (galaxy.datatypes.plant_tribes.PlantTribesKsComponents method) (galaxy.datatypes.plant_tribes.Smat method) (galaxy.datatypes.proteomics.Dta2d method) (galaxy.datatypes.proteomics.Edta method) (galaxy.datatypes.proteomics.Kroenik method) (galaxy.datatypes.proteomics.MascotDat method) (galaxy.datatypes.proteomics.Mgf method) (galaxy.datatypes.proteomics.Ms2 method) (galaxy.datatypes.proteomics.Msp method) (galaxy.datatypes.proteomics.MzTab method) (galaxy.datatypes.proteomics.PEFF method) (galaxy.datatypes.proteomics.PepList method) (galaxy.datatypes.proteomics.PSMS method) (galaxy.datatypes.proteomics.SPLib method) (galaxy.datatypes.proteomics.ThermoRAW method) (galaxy.datatypes.qiime2.QIIME2Artifact method) (galaxy.datatypes.qiime2.QIIME2Metadata method) (galaxy.datatypes.qiime2.QIIME2Visualization method) (galaxy.datatypes.qualityscore.QualityScore454 method) (galaxy.datatypes.qualityscore.QualityScoreSOLiD method) (galaxy.datatypes.sequence.Axt method) (galaxy.datatypes.sequence.BaseFastq method) (galaxy.datatypes.sequence.csFasta method) (galaxy.datatypes.sequence.DotBracket method) (galaxy.datatypes.sequence.Fasta method) (galaxy.datatypes.sequence.Fastg method) (galaxy.datatypes.sequence.Genbank method) (galaxy.datatypes.sequence.Lav method) (galaxy.datatypes.sequence.Maf method) (galaxy.datatypes.sequence.MemePsp method) (galaxy.datatypes.sequence.RNADotPlotMatrix method) (galaxy.datatypes.sequence.SequenceSplitLocations method) (galaxy.datatypes.speech.BPF method) (galaxy.datatypes.speech.TextGrid method) (galaxy.datatypes.tabular.BaseCSV method) (galaxy.datatypes.tabular.BaseVcf method) (galaxy.datatypes.tabular.CMAP method) (galaxy.datatypes.tabular.ConnectivityTable method) (galaxy.datatypes.tabular.Eland method) (galaxy.datatypes.tabular.ElandMulti method) (galaxy.datatypes.tabular.MatrixMarket method) (galaxy.datatypes.tabular.Pileup method) (galaxy.datatypes.tabular.Psl method) (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.VcfGz method) (galaxy.datatypes.text.Arff method) (galaxy.datatypes.text.BCSLmodel method) (galaxy.datatypes.text.BCSLts method) (galaxy.datatypes.text.Biom1 method) (galaxy.datatypes.text.Castep method) (galaxy.datatypes.text.CTLresult method) (galaxy.datatypes.text.FormattedDensity method) (galaxy.datatypes.text.GeoJson method) (galaxy.datatypes.text.Gfa1 method) (galaxy.datatypes.text.Gfa2 method) (galaxy.datatypes.text.Html method) (galaxy.datatypes.text.ImgtJson method) (galaxy.datatypes.text.Ipynb method) (galaxy.datatypes.text.IQTree method) (galaxy.datatypes.text.Json method) (galaxy.datatypes.text.Obo method) (galaxy.datatypes.text.Paf method) (galaxy.datatypes.text.Param method) (galaxy.datatypes.text.PithyaModel method) (galaxy.datatypes.text.PithyaProperty method) (galaxy.datatypes.text.PithyaResult method) (galaxy.datatypes.text.StormCheck method) (galaxy.datatypes.text.StormSample method) (galaxy.datatypes.text.Yaml method) (galaxy.datatypes.tracks.UCSCTrackHub method) (galaxy.datatypes.triples.HDT method) (galaxy.datatypes.triples.Jsonld method) (galaxy.datatypes.triples.N3 method) (galaxy.datatypes.triples.NTriples method) (galaxy.datatypes.triples.Rdf method) (galaxy.datatypes.triples.Sbol method) (galaxy.datatypes.triples.Triples method) (galaxy.datatypes.triples.Turtle method) (galaxy.datatypes.xml.CisML method) (galaxy.datatypes.xml.GenericXml method) (galaxy.datatypes.xml.MEMEXml method) sniff_prefix() (galaxy.datatypes.annotation.SnapHmm method) (galaxy.datatypes.assembly.Amos method) (galaxy.datatypes.assembly.Roadmaps method) (galaxy.datatypes.assembly.Sequences method) (galaxy.datatypes.binary.BigWig method) (galaxy.datatypes.binary.Bref3 method) (galaxy.datatypes.binary.DAA method) (galaxy.datatypes.binary.DMND method) (galaxy.datatypes.binary.ExcelXls method) (galaxy.datatypes.binary.GmxBinary method) (galaxy.datatypes.binary.Grib method) (galaxy.datatypes.binary.NetCDF method) (galaxy.datatypes.binary.Numpy method) (galaxy.datatypes.binary.Parquet method) (galaxy.datatypes.binary.Pretext method) (galaxy.datatypes.binary.RData method) (galaxy.datatypes.binary.RDS method) (galaxy.datatypes.binary.RMA6 method) (galaxy.datatypes.binary.Sff method) (galaxy.datatypes.binary.Sra method) (galaxy.datatypes.binary.TwoBit method) (galaxy.datatypes.binary.Xlsx method) (galaxy.datatypes.blast.BlastXml method) (galaxy.datatypes.constructive_solid_geometry.GmshMsh method) (galaxy.datatypes.constructive_solid_geometry.NeperTesr method) (galaxy.datatypes.constructive_solid_geometry.NeperTess method) (galaxy.datatypes.constructive_solid_geometry.Ply method) (galaxy.datatypes.constructive_solid_geometry.Vtk method) (galaxy.datatypes.data.Nexus method) (galaxy.datatypes.flow.FCS method) (galaxy.datatypes.genetics.AllegroLOD method) (galaxy.datatypes.genetics.DataIn method) (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.genetics.GenotypeMatrix method) (galaxy.datatypes.genetics.MarkerMap method) (galaxy.datatypes.goldenpath.GoldenPath method) (galaxy.datatypes.images.Gifti method) (galaxy.datatypes.images.Nifti1 method) (galaxy.datatypes.images.Nifti2 method) (galaxy.datatypes.images.Star method) (galaxy.datatypes.images.Tck method) (galaxy.datatypes.images.Trk method) (galaxy.datatypes.interval.Bed method) (galaxy.datatypes.interval.CustomTrack method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Gff3 method) (galaxy.datatypes.interval.Gtf method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.IntervalTabix method) (galaxy.datatypes.interval.ScIdx method) (galaxy.datatypes.interval.Wiggle method) (galaxy.datatypes.metacyto.mStats method) (galaxy.datatypes.metacyto.mSummary method) (galaxy.datatypes.microarrays.Gal method) (galaxy.datatypes.microarrays.Gpr method) (galaxy.datatypes.molecules.Cell method) (galaxy.datatypes.molecules.CIF method) (galaxy.datatypes.molecules.CML method) (galaxy.datatypes.molecules.ExtendedXYZ method) (galaxy.datatypes.molecules.FPS method) (galaxy.datatypes.molecules.GRO method) (galaxy.datatypes.molecules.InChI method) (galaxy.datatypes.molecules.Magres method) (galaxy.datatypes.molecules.MOL2 method) (galaxy.datatypes.molecules.PDB method) (galaxy.datatypes.molecules.PDBQT method) (galaxy.datatypes.molecules.PQR method) (galaxy.datatypes.molecules.SDF method) (galaxy.datatypes.molecules.XYZ method) (galaxy.datatypes.mothur.Axes method) (galaxy.datatypes.mothur.Frequency method) (galaxy.datatypes.mothur.GroupAbund method) (galaxy.datatypes.mothur.LaneMask method) (galaxy.datatypes.mothur.LowerTriangleDistanceMatrix method) (galaxy.datatypes.mothur.Oligos method) (galaxy.datatypes.mothur.Otu method) (galaxy.datatypes.mothur.PairwiseDistanceMatrix method) (galaxy.datatypes.mothur.Quantile method) (galaxy.datatypes.mothur.RefTaxonomy method) (galaxy.datatypes.mothur.Sabund method) (galaxy.datatypes.mothur.SecondaryStructureMap method) (galaxy.datatypes.mothur.SquareDistanceMatrix method) (galaxy.datatypes.msa.Hmmer method) (galaxy.datatypes.msa.Hmmer2 method) (galaxy.datatypes.msa.Hmmer3 method) (galaxy.datatypes.msa.InfernalCM method) (galaxy.datatypes.msa.MauveXmfa method) (galaxy.datatypes.msa.Stockholm_1_0 method) (galaxy.datatypes.phylip.Phylip method) (galaxy.datatypes.plant_tribes.Smat method) (galaxy.datatypes.proteomics.Dta2d method) (galaxy.datatypes.proteomics.Edta method) (galaxy.datatypes.proteomics.Kroenik method) (galaxy.datatypes.proteomics.Ms2 method) (galaxy.datatypes.proteomics.Msp method) (galaxy.datatypes.proteomics.MzTab method) (galaxy.datatypes.proteomics.PEFF method) (galaxy.datatypes.proteomics.PepList method) (galaxy.datatypes.proteomics.ProteomicsXml method) (galaxy.datatypes.proteomics.PSMS method) (galaxy.datatypes.proteomics.SPLib method) (galaxy.datatypes.qiime2.QIIME2Metadata method) (galaxy.datatypes.qualityscore.QualityScore454 method) (galaxy.datatypes.qualityscore.QualityScoreSOLiD method) (galaxy.datatypes.sequence.Axt method) (galaxy.datatypes.sequence.BaseFastq method) (galaxy.datatypes.sequence.csFasta method) (galaxy.datatypes.sequence.DotBracket method) (galaxy.datatypes.sequence.Fasta method) (galaxy.datatypes.sequence.Fastg method) (galaxy.datatypes.sequence.FastqIllumina method) (galaxy.datatypes.sequence.FastqSolexa method) (galaxy.datatypes.sequence.Genbank method) (galaxy.datatypes.sequence.Lav method) (galaxy.datatypes.sequence.Maf method) (galaxy.datatypes.sequence.MemePsp method) (galaxy.datatypes.sequence.SequenceSplitLocations method) (galaxy.datatypes.tabular.CMAP method) (galaxy.datatypes.tabular.ConnectivityTable method) (galaxy.datatypes.tabular.Eland method) (galaxy.datatypes.tabular.ElandMulti method) (galaxy.datatypes.tabular.MatrixMarket method) (galaxy.datatypes.tabular.Pileup method) (galaxy.datatypes.tabular.Psl method) (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.Vcf method) (galaxy.datatypes.text.Arff method) (galaxy.datatypes.text.BCSLmodel method) (galaxy.datatypes.text.BCSLts method) (galaxy.datatypes.text.Biom1 method) (galaxy.datatypes.text.Castep method) (galaxy.datatypes.text.CTLresult method) (galaxy.datatypes.text.FormattedDensity method) (galaxy.datatypes.text.GeoJson method) (galaxy.datatypes.text.Gfa1 method) (galaxy.datatypes.text.Gfa2 method) (galaxy.datatypes.text.Html method) (galaxy.datatypes.text.ImgtJson method) (galaxy.datatypes.text.Ipynb method) (galaxy.datatypes.text.IQTree method) (galaxy.datatypes.text.Json method) (galaxy.datatypes.text.Obo method) (galaxy.datatypes.text.Paf method) (galaxy.datatypes.text.Param method) (galaxy.datatypes.text.PithyaModel method) (galaxy.datatypes.text.PithyaProperty method) (galaxy.datatypes.text.PithyaResult method) (galaxy.datatypes.text.StormCheck method) (galaxy.datatypes.text.StormSample method) (galaxy.datatypes.text.Yaml method) (galaxy.datatypes.triples.Jsonld method) (galaxy.datatypes.triples.NTriples method) (galaxy.datatypes.triples.Rdf method) (galaxy.datatypes.triples.Sbol method) (galaxy.datatypes.triples.Turtle method) (galaxy.datatypes.xml.CisML method) (galaxy.datatypes.xml.Dzi method) (galaxy.datatypes.xml.GenericXml method) (galaxy.datatypes.xml.MEMEXml method) (galaxy.datatypes.xml.Owl method) (galaxy.datatypes.xml.Phyloxml method) (galaxy.datatypes.xml.Sbml method) sniff_relaxed_interleaved() (galaxy.datatypes.phylip.Phylip method) sniff_strict_interleaved() (galaxy.datatypes.phylip.Phylip method) sniff_strict_sequential() (galaxy.datatypes.phylip.Phylip method) sniff_table_names() (galaxy.datatypes.binary.SQlite method) sniff_with_cls() (in module galaxy.datatypes.sniff) sniffers() (galaxy.webapps.galaxy.api.datatypes.FastAPIDatatypes method) SnpEffDb (class in galaxy.datatypes.text) SNPMatrix (class in galaxy.datatypes.genetics) SnpSiftDbNSFP (class in galaxy.datatypes.text) Snptest (class in galaxy.datatypes.genetics) social_auth (galaxy.model.User attribute) sort() (galaxy.job_execution.output_collect.DatasetCollector method) (galaxy.web.framework.helpers.grids.GridColumn method) (galaxy.web.legacy_framework.grids.BooleanColumn method) (galaxy.web.legacy_framework.grids.CommunityRatingColumn method) (galaxy.web.legacy_framework.grids.DateTimeColumn method) (galaxy.web.legacy_framework.grids.GridColumn method) (galaxy.web.legacy_framework.grids.IntegerColumn method) (galaxy.web.legacy_framework.grids.OwnerColumn method) (galaxy.web.legacy_framework.grids.ReverseSortColumn method) (galaxy.web.legacy_framework.grids.TextColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.DiskUsageColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.LastLoginColumn method) sort_block_components_by_block() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) sort_by (galaxy.schema.schema.InvocationIndexQueryPayload attribute) (galaxy.schema.schema.PageIndexQueryPayload attribute) (galaxy.schema.schema.WorkflowIndexQueryPayload attribute) sort_by_attr() (galaxy.model.security.GalaxyRBACAgent method) (in module galaxy.webapps.base.controller) (in module tool_shed.webapp.model) sort_desc (galaxy.schema.schema.InvocationIndexQueryPayload attribute) (galaxy.schema.schema.LibraryFolderContentsIndexQueryPayload attribute) (galaxy.schema.schema.PageIndexQueryPayload attribute) (galaxy.schema.schema.WorkflowIndexQueryPayload attribute) sort_flag (galaxy.datatypes.binary.BamInputSorted attribute) (galaxy.datatypes.binary.BamNative attribute) (galaxy.datatypes.binary.BamQuerynameSorted attribute) sort_map (galaxy.managers.base.StorageCleanerManager attribute) (galaxy.managers.hdas.HDAStorageCleanerManager attribute) (galaxy.managers.histories.HistoryStorageCleanerManager attribute) SortableManager (class in galaxy.managers.base) SortByColumnFilter (class in galaxy.tools.parameters.dynamic_options) sorter() (in module galaxy.webapps.reports.controllers.jobs) SortRuleDefinition (class in galaxy.util.rules_dsl) SortTool (class in galaxy.tools) source (galaxy.model.DatasetSourceHash attribute) (galaxy.model.Notification attribute) (galaxy.objectstore.QuotaModel attribute) (galaxy.schema.schema.MaterializeDatasetInstanceAPIRequest attribute) (galaxy.schema.tasks.MaterializeDatasetInstanceTaskRequest attribute) (galaxy.util.plugin_config.PluginConfigSource attribute) (galaxy.webapps.galaxy.api.tool_data.ImportToolDataBundle attribute) (galaxy.webapps.galaxy.services.sharable.SharedItemNotificationFactory attribute) source_dataset_chain (galaxy.model.DatasetInstance property) source_environment (galaxy.tool_util.deps.container_classes.Container property) source_library_dataset (galaxy.model.DatasetInstance property) source_metadata (galaxy.model.Workflow attribute) source_path (galaxy.tool_util.parser.cwl.CwlToolSource property) (galaxy.tool_util.parser.interface.ToolSource property) (galaxy.tool_util.parser.ToolSource property) (galaxy.tool_util.parser.xml.XmlToolSource property) (galaxy.tool_util.parser.yaml.YamlToolSource property) source_step (galaxy.schema.schema.InputStep attribute) source_to_import_store() (in module galaxy.model.store) source_uri (galaxy.model.DatasetSource attribute) (galaxy.schema.schema.DatasetSource attribute) (galaxy.schema.tasks.ImportModelStoreTaskRequest attribute) sources (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance property) (galaxy.model.store.discover.JsonCollectedDatasetMatch property) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) space_to_tab (galaxy.schema.fetch_data.BaseDataElement attribute) (galaxy.tools.parameters.grouping.Dataset attribute) SpalnNuclDb (class in galaxy.datatypes.spaln) SpalnProtDb (class in galaxy.datatypes.spaln) spdxUrl (galaxy.managers.licenses.LicenseMetadataModel attribute) spec (galaxy.datatypes.metadata.MetadataCollection property) (galaxy.model.metadata.MetadataCollection property) SpecificationAwareDependencyResolver (class in galaxy.tool_util.deps.resolvers) SpecificationPatternDependencyResolver (class in galaxy.tool_util.deps.resolvers) specified_date() (galaxy.webapps.reports.controllers.users.Users method) specified_date_handler() (galaxy.webapps.reports.controllers.jobs.Jobs method) (galaxy.webapps.reports.controllers.workflows.Workflows method) specified_date_list_grid (galaxy.webapps.reports.controllers.jobs.Jobs attribute) (galaxy.webapps.reports.controllers.workflows.Workflows attribute) specified_month() (galaxy.webapps.reports.controllers.users.Users method) specified_month_all() (galaxy.webapps.reports.controllers.jobs.Jobs method) specified_month_in_error() (galaxy.webapps.reports.controllers.jobs.Jobs method) SpecifiedDateListGrid (class in galaxy.webapps.reports.controllers.jobs) (class in galaxy.webapps.reports.controllers.workflows) SpecifiedDateListGrid.CreateTimeColumn (class in galaxy.webapps.reports.controllers.jobs) (class in galaxy.webapps.reports.controllers.workflows) SpecifiedDateListGrid.DestinationIdColumn (class in galaxy.webapps.reports.controllers.jobs) SpecifiedDateListGrid.EmailColumn (class in galaxy.webapps.reports.controllers.jobs) (class in galaxy.webapps.reports.controllers.workflows) SpecifiedDateListGrid.JobIdColumn (class in galaxy.webapps.reports.controllers.jobs) SpecifiedDateListGrid.SpecifiedDateColumn (class in galaxy.webapps.reports.controllers.jobs) (class in galaxy.webapps.reports.controllers.workflows) SpecifiedDateListGrid.StateColumn (class in galaxy.webapps.reports.controllers.jobs) SpecifiedDateListGrid.ToolColumn (class in galaxy.webapps.reports.controllers.jobs) SpecifiedDateListGrid.UserColumn (class in galaxy.webapps.reports.controllers.jobs) (class in galaxy.webapps.reports.controllers.workflows) SpecifiedDateListGrid.WorkflowNameColumn (class in galaxy.webapps.reports.controllers.workflows) specifies_version (galaxy.tool_util.deps.requirements.RequirementSpecification property) SPLib (class in galaxy.datatypes.proteomics) SPLibNoIndex (class in galaxy.datatypes.proteomics) SplicedAlignment (class in galaxy.datatypes.util.maf_utilities) (class in galaxy.tools.util.maf_utilities) split() (galaxy.datatypes.data.Text class method) (galaxy.datatypes.molecules.CML class method) (galaxy.datatypes.molecules.FPS class method) (galaxy.datatypes.molecules.MOL2 class method) (galaxy.datatypes.molecules.OBFS class method) (galaxy.datatypes.molecules.SDF class method) (galaxy.datatypes.msa.Stockholm_1_0 class method) (galaxy.datatypes.sequence.Alignment class method) (galaxy.datatypes.sequence.BaseFastq class method) (galaxy.datatypes.sequence.Fasta class method) (galaxy.datatypes.sequence.Sequence class method) split_container_name() (in module galaxy.tool_util.deps.mulled.util) split_dataset_collection_instance() (in module galaxy.model.dataset_collections.subcollections) split_output_name() (galaxy.tool_util.parser.output_objects.ToolOutputCollectionPart static method) (galaxy.tool_util.parser.ToolOutputCollectionPart static method) split_params() (in module galaxy.jobs.runners.util.cli) split_port() (in module galaxy.files.uris) split_tag() (in module galaxy.tool_util.deps.mulled.util) SplitColumnsRuleDefinition (class in galaxy.util.rules_dsl) splitLinebyWhitespaces() (galaxy.visualization.data_providers.phyloviz.nexusparser.Nexus_Parser method) sqlalchemy_engine() (in module galaxy.model.database_utils) SQLDebugMiddleware (class in galaxy.web.framework.middleware.sqldebug) SQlite (class in galaxy.datatypes.binary) sqlite_datadictprovider() (galaxy.datatypes.binary.SQlite method) sqlite_dataprovider() (galaxy.datatypes.binary.SQlite method) sqlite_datatableprovider() (galaxy.datatypes.binary.SQlite method) SqliteDatabaseManager (class in galaxy.model.database_utils) SQliteDataDictProvider (class in galaxy.datatypes.dataproviders.dataset) SQliteDataProvider (class in galaxy.datatypes.dataproviders.dataset) SQliteDataTableProvider (class in galaxy.datatypes.dataproviders.dataset) SqliteProxyIpc (class in galaxy.web.proxy) SQmass (class in galaxy.datatypes.binary) SquareDistanceMatrix (class in galaxy.datatypes.mothur) Sra (class in galaxy.datatypes.binary) SraManifest (class in galaxy.datatypes.tabular) Src (class in galaxy.schema.fetch_data) src (galaxy.schema.fetch_data.CompositeDataElement attribute) (galaxy.schema.fetch_data.ExtraFiles attribute) (galaxy.schema.fetch_data.FileDataElement attribute) (galaxy.schema.fetch_data.FtpImportElement attribute) (galaxy.schema.fetch_data.FtpImportTarget attribute) (galaxy.schema.fetch_data.ItemsFromModel attribute) (galaxy.schema.fetch_data.PastedDataElement attribute) (galaxy.schema.fetch_data.PathDataElement attribute) (galaxy.schema.fetch_data.ServerDirElement attribute) (galaxy.schema.fetch_data.UrlDataElement attribute) (galaxy.schema.schema.CollectionElementIdentifier attribute) (galaxy.schema.schema.DatasetSourceIdBase attribute) (galaxy.schema.schema.EncodedDataItemSourceId attribute) (galaxy.schema.schema.ImportToolDataBundleDatasetSource attribute) (galaxy.schema.schema.ImportToolDataBundleUriSource attribute) src_id_to_item() (in module galaxy.tools.parameters.basic) src_merge() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) src_split() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) SshFilesSource (class in galaxy.files.sources.ssh) SSHKeys (class in galaxy.security.ssh_util) stage() (galaxy.tool_util.client.staging.StagingInterface method) stage_addition() (galaxy.model.History method) stage_data_async() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) stage_data_in_history() (in module galaxy.tool_util.verify.interactor) stage_inputs() (in module galaxy_test.base.populators) stage_rules_example() (in module galaxy_test.base.populators) stagedir (galaxy.tool_util.cwl.cwltool_deps.RuntimeContext attribute) StagingInterface (class in galaxy.tool_util.client.staging) stamp_model_head() (galaxy.model.migrations.AlembicManager method) StandaloneToolShedInstallationClient (class in tool_shed.test.base.twilltestcase) standard_filters (galaxy.web.legacy_framework.grids.Grid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) Star (class in galaxy.datatypes.images) start (galaxy.datatypes.util.maf_utilities.SplicedAlignment property) (galaxy.tools.util.maf_utilities.SplicedAlignment property) start() (galaxy.authnz.psa_authnz.Strategy method) (galaxy.config_watchers.ConfigWatchers method) (galaxy.jobs.handler.DefaultJobDispatcher method) (galaxy.jobs.handler.JobHandler method) (galaxy.jobs.handler.JobHandlerI method) (galaxy.jobs.handler.JobHandlerQueue method) (galaxy.jobs.handler.JobHandlerStopQueue method) (galaxy.jobs.manager.JobManager method) (galaxy.jobs.manager.NoopHandler method) (galaxy.jobs.runners.BaseJobRunner method) (galaxy.model.database_heartbeat.DatabaseHeartbeat method) (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.irods.IRODSObjectStore method) (galaxy.tool_util.toolbox.watcher.ToolConfWatcher method) (galaxy.util.task.IntervalTask method) (galaxy.util.watcher.BaseWatcher method) (galaxy.util.watcher.NullWatcher method) (galaxy.web_stack.ApplicationStack method) (galaxy.web_stack.transport.ApplicationStackTransport method) (galaxy.webapps.reports.controllers.jobs.Timer method) (galaxy.workflow.scheduling_manager.WorkflowRequestMonitor method) start_cache_monitor() (galaxy.objectstore.cloud.Cloud method) (galaxy.objectstore.s3.S3ObjectStore method) start_connection_pool_monitor() (galaxy.objectstore.irods.IRODSObjectStore method) start_if_needed() (galaxy.web_stack.transport.ApplicationStackTransport method) start_methods (galaxy.jobs.runners.BaseJobRunner attribute) start_monitoring() (galaxy.util.monitors.Monitors method) start_process() (galaxy.util.lazy_process.LazyProcess method) (galaxy.util.lazy_process.NoOpLazyProcess method) startswith() (galaxy.datatypes.sniff.FilePrefix method) startswith_bytes() (galaxy.datatypes.sniff.FilePrefix method) startup() (galaxy.workflow.schedulers.core.CoreWorkflowSchedulingPlugin method) (galaxy.workflow.schedulers.WorkflowSchedulingPlugin method) state (galaxy.datatypes.display_applications.parameters.DatasetLikeObject attribute) (galaxy.model.Dataset attribute) (galaxy.model.DatasetCollection property) (galaxy.model.DatasetCollectionInstance property) (galaxy.model.DatasetInstance property) (galaxy.model.Job attribute) (galaxy.model.JobStateHistory attribute) (galaxy.model.store.DatasetAttributeImportModel attribute) (galaxy.model.store.discover.DiscoveredResultState attribute) (galaxy.model.Task attribute) (galaxy.model.UserAddress attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowStep attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.DatasetSummary attribute) (galaxy.schema.schema.FileLibraryFolderItem attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDAInaccessible attribute) (galaxy.schema.schema.HDAObject attribute) (galaxy.schema.schema.HDASummary attribute) (galaxy.schema.schema.HistoryDetailed attribute) (galaxy.schema.schema.JobBaseModel attribute) state() (galaxy.webapps.galaxy.api.tasks.FastAPITasks method) state_counts() (galaxy.managers.history_contents.HistoryContentsManager method) state_details (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.HistoryDetailed attribute) state_history (galaxy.model.Job attribute) state_ids (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.HistoryDetailed attribute) StateColumn (class in galaxy.web.legacy_framework.grids) Statement (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) states (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance attribute) (galaxy.model.Job attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.schema.schema.ItemStateSummary attribute) (galaxy.schema.schema.JobIndexQueryPayload attribute) StaticFileVisualizationPlugin (class in galaxy.visualization.plugins.plugin) StaticToolBoxView (class in galaxy.tool_util.toolbox.views.definitions) StaticToolBoxViewSources (class in galaxy.tool_util.toolbox.views.sources) StaticToolBoxViewTypeEnum (class in galaxy.tool_util.toolbox.views.definitions) StaticToolPanelView (class in galaxy.tool_util.toolbox.views.static) StaticValueFilter (class in galaxy.tools.parameters.dynamic_options) stats (galaxy.schema.schema.HistoryContentsWithStatsResult attribute) StatsdMiddleware (class in galaxy.web.framework.middleware.statsd) StatsdStructuredExecutionTimer (class in galaxy.app) status (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.schema.schema.CheckForUpdatesResponse attribute) (galaxy.schema.schema.InstalledToolShedRepository attribute) (galaxy.webapps.galaxy.controllers.admin.DatatypesEntryT attribute) status_code (galaxy.exceptions.AcceptedRetryLater attribute) (galaxy.exceptions.ActionInputError attribute) (galaxy.exceptions.AdminRequiredException attribute) (galaxy.exceptions.AuthenticationFailed attribute) (galaxy.exceptions.AuthenticationRequired attribute) (galaxy.exceptions.ConfigDoesNotAllowException attribute) (galaxy.exceptions.ConfigurationError attribute) (galaxy.exceptions.Conflict attribute) (galaxy.exceptions.DeprecatedMethod attribute) (galaxy.exceptions.DuplicatedIdentifierException attribute) (galaxy.exceptions.DuplicatedSlugException attribute) (galaxy.exceptions.InconsistentDatabase attribute) (galaxy.exceptions.InsufficientPermissionsException attribute) (galaxy.exceptions.InternalServerError attribute) (galaxy.exceptions.InvalidFileFormatError attribute) (galaxy.exceptions.ItemAccessibilityException attribute) (galaxy.exceptions.ItemImmutableException attribute) (galaxy.exceptions.ItemOwnershipException attribute) (galaxy.exceptions.MalformedContents attribute) (galaxy.exceptions.MalformedId attribute) (galaxy.exceptions.MessageException attribute) (galaxy.exceptions.NoContentException attribute) (galaxy.exceptions.NotImplemented attribute) (galaxy.exceptions.ObjectAttributeInvalidException attribute) (galaxy.exceptions.ObjectAttributeMissingException attribute) (galaxy.exceptions.ObjectNotFound attribute) (galaxy.exceptions.RealUserRequiredException attribute) (galaxy.exceptions.ReferenceDataError attribute) (galaxy.exceptions.RequestParameterInvalidException attribute) (galaxy.exceptions.RequestParameterMissingException attribute) (galaxy.exceptions.ServerNotConfiguredForRequest attribute) (galaxy.exceptions.ToolExecutionError attribute) (galaxy.exceptions.ToolInputsNotOKException attribute) (galaxy.exceptions.ToolInputsNotReadyException attribute) (galaxy.exceptions.ToolMetaParameterException attribute) (galaxy.exceptions.ToolMissingException attribute) (galaxy.exceptions.UnknownContentsType attribute) (galaxy.exceptions.UserActivationRequiredException attribute) (galaxy.exceptions.UserCannotRunAsException attribute) (galaxy.exceptions.UserInvalidRunAsException attribute) stderr (galaxy.model.JobLike property) (galaxy.schema.schema.JobFullDetails attribute) (galaxy.tool_util.parser.interface.ToolSourceTest attribute) (galaxy.tool_util.verify.interactor.ToolTestDescription attribute) (galaxy.tool_util.verify.interactor.ToolTestDescriptionDict attribute) (galaxy.tool_util.verify.interactor.ValidToolTestDict attribute) StdFsAccess (class in galaxy.tool_util.cwl.cwltool_deps) stdio_exit_codes (galaxy.tools.ApplyRulesTool attribute) (galaxy.tools.AsyncDataSourceTool attribute) (galaxy.tools.BuildListCollectionTool attribute) (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.DataDestinationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.DuplicateFileToCollectionTool attribute) (galaxy.tools.ExportHistoryTool attribute) (galaxy.tools.ExpressionTool attribute) (galaxy.tools.ExtractDatasetCollectionTool attribute) (galaxy.tools.FilterDatasetsTool attribute) (galaxy.tools.FilterEmptyDatasetsTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) (galaxy.tools.FilterFromFileTool attribute) (galaxy.tools.FlattenTool attribute) (galaxy.tools.HarmonizeTool attribute) (galaxy.tools.ImportHistoryTool attribute) (galaxy.tools.InteractiveTool attribute) (galaxy.tools.KeepSuccessDatasetsTool attribute) (galaxy.tools.MergeCollectionTool attribute) (galaxy.tools.OutputParameterJSONTool attribute) (galaxy.tools.RelabelFromFileTool attribute) (galaxy.tools.SortTool attribute) (galaxy.tools.TagFromFileTool attribute) (galaxy.tools.UnzipCollectionTool attribute) (galaxy.tools.ZipCollectionTool attribute) stdio_regexes (galaxy.tools.ApplyRulesTool attribute) (galaxy.tools.AsyncDataSourceTool attribute) (galaxy.tools.BuildListCollectionTool attribute) (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.DataDestinationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.DuplicateFileToCollectionTool attribute) (galaxy.tools.ExportHistoryTool attribute) (galaxy.tools.ExpressionTool attribute) (galaxy.tools.ExtractDatasetCollectionTool attribute) (galaxy.tools.FilterDatasetsTool attribute) (galaxy.tools.FilterEmptyDatasetsTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) (galaxy.tools.FilterFromFileTool attribute) (galaxy.tools.FlattenTool attribute) (galaxy.tools.HarmonizeTool attribute) (galaxy.tools.ImportHistoryTool attribute) (galaxy.tools.InteractiveTool attribute) (galaxy.tools.KeepSuccessDatasetsTool attribute) (galaxy.tools.MergeCollectionTool attribute) (galaxy.tools.OutputParameterJSONTool attribute) (galaxy.tools.RelabelFromFileTool attribute) (galaxy.tools.SortTool attribute) (galaxy.tools.TagFromFileTool attribute) (galaxy.tools.UnzipCollectionTool attribute) (galaxy.tools.ZipCollectionTool attribute) StdIOAbsence (class in galaxy.tool_util.linters.stdio) StdIOAbsenceLegacy (class in galaxy.tool_util.linters.stdio) StdioErrorLevel (class in galaxy.tool_util.parser.stdio) StdioParser (class in galaxy.tool_util.parser.xml) StdIORegex (class in galaxy.tool_util.linters.stdio) stdout (galaxy.datatypes.upload_util.HandleUploadResponse attribute) (galaxy.model.JobLike property) (galaxy.schema.schema.JobFullDetails attribute) (galaxy.tool_util.parser.interface.ToolSourceTest attribute) (galaxy.tool_util.verify.interactor.ToolTestDescription attribute) (galaxy.tool_util.verify.interactor.ToolTestDescriptionDict attribute) (galaxy.tool_util.verify.interactor.ValidToolTestDict attribute) step (galaxy.workflow.refactor.schema.FillStepDefaultsAction attribute) (galaxy.workflow.refactor.schema.UpdateStepLabelAction attribute) (galaxy.workflow.refactor.schema.UpdateStepPositionAction attribute) (galaxy.workflow.refactor.schema.UpgradeSubworkflowAction attribute) (galaxy.workflow.refactor.schema.UpgradeToolAction attribute) step_by_index() (galaxy.model.Workflow method) step_by_label() (galaxy.model.Workflow method) step_count (galaxy.model.Workflow attribute) step_effective_outputs (galaxy.model.WorkflowInvocationStepObjectStores attribute) step_id (galaxy.model.EffectiveOutput attribute) step_invocation_for_label() (galaxy.model.WorkflowInvocation method) step_invocation_for_step_id() (galaxy.model.WorkflowInvocation method) step_invocations_by_step_id() (galaxy.model.WorkflowInvocation method) step_label (galaxy.workflow.refactor.schema.RefactorActionExecutionMessage attribute) step_output (galaxy.schema.schema.InputStep attribute) STEP_PARAMETERS (galaxy.model.WorkflowRequestInputParameter.types attribute) step_state_to_tool_state() (galaxy.workflow.modules.InputModule method) (galaxy.workflow.modules.InputParameterModule method) (galaxy.workflow.modules.WorkflowModule method) step_states (galaxy.model.WorkflowInvocation attribute) step_states_by_step_id() (galaxy.model.WorkflowInvocation method) STEP_TYPE_TO_INPUT_TYPE (galaxy.model.WorkflowStep attribute) StepReferenceByLabel (class in galaxy.workflow.refactor.schema) StepReferenceByOrderIndex (class in galaxy.workflow.refactor.schema) steps (galaxy.model.Workflow attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.schema.schema.WorkflowToExport attribute) (galaxy.tours.TourDetails attribute) steps_by_id (galaxy.model.Workflow property) STL (class in galaxy.datatypes.constructive_solid_geometry) stock (galaxy.files.sources.PluginKind attribute) Stockholm_1_0 (class in galaxy.datatypes.msa) stop (galaxy.app_unittest_utils.galaxy_mock.MockApp attribute) (galaxy.model.JobStateSummary attribute) stop() (galaxy.jobs.handler.DefaultJobDispatcher method) (galaxy.jobs.manager.JobManager method) (galaxy.jobs.manager.NoopManager method) (galaxy.managers.interactivetool.InteractiveToolManager method) (galaxy.managers.jobs.JobManager method) (galaxy.webapps.reports.controllers.jobs.Timer method) stop_creating_job() (galaxy.managers.datasets.DatasetAssociationManager method) stop_entry_point() (galaxy.webapps.galaxy.api.tool_entry_points.ToolEntryPointsAPIController method) stop_err() (in module galaxy.datatypes.converters.fastqsolexa_to_fasta_converter) (in module galaxy.datatypes.converters.fastqsolexa_to_qual_converter) (in module galaxy.datatypes.converters.interval_to_bed_converter) (in module galaxy.datatypes.converters.interval_to_bedstrict_converter) stop_if_unneeded() (galaxy.web_stack.transport.ApplicationStackTransport method) stop_job (galaxy.schema.schema.DeleteHistoryContentPayload attribute) stop_job() (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.chronos.ChronosJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.condor.CondorJobRunner method) (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) (galaxy.jobs.runners.godocker.GodockerJobRunner method) (galaxy.jobs.runners.kubernetes.KubernetesJobRunner method) (galaxy.jobs.runners.local.LocalJobRunner method) (galaxy.jobs.runners.pbs.PBSJobRunner method) (galaxy.jobs.runners.tasks.TaskedJobRunner method) stop_monitoring() (galaxy.util.monitors.Monitors method) stop_servers() (galaxy_test.driver.driver_util.TestDriver method) STOP_SIGNAL (galaxy.jobs.handler.BaseJobHandlerQueue attribute) stopped (galaxy.model.JobStateSummary attribute) STOPPED (galaxy.schema.schema.JobState attribute) STOPPING (galaxy.schema.schema.JobState attribute) StopSignalException StorableObject (class in galaxy.model) Storage (class in galaxy.authnz.psa_authnz) storage_request_id (galaxy.schema.schema.AsyncFile attribute) StorageCleanerManager (class in galaxy.managers.base) store() (galaxy.model.PSAAssociation class method) store_by (galaxy.model.Dataset property) (galaxy.objectstore.BaseObjectStore attribute) (galaxy.objectstore.DiskObjectStore attribute) (galaxy.objectstore.DistributedObjectStore attribute) (galaxy.objectstore.HierarchicalObjectStore attribute) (galaxy.objectstore.irods.IRODSObjectStore attribute) (galaxy.objectstore.NestedObjectStore attribute) (galaxy.objectstore.pithos.PithosObjectStore attribute) (galaxy.objectstore.pulsar.PulsarObjectStore attribute) (galaxy.objectstore.s3.GenericS3ObjectStore attribute) store_content_uri (galaxy.schema.schema.CreateHistoryFromStore attribute) (galaxy.schema.schema.CreateLibrariesFromStore attribute) (galaxy.schema.schema.StoreContentSource attribute) store_dict (galaxy.schema.schema.CreateHistoryFromStore attribute) (galaxy.schema.schema.CreateLibrariesFromStore attribute) (galaxy.schema.schema.StoreContentSource attribute) store_directory (galaxy.schema.tasks.SetupHistoryExportJob attribute) store_errors_even_if_ignored (galaxy.celery.GalaxyTask attribute) store_jobtemplate() (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) store_type (galaxy.objectstore.azure_blob.AzureBlobObjectStore attribute) (galaxy.objectstore.BaseObjectStore attribute) (galaxy.objectstore.cloud.Cloud attribute) (galaxy.objectstore.DiskObjectStore attribute) (galaxy.objectstore.DistributedObjectStore attribute) (galaxy.objectstore.HierarchicalObjectStore attribute) (galaxy.objectstore.irods.IRODSObjectStore attribute) (galaxy.objectstore.NestedObjectStore attribute) (galaxy.objectstore.pithos.PithosObjectStore attribute) (galaxy.objectstore.pulsar.PulsarObjectStore attribute) (galaxy.objectstore.s3.GenericS3ObjectStore attribute) (galaxy.objectstore.s3.S3ObjectStore attribute) store_workflow_artifacts() (galaxy.managers.workflows.WorkflowContentsManager method) store_workflow_to_path() (galaxy.managers.workflows.WorkflowContentsManager method) StoreAppProtocol (class in galaxy.model.store) StoreContentSource (class in galaxy.schema.schema) stored_workflow (galaxy.managers.workflows.CreatedWorkflow attribute) (galaxy.model.StoredWorkflowAnnotationAssociation attribute) (galaxy.model.StoredWorkflowMenuEntry attribute) (galaxy.model.StoredWorkflowRatingAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.StoredWorkflowUserShareAssociation attribute) (galaxy.model.Workflow attribute) stored_workflow_id (galaxy.model.StoredWorkflowAnnotationAssociation attribute) (galaxy.model.StoredWorkflowMenuEntry attribute) (galaxy.model.StoredWorkflowRatingAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.StoredWorkflowUserShareAssociation attribute) (galaxy.model.Workflow attribute) stored_workflow_menu_entries (galaxy.model.User attribute) stored_workflows (galaxy.model.User attribute) StoredWorkflow (class in galaxy.model) (galaxy.managers.tags.TaggableItemClass attribute) StoredWorkflowAnnotationAssociation (class in galaxy.model) StoredWorkflowMenuEntry (class in galaxy.model) StoredWorkflowRatingAssociation (class in galaxy.model) StoredWorkflowSummary (class in galaxy.schema.schema) StoredWorkflowTagAssociation (class in galaxy.model) StoredWorkflowUserShareAssociation (class in galaxy.model) StoreExportAssociation (class in galaxy.model) StoreExportPayload (class in galaxy.schema.schema) StormCheck (class in galaxy.datatypes.text) StormSample (class in galaxy.datatypes.text) str_removeprefix() (in module galaxy.util) str_to_bytes() (in module galaxy.jobs.dynamic_tool_destination) Strategy (class in galaxy.authnz.psa_authnz) stream_dataset_collection() (in module galaxy.managers.hdcas) stream_to_file() (in module galaxy.files.uris) stream_to_open_named_file() (in module galaxy.util) stream_url_to_file() (in module galaxy.files.uris) stream_url_to_str() (in module galaxy.files.uris) strict_width (galaxy.datatypes.tabular.BaseCSV property) (galaxy.datatypes.tabular.CSV attribute) (galaxy.datatypes.tabular.TSV attribute) string_as_bool() (in module galaxy.util) string_as_bool_or_none() (in module galaxy.util) string_io() (galaxy.datatypes.sniff.FilePrefix method) string_standard_ops() (galaxy.managers.base.ModelFilterParser method) string_to_object() (in module galaxy.util) StringFunctionFilter (class in galaxy.tool_util.parser.output_actions) stringify() (in module galaxy.tool_shed.util.basic_util) (in module tool_shed.util.basic_util) stringify_dictionary_keys() (in module galaxy.util) strip_control_characters() (in module galaxy.util) strip_or_none() (in module galaxy.tools.parameters.dynamic_options) strip_path() (in module galaxy.tool_shed.util.basic_util) (in module tool_shed.util.basic_util) strip_tzinfo() (in module galaxy.schema.types) stripwd() (in module galaxy.model.orm.engine_factory) structure (galaxy.model.dataset_collections.matching.MatchingCollections property) structure_regexp (galaxy.datatypes.sequence.DotBracket attribute) (galaxy.datatypes.tabular.ConnectivityTable attribute) StructuredApp (class in galaxy.structured_app) StructuredExecutionTimer (class in galaxy.util) stub_label() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) stub_tool() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) stub_workflow() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) style (galaxy.managers.workflows.RefactorRequest attribute) stylesheet_link() (in module galaxy.web.framework.helpers.tags) subcollection_mapping_type() (galaxy.model.dataset_collections.matching.MatchingCollections method) subcollection_type_description() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) subcontainer_class (galaxy.managers.history_contents.HistoryContentsManager attribute) subcontainer_class_manager_class (galaxy.managers.history_contents.HistoryContentsManager attribute) subcontainer_class_type_name (galaxy.managers.history_contents.HistoryContentsManager attribute) SubElement() (in module galaxy.util) submission_params() (in module galaxy.jobs.runners.util.condor) submit() (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.util.cli.job.BaseJobExec method) (galaxy.jobs.runners.util.cli.job.lsf.LSF method) (galaxy.jobs.runners.util.cli.job.slurm.Slurm method) (galaxy.jobs.runners.util.cli.job.torque.Torque method) submit_form() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) submit_login() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) submit_report() (galaxy.tools.error_reports.ErrorPlugin method) (galaxy.tools.error_reports.NullErrorPlugin method) (galaxy.tools.error_reports.plugins.email.EmailPlugin method) (galaxy.tools.error_reports.plugins.ErrorPlugin method) (galaxy.tools.error_reports.plugins.github.GithubPlugin method) (galaxy.tools.error_reports.plugins.gitlab.GitLabPlugin method) (galaxy.tools.error_reports.plugins.influxdb.InfluxDBPlugin method) (galaxy.tools.error_reports.plugins.json.JsonPlugin method) (galaxy.tools.error_reports.plugins.sentry.SentryPlugin method) subprocess() (galaxy.datatypes.dataproviders.external.SubprocessDataProvider method) SubprocessDataProvider (class in galaxy.datatypes.dataproviders.external) subset (galaxy.model.HistoryDatasetAssociationSubset attribute) subtype (galaxy.datatypes.constructive_solid_geometry.Ply attribute) (galaxy.datatypes.constructive_solid_geometry.PlyAscii attribute) (galaxy.datatypes.constructive_solid_geometry.PlyBinary attribute) (galaxy.datatypes.constructive_solid_geometry.Vtk attribute) (galaxy.datatypes.constructive_solid_geometry.VtkAscii attribute) (galaxy.datatypes.constructive_solid_geometry.VtkBinary attribute) subworkflow (galaxy.model.WorkflowStep attribute) (galaxy.schema.schema.SubworkflowStepToExport attribute) (galaxy.workflow.modules.SubWorkflowModule attribute) subworkflow_id (galaxy.model.WorkflowStep attribute) subworkflow_invocation (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute) subworkflow_invocation_id (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute) subworkflow_invocations (galaxy.model.WorkflowInvocation attribute) SubWorkflowModule (class in galaxy.workflow.modules) SubworkflowStep (class in galaxy.schema.schema) SubworkflowStepToExport (class in galaxy.schema.schema) success (galaxy.schema.schema.ExportObjectResultMetadata attribute) success_count (galaxy.schema.schema.HistoryContentBulkOperationResult attribute) sudo_popen() (in module galaxy.jobs.runners.util.sudo) suggestions (galaxy.workflow.refactor.schema.AddInputAction attribute) sum_job_runtime() (galaxy.jobs.rule_helper.RuleHelper method) summarize() (in module galaxy.workflow.extract) summarize_condor_log() (in module galaxy.jobs.runners.util.condor) summarize_destination_params() (in module galaxy.managers.jobs) summarize_instance_history_on_error() (in module galaxy_test.base.populators) summarize_invocation_jobs() (in module galaxy.managers.jobs) summarize_job_metrics() (in module galaxy.managers.jobs) summarize_job_outputs() (in module galaxy.managers.jobs) summarize_job_parameters() (in module galaxy.managers.jobs) summarize_jobs_to_dict() (in module galaxy.managers.jobs) summarize_requirements() (galaxy.tool_util.deps.views.DependencyResolversView method) summarize_toolbox() (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) summarize_tools() (galaxy.tool_util.deps.views.DependencyResolversView method) Summary (class in galaxy.datatypes.mothur) supported_display_apps (galaxy.datatypes.data.Data attribute) supported_field_types (galaxy.model.FormDefinition attribute) supports_container() (galaxy.jobs.rule_helper.RuleHelper method) supports_docker() (galaxy.jobs.rule_helper.RuleHelper method) supports_returning() (galaxy.web_stack.ApplicationStack method) (in module galaxy.model.database_utils) supports_singularity() (galaxy.jobs.rule_helper.RuleHelper method) supports_skip_locked() (galaxy.web_stack.ApplicationStack method) (in module galaxy.model.database_utils) supports_test_data_download (galaxy.tool_util.verify.interactor.GalaxyInteractorApi property) SupportsBrowsing (class in galaxy.files.sources) SwapColumnsRuleDefinition (class in galaxy.util.rules_dsl) switch_param_type() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) switch_to_history() (galaxy.webapps.galaxy.controllers.history.HistoryController method) switch_to_main_panel() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) synchronized() (in module galaxy.util) synopsis (galaxy.model.Library attribute) (galaxy.schema.fetch_data.LibraryDestination attribute) (galaxy.schema.schema.CreateLibraryPayload attribute) (galaxy.schema.schema.LibraryLegacySummary attribute) (galaxy.schema.schema.UpdateLibraryPayload attribute) System (class in galaxy.webapps.reports.controllers.system) SYSTEM (galaxy.model.Role.types attribute) system_user_pwent() (galaxy.model.User method)

T

t_data_downloader_for() (in module galaxy.tool_util.unittest_utils) tab_to() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) TabixDataProvider (class in galaxy.visualization.data_providers.genome) table (galaxy.model.APIKeys attribute) (galaxy.model.CeleryUserRateLimit attribute) (galaxy.model.CleanupEvent attribute) (galaxy.model.CleanupEventDatasetAssociation attribute) (galaxy.model.CleanupEventHistoryAssociation attribute) (galaxy.model.CleanupEventHistoryDatasetAssociationAssociation attribute) (galaxy.model.CleanupEventImplicitlyConvertedDatasetAssociationAssociation attribute) (galaxy.model.CleanupEventLibraryAssociation attribute) (galaxy.model.CleanupEventLibraryDatasetAssociation attribute) (galaxy.model.CleanupEventLibraryDatasetDatasetAssociationAssociation attribute) (galaxy.model.CleanupEventLibraryFolderAssociation attribute) (galaxy.model.CleanupEventMetadataFileAssociation attribute) (galaxy.model.CloudAuthz attribute) (galaxy.model.CustosAuthnzToken attribute) (galaxy.model.DataManagerHistoryAssociation attribute) (galaxy.model.DataManagerJobAssociation attribute) (galaxy.model.Dataset attribute) (galaxy.model.DatasetCollection attribute) (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.DatasetHash attribute) (galaxy.model.DatasetPermissions attribute) (galaxy.model.DatasetSource attribute) (galaxy.model.DatasetSourceHash attribute) (galaxy.model.DefaultHistoryPermissions attribute) (galaxy.model.DefaultQuotaAssociation attribute) (galaxy.model.DefaultUserPermissions attribute) (galaxy.model.DynamicTool attribute) (galaxy.model.Event attribute) (galaxy.model.ExtendedMetadata attribute) (galaxy.model.ExtendedMetadataIndex attribute) (galaxy.model.FormDefinition attribute) (galaxy.model.FormDefinitionCurrent attribute) (galaxy.model.FormValues attribute) (galaxy.model.GalaxySession attribute) (galaxy.model.GalaxySessionToHistoryAssociation attribute) (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.Group attribute) (galaxy.model.GroupQuotaAssociation attribute) (galaxy.model.GroupRoleAssociation attribute) (galaxy.model.History attribute) (galaxy.model.HistoryAnnotationAssociation attribute) (galaxy.model.HistoryAudit attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization attribute) (galaxy.model.HistoryDatasetAssociationHistory attribute) (galaxy.model.HistoryDatasetAssociationRatingAssociation attribute) (galaxy.model.HistoryDatasetAssociationSubset attribute) (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetCollectionRatingAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryRatingAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.HistoryUserShareAssociation attribute) (galaxy.model.ImplicitCollectionJobs attribute) (galaxy.model.ImplicitCollectionJobsJobAssociation attribute) (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) (galaxy.model.ImplicitlyCreatedDatasetCollectionInput attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.Job attribute) (galaxy.model.JobContainerAssociation attribute) (galaxy.model.JobExportHistoryArchive attribute) (galaxy.model.JobExternalOutputMetadata attribute) (galaxy.model.JobImportHistoryArchive attribute) (galaxy.model.JobMetricNumeric attribute) (galaxy.model.JobMetricText attribute) (galaxy.model.JobParameter attribute) (galaxy.model.JobStateHistory attribute) (galaxy.model.JobToImplicitOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetAssociation attribute) (galaxy.model.JobToInputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetCollectionElementAssociation attribute) (galaxy.model.JobToInputLibraryDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToOutputLibraryDatasetAssociation attribute) (galaxy.model.Library attribute) (galaxy.model.LibraryDataset attribute) (galaxy.model.LibraryDatasetCollectionAnnotationAssociation attribute) (galaxy.model.LibraryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetCollectionRatingAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationPermissions attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) (galaxy.model.LibraryDatasetPermissions attribute) (galaxy.model.LibraryFolder attribute) (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryFolderPermissions attribute) (galaxy.model.LibraryInfoAssociation attribute) (galaxy.model.LibraryPermissions attribute) (galaxy.model.MetadataFile attribute) (galaxy.model.Notification attribute) (galaxy.model.Page attribute) (galaxy.model.PageAnnotationAssociation attribute) (galaxy.model.PageRatingAssociation attribute) (galaxy.model.PageRevision attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.PageUserShareAssociation attribute) (galaxy.model.PasswordResetToken attribute) (galaxy.model.PostJobAction attribute) (galaxy.model.PostJobActionAssociation attribute) (galaxy.model.PSAAssociation attribute) (galaxy.model.PSACode attribute) (galaxy.model.PSANonce attribute) (galaxy.model.PSAPartial attribute) (galaxy.model.Quota attribute) (galaxy.model.Role attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.StoredWorkflowAnnotationAssociation attribute) (galaxy.model.StoredWorkflowMenuEntry attribute) (galaxy.model.StoredWorkflowRatingAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.StoredWorkflowUserShareAssociation attribute) (galaxy.model.StoreExportAssociation attribute) (galaxy.model.Tag attribute) (galaxy.model.Task attribute) (galaxy.model.TaskMetricNumeric attribute) (galaxy.model.TaskMetricText attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.User attribute) (galaxy.model.UserAction attribute) (galaxy.model.UserAddress attribute) (galaxy.model.UserAuthnzToken attribute) (galaxy.model.UserGroupAssociation attribute) (galaxy.model.UserNotificationAssociation attribute) (galaxy.model.UserPreference attribute) (galaxy.model.UserQuotaAssociation attribute) (galaxy.model.UserQuotaSourceUsage attribute) (galaxy.model.UserRoleAssociation attribute) (galaxy.model.Vault attribute) (galaxy.model.Visualization attribute) (galaxy.model.VisualizationAnnotationAssociation attribute) (galaxy.model.VisualizationRatingAssociation attribute) (galaxy.model.VisualizationRevision attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.VisualizationUserShareAssociation attribute) (galaxy.model.WorkerProcess attribute) (galaxy.model.Workflow attribute) (galaxy.model.WorkflowComment attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowInvocationMessage attribute) (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationOutputValue attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute) (galaxy.model.WorkflowOutput attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.model.WorkflowRequestInputStepParameter attribute) (galaxy.model.WorkflowRequestStepState attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowStep attribute) (galaxy.model.WorkflowStepAnnotationAssociation attribute) (galaxy.model.WorkflowStepConnection attribute) (galaxy.model.WorkflowStepInput attribute) (galaxy.model.WorkflowStepTagAssociation attribute) (tool_shed.webapp.model.APIKeys attribute) (tool_shed.webapp.model.Category attribute) (tool_shed.webapp.model.GalaxySession attribute) (tool_shed.webapp.model.Group attribute) (tool_shed.webapp.model.GroupRoleAssociation attribute) (tool_shed.webapp.model.PasswordResetToken attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.RepositoryCategoryAssociation attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) (tool_shed.webapp.model.RepositoryRatingAssociation attribute) (tool_shed.webapp.model.RepositoryRoleAssociation attribute) (tool_shed.webapp.model.Role attribute) (tool_shed.webapp.model.Tag attribute) (tool_shed.webapp.model.User attribute) (tool_shed.webapp.model.UserGroupAssociation attribute) (tool_shed.webapp.model.UserRoleAssociation attribute) table_exists() (in module galaxy.model.migrations.util) Tabular (class in galaxy.datatypes.tabular) TabularData (class in galaxy.datatypes.tabular) TabularToolDataField (class in galaxy.tools.data) TabularToolDataTable (class in galaxy.tools.data) Tag (class in galaxy.model) (class in tool_shed.webapp.model) tag (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.WorkflowStepTagAssociation attribute) (galaxy.tool_util.parser.interface.AssertionDict attribute) (galaxy.tool_util.parser.output_actions.BooleanFilter attribute) (galaxy.tool_util.parser.output_actions.ColumnReplaceFilter attribute) (galaxy.tool_util.parser.output_actions.ColumnStripFilter attribute) (galaxy.tool_util.parser.output_actions.DatatypeIsInstanceToolOutputActionConditionalWhen attribute) (galaxy.tool_util.parser.output_actions.FormatToolOutputAction attribute) (galaxy.tool_util.parser.output_actions.FromDataTableOutputActionOption attribute) (galaxy.tool_util.parser.output_actions.FromFileToolOutputActionOption attribute) (galaxy.tool_util.parser.output_actions.FromParamToolOutputActionOption attribute) (galaxy.tool_util.parser.output_actions.InsertColumnToolOutputActionOptionFilter attribute) (galaxy.tool_util.parser.output_actions.MetadataToolOutputAction attribute) (galaxy.tool_util.parser.output_actions.MetadataValueFilter attribute) (galaxy.tool_util.parser.output_actions.MultipleSplitterFilter attribute) (galaxy.tool_util.parser.output_actions.NullToolOutputActionOption attribute) (galaxy.tool_util.parser.output_actions.ParamValueToolOutputActionOptionFilter attribute) (galaxy.tool_util.parser.output_actions.StringFunctionFilter attribute) (galaxy.tool_util.parser.output_actions.ToolOutputAction attribute) (galaxy.tool_util.parser.output_actions.ToolOutputActionConditional attribute) (galaxy.tool_util.parser.output_actions.ToolOutputActionConditionalWhen attribute) (galaxy.tool_util.parser.output_actions.ToolOutputActionGroup attribute) (galaxy.tool_util.parser.output_actions.ToolOutputActionOption attribute) (galaxy.tool_util.parser.output_actions.ToolOutputActionOptionFilter attribute) (galaxy.tool_util.parser.output_actions.ValueToolOutputActionConditionalWhen attribute) (galaxy.webapps.galaxy.api.IndexQueryTag attribute) (galaxy.workflow.modules.InputModuleState attribute) tag_assoc (galaxy.managers.hdas.HDAManager attribute) (galaxy.managers.hdcas.HDCAManager attribute) (galaxy.managers.histories.HistoryManager attribute) (galaxy.managers.pages.PageManager attribute) (galaxy.managers.visualizations.VisualizationManager attribute) tag_autocomplete_data() (galaxy.webapps.galaxy.controllers.tag.TagsController method) tag_dataset() (galaxy_test.base.populators.BaseDatasetPopulator method) tag_filter() (in module galaxy.model.index_filter_util) tag_handler (galaxy.app_unittest_utils.galaxy_mock.MockTrans property) (galaxy.job_execution.output_collect.JobContext property) (galaxy.managers.context.ProvidesUserContext property) (galaxy.managers.taggable.TaggableDeserializerMixin attribute) (galaxy.managers.visualizations.VisualizationDeserializer attribute) (galaxy.model.store.discover.ModelPersistenceContext property) (galaxy.model.store.discover.SessionlessModelPersistenceContext property) (galaxy.model.store.StoreAppProtocol attribute) (galaxy.structured_app.MinimalApp attribute) tag_id (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.WorkflowStepTagAssociation attribute) tag_list (galaxy.model.store.discover.JsonCollectedDatasetMatch property) tag_using_filenames (galaxy.tools.parameters.grouping.Dataset attribute) TagAttributeHandler (class in tool_shed.dependencies.tool.tag_attribute_handler) TagCollection (class in galaxy.schema.schema) TagDatasetAction (class in galaxy.job_execution.actions.post) TagFromFileTool (class in galaxy.tools) TaggableDeserializerMixin (class in galaxy.managers.taggable) TaggableFilterMixin (class in galaxy.managers.taggable) TaggableItemClass (class in galaxy.managers.tags) TaggableSerializerMixin (class in galaxy.managers.taggable) tagged_item_id (galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController attribute) (galaxy.webapps.galaxy.api.annotations.HistoryAnnotationsController attribute) (galaxy.webapps.galaxy.api.annotations.HistoryContentAnnotationsController attribute) (galaxy.webapps.galaxy.api.annotations.WorkflowAnnotationsController attribute) tagging_add() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) TagHandler (class in galaxy.model.tags) TagOperationParams (class in galaxy.schema.schema) tags (galaxy.model.HasTags attribute) (galaxy.model.History attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.Page attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.Visualization attribute) (galaxy.model.WorkflowStep attribute) (galaxy.schema.fetch_data.BaseCollectionTarget attribute) (galaxy.schema.fetch_data.BaseDataElement attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.ArchivedHistorySummary attribute) (galaxy.schema.schema.CollectionElementIdentifier attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.FileLibraryFolderItem attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDAObject attribute) (galaxy.schema.schema.HistoryItemCommon attribute) (galaxy.schema.schema.HistorySummary attribute) (galaxy.schema.schema.PageSummary attribute) (galaxy.schema.schema.StoredWorkflowSummary attribute) (galaxy.schema.schema.TagOperationParams attribute) (galaxy.schema.schema.UpdateHistoryContentsPayload attribute) (galaxy.schema.schema.WorkflowToExport attribute) (galaxy.tools.actions.upload_common.LibraryParams attribute) (galaxy.tools.parameters.grouping.Dataset attribute) (galaxy.tours.TourCore attribute) (galaxy.webapps.galaxy.api.Router attribute) tags_used (galaxy.schema.schema.DetailedUserModel attribute) tags_used() (galaxy.managers.users.UserManager method) TagsController (class in galaxy.webapps.galaxy.controllers.tag) TagsManager (class in galaxy.managers.tags) TandemXML (class in galaxy.datatypes.proteomics) tap_path (galaxy.tool_util.deps.brew_exts.RecipeContext property) TAR (galaxy.schema.schema.ModelStoreFormat attribute) TAR_DOT_GZ (galaxy.schema.schema.ModelStoreFormat attribute) tar_export_directory() (in module galaxy.model.store) tar_open() (in module tool_shed.util.repository_content_util) target (galaxy.schema.remote_files.CreateEntryPayload attribute) (galaxy.schema.schema.Hyperlink attribute) (galaxy.web_stack.message.ApplicationStackMessage property) (galaxy.web_stack.message.JobHandlerMessage attribute) (galaxy.web_stack.message.WorkflowSchedulingMessage attribute) target_galaxy_version (galaxy.tool_util.verify.interactor.GalaxyInteractorApi property) target_history() (galaxy.model.store.ModelImportStore method) target_if_active() (galaxy.managers.interactivetool.InteractiveToolManager method) target_uri (galaxy.schema.schema.ExportRecordData attribute) (galaxy.schema.schema.WriteStoreToPayload attribute) TARGET_URL (galaxy.datatypes.binary.H5MLM attribute) target_url_from_selenium (galaxy.selenium.context.GalaxySeleniumContext attribute) (galaxy.selenium.context.GalaxySeleniumContextImpl attribute) (galaxy.selenium.jupyter_context.JupyterContextImpl attribute) (galaxy_test.selenium.jupyter_context.JupyterTestContextImpl attribute) target_url_parts() (in module galaxy_test.base.env) targets (galaxy.schema.fetch_data.FetchDataFormPayload attribute) (galaxy.schema.fetch_data.FetchDataPayload attribute) targets_string_to_json() (galaxy.schema.fetch_data.BaseDataPayload class method) TarModelExportStore (class in galaxy.model.store) Task (class in galaxy.model) task (galaxy.schema.schema.AsyncFile attribute) (galaxy.web_stack.message.TaskMessage property) Task.states (class in galaxy.model) task_based (galaxy_test.api.test_histories.ImportExportTests attribute) (galaxy_test.api.test_histories.TestImportExportHistory attribute) task_id (galaxy.model.TaskMetricNumeric attribute) (galaxy.model.TaskMetricText attribute) task_runner_external_id (galaxy.model.Task attribute) task_runner_name (galaxy.model.Task attribute) task_suspend() (galaxy.jobs.runners.godocker.GodockerJobRunner method) task_uuid (galaxy.model.StoreExportAssociation attribute) (galaxy.schema.schema.ObjectExportTaskResponse attribute) TaskedJobRunner (class in galaxy.jobs.runners.tasks) TaskMessage (class in galaxy.web_stack.message) TaskMetricNumeric (class in galaxy.model) TaskMetricText (class in galaxy.model) TaskPathRewriter (class in galaxy.job_execution.datasets) tasks (galaxy.model.Job attribute) TaskWrapper (class in galaxy.jobs) Taxonomy (class in galaxy.datatypes.tabular) TaxonomySummary (class in galaxy.datatypes.mothur) Tck (class in galaxy.datatypes.images) TdfTar (class in galaxy.datatypes.binary) TDirectoryClass (class in galaxy.files.sources) tear_down() (galaxy_test.driver.driver_util.TestDriver method) tear_down_app() (galaxy.app_unittest_utils.tools_support.UsesApp method) tear_down_pool() (in module galaxy.celery) tearDown() (galaxy_test.base.api.UsesApiTestCaseMixin method) (galaxy_test.driver.integration_util.IntegrationInstance method) tearDownClass() (galaxy_test.base.testcase.FunctionalTestCase class method) (galaxy_test.driver.integration_util.IntegrationInstance class method) telephone (galaxy.schema.schema.Creator attribute) temp_config_dir() (galaxy_test.driver.integration_util.IntegrationInstance class method) temp_directory (galaxy.model.JobExportHistoryArchive property) temp_input_connections (galaxy.model.WorkflowStep attribute) TempfileDataProvider (class in galaxy.datatypes.dataproviders.external) TempFileHandler (class in galaxy.datatypes.util.maf_utilities) (class in galaxy.tools.util.maf_utilities) template (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryInfoAssociation attribute) (galaxy.model.migrations.DatabaseConfig attribute) (galaxy.tools.actions.upload_common.LibraryParams attribute) (galaxy.web.legacy_framework.grids.Grid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) template_context (galaxy.webapps.base.webapp.GalaxyWebTransaction attribute) template_field_contents (galaxy.tools.actions.upload_common.LibraryParams attribute) template_macro_params() (in module galaxy.tool_util.loader) (in module galaxy.util.xml_macros) template_or_none() (in module galaxy.tools.parameters.dynamic_options) TEMPLATE_PATHS_CONFIG (galaxy.visualization.plugins.registry.VisualizationsRegistry attribute) terminal_states (galaxy.model.Dataset attribute) (galaxy.model.Job attribute) test_0000_create_or_login_admin_user() (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository method) (tool_shed.test.functional.test_0070_invalid_tool.TestBismarkRepository method) (tool_shed.test.functional.test_1070_invalid_tool.TestFreebayesRepository method) (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies method) (tool_shed.test.functional.test_1100_install_updated_repository_dependencies.TestRepositoryDependencies method) test_0000_initiate_users() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) (tool_shed.test.functional.test_0020_basic_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies method) (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_0080_advanced_circular_dependencies.TestRepositoryCircularDependencies method) (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain method) (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies method) (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners.TestRepositoryMultipleOwners method) (tool_shed.test.functional.test_0140_tool_help_images.TestToolHelpImages method) (tool_shed.test.functional.test_0150_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_0160_circular_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_0170_complex_prior_installation_required.TestComplexPriorInstallation method) (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) (tool_shed.test.functional.test_0310_hg_api_features.TestHgWebFeatures method) (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs method) (tool_shed.test.functional.test_0430_browse_utilities.TestToolShedBrowseUtilities method) (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole method) (tool_shed.test.functional.test_0550_metadata_updated_dependencies.TestGetUpdatedMetadata method) (tool_shed.test.functional.test_1000_install_basic_repository.TestBasicToolShedFeatures method) (tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies.TestToolWithToolDependencies method) (tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies.TestToolWithRepositoryDependencies method) (tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions.TestRepositoryWithDependencyRevisions method) (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners method) (tool_shed.test.functional.test_1160_tool_help_images.TestToolHelpImages method) (tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1190_complex_prior_installation_required.TestComplexPriorInstallation method) (tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository.TestUninstallingAndReinstallingRepositories method) (tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies.TestUninstallingAndReinstallingRepositories method) (tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions.TestUninstallingAndReinstallingRepositories method) (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) (tool_shed.test.functional.test_1410_update_manager.TestUpdateManager method) (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository method) test_0000_initiate_users_and_category() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) (tool_shed.test.functional.test_0480_tool_dependency_xml_verification.TestDependencyDefinitionValidation method) (tool_shed.test.functional.test_1430_repair_installed_repository.TestRepairRepository method) (tool_shed.test.functional.test_1460_data_managers.TestDataManagers method) test_0005_create_and_populate_column_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies method) (tool_shed.test.functional.test_1100_install_updated_repository_dependencies.TestRepositoryDependencies method) test_0005_create_bwa_base_repository() (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain method) test_0005_create_bwa_package_repository() (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies method) (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0005_create_categories() (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) test_0005_create_category() (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository method) (tool_shed.test.functional.test_0020_basic_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies method) (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies method) test_0005_create_category_and_repository() (tool_shed.test.functional.test_0070_invalid_tool.TestBismarkRepository method) test_0005_create_column_maker_repository() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0005_create_column_repository() (tool_shed.test.functional.test_0080_advanced_circular_dependencies.TestRepositoryCircularDependencies method) test_0005_create_convert_repository() (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_0080_advanced_circular_dependencies.TestRepositoryCircularDependencies method) (tool_shed.test.functional.test_0150_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_0160_circular_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) (tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) test_0005_create_datatypes_repository() (tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners.TestRepositoryMultipleOwners method) (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners method) test_0005_create_filter_repository() (tool_shed.test.functional.test_1430_repair_installed_repository.TestRepairRepository method) test_0005_create_filtering_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) (tool_shed.test.functional.test_0310_hg_api_features.TestHgWebFeatures method) (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole method) (tool_shed.test.functional.test_1410_update_manager.TestUpdateManager method) (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository method) test_0005_create_freebayes_repository() (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies method) test_0005_create_htseq_count_repository() (tool_shed.test.functional.test_0140_tool_help_images.TestToolHelpImages method) (tool_shed.test.functional.test_1160_tool_help_images.TestToolHelpImages method) test_0005_create_libx11_repository() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) test_0005_create_matplotlib_repository() (tool_shed.test.functional.test_0170_complex_prior_installation_required.TestComplexPriorInstallation method) (tool_shed.test.functional.test_1190_complex_prior_installation_required.TestComplexPriorInstallation method) test_0005_create_repository() (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs method) test_0005_create_repository_without_categories() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0005_create_tool_dependency_repository() (tool_shed.test.functional.test_0480_tool_dependency_xml_verification.TestDependencyDefinitionValidation method) test_0005_ensure_existence_of_repository_and_category() (tool_shed.test.functional.test_1070_invalid_tool.TestFreebayesRepository method) test_0005_ensure_repositories_and_categories_exist() (tool_shed.test.functional.test_1000_install_basic_repository.TestBasicToolShedFeatures method) (tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies.TestToolWithToolDependencies method) (tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies.TestToolWithRepositoryDependencies method) (tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions.TestRepositoryWithDependencyRevisions method) (tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository.TestUninstallingAndReinstallingRepositories method) (tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies.TestUninstallingAndReinstallingRepositories method) (tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions.TestUninstallingAndReinstallingRepositories method) test_0005_freebayes_repository() (tool_shed.test.functional.test_0550_metadata_updated_dependencies.TestGetUpdatedMetadata method) test_0010_browse_tool_shed() (tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies.TestToolWithToolDependencies method) (tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies.TestToolWithRepositoryDependencies method) (tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions.TestRepositoryWithDependencyRevisions method) (tool_shed.test.functional.test_1070_invalid_tool.TestFreebayesRepository method) test_0010_browse_tool_sheds() (tool_shed.test.functional.test_1000_install_basic_repository.TestBasicToolShedFeatures method) test_0010_clone() (tool_shed.test.functional.test_0310_hg_api_features.TestHgWebFeatures method) test_0010_create_and_populate_convert_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies method) (tool_shed.test.functional.test_1100_install_updated_repository_dependencies.TestRepositoryDependencies method) test_0010_create_bwa_base_repository() (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies method) (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0010_create_bwa_color_repository() (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain method) test_0010_create_bwa_package_repository() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0010_create_categories() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0010_create_column_maker_repository() (tool_shed.test.functional.test_0020_basic_repository_dependencies.TestBasicRepositoryDependencies method) test_0010_create_column_repository() (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_0150_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_0160_circular_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) (tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1430_repair_installed_repository.TestRepairRepository method) test_0010_create_convert_chars_repository() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0010_create_data_manager_repository() (tool_shed.test.functional.test_1460_data_managers.TestDataManagers method) test_0010_create_emboss_5_0_0_repository() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) test_0010_create_emboss_5_repository() (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) test_0010_create_emboss_datatypes_repository_and_upload_tarball() (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies method) test_0010_create_emboss_dependendent_column_maker_repository_and_upload_tarball() (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies method) test_0010_create_emboss_repository() (tool_shed.test.functional.test_0430_browse_utilities.TestToolShedBrowseUtilities method) test_0010_create_freebayes_repository() (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies method) (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0010_create_freebayes_repository_and_upload_tool_xml() (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository method) test_0010_create_numpy_repository() (tool_shed.test.functional.test_0170_complex_prior_installation_required.TestComplexPriorInstallation method) (tool_shed.test.functional.test_1190_complex_prior_installation_required.TestComplexPriorInstallation method) test_0010_create_repositories_from_0000_series() (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) test_0010_create_samtools_repository() (tool_shed.test.functional.test_0550_metadata_updated_dependencies.TestGetUpdatedMetadata method) test_0010_install_emboss_repository() (tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions.TestUninstallingAndReinstallingRepositories method) test_0010_install_filtering_repository() (tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository.TestUninstallingAndReinstallingRepositories method) (tool_shed.test.functional.test_1410_update_manager.TestUpdateManager method) test_0010_install_filtering_to_galaxy() (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository method) test_0010_install_freebayes_repository() (tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies.TestUninstallingAndReinstallingRepositories method) test_0010_load_tool_page() (tool_shed.test.functional.test_0140_tool_help_images.TestToolHelpImages method) (tool_shed.test.functional.test_1160_tool_help_images.TestToolHelpImages method) test_0010_populate_tool_dependency_repository() (tool_shed.test.functional.test_0480_tool_dependency_xml_verification.TestDependencyDefinitionValidation method) test_0010_upload_new_file_to_repository() (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs method) test_0010_verify_datatypes_repository() (tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners.TestRepositoryMultipleOwners method) (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners method) test_0010_verify_repository_admin_role_exists() (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole method) test_0015_browse_test_0000_category() (tool_shed.test.functional.test_1000_install_basic_repository.TestBasicToolShedFeatures method) test_0015_create_and_upload_dependency_files() (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies method) test_0015_create_complex_repository_dependency() (tool_shed.test.functional.test_0170_complex_prior_installation_required.TestComplexPriorInstallation method) (tool_shed.test.functional.test_1190_complex_prior_installation_required.TestComplexPriorInstallation method) test_0015_create_datatypes_0020_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0015_create_dependency_on_convert_chars() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0015_create_emboss_5_repository() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) test_0015_create_emboss_6_repository() (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) test_0015_create_emboss_datatypes_repository() (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0015_create_filtering_repository() (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies method) (tool_shed.test.functional.test_0160_circular_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_0550_metadata_updated_dependencies.TestGetUpdatedMetadata method) (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies method) (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) test_0015_create_repositories_from_0010_series() (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) test_0015_create_repository() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0015_create_repository_dependency() (tool_shed.test.functional.test_0150_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1430_repair_installed_repository.TestRepairRepository method) test_0015_create_tool_dependency_repositories() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0015_create_tool_repository() (tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners.TestRepositoryMultipleOwners method) (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners method) test_0015_generate_complex_repository_dependency_invalid_shed_url() (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies method) (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0015_install_and_uninstall_column_repository() (tool_shed.test.functional.test_1100_install_updated_repository_dependencies.TestRepositoryDependencies method) test_0015_install_emboss_repository() (tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies.TestToolWithRepositoryDependencies method) (tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions.TestRepositoryWithDependencyRevisions method) test_0015_install_freebayes_repository() (tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies.TestToolWithToolDependencies method) (tool_shed.test.functional.test_1070_invalid_tool.TestFreebayesRepository method) test_0015_load_user_view_page() (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs method) test_0015_uninstall_emboss_repository() (tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions.TestUninstallingAndReinstallingRepositories method) test_0015_uninstall_filtering_repository() (tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository.TestUninstallingAndReinstallingRepositories method) test_0015_uninstall_freebayes_repository() (tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies.TestUninstallingAndReinstallingRepositories method) test_0015_update_repository() (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository method) test_0015_upload_dependency_xml_if_needed() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0015_upload_missing_tool_data_table_conf_file() (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository method) test_0015_upload_readme_file() (tool_shed.test.functional.test_1410_update_manager.TestUpdateManager method) test_0015_verify_repository_role_association() (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole method) test_0020_check_for_displayed_update() (tool_shed.test.functional.test_1410_update_manager.TestUpdateManager method) test_0020_check_repository_dependency() (tool_shed.test.functional.test_0550_metadata_updated_dependencies.TestGetUpdatedMetadata method) test_0020_create_dependency_on_freebayes() (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies method) test_0020_create_dependent_repository() (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) test_0020_create_emboss_0020_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0020_create_emboss_5_repository_and_upload_files() (tool_shed.test.functional.test_0020_basic_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies method) test_0020_create_emboss_repository() (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0020_create_repositories_from_0020_series() (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) test_0020_create_repository_dependencies() (tool_shed.test.functional.test_0080_advanced_circular_dependencies.TestRepositoryCircularDependencies method) (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies method) test_0020_create_repository_dependency() (tool_shed.test.functional.test_0160_circular_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) test_0020_create_tool_dependency_repository() (tool_shed.test.functional.test_0430_browse_utilities.TestToolShedBrowseUtilities method) test_0020_edit_repository() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0020_generate_complex_repository_dependency_invalid_repository_name() (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies method) (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0020_get_repository_updates() (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository method) test_0020_install_column_repository() (tool_shed.test.functional.test_1430_repair_installed_repository.TestRepairRepository method) test_0020_install_convert_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0020_install_data_manager_repository() (tool_shed.test.functional.test_1460_data_managers.TestDataManagers method) test_0020_install_repositories() (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies method) test_0020_load_repository_view_page() (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs method) test_0020_populate_complex_dependency_test_1_0460() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0020_preview_filtering_repository() (tool_shed.test.functional.test_1000_install_basic_repository.TestBasicToolShedFeatures method) test_0020_reinstall_emboss_repository() (tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions.TestUninstallingAndReinstallingRepositories method) test_0020_reinstall_filtering_repository() (tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository.TestUninstallingAndReinstallingRepositories method) test_0020_reinstall_freebayes_repository() (tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies.TestUninstallingAndReinstallingRepositories method) test_0020_rename_repository() (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole method) test_0020_upload_dependency_xml() (tool_shed.test.functional.test_1100_install_updated_repository_dependencies.TestRepositoryDependencies method) test_0020_upload_missing_sample_loc_file() (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository method) test_0020_upload_updated_tool_dependency_to_package_x11() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) test_0020_verify_dependency_metadata() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0020_verify_generated_dependency() (tool_shed.test.functional.test_0170_complex_prior_installation_required.TestComplexPriorInstallation method) (tool_shed.test.functional.test_1190_complex_prior_installation_required.TestComplexPriorInstallation method) test_0020_verify_installed_repository_metadata() (tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies.TestToolWithToolDependencies method) (tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies.TestToolWithRepositoryDependencies method) test_0020_verify_repository_dependency() (tool_shed.test.functional.test_0150_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation method) test_0020_verify_tool_repository() (tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners.TestRepositoryMultipleOwners method) (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners method) test_0025_change_repository_category() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0025_create_dependency_on_filtering() (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies method) (tool_shed.test.functional.test_0080_advanced_circular_dependencies.TestRepositoryCircularDependencies method) test_0025_create_emboss_datatypes_0030_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0025_create_emboss_repository() (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) test_0025_create_filtering_repository() (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0025_create_repositories_from_0030_series() (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) test_0025_create_repository_dependency() (tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners.TestRepositoryMultipleOwners method) (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners method) test_0025_deactivate_datatypes_repository() (tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies.TestToolWithRepositoryDependencies method) test_0025_deactivate_emboss_repository() (tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions.TestUninstallingAndReinstallingRepositories method) test_0025_deactivate_filtering_repository() (tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository.TestUninstallingAndReinstallingRepositories method) test_0025_deactivate_freebayes_repository() (tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies.TestUninstallingAndReinstallingRepositories method) test_0025_delete_repository_dependency() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0025_generate_and_upload_repository_dependencies_xml() (tool_shed.test.functional.test_0020_basic_repository_dependencies.TestBasicRepositoryDependencies method) test_0025_generate_complex_repository_dependency_invalid_owner_name() (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies method) (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0025_generate_repository_dependency_with_invalid_url() (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies method) test_0025_install_column_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) (tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation method) test_0025_install_filtering_repository() (tool_shed.test.functional.test_1000_install_basic_repository.TestBasicToolShedFeatures method) test_0025_install_freebayes_repository() (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies method) test_0025_install_matplotlib_repository() (tool_shed.test.functional.test_1190_complex_prior_installation_required.TestComplexPriorInstallation method) test_0025_load_view_page_for_previous_revision() (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs method) test_0025_populate_complex_dependency_test_2_0460() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0025_uninstall_column_repository() (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies method) test_0025_uninstall_filter_repository() (tool_shed.test.functional.test_1430_repair_installed_repository.TestRepairRepository method) test_0025_uninstall_repository() (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository method) test_0025_update_dependent_repositories() (tool_shed.test.functional.test_0550_metadata_updated_dependencies.TestGetUpdatedMetadata method) test_0025_upload_malformed_tool_dependency_xml() (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository method) test_0025_upload_updated_tool_dependency_to_package_emboss() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) test_0025_verify_installed_repository_metadata() (tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions.TestRepositoryWithDependencyRevisions method) test_0025_verify_repository_dependency() (tool_shed.test.functional.test_0160_circular_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1100_install_updated_repository_dependencies.TestRepositoryDependencies method) (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) test_0025_verify_sample_files() (tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies.TestToolWithToolDependencies method) test_0030_browse_tools() (tool_shed.test.functional.test_0430_browse_utilities.TestToolShedBrowseUtilities method) test_0030_create_bwa_package_repository() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0030_create_emboss_5_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0030_create_freebayes_repository() (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0030_create_repositories_from_0040_series() (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) test_0030_deactivate_convert_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0030_generate_complex_repository_dependency_invalid_changeset_revision() (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies method) (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0030_generate_repository_dependencies_for_emboss_5() (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) test_0030_generate_repository_dependency_with_invalid_name() (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies method) test_0030_grant_write_access() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0030_install_filtering_repository() (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) test_0030_install_filtering_repository_again() (tool_shed.test.functional.test_1000_install_basic_repository.TestBasicToolShedFeatures method) test_0030_load_sharable_url_with_invalid_changeset_revision() (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs method) test_0030_populate_complex_dependency_test_3_0460() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0030_reactivate_datatypes_repository() (tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies.TestToolWithRepositoryDependencies method) test_0030_reactivate_emboss_repository() (tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions.TestUninstallingAndReinstallingRepositories method) test_0030_reactivate_filtering_repository() (tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository.TestUninstallingAndReinstallingRepositories method) test_0030_reactivate_freebayes_repository() (tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies.TestUninstallingAndReinstallingRepositories method) test_0030_reinstall_column_repository() (tool_shed.test.functional.test_1100_install_updated_repository_dependencies.TestRepositoryDependencies method) test_0030_reinstall_repository() (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository method) test_0030_uninstall_convert_repository() (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies method) test_0030_uninstall_filtering_repository() (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies method) test_0030_upload_invalid_tool_dependency_xml() (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository method) test_0030_upload_updated_tool_dependency_to_emboss_5_repository() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) test_0030_verify_access_denied() (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole method) test_0030_verify_data_manager_tool() (tool_shed.test.functional.test_1460_data_managers.TestDataManagers method) test_0030_verify_emboss_5_dependencies() (tool_shed.test.functional.test_0020_basic_repository_dependencies.TestBasicRepositoryDependencies method) test_0030_verify_installation_order() (tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1190_complex_prior_installation_required.TestComplexPriorInstallation method) test_0030_verify_repository_dependencies() (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies method) (tool_shed.test.functional.test_0080_advanced_circular_dependencies.TestRepositoryCircularDependencies method) test_0035_create_and_upload_dependency_definitions() (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain method) test_0035_create_bismark_repository() (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0035_create_bwa_base_repository() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0035_create_emboss_6_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0035_create_repositories_for_url_upload() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0035_create_repositories_from_0050_series() (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) test_0035_generate_complex_repository_dependency() (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies method) test_0035_generate_repository_dependencies_for_emboss_6() (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) test_0035_generate_repository_dependency_with_invalid_owner() (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies method) test_0035_generate_valid_complex_repository_dependency() (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0035_grant_admin_role() (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole method) test_0035_load_sharable_url_with_invalid_repository_name() (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs method) test_0035_modify_package_x11_repository_type() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) test_0035_reactivate_convert_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0035_reactivate_filtering_repository() (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies method) test_0035_reinstall_column_repository() (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies method) test_0035_upload_filtering_1_1_0() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0035_upload_valid_tool_dependency_xml() (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository method) test_0035_verify_absence_of_ghosts() (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository method) test_0035_verify_installation_order() (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) test_0035_verify_installed_repository_metadata() (tool_shed.test.functional.test_1000_install_basic_repository.TestBasicToolShedFeatures method) test_0035_verify_repository_metadata() (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies method) (tool_shed.test.functional.test_0080_advanced_circular_dependencies.TestRepositoryCircularDependencies method) test_0040_browse_tool_dependencies() (tool_shed.test.functional.test_0430_browse_utilities.TestToolShedBrowseUtilities method) test_0040_create_and_upload_dependency_definitions() (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0040_create_dependency_on_bwa_package_repository() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0040_create_emboss_0030_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0040_deactivate_all_repositories() (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) test_0040_deactivate_column_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0040_generate_repository_dependency_on_emboss_5() (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) test_0040_generate_repository_dependency_with_invalid_changeset_revision() (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies method) test_0040_generate_tool_dependency() (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies method) test_0040_load_sharable_url_with_invalid_owner() (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs method) test_0040_modify_package_emboss_repository_type() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) test_0040_reinstall_convert_repository() (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies method) test_0040_rename_repository_as_repository_admin() (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole method) test_0040_uninstall_freebayes_repository() (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies method) test_0040_update_tool_repository() (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0040_verify_data_manager_data_table() (tool_shed.test.functional.test_1460_data_managers.TestDataManagers method) test_0040_verify_repository() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0040_verify_repository_dependencies() (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain method) test_0040_verify_repository_dependency() (tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners.TestRepositoryMultipleOwners method) (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners method) test_0040_verify_repository_metadata() (tool_shed.test.functional.test_0020_basic_repository_dependencies.TestBasicRepositoryDependencies method) test_0040_verify_tool_dependencies() (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository method) (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies method) test_0045_alter_repository_states() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0045_create_repository_dependencies_for_0030() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0045_deactivate_convert_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0045_deactivate_filtering_repository() (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies method) test_0045_generate_repository_dependency_on_emboss_6() (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) test_0045_install_base_repository() (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0045_install_blastxml_to_top_descr() (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners method) test_0045_install_repository_with_invalid_repository_dependency() (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies method) test_0045_reactivate_filter_repository() (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) test_0045_reset_repository_metadata() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) test_0045_verify_dependency_metadata() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0045_verify_repository_dependencies() (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0050_create_freebayes_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0050_create_repositories_for_simple_dependencies() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0050_delete_complex_repository_dependency() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0050_display_repository_tip_file() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0050_reactivate_column_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0050_reset_emboss_5_metadata() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) test_0050_verify_installed_repositories() (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0050_verify_reinstallation_order() (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) test_0050_verify_repository_dependency_revisions() (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) test_0050_verify_repository_installation() (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners method) test_0050_verify_tool_dependencies() (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0055_create_bwa_tool_dependency_repository() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0055_create_filtering_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0055_install_column_repository() (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0055_populate_repository_dependency_test_1_0460() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0055_reactivate_convert_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0055_upload_filtering_txt_file() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0055_verify_repository_metadata() (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) test_0060_create_dependency_structure() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0060_delete_bwa_tool_dependency_definition() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0060_install_emboss_repository() (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0060_populate_repository_dependency_test_2_0460() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0060_uninstall_column_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0060_upload_filtering_test_data() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0065_create_convert_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0065_deactivate_bismark_repository() (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0065_populate_repository_dependency_test_3_0460() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0065_reinstall_column_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0065_reupload_bwa_tool_dependency_definition() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0065_upload_filtering_2_2_0() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0070_create_column_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0070_create_repositories_for_url_upload() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0070_uninstall_convert_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0070_uninstall_emboss_repository() (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0070_verify_filtering_repository() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0075_create_emboss_datatypes_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0075_install_freebayes_repository() (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0075_uninstall_column_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0075_upload_readme_txt_file() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0080_create_emboss_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0080_delete_readme_txt_file() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0080_reinstall_convert_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0085_create_filtering_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0085_search_for_valid_filter_tool() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0090_create_freebayes_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0090_verify_repository_metadata() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0095_create_bismark_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0095_verify_reserved_repository_name_handling() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0100_create_and_upload_dependency_definitions() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0100_verify_reserved_username_handling() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0105_contact_repository_owner() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0110_delete_filtering_repository() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0110_reset_metadata_on_all_repositories() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0115_undelete_filtering_repository() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0120_enable_email_notifications() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0125_upload_new_readme_file() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0130_verify_handling_of_invalid_characters() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0135_api_get_repositories_in_category() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0140_view_invalid_changeset() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_400_on_delete_invalid_page_id() (galaxy_test.api.test_pages.TestPagesApi method) test_400_on_download_pdf_when_unsupported_content_format() (galaxy_test.api.test_pages.TestPagesApi method) test_400_on_index_deleted_shared() (galaxy_test.api.test_pages.TestPagesApi method) test_400_on_invalid_embedded_content() (galaxy_test.api.test_pages.TestPagesApi method) test_400_on_invalid_id_encoding() (galaxy_test.api.test_pages.TestPagesApi method) test_400_on_invalid_id_encoding_markdown() (galaxy_test.api.test_pages.TestPagesApi method) test_400_on_invalid_markdown_call() (galaxy_test.api.test_pages.TestPagesApi method) test_400_on_invalid_workflow_id() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_403_if_create_revision_on_unowned_page() (galaxy_test.api.test_page_revisions.TestPageRevisionsApi method) test_403_on_delete_unowned_page() (galaxy_test.api.test_pages.TestPagesApi method) test_403_on_unowner_show() (galaxy_test.api.test_pages.TestPagesApi method) test_404_on_unknown_license() (galaxy_test.api.test_licenses.TestLicensesApi method) test_501_on_download_pdf_when_service_unavailable() (galaxy_test.api.test_pages.TestPagesApi method) test_9900_install_all_missing_repositories() (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) test_9905_reset_metadata_on_all_repositories() (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) test_abort_fetch_job() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_admin_can_update_permissions() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_admin_data_manager() (galaxy_test.selenium.test_admin_app.TestAdminApp method) test_admin_dependencies_display() (galaxy_test.selenium.test_admin_app.TestAdminApp method) test_admin_job_list() (galaxy_test.api.test_jobs.TestJobsApi method) test_admin_jobs_display() (galaxy_test.selenium.test_admin_app.TestAdminApp method) test_admin_only() (galaxy_test.api.test_tool_data.TestToolDataApi method) test_admin_server_display() (galaxy_test.selenium.test_admin_app.TestAdminApp method) test_admin_toolshed() (galaxy_test.selenium.test_admin_app.TestAdminApp method) test_admin_update() (galaxy_test.api.test_users.TestUsersApi method) test_admin_user_configuration() (galaxy_test.api.test_configuration.TestConfigurationApi method) test_admin_user_display() (galaxy_test.selenium.test_admin_app.TestAdminApp method) test_advanced_search() (galaxy_test.selenium.test_histories_list.TestSavedHistories method) test_anon_can_download_importable_workflow() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_anon_can_download_public_workflow() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_anon_can_see_workflow_preview() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_anon_get_content_as_text() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_anon_history_after_registration() (galaxy_test.selenium.test_anon_history.TestAnonymousHistories method) test_anon_history_creation() (galaxy_test.api.test_authenticate.TestAuthenticateApi method) test_anon_history_landing() (galaxy_test.selenium.test_anon_history.TestAnonymousHistories method) test_anon_history_upload() (galaxy_test.selenium.test_anon_history.TestAnonymousHistories method) test_anon_private_get_content_as_text() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_anon_tag_permissions() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_anonymous_can_import_published() (galaxy_test.api.test_histories.TestHistoriesApi method) test_anonymous_published() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_api_key() (galaxy_test.selenium.test_personal_information.TestManageInformation method) test_apply_rules_1() (galaxy_test.api.test_tools.TestToolsApi method) test_apply_rules_2() (galaxy_test.api.test_tools.TestToolsApi method) test_apply_rules_3() (galaxy_test.api.test_tools.TestToolsApi method) test_apply_rules_4() (galaxy_test.api.test_tools.TestToolsApi method) test_apply_rules_5() (galaxy_test.api.test_tools.TestToolsApi method) test_apply_rules_6() (galaxy_test.api.test_tools.TestToolsApi method) test_archive() (galaxy_test.api.test_histories.TestArchivingHistoriesWithoutExportRecord method) test_archived_histories_are_not_listed_by_default() (galaxy_test.api.test_histories.TestArchivingHistoriesWithoutExportRecord method) test_archived_histories_filtering_and_sorting() (galaxy_test.api.test_histories.TestArchivingHistoriesWithoutExportRecord method) test_archived_histories_index() (galaxy_test.api.test_histories.TestArchivingHistoriesWithoutExportRecord method) test_archiving_an_archived_history_conflicts() (galaxy_test.api.test_histories.TestArchivingHistoriesWithoutExportRecord method) test_aria_connections_menu() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_assign_column_pja() (galaxy_test.api.test_workflows.ChangeDatatypeTests method) test_auth() (galaxy_test.api.test_authenticate.TestAuthenticateApi method) test_back_to_history_button() (galaxy_test.selenium.test_history_panel_collections.TestHistoryPanelCollections method) test_bad_emails() (galaxy_test.selenium.test_registration.TestRegistration method) test_bad_usernames() (galaxy_test.selenium.test_registration.TestRegistration method) test_bam_chunking_through_display_endpoint() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_bam_state_regression() (galaxy_test.api.test_tools.TestToolsApi method) test_base64_import() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_basics() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_bibtex_rendering() (galaxy_test.selenium.test_tool_form.TestToolForm method) test_build_add() (galaxy_test.selenium.test_custom_builds.TestCustomBuilds method) test_build_delete() (galaxy_test.selenium.test_custom_builds.TestCustomBuilds method) test_build_list_and_show_items() (galaxy_test.selenium.test_collection_builders.TestCollectionBuilders method) test_build_list_simple_hidden() (galaxy_test.selenium.test_collection_builders.TestCollectionBuilders method) test_build_pair_simple_hidden() (galaxy_test.selenium.test_collection_builders.TestCollectionBuilders method) test_build_paired_list_show_original() (galaxy_test.selenium.test_collection_builders.TestCollectionBuilders method) test_build_paired_list_simple() (galaxy_test.selenium.test_collection_builders.TestCollectionBuilders method) test_build_simple_list_via_rules_hidden() (galaxy_test.selenium.test_collection_builders.TestCollectionBuilders method) test_bulk_datatype_change() (galaxy_test.api.test_history_contents.TestHistoryContentsApiBulkOperation method) test_bulk_datatype_change_auto() (galaxy_test.api.test_history_contents.TestHistoryContentsApiBulkOperation method) test_bulk_datatype_change_collection() (galaxy_test.api.test_history_contents.TestHistoryContentsApiBulkOperation method) test_bulk_datatype_change_errors() (galaxy_test.api.test_history_contents.TestHistoryContentsApiBulkOperation method) test_bulk_datatype_change_should_skip_set_metadata_on_deferred_data() (galaxy_test.api.test_history_contents.TestHistoryContentsApiBulkOperation method) test_bulk_dbkey_change() (galaxy_test.api.test_history_contents.TestHistoryContentsApiBulkOperation method) test_bulk_dbkey_change_dataset_collection() (galaxy_test.api.test_history_contents.TestHistoryContentsApiBulkOperation method) test_bulk_operations() (galaxy_test.api.test_history_contents.TestHistoryContentsApiBulkOperation method) test_bulk_tag_changes() (galaxy_test.api.test_history_contents.TestHistoryContentsApiBulkOperation method) test_byte_range_support() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_cancel_new_workflow_when_history_deleted() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_cancel_ready_workflow_when_history_deleted() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_cancel_workflow_invocation() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_cancel_workflow_invocation_deletes_jobs() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_cannot_create_page_with_invalid_content_format() (galaxy_test.api.test_pages.TestPagesApi method) test_cannot_create_pages_with_invalid_slug() (galaxy_test.api.test_pages.TestPagesApi method) test_cannot_create_pages_with_same_slug() (galaxy_test.api.test_pages.TestPagesApi method) test_cannot_download_private_workflow() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_cannot_map_over_incompatible_collections() (galaxy_test.api.test_tools.TestToolsApi method) test_cannot_modify_tags_on_immutable_history() (galaxy_test.api.test_histories.TestHistoriesApi method) test_cannot_run_against_other_users_history() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_cannot_run_bootstrap_admin_workflow() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_cannot_run_inaccessible_workflow() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_cannot_run_tools_on_immutable_histories() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_cannot_run_workflow_as_anon() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_cannot_run_workflow_on_immutable_history() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_cannot_show_private_workflow() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_cannot_update_dataset_collection_on_immutable_history() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_cannot_update_dataset_on_immutable_history() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_cannot_update_datatype_on_immutable_history() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_change_datatype() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_change_datatype_collection_map_over() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_change_datatype_discovered_outputs() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_change_datatype_in_subworkflow() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_change_datatype_post_job_action_lost_regression() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_change_datatype_simple_list() (galaxy_test.selenium.test_collection_edit.TestCollectionEdit method) test_change_dbkey_simple_list() (galaxy_test.selenium.test_collection_edit.TestCollectionEdit method) test_change_email() (galaxy_test.selenium.test_personal_information.TestManageInformation method) test_change_password() (galaxy_test.selenium.test_change_password.TestChangePassword method) test_clean_anon_history_after_logout() (galaxy_test.selenium.test_anon_history.TestAnonymousHistories method) test_click_error() (galaxy_test.selenium.test_navigates_galaxy.TestNavigatesGalaxySelenium method) test_collection_contents_empty_root() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_collection_contents_invalid_collection() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_collection_contents_limit_offset() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_collection_contents_security() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_collection_input() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_collection_job_details() (galaxy_test.selenium.test_history_panel_collections.TestHistoryPanelCollections method) test_collection_operation_collection_input_permissions() (galaxy_test.api.test_tools.TestToolsApi method) test_collection_operation_dataset_input_permissions() (galaxy_test.api.test_tools.TestToolsApi method) test_collection_parameter() (galaxy_test.api.test_tools.TestToolsApi method) test_collection_tools_tag_propagation() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_column_legal_values() (galaxy_test.api.test_tools.TestToolsApi method) test_combined_mapping_and_subcollection_mapping() (galaxy_test.api.test_tools.TestToolsApi method) test_comma_separated_columns() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_comma_separated_columns_with_trailing_newline() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_common_problems() (galaxy_test.api.test_jobs.TestJobsApi method) test_composite_datatype() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_composite_datatype_download() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_composite_datatype_fetch() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_composite_datatype_isatab() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_composite_datatype_pbed_stage_fetch() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_composite_datatype_posix_lines() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_composite_datatype_space_to_tab() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_composite_datatype_stage_fetch() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_composite_datatype_stage_upload1() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_compute_md5_on_primary_dataset() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_compute_sha1_on_composite_dataset() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_conditional_ints() (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi method) test_conditional_subworkflow_step() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_connecting_display_in_upload_false_connections() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_connectivity_table_chunking_through_display_endpoint() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_convert_dataset_explicit_history() (galaxy_test.api.test_tools.TestToolsApi method) test_convert_dataset_implicit_history() (galaxy_test.api.test_tools.TestToolsApi method) test_convert_hdca() (galaxy_test.api.test_tools.TestToolsApi method) test_converter_present_after_toolbox_reload() (galaxy_test.api.test_datatypes.TestDatatypesApi method) test_converters() (galaxy_test.api.test_datatypes.TestDatatypesApi method) test_copy_hdca() (galaxy_test.selenium.test_history_copy_elements.TestHistoryCopyElements method) test_copy_history() (galaxy_test.api.test_histories.TestHistoriesApi method) test_core_deferred() (galaxy_test.selenium.test_stock_tours.TestStockToursTestCase method) test_core_galaxy_ui() (galaxy_test.selenium.test_stock_tours.TestStockToursTestCase method) test_core_history() (galaxy_test.selenium.test_stock_tours.TestStockToursTestCase method) test_core_windows() (galaxy_test.selenium.test_stock_tours.TestStockToursTestCase method) test_create() (galaxy_test.api.test_folders.TestFoldersApi method) (galaxy_test.api.test_libraries.TestLibrariesApi method) (galaxy_test.api.test_page_revisions.TestPageRevisionsApi method) (galaxy_test.api.test_pages.TestPagesApi method) (galaxy_test.api.test_visualizations.TestVisualizationsApi method) test_create_anonymous_fails() (galaxy_test.api.test_histories.TestHistoriesApi method) test_create_dataset() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_create_dataset_bootstrap_admin_user() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_create_dataset_denied() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_create_dataset_in_folder() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_create_dataset_in_subfolder() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_create_datasets_in_folder_from_collection() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_create_datasets_in_library_from_collection() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_create_duplicated_name_raises_409() (galaxy_test.api.test_groups.TestGroupsApi method) test_create_fails_with_bad_slug() (galaxy_test.api.test_visualizations.TestVisualizationsApi method) test_create_fails_with_invalid_config() (galaxy_test.api.test_visualizations.TestVisualizationsApi method) test_create_fails_without_title() (galaxy_test.api.test_visualizations.TestVisualizationsApi method) test_create_from_report() (galaxy_test.api.test_pages.TestPagesApi method) test_create_from_store() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_create_hda_with_ldda_message() (galaxy_test.api.test_folder_contents.TestFolderContentsApi method) test_create_hdca_with_ldda_message() (galaxy_test.api.test_folder_contents.TestFolderContentsApi method) test_create_history() (galaxy_test.api.test_histories.TestHistoriesApi method) test_create_history_json() (galaxy_test.api.test_histories.TestHistoriesApi method) test_create_invalid_params() (galaxy_test.api.test_roles.TestRolesApi method) test_create_invalid_params_raises_400() (galaxy_test.api.test_groups.TestGroupsApi method) test_create_library_dataset_bootstrap_user() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_create_list_from_history() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_create_list_of_existing_pairs() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_create_list_of_new_pairs() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_create_new() (galaxy_test.selenium.test_library_landing.TestLibraryLanding method) test_create_new_close() (galaxy_test.selenium.test_library_landing.TestLibraryLanding method) test_create_only_admin() (galaxy_test.api.test_groups.TestGroupsApi method) (galaxy_test.api.test_roles.TestRolesApi method) test_create_pair_from_history() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_create_private_library_legacy_permissions() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_create_private_library_permissions() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_create_tag() (galaxy_test.api.test_histories.TestHistoriesApi method) test_create_valid() (galaxy_test.api.test_groups.TestGroupsApi method) (galaxy_test.api.test_roles.TestRolesApi method) test_create_without_name_raises_400() (galaxy_test.api.test_folders.TestFoldersApi method) test_create_without_session_fails() (galaxy_test.api.test_histories.TestHistoriesApi method) test_csv_fetch() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_csv_sniff_fetch() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_csv_upload() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_csv_upload_auto() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_currect_password_incorrect() (galaxy_test.selenium.test_change_password.TestChangePassword method) test_data() (galaxy.tool_util.verify.interactor.ToolTestDescription method) (galaxy.webapps.galaxy.api.tools.ToolsController method) test_data_column_input_editing() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_data_download() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) (galaxy.webapps.galaxy.api.tools.ToolsController method) test_data_input() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_data_iter() (in module galaxy.tool_util.verify.interactor) test_data_path() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) (galaxy.tools.Tool method) (galaxy.webapps.galaxy.api.tools.ToolsController method) test_data_resolver (galaxy.structured_app.StructuredApp attribute) (galaxy_test.api.test_pages.TestPagesApi attribute) (galaxy_test.api.test_workflows.TestAdminWorkflowsApi attribute) (galaxy_test.api.test_workflows_cwl.BaseCwlWorkflowsApiTestCase attribute) (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi attribute) (galaxy_test.base.testcase.FunctionalTestCase attribute) (galaxy_test.driver.testcase.DrivenFunctionalTestCase attribute) (galaxy_test.selenium.test_admin_app.TestAdminApp attribute) (galaxy_test.selenium.test_anon_history.TestAnonymousHistories attribute) (galaxy_test.selenium.test_change_password.TestChangePassword attribute) (galaxy_test.selenium.test_collection_builders.TestCollectionBuilders attribute) (galaxy_test.selenium.test_collection_edit.TestCollectionEdit attribute) (galaxy_test.selenium.test_data_source_tools.TestDataSource attribute) (galaxy_test.selenium.test_dataset_metadata_download.TestHistoryDatasetState attribute) (galaxy_test.selenium.test_histories_list.TestSavedHistories attribute) (galaxy_test.selenium.test_history_copy_elements.TestHistoryCopyElements attribute) (galaxy_test.selenium.test_history_dataset_state.TestHistoryDatasetState attribute) (galaxy_test.selenium.test_history_multi_view.TestHistoryMultiView attribute) (galaxy_test.selenium.test_history_options.TestHistoryOptions attribute) (galaxy_test.selenium.test_history_panel.TestHistoryPanel attribute) (galaxy_test.selenium.test_history_panel_collections.TestHistoryPanelCollections attribute) (galaxy_test.selenium.test_history_sharing.TestHistoryRequiresLoginSelenium attribute) (galaxy_test.selenium.test_history_sharing.TestHistorySharing attribute) (galaxy_test.selenium.test_invocation_grid.TestInvocationGridSelenium attribute) (galaxy_test.selenium.test_library_contents.TestLibraryContents attribute) (galaxy_test.selenium.test_library_landing.TestLibraryLanding attribute) (galaxy_test.selenium.test_library_to_collections.TestLibraryToCollections attribute) (galaxy_test.selenium.test_login.TestLogin attribute) (galaxy_test.selenium.test_navigates_galaxy.TestNavigatesGalaxySelenium attribute) (galaxy_test.selenium.test_pages.TestPages attribute) (galaxy_test.selenium.test_personal_information.TestDeleteCurrentAccount attribute) (galaxy_test.selenium.test_personal_information.TestManageInformation attribute) (galaxy_test.selenium.test_registration.TestRegistration attribute) (galaxy_test.selenium.test_sign_out.TestSignOut attribute) (galaxy_test.selenium.test_sizzle_loading.TestSizzleLoading attribute) (galaxy_test.selenium.test_stock_tours.TestStockToursTestCase attribute) (galaxy_test.selenium.test_tool_describing_tours.TestToolDescribingTours attribute) (galaxy_test.selenium.test_tool_form.TestLoggedInToolForm attribute) (galaxy_test.selenium.test_tool_form.TestToolForm attribute) (galaxy_test.selenium.test_uploads.TestUploads attribute) (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor attribute) (galaxy_test.selenium.test_workflow_invocation_details.TestWorkflowInvocationDetails attribute) (galaxy_test.selenium.test_workflow_management.TestWorkflowManagement attribute) (galaxy_test.selenium.test_workflow_run.TestWorkflowRun attribute) (galaxy_test.selenium.test_workflow_sharing.TestWorkflowSharing attribute) (galaxy_test.selenium.test_workflow_sharing.TestWorkflowSharingRedirect attribute) (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures attribute) (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository attribute) (tool_shed.test.functional.test_0020_basic_repository_dependencies.TestBasicRepositoryDependencies attribute) (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions attribute) (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies attribute) (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels attribute) (tool_shed.test.functional.test_0070_invalid_tool.TestBismarkRepository attribute) (tool_shed.test.functional.test_0080_advanced_circular_dependencies.TestRepositoryCircularDependencies attribute) (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain attribute) (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies attribute) (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies attribute) (tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners.TestRepositoryMultipleOwners attribute) (tool_shed.test.functional.test_0140_tool_help_images.TestToolHelpImages attribute) (tool_shed.test.functional.test_0150_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_0160_circular_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_0170_complex_prior_installation_required.TestComplexPriorInstallation attribute) (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata attribute) (tool_shed.test.functional.test_0310_hg_api_features.TestHgWebFeatures attribute) (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs attribute) (tool_shed.test.functional.test_0430_browse_utilities.TestToolShedBrowseUtilities attribute) (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies attribute) (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision attribute) (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance attribute) (tool_shed.test.functional.test_0480_tool_dependency_xml_verification.TestDependencyDefinitionValidation attribute) (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole attribute) (tool_shed.test.functional.test_0550_metadata_updated_dependencies.TestGetUpdatedMetadata attribute) (tool_shed.test.functional.test_1000_install_basic_repository.TestBasicToolShedFeatures attribute) (tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies.TestToolWithToolDependencies attribute) (tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies.TestToolWithRepositoryDependencies attribute) (tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions.TestRepositoryWithDependencyRevisions attribute) (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies attribute) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies attribute) (tool_shed.test.functional.test_1070_invalid_tool.TestFreebayesRepository attribute) (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies attribute) (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies attribute) (tool_shed.test.functional.test_1100_install_updated_repository_dependencies.TestRepositoryDependencies attribute) (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies attribute) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies attribute) (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners attribute) (tool_shed.test.functional.test_1160_tool_help_images.TestToolHelpImages attribute) (tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_1190_complex_prior_installation_required.TestComplexPriorInstallation attribute) (tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository.TestUninstallingAndReinstallingRepositories attribute) (tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies.TestUninstallingAndReinstallingRepositories attribute) (tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions.TestUninstallingAndReinstallingRepositories attribute) (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata attribute) (tool_shed.test.functional.test_1410_update_manager.TestUpdateManager attribute) (tool_shed.test.functional.test_1430_repair_installed_repository.TestRepairRepository attribute) (tool_shed.test.functional.test_1460_data_managers.TestDataManagers attribute) (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository attribute) test_data_source_build_request() (galaxy_test.api.test_tools.TestToolsApi method) test_data_source_ok_request() (galaxy_test.api.test_tools.TestToolsApi method) test_data_source_sniff_fastqsanger() (galaxy_test.api.test_tools.TestToolsApi method) test_data_sources_block_file_parameters() (galaxy_test.api.test_tools.TestToolsApi method) test_data_table_requirement_annotated() (galaxy_test.api.test_tools.TestToolsApi method) test_database_operation_tool_with_pending_inputs() (galaxy_test.api.test_tools.TestToolsApi method) test_dataprovider_chunk() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_dataset_change_dbkey() (galaxy_test.selenium.test_history_dataset_state.TestHistoryDatasetState method) test_dataset_collection_create_from_exisiting_datasets_with_new_tags() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_dataset_collection_creation_on_contents() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_dataset_collection_creation_on_typed_contents() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_dataset_collection_element_security() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_dataset_collection_hide_originals() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_dataset_hidden_after_job_finish() (galaxy_test.api.test_tools.TestToolsApi method) test_dataset_metadata_download() (galaxy_test.selenium.test_dataset_metadata_download.TestHistoryDatasetState method) test_dataset_state() (galaxy_test.selenium.test_history_dataset_state.TestHistoryDatasetState method) test_dataset_state_deferred() (galaxy_test.selenium.test_history_dataset_state.TestHistoryDatasetState method) test_dataset_state_discarded() (galaxy_test.selenium.test_history_dataset_state.TestHistoryDatasetState method) test_dataset_state_filtering() (galaxy_test.selenium.test_tool_form.TestLoggedInToolForm method) test_dce_submission_security() (galaxy_test.api.test_jobs.TestJobsApi method) test_default_identifier_source_map_over() (galaxy_test.api.test_tools.TestToolsApi method) test_default_xframe_options() (galaxy_test.api.test_framework.TestApiFramework method) test_defaults_editor() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_deferred_map_over_nested_collections() (galaxy_test.api.test_tools.TestToolsApi method) test_delete() (galaxy_test.api.test_folders.TestFoldersApi method) (galaxy_test.api.test_group_roles.TestGroupRolesApi method) (galaxy_test.api.test_group_users.TestGroupUsersApi method) (galaxy_test.api.test_groups.TestGroupsApi method) (galaxy_test.api.test_histories.TestHistoriesApi method) (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) (galaxy_test.api.test_libraries.TestLibrariesApi method) (galaxy_test.api.test_pages.TestPagesApi method) (galaxy_test.api.test_roles.TestRolesApi method) (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_delete_account() (galaxy_test.selenium.test_personal_information.TestDeleteCurrentAccount method) test_delete_and_undelete_history() (galaxy_test.selenium.test_histories_list.TestSavedHistories method) test_delete_and_undelete_multiple_histories() (galaxy_test.selenium.test_histories_list.TestSavedHistories method) test_delete_anon() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_delete_batch() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_delete_batch_error() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_delete_cancels_job() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_delete_cancels_job_with_query_params() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_delete_dataset() (galaxy_test.selenium.test_library_contents.TestLibraryContents method) test_delete_duplicating_name_raises_409() (galaxy_test.api.test_groups.TestGroupsApi method) (galaxy_test.api.test_roles.TestRolesApi method) test_delete_intermediate_datasets_pja_1() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_delete_job() (galaxy_test.api.test_jobs.TestJobsApi method) test_delete_only_admin() (galaxy_test.api.test_group_roles.TestGroupRolesApi method) (galaxy_test.api.test_group_users.TestGroupUsersApi method) test_delete_permission_denied() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_delete_unknown_raises_400() (galaxy_test.api.test_group_roles.TestGroupRolesApi method) (galaxy_test.api.test_group_users.TestGroupUsersApi method) test_delete_user() (galaxy_test.api.test_users.TestUsersApi method) test_delete_user_cancel_all_jobs() (galaxy_test.api.test_users.TestUsersApi method) test_delete_with_wrong_values_raises_400() (galaxy_test.api.test_tool_data.TestToolDataApi method) test_delete_without_payload_raises_400() (galaxy_test.api.test_tool_data.TestToolDataApi method) test_delete_without_values_raises_400() (galaxy_test.api.test_tool_data.TestToolDataApi method) test_deleting_collection_should_delete_contents() (galaxy_test.api.test_history_contents.TestHistoryContentsApiBulkOperation method) test_deleting_output_keep_running_until_all_deleted() (galaxy_test.api.test_jobs.TestJobsApi method) test_destination_params() (galaxy_test.api.test_jobs.TestJobsApi method) test_detect_datatype_of_dataset_in_folder() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_display() (galaxy_test.api.test_datasets.TestDatasetsApi method) (galaxy_test.selenium.test_history_multi_view.TestHistoryMultiView method) test_display_application_link() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_display_error_handling() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_download() (galaxy_test.selenium.test_workflow_management.TestWorkflowManagement method) test_download_field_file() (galaxy_test.api.test_tool_data.TestToolDataApi method) test_download_field_unknown_file_raises_404() (galaxy_test.api.test_tool_data.TestToolDataApi method) test_download_non_english_characters() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_drilldown_tool() (galaxy_test.selenium.test_tool_form.TestToolForm method) test_duplicated_hash_requests_on_extra_files() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_duplicated_hash_requests_on_primary() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_dynamic_list_output() (galaxy_test.api.test_tools.TestToolsApi method) test_dynamic_list_output_datasets_in_failed_state() (galaxy_test.api.test_tools.TestToolsApi method) test_dynamic_parameter_error_handling() (galaxy_test.api.test_tools.TestToolsApi method) test_dynamic_query_selection() (galaxy_test.api.test_history_contents.TestHistoryContentsApiBulkOperation method) test_dynamic_tool_1() (galaxy_test.api.test_tools.TestToolsApi method) test_dynamic_tool_from_path() (galaxy_test.api.test_tools.TestToolsApi method) test_dynamic_tool_no_id() (galaxy_test.api.test_tools.TestToolsApi method) test_edam_data() (galaxy_test.api.test_datatypes.TestDatatypesApi method) test_edam_formats() (galaxy_test.api.test_datatypes.TestDatatypesApi method) test_edit_annotation() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_edit_license() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_edit_name() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_edit_subworkflow() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_editor_create_conditional_step() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_editor_duplicate_node() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_editor_embed_workflow() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_editor_insert_steps() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_editor_invalid_tool_state() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_editor_place_comments() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_editor_snapping() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_editor_subworkflow_tool_upgrade_message() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_editor_tool_upgrade() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_editor_tool_upgrade_message() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_elements_datatypes_field() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_empty_collection_sort() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_empty_create() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_empty_file_data_column_specified() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_empty_list_mapping() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_empty_list_reduction() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_enforces_unique_names() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_error_outputs_with_purged_inputs() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_exceptions (galaxy.tool_util.verify.script.Results attribute) test_execution_with_custom_invocation_report() (galaxy_test.selenium.test_workflow_run.TestWorkflowRun method) test_execution_with_multiple_inputs() (galaxy_test.selenium.test_workflow_run.TestWorkflowRun method) test_execution_with_null_optional_select_from_data() (galaxy_test.selenium.test_workflow_run.TestWorkflowRun method) test_execution_with_rules() (galaxy_test.selenium.test_workflow_run.TestWorkflowRun method) test_execution_with_text_default_value_connected_to_restricted_select() (galaxy_test.selenium.test_workflow_run.TestWorkflowRun method) test_execution_with_tool_upgrade() (galaxy_test.selenium.test_workflow_run.TestWorkflowRun method) test_existing_connections() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_expanded_execution_of_simple_workflow() (galaxy_test.selenium.test_workflow_run.TestWorkflowRun method) test_explicit_items_selection() (galaxy_test.api.test_history_contents.TestHistoryContentsApiBulkOperation method) test_export() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_export_editor() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_export_editor_collection_type_source() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_export_editor_filtered_outputs() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_export_editor_filtered_outputs_exception_handling() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_export_editor_subworkflow_collection_type_source() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_export_format2() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_export_invocation_bco() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_export_invocation_ro_crate() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_export_invocation_ro_crate_adv() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_export_pairs_list() (galaxy_test.selenium.test_library_to_collections.TestLibraryToCollections method) test_export_pairs_list_new_history() (galaxy_test.selenium.test_library_to_collections.TestLibraryToCollections method) test_export_workflow_with_login_redirect() (galaxy_test.selenium.test_workflow_sharing.TestWorkflowSharingRedirect method) test_expression_tool_map_over() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_extract_copied_mapping_from_history() (galaxy_test.api.test_workflow_extraction.TestWorkflowExtractionApi method) test_extract_copied_mapping_from_history_reimported() (galaxy_test.api.test_workflow_extraction.TestWorkflowExtractionApi method) test_extract_dataset_invalid_element_identifier() (galaxy_test.api.test_tools.TestToolsApi method) test_extract_from_history() (galaxy_test.api.test_workflow_extraction.TestWorkflowExtractionApi method) test_extract_mapping_workflow_from_history() (galaxy_test.api.test_workflow_extraction.TestWorkflowExtractionApi method) test_extract_reduction_from_history() (galaxy_test.api.test_workflow_extraction.TestWorkflowExtractionApi method) test_extract_with_copied_inputs() (galaxy_test.api.test_workflow_extraction.TestWorkflowExtractionApi method) test_extract_with_copied_inputs_reimported() (galaxy_test.api.test_workflow_extraction.TestWorkflowExtractionApi method) test_extract_with_mapped_output_collections() (galaxy_test.api.test_workflow_extraction.TestWorkflowExtractionApi method) test_extract_workflow_with_output_collections() (galaxy_test.api.test_workflow_extraction.TestWorkflowExtractionApi method) test_extract_workflows_with_dataset_collections() (galaxy_test.api.test_workflow_extraction.TestWorkflowExtractionApi method) test_favorites() (galaxy_test.api.test_users.TestUsersApi method) test_fetch_bagit_archive_to_folder() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_fetch_bam_file() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_fetch_bam_file_from_url_with_extension_set() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_fetch_compressed_auto_decompress_target() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_fetch_compressed_default() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_fetch_compressed_with_auto() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_fetch_compressed_with_explicit_type() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_fetch_failed_validation() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_fetch_html_from_url() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_fetch_metadata() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_fetch_posix_unaltered() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_fetch_post_lines_option() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_fetch_post_lines_trailing_if_to_posix() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_fetch_post_lines_trailing_off_by_default() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_fetch_single_url_to_folder() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_fetch_single_url_with_invalid_datatype() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_fetch_tab_to_space() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_fetch_tab_to_space_doesnt_swap_newlines() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_fetch_tab_to_space_off_by_default() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_fetch_upload_to_folder() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_fetch_url_archive_to_folder() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_fetch_zip_to_folder() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_files (galaxy.datatypes.genetics.LinkageStudies attribute) test_filter_failed_list() (galaxy_test.api.test_tools.TestToolsApi method) test_filter_failed_list_paired() (galaxy_test.api.test_tools.TestToolsApi method) test_filter_failed_mapping() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_full_index() (galaxy_test.api.test_datatypes.TestDatatypesApi method) test_galaxy_expression_metadata() (galaxy_test.api.test_tools.TestToolsApi method) test_galaxy_expression_tool_simple() (galaxy_test.api.test_tools.TestToolsApi method) test_galaxy_expression_tool_simplest() (galaxy_test.api.test_tools.TestToolsApi method) test_generate_tour_no_data() (galaxy_test.selenium.test_tool_describing_tours.TestToolDescribingTours method) test_generate_tour_with_data() (galaxy_test.selenium.test_tool_describing_tours.TestToolDescribingTours method) test_get_all() (galaxy_test.api.test_webhooks.TestWebhooksApi method) test_get_content_as_text() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_get_content_as_text_with_compressed_text_data() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_get_data() (galaxy_test.api.test_webhooks.TestWebhooksApi method) test_get_inputs_and_outputs() (galaxy_test.api.test_jobs.TestJobsApi method) test_get_library_available_permissions() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_get_library_available_permissions_with_query() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_get_library_current_permissions() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_get_license() (galaxy_test.api.test_licenses.TestLicensesApi method) test_get_prov() (galaxy_test.api.test_history_contents_provenance.TestProvenance method) test_get_suitable_converters_different_datatypes_matches() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_get_suitable_converters_different_datatypes_no_matches() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_get_suitable_converters_single_datatype() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_grid() (galaxy_test.selenium.test_invocation_grid.TestInvocationGridSelenium method) test_group_tag_selection() (galaxy_test.api.test_tools.TestToolsApi method) test_group_tag_selection_multiple() (galaxy_test.api.test_tools.TestToolsApi method) test_guess_derived_permissions() (galaxy_test.api.test_tools.TestToolsApi method) test_guess_derived_permissions_collections() (galaxy_test.api.test_tools.TestToolsApi method) test_hda_copy() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_hda_security() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_hdca_copy() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_hdca_copy_and_elements() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_hdca_copy_with_new_dbkey() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_hdca_from_inaccessible_library_datasets() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_hdca_from_library_datasets() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_head() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_hidden_param_in_workflow() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_histories_count() (galaxy_test.api.test_histories.TestHistoriesApi method) test_histories_list() (galaxy_test.selenium.test_histories_list.TestSavedHistories method) test_history() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) (galaxy_test.base.populators.BaseDatasetPopulator method) test_history_for() (galaxy_test.base.populators.BaseDatasetPopulator method) test_history_links() (galaxy_test.selenium.test_pages.TestPages method) test_history_panel_annotations_change() (galaxy_test.selenium.test_history_panel.TestHistoryPanel method) test_history_panel_landing_state() (galaxy_test.selenium.test_history_panel.TestHistoryPanel method) test_history_panel_rename() (galaxy_test.selenium.test_history_panel.TestHistoryPanel method) test_history_panel_tags_change() (galaxy_test.selenium.test_history_panel.TestHistoryPanel method) test_history_publish() (galaxy_test.selenium.test_histories_list.TestSavedHistories method) test_history_rename_cancel_with_escape() (galaxy_test.selenium.test_history_panel.TestHistoryPanel method) test_history_switch() (galaxy_test.selenium.test_histories_list.TestSavedHistories method) test_history_tags_and_annotations_buttons() (galaxy_test.selenium.test_history_panel.TestHistoryPanel method) test_history_view() (galaxy_test.selenium.test_histories_list.TestSavedHistories method) test_html_allowlist() (galaxy_test.selenium.test_admin_app.TestAdminApp method) test_identifier_in_actions() (galaxy_test.api.test_tools.TestToolsApi method) test_identifier_in_map() (galaxy_test.api.test_tools.TestToolsApi method) test_identifier_in_multiple_reduce() (galaxy_test.api.test_tools.TestToolsApi method) test_identifier_map_over_input_in_conditional() (galaxy_test.api.test_tools.TestToolsApi method) test_identifier_map_over_multiple_input_in_conditional() (galaxy_test.api.test_tools.TestToolsApi method) test_identifier_map_over_multiple_input_in_conditional_new_payload_form() (galaxy_test.api.test_tools.TestToolsApi method) test_identifier_multiple_in_conditional() (galaxy_test.api.test_tools.TestToolsApi method) test_identifier_multiple_reduce_in_conditional() (galaxy_test.api.test_tools.TestToolsApi method) test_identifier_multiple_reduce_in_repeat() (galaxy_test.api.test_tools.TestToolsApi method) test_identifier_multiple_reduce_in_repeat_new_payload_form() (galaxy_test.api.test_tools.TestToolsApi method) test_identifier_outside_map() (galaxy_test.api.test_tools.TestToolsApi method) test_identifier_single_in_repeat() (galaxy_test.api.test_tools.TestToolsApi method) test_identifier_with_data_collection() (galaxy_test.api.test_tools.TestToolsApi method) test_identifier_with_multiple_normal_datasets() (galaxy_test.api.test_tools.TestToolsApi method) test_image_upload_auto() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_immutable_history_cannot_add_datasets() (galaxy_test.api.test_histories.TestHistoriesApi method) test_immutable_history_update_fails() (galaxy_test.api.test_histories.TestHistoriesApi method) test_implicit_collection_jobs() (galaxy_test.api.test_jobs.TestJobsApi method) test_implicit_connections() (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi method) test_implicit_conversion_and_reduce() (galaxy_test.api.test_tools.TestToolsApi method) test_implicit_conversion_and_reduce_invalid_param() (galaxy_test.api.test_tools.TestToolsApi method) test_implicit_reduce_with_mapping() (galaxy_test.api.test_tools.TestToolsApi method) test_import_1901_histories() (galaxy_test.api.test_histories.ImportExportTests method) test_import_accessibility() (galaxy_test.selenium.test_workflow_management.TestWorkflowManagement method) test_import_annotations() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_import_dataset_from_history() (galaxy_test.selenium.test_library_contents.TestLibraryContents method) test_import_dataset_from_import_dir() (galaxy_test.selenium.test_library_contents.TestLibraryContents method) test_import_dataset_from_path() (galaxy_test.selenium.test_library_contents.TestLibraryContents method) test_import_deprecated() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_import_export() (galaxy_test.api.test_histories.ImportExportTests method) test_import_export_collection() (galaxy_test.api.test_histories.ImportExportTests method) test_import_export_dynamic() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_import_export_dynamic_tools() (galaxy_test.api.test_workflows.TestAdminWorkflowsApi method) test_import_export_failed_job() (galaxy_test.api.test_histories.ImportExportTests method) test_import_export_include_deleted() (galaxy_test.api.test_histories.ImportExportTests method) test_import_export_nested_collection() (galaxy_test.api.test_histories.ImportExportTests method) test_import_export_with_runtime_inputs() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_import_folder_to_history() (galaxy_test.api.test_folders.TestFoldersApi method) test_import_from_model_store_dict() (galaxy_test.api.test_histories.TestHistoriesApi method) test_import_from_url() (galaxy_test.selenium.test_workflow_management.TestWorkflowManagement method) test_import_metadata_regeneration() (galaxy_test.api.test_histories.ImportExportTests method) test_import_missing_tool() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_import_no_tool_id() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_import_paired_collection() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_import_published() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_import_published_api() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_import_subworkflows() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_import_tools_requires_admin() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_index (galaxy.tool_util.verify.interactor.InvalidToolTestDict attribute) (galaxy.tool_util.verify.interactor.ToolTestDescriptionDict attribute) (galaxy.tool_util.verify.interactor.ValidToolTestDict attribute) (galaxy.tool_util.verify.script.TestReference attribute) test_index() (galaxy_test.api.test_datasets.TestDatasetsApi method) (galaxy_test.api.test_datatypes.TestDatatypesApi method) (galaxy_test.api.test_display_applications.TestDisplayApplicationsApi method) (galaxy_test.api.test_folder_contents.TestFolderContentsApi method) (galaxy_test.api.test_group_roles.TestGroupRolesApi method) (galaxy_test.api.test_group_users.TestGroupUsersApi method) (galaxy_test.api.test_groups.TestGroupsApi method) (galaxy_test.api.test_jobs.TestJobsApi method) (galaxy_test.api.test_libraries.TestLibrariesApi method) (galaxy_test.api.test_licenses.TestLicensesApi method) (galaxy_test.api.test_pages.TestPagesApi method) (galaxy_test.api.test_tools.TestToolsApi method) (galaxy_test.api.test_tours.TestToursApi method) (galaxy_test.api.test_users.TestUsersApi method) (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_index_advanced_filter() (galaxy_test.api.test_histories.TestHistoriesApi method) test_index_advanced_search() (galaxy_test.selenium.test_workflow_management.TestWorkflowManagement method) test_index_and_show() (galaxy_test.api.test_visualizations.TestVisualizationsApi method) test_index_case_insensitive_contains_query() (galaxy_test.api.test_histories.TestHistoriesApi method) test_index_date_filter() (galaxy_test.api.test_jobs.TestJobsApi method) test_index_deleted() (galaxy_test.api.test_pages.TestPagesApi method) (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_index_detail_parameter_error() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_index_does_not_show_unavailable_pages() (galaxy_test.api.test_pages.TestPagesApi method) test_index_filter_by_name_ignores_case() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_index_filter_by_related_items() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_index_filter_by_type() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_index_filtering() (galaxy_test.api.test_visualizations.TestVisualizationsApi method) test_index_handler_runner_filters() (galaxy_test.api.test_jobs.TestJobsApi method) test_index_hda_all_details() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_index_hda_detail_by_id() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_index_hda_summary() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_index_hidden() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_index_history() (galaxy_test.api.test_jobs.TestJobsApi method) test_index_include_deleted() (galaxy_test.api.test_folder_contents.TestFolderContentsApi method) test_index_limit_and_offset() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_index_limit_and_offset_filter() (galaxy_test.api.test_jobs.TestJobsApi method) test_index_limit_offset() (galaxy_test.api.test_pages.TestPagesApi method) test_index_multiple_states_filter() (galaxy_test.api.test_jobs.TestJobsApi method) test_index_only_admin() (galaxy_test.api.test_group_roles.TestGroupRolesApi method) (galaxy_test.api.test_group_users.TestGroupUsersApi method) (galaxy_test.api.test_groups.TestGroupsApi method) test_index_only_self_for_nonadmins() (galaxy_test.api.test_users.TestUsersApi method) test_index_order() (galaxy_test.api.test_histories.TestHistoriesApi method) test_index_order_by() (galaxy_test.api.test_folder_contents.TestFolderContentsApi method) test_index_order_by_size() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_index_ordering() (galaxy_test.api.test_pages.TestPagesApi method) (galaxy_test.api.test_visualizations.TestVisualizationsApi method) (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_index_owner() (galaxy_test.api.test_pages.TestPagesApi method) (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_index_pagination() (galaxy_test.api.test_folder_contents.TestFolderContentsApi method) test_index_parameter_invalid_combinations() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_index_permissions() (galaxy_test.api.test_folder_contents.TestFolderContentsApi method) test_index_permissions_include_deleted() (galaxy_test.api.test_folder_contents.TestFolderContentsApi method) test_index_published() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_index_query() (galaxy_test.api.test_histories.TestHistoriesApi method) test_index_returns_expected_total_matches() (galaxy_test.api.test_history_contents.TestHistoryContentsApiBulkOperation method) test_index_search() (galaxy_test.api.test_workflows.TestWorkflowsApi method) (galaxy_test.selenium.test_workflow_management.TestWorkflowManagement method) test_index_search_filter_email() (galaxy_test.api.test_jobs.TestJobsApi method) test_index_search_filter_tool_id() (galaxy_test.api.test_jobs.TestJobsApi method) test_index_search_filters() (galaxy_test.selenium.test_workflow_management.TestWorkflowManagement method) test_index_search_is_tags() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_index_search_mode_views() (galaxy_test.api.test_histories.TestHistoriesApi method) test_index_search_name() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_index_search_name_exact_vs_inexact() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_index_search_sharing_tags() (galaxy_test.api.test_pages.TestPagesApi method) test_index_search_slug() (galaxy_test.api.test_pages.TestPagesApi method) test_index_search_tags() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_index_search_tags_exact() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_index_search_tags_multiple() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_index_search_text() (galaxy_test.api.test_folder_contents.TestFolderContentsApi method) test_index_search_title() (galaxy_test.api.test_pages.TestPagesApi method) test_index_show_published() (galaxy_test.api.test_pages.TestPagesApi method) test_index_show_shared() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_index_show_shared_with_me() (galaxy_test.api.test_pages.TestPagesApi method) test_index_show_shared_with_me_deleted() (galaxy_test.api.test_pages.TestPagesApi method) test_index_skip_step_counts() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_index_sort_by() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_index_state_filter() (galaxy_test.api.test_jobs.TestJobsApi method) test_index_total_matches() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_index_unknown_group_raises_400() (galaxy_test.api.test_group_roles.TestGroupRolesApi method) (galaxy_test.api.test_group_users.TestGroupUsersApi method) test_index_upload_only() (galaxy_test.api.test_datatypes.TestDatatypesApi method) test_index_user_filter() (galaxy_test.api.test_jobs.TestJobsApi method) test_index_user_id_security() (galaxy_test.api.test_pages.TestPagesApi method) test_index_user_published() (galaxy_test.api.test_pages.TestPagesApi method) test_index_using_keys() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_index_views() (galaxy_test.api.test_histories.TestHistoriesApi method) test_index_with_stats_fails_with_non_orm_filters() (galaxy_test.api.test_history_contents.TestHistoryContentsApiBulkOperation method) test_index_with_stats_has_extra_serialization() (galaxy_test.api.test_history_contents.TestHistoryContentsApiBulkOperation method) test_index_workflow_and_invocation_filter() (galaxy_test.api.test_jobs.TestJobsApi method) test_index_workflow_filter_implicit_jobs() (galaxy_test.api.test_jobs.TestJobsApi method) test_information() (galaxy_test.api.test_users.TestUsersApi method) test_inheritance_chain() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_inputs_to_steps() (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi method) test_insert_input_handling() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_integer_input() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_invalid_create_multiple_types() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_invalid_keys() (galaxy_test.api.test_histories.TestHistoriesApi method) test_invalid_logins() (galaxy_test.selenium.test_login.TestLogin method) test_invalid_passwords() (galaxy_test.selenium.test_login.TestLogin method) test_invalid_search() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_invalid_update_dataset_in_folder() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_invocation_filtering() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_invocation_filtering_exclude_subworkflow() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_invocation_map_over() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_invocation_map_over_inner_collection() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_invocation_map_over_inner_collection_with_tool_collection_input() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_invocation_usage() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_invocation_with_collection_mapping() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_invocations_accessible_imported_workflow() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_invocations_accessible_published_workflow() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_invocations_not_accessible_by_different_user_for_published_workflow() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_job_build_for_rerun() (galaxy_test.api.test_jobs.TestJobsApi method) test_job_build_for_rerun_list_list() (galaxy_test.api.test_jobs.TestJobsApi method) test_job_details() (galaxy_test.selenium.test_workflow_invocation_details.TestWorkflowInvocationDetails method) test_job_list_collection_view() (galaxy_test.api.test_jobs.TestJobsApi method) test_job_list_default_view() (galaxy_test.api.test_jobs.TestJobsApi method) test_job_metrics() (galaxy_test.api.test_jobs.TestJobsApi method) test_job_state_summary_field() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_jobs_summary_implicit_hdca() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_jobs_summary_simple_hdca() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_keep_success_mapping_error() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_keep_success_mapping_paused() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_landing() (galaxy_test.selenium.test_registration.TestRegistration method) test_ldda_collection_import_to_history() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_ldda_collection_import_to_history_hide_source() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_legacy_biotools_xref_injection() (galaxy_test.api.test_tools.TestToolsApi method) test_legacy_upload_unknown_datatype() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_library_collection_export() (galaxy_test.selenium.test_library_to_collections.TestLibraryToCollections method) test_library_collection_export_new_history() (galaxy_test.selenium.test_library_to_collections.TestLibraryToCollections method) test_library_copy() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_library_data_param() (galaxy_test.api.test_tools.TestToolsApi method) test_library_pair_export() (galaxy_test.selenium.test_library_to_collections.TestLibraryToCollections method) test_library_pair_export_new_history() (galaxy_test.selenium.test_library_to_collections.TestLibraryToCollections method) test_list() (galaxy_test.api.test_tool_data.TestToolDataApi method) test_list_and_show() (galaxy_test.api.test_roles.TestRolesApi method) test_list_collection_output() (galaxy_test.api.test_tools.TestToolsApi method) test_list_collection_output_format_source() (galaxy_test.api.test_tools.TestToolsApi method) test_list_display() (galaxy_test.selenium.test_history_panel_collections.TestHistoryPanelCollections method) test_list_download() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_list_library() (galaxy_test.api.test_folders.TestFoldersApi method) test_list_list_display() (galaxy_test.selenium.test_history_multi_view.TestHistoryMultiView method) (galaxy_test.selenium.test_history_panel_collections.TestHistoryPanelCollections method) test_list_list_download() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_list_list_list_download() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_list_pair_download() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_list_paired_display() (galaxy_test.selenium.test_history_panel_collections.TestHistoryPanelCollections method) test_list_selectable_in_multidata_input() (galaxy_test.api.test_tools.TestToolsApi method) test_logging_in() (galaxy_test.selenium.test_login.TestLogin method) test_login() (galaxy_test.selenium.jupyter_context.JupyterTestContextImpl method) test_login_accessibility() (galaxy_test.selenium.test_login.TestLogin method) test_logout() (galaxy_test.selenium.test_registration.TestRegistration method) test_make_private_and_public() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_malformed_id_if_index_unknown_page() (galaxy_test.api.test_page_revisions.TestPageRevisionsApi method) test_manage_api_key() (galaxy_test.api.test_users.TestUsersApi method) test_manage_beacon_settings() (galaxy_test.api.test_users.TestUsersApi method) test_map_over_collected_and_individual_datasets() (galaxy_test.api.test_tools.TestToolsApi method) test_map_over_collection() (galaxy_test.api.test_tools.TestToolsApi method) test_map_over_collection_output() (galaxy_test.api.test_tools.TestToolsApi method) test_map_over_collection_structured_like() (galaxy_test.api.test_tools.TestToolsApi method) test_map_over_collection_type_source() (galaxy_test.api.test_tools.TestToolsApi method) test_map_over_empty_collection() (galaxy_test.api.test_tools.TestToolsApi method) test_map_over_nested_collections() (galaxy_test.api.test_tools.TestToolsApi method) test_map_over_output_indicator() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_map_over_two_collections() (galaxy_test.api.test_tools.TestToolsApi method) test_map_over_two_collections_unlinked() (galaxy_test.api.test_tools.TestToolsApi method) test_map_over_with_complex_output_actions() (galaxy_test.api.test_tools.TestToolsApi method) test_map_over_with_discovered_output_collection_elements() (galaxy_test.api.test_tools.TestToolsApi method) test_map_over_with_nested_paired_output_format_actions() (galaxy_test.api.test_tools.TestToolsApi method) test_map_over_with_output_filter_no_filtering() (galaxy_test.api.test_tools.TestToolsApi method) test_map_over_with_output_filter_on_optional_input() (galaxy_test.api.test_tools.TestToolsApi method) test_map_over_with_output_filter_one_filtered() (galaxy_test.api.test_tools.TestToolsApi method) test_map_over_with_output_format_actions() (galaxy_test.api.test_tools.TestToolsApi method) test_mapping() (galaxy_test.api.test_datatypes.TestDatatypesApi method) test_mapping_and_subcollection_mapping() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_mapping_collection_states_running() (galaxy_test.selenium.test_history_panel_collections.TestHistoryPanelCollections method) test_mapping_collection_states_terminal() (galaxy_test.selenium.test_history_panel_collections.TestHistoryPanelCollections method) test_merge_collection_scheduling() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_metadata_validator_can_fail_on_deferred_input() (galaxy_test.api.test_tools.TestToolsApi method) test_metadata_validator_on_deferred_input() (galaxy_test.api.test_tools.TestToolsApi method) test_missing_tools() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_model_attributes_sanitization() (galaxy_test.api.test_tools.TestToolsApi method) test_multi_select_as_list() (galaxy_test.api.test_tools.TestToolsApi method) test_multi_select_optional() (galaxy_test.api.test_tools.TestToolsApi method) test_multidata_param() (galaxy_test.api.test_tools.TestToolsApi method) test_multiple_files_posix_lines() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_multirun_cat1() (galaxy_test.api.test_tools.TestToolsApi method) test_multirun_in_repeat() (galaxy_test.api.test_tools.TestToolsApi method) test_multirun_in_repeat_mismatch() (galaxy_test.api.test_tools.TestToolsApi method) test_multirun_non_data_parameter() (galaxy_test.api.test_tools.TestToolsApi method) test_multirun_on_multiple_inputs() (galaxy_test.api.test_tools.TestToolsApi method) test_multirun_on_multiple_inputs_unlinked() (galaxy_test.api.test_tools.TestToolsApi method) test_name_tags_display() (galaxy_test.selenium.test_history_panel_collections.TestHistoryPanelCollections method) test_nested_workflow_rerun_with_use_cached_job() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_new_password_password() (galaxy_test.selenium.test_change_password.TestChangePassword method) test_new_password_same_password() (galaxy_test.selenium.test_change_password.TestChangePassword method) test_new_password_short() (galaxy_test.selenium.test_change_password.TestChangePassword method) test_newlines_stage_fetch() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_newlines_stage_fetch_configured() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_no_hide_on_rerun() (galaxy_test.api.test_jobs.TestJobsApi method) test_no_panel_index() (galaxy_test.api.test_tools.TestToolsApi method) test_no_password_confirmation() (galaxy_test.selenium.test_change_password.TestChangePassword method) test_no_unhide_on_error_if_mapped_over() (galaxy_test.api.test_jobs.TestJobsApi method) test_non_data_connections() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_non_data_map_over_carried_through() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_nonadmin() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_nonadmin_users_cannot_create_tools() (galaxy_test.api.test_tools.TestToolsApi method) test_normal_user_configuration() (galaxy_test.api.test_configuration.TestConfigurationApi method) test_normal_user_decode_id() (galaxy_test.api.test_configuration.TestConfigurationApi method) test_not_importable_prevents_import() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_only_admin_can_manage_other_users_api_key() (galaxy_test.api.test_users.TestUsersApi method) test_only_own_invocations_indexed_and_accessible() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_only_owner_can_apply_bulk_operations() (galaxy_test.api.test_history_contents.TestHistoryContentsApiBulkOperation method) test_optional_select_data_field() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_optional_workflow_output() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_options() (galaxy_test.selenium.test_history_options.TestHistoryOptions method) test_other_cannot_delete() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_other_cannot_undelete() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_other_users_cannot_archive_history() (galaxy_test.api.test_histories.TestArchivingHistoriesWithoutExportRecord method) test_other_users_cannot_restore_history() (galaxy_test.api.test_histories.TestArchivingHistoriesWithoutExportRecord method) test_output_collection_states_running() (galaxy_test.selenium.test_history_panel_collections.TestHistoryPanelCollections method) test_output_collection_states_terminal() (galaxy_test.selenium.test_history_panel_collections.TestHistoryPanelCollections method) test_outputs() (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi method) test_page_requires_name() (galaxy_test.api.test_pages.TestPagesApi method) test_page_requires_slug() (galaxy_test.api.test_pages.TestPagesApi method) test_pair_download() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_paired_collection_output() (galaxy_test.api.test_tools.TestToolsApi method) test_paired_display() (galaxy_test.selenium.test_history_panel_collections.TestHistoryPanelCollections method) test_paired_input_conditional_map_over_nested_collections() (galaxy_test.api.test_tools.TestToolsApi method) test_paired_input_map_over_nested_collections() (galaxy_test.api.test_tools.TestToolsApi method) test_parameter_default_rep() (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi method) test_parameter_substitution_sanitization() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_parameter_substitution_validation_value_errors_0() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_parameter_substitution_validation_value_errors_1() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_parameters_display() (galaxy_test.api.test_jobs.TestJobsApi method) test_password_confirmation() (galaxy_test.selenium.test_registration.TestRegistration method) test_pause() (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi method) test_pause_outputs_with_deleted_inputs() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_pdf_when_service_available() (galaxy_test.api.test_pages.TestPagesApi method) test_permanently_delete_history() (galaxy_test.selenium.test_histories_list.TestSavedHistories method) test_permissions() (galaxy_test.api.test_folders.TestFoldersApi method) test_pja_import_export() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_placements_from_text_inputs() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_placements_from_text_inputs_nested() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_post_lines_trailing() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_post_lines_trailing_off() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_public_name() (galaxy_test.selenium.test_personal_information.TestManageInformation method) test_published_collection_contents_accessible() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_purge() (galaxy_test.api.test_groups.TestGroupsApi method) (galaxy_test.api.test_histories.TestHistoriesApi method) (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) (galaxy_test.api.test_roles.TestRolesApi method) test_purge_can_reuse_name() (galaxy_test.api.test_groups.TestGroupsApi method) (galaxy_test.api.test_roles.TestRolesApi method) test_purge_does_not_reset_file_size() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_purge_user() (galaxy_test.api.test_users.TestUsersApi method) test_purging_collection_should_purge_contents() (galaxy_test.api.test_history_contents.TestHistoryContentsApiBulkOperation method) test_purging_output_cleaned_after_ok_run() (galaxy_test.api.test_jobs.TestJobsApi method) test_purging_output_keep_running_until_all_purged() (galaxy_test.api.test_jobs.TestJobsApi method) test_qc_messages() (galaxy_test.api.test_tools.TestToolsApi method) test_rdata_not_decompressed() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_reconnecting_nodes() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_recover_mapping_in_subworkflow() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_reduce_collections() (galaxy_test.api.test_tools.TestToolsApi method) test_reduce_collections_in_repeat() (galaxy_test.api.test_tools.TestToolsApi method) test_reduce_collections_in_repeat_legacy() (galaxy_test.api.test_tools.TestToolsApi method) test_reduce_collections_legacy() (galaxy_test.api.test_tools.TestToolsApi method) test_reduce_multiple_lists_on_multi_data() (galaxy_test.api.test_tools.TestToolsApi method) test_refactor() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_refactor_tool_state_upgrade() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_refresh_preserves_state() (galaxy_test.selenium.test_history_panel.TestHistoryPanel method) test_registration() (galaxy_test.selenium.test_registration.TestRegistration method) test_registration_accessibility() (galaxy_test.selenium.test_registration.TestRegistration method) test_reload() (galaxy_test.api.test_tool_data.TestToolDataApi method) test_reload_as_admin() (galaxy_test.api.test_display_applications.TestDisplayApplicationsApi method) test_reload_as_non_admin_returns_403() (galaxy_test.api.test_display_applications.TestDisplayApplicationsApi method) test_reload_unknown_raises_404() (galaxy_test.api.test_tool_data.TestToolDataApi method) test_reload_unknown_returns_as_failed() (galaxy_test.api.test_display_applications.TestDisplayApplicationsApi method) test_reload_with_some_ids() (galaxy_test.api.test_display_applications.TestDisplayApplicationsApi method) test_rename() (galaxy_test.selenium.test_library_landing.TestLibraryLanding method) (galaxy_test.selenium.test_workflow_management.TestWorkflowManagement method) test_rename_collection() (galaxy_test.selenium.test_history_panel_collections.TestHistoryPanelCollections method) test_rename_history() (galaxy_test.selenium.test_histories_list.TestSavedHistories method) test_rendering_output_collection_connections() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_rendering_rules_workflow_1() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_rendering_rules_workflow_2() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_rendering_simple_nested_workflow() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_repeat_reordering() (galaxy_test.selenium.test_tool_form.TestToolForm method) test_replacement_parameters() (galaxy_test.selenium.test_workflow_run.TestWorkflowRun method) test_replacement_parameters_on_subworkflows() (galaxy_test.selenium.test_workflow_run.TestWorkflowRun method) test_report_error() (galaxy_test.api.test_jobs.TestJobsApi method) test_report_error_anon() (galaxy_test.api.test_jobs.TestJobsApi method) test_report_error_bootstrap_admin() (galaxy_test.api.test_jobs.TestJobsApi method) test_require_unique_step_labels() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_require_unique_step_uuids() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_requirements() (galaxy_test.api.test_tools.TestToolsApi method) test_reregister_email_fails() (galaxy_test.selenium.test_registration.TestRegistration method) test_reregister_username_fails() (galaxy_test.selenium.test_registration.TestRegistration method) test_rerun() (galaxy_test.selenium.test_tool_form.TestToolForm method) test_rerun_dataset_collection_element() (galaxy_test.selenium.test_tool_form.TestToolForm method) test_rerun_deleted_dataset() (galaxy_test.selenium.test_tool_form.TestToolForm method) test_restore() (galaxy_test.api.test_histories.TestArchivingHistoriesWithoutExportRecord method) test_resume_job() (galaxy_test.api.test_jobs.TestJobsApi method) test_revision_index() (galaxy_test.api.test_page_revisions.TestPageRevisionsApi method) test_rules_deferred_datasets() (galaxy_test.selenium.test_uploads.TestUploads method) test_rules_deferred_list() (galaxy_test.selenium.test_uploads.TestUploads method) test_rules_example_1_datasets() (galaxy_test.selenium.test_uploads.TestUploads method) test_rules_example_2_list() (galaxy_test.selenium.test_uploads.TestUploads method) test_rules_example_3_list_pairs() (galaxy_test.selenium.test_uploads.TestUploads method) test_rules_example_4_accessions() (galaxy_test.selenium.test_uploads.TestUploads method) test_rules_example_5_matching_collections() (galaxy_test.selenium.test_uploads.TestUploads method) test_rules_example_6_nested_lists() (galaxy_test.selenium.test_uploads.TestUploads method) test_run_add_tag_on_collection_output() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_add_tag_on_database_operation_output() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_add_tag_on_mapped_over_collection() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_apply_rules_1() (galaxy_test.selenium.test_tool_form.TestLoggedInToolForm method) test_run_apply_rules_2() (galaxy_test.selenium.test_tool_form.TestLoggedInToolForm method) test_run_apply_rules_3() (galaxy_test.selenium.test_tool_form.TestLoggedInToolForm method) test_run_apply_rules_4() (galaxy_test.selenium.test_tool_form.TestLoggedInToolForm method) test_run_apply_rules_tutorial() (galaxy_test.selenium.test_tool_form.TestLoggedInToolForm method) test_run_as_invalid_user() (galaxy_test.api.test_framework.TestApiFramework method) test_run_as_valid_user() (galaxy_test.api.test_framework.TestApiFramework method) test_run_batch() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_batch_inputs() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_build_list_change_datatype_collection_output() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_build_list_change_datatype_new_metadata_file_parameter() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_build_list_delete_intermediate_collection_output() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_build_list_hide_collection_output() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_build_list_rename_collection_output() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_by_versions() (galaxy_test.api.test_tools.TestToolsApi method) test_run_cat1() (galaxy_test.api.test_tools.TestToolsApi method) test_run_cat1_listified_param() (galaxy_test.api.test_tools.TestToolsApi method) test_run_cat1_single_meta_wrapper() (galaxy_test.api.test_tools.TestToolsApi method) test_run_cat1_use_cached_job() (galaxy_test.api.test_tools.TestToolsApi method) test_run_cat1_with_two_inputs() (galaxy_test.api.test_tools.TestToolsApi method) test_run_data() (galaxy_test.selenium.test_tool_form.TestToolForm method) test_run_deferred_dataset() (galaxy_test.api.test_tools.TestToolsApi method) test_run_deferred_dataset_with_metadata_options_filter() (galaxy_test.api.test_tools.TestToolsApi method) test_run_deferred_list_multi_data_reduction() (galaxy_test.api.test_tools.TestToolsApi method) test_run_deferred_mapping() (galaxy_test.api.test_tools.TestToolsApi method) test_run_deferred_nested_list_input() (galaxy_test.api.test_tools.TestToolsApi method) test_run_form_safe_upgrade_handling() (galaxy_test.selenium.test_workflow_run.TestWorkflowRun method) test_run_hide_on_collection_output() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_hide_on_mapped_over_collection() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_nested_conditional_workflow_steps() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_remove_tag_on_collection_output() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_rename_based_on_input() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_rename_based_on_input_collection() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_rename_based_on_input_conditional() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_rename_based_on_input_conditional_legacy_pja_reference() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_rename_based_on_input_recursive() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_rename_based_on_input_repeat() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_rename_based_on_inputs_on_mapped_over_collection() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_rename_collection_output() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_rename_multiple_outputs() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_rename_on_mapped_over_collection() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_rename_when_resuming_jobs() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_replace_params_by_steps() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_replace_params_by_tool() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_replace_params_by_uuid() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_replace_params_nested() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_replace_params_nested_normalized() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_replace_params_over_default() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_replace_params_over_default_delayed() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_runtime_parameters_after_pause() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_simple() (galaxy_test.performance.test_workflow_framework_performance.TestWorkflowFrameworkPerformance method) test_run_subworkflow_auto_labels() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_subworkflow_replacement_parameters() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_subworkflow_runtime_parameters() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_subworkflow_simple() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_subworkflow_with_optional_data_unspecified() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_tool_verify_contents_by_peek() (galaxy_test.selenium.test_tool_form.TestToolForm method) test_run_tool_verify_dataset_details() (galaxy_test.selenium.test_tool_form.TestToolForm method) test_run_two_output() (galaxy_test.performance.test_workflow_framework_performance.TestWorkflowFrameworkPerformance method) test_run_versioned_tools() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_wave() (galaxy_test.performance.test_workflow_framework_performance.TestWorkflowFrameworkPerformance method) test_run_with_default_file_dataset_input() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_with_default_file_dataset_input_and_explicit_input() (galaxy_test.api.test_workflows.TestWorkflowsApi method)

test_run_with_default_file_in_step_inline() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_with_delayed_runtime_pja() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_with_implicit_collection_map_over() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_with_implicit_connection() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_with_int_parameter() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_with_int_parameter_nested() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_with_non_optional_collection_unspecified_fails_invocation() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_with_non_optional_data_unspecified_fails_invocation() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_with_numeric_input_connection() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_with_optional_collection_specified() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_with_optional_collection_unspecified() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_with_optional_data_specified_to_multi_data() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_with_optional_data_unspecified_survives_delayed_step() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_with_optional_data_unspecified_to_multi_data() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_with_pja() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_with_runtime_pja() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_with_text_input_connection() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_with_validated_parameter_connection_default_values() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_with_validated_parameter_connection_invalid() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_with_validated_parameter_connection_optional() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_workflow() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_workflow_by_index() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_workflow_by_name() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_workflow_by_uuid() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_workflow_by_uuid_implicitly() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_workflow_conditional_step_map_over_expression_tool() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_workflow_conditional_step_map_over_expression_tool_pick_value() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_workflow_conditional_subworkflow_step_map_over_expression_tool() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_workflow_conditional_subworkflow_step_map_over_expression_tool_with_extra_nesting() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_workflow_conditional_subworkflow_step_map_over_expression_tool_with_extra_nesting_skip_all() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_workflow_fails_when_expression_not_boolean() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_workflow_invalid_when_expression() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_workflow_pick_value_bam_pja() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_workflow_simple_conditional_step() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_workflow_simple_conditional_step_with_nested_tool_state() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_workflow_subworkflow_conditional_step() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_run_workflow_subworkflow_conditional_with_simple_mapping_step() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_runtime_data_column_parameter() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_runtime_inputs() (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi method) test_runtime_parameters_simple() (galaxy_test.selenium.test_workflow_run.TestWorkflowRun method) test_save_as() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_search() (galaxy_test.api.test_jobs.TestJobsApi method) test_search_by_extension() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_search_by_tag() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_search_by_tag_case_insensitive() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_search_by_tool_id() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_search_casing() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_search_cat() (galaxy_test.api.test_tools.TestToolsApi method) test_search_datasets() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_search_delete_hdca_output() (galaxy_test.api.test_jobs.TestJobsApi method) test_search_delete_outputs() (galaxy_test.api.test_jobs.TestJobsApi method) test_search_favorites() (galaxy_test.api.test_users.TestUsersApi method) test_search_grep() (galaxy_test.api.test_tools.TestToolsApi method) test_search_handle_identifiers() (galaxy_test.api.test_jobs.TestJobsApi method) test_search_returns_only_accessible() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_search_trimmer() (galaxy_test.api.test_tools.TestToolsApi method) test_search_with_hdca_list_input() (galaxy_test.api.test_jobs.TestJobsApi method) test_search_with_hdca_list_pair_collection_mapped_over_pair_input() (galaxy_test.api.test_jobs.TestJobsApi method) test_search_with_hdca_list_pair_input() (galaxy_test.api.test_jobs.TestJobsApi method) test_search_with_hdca_pair_input() (galaxy_test.api.test_jobs.TestJobsApi method) test_select_legal_values() (galaxy_test.api.test_tools.TestToolsApi method) test_set_permissions_add_admin_datasets() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_set_permissions_add_admin_history_contents() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_set_slug() (galaxy_test.api.sharable.SharingApiTests method) test_set_theme() (galaxy_test.api.test_users.TestUsersApi method) test_share_history_login_redirect() (galaxy_test.selenium.test_history_sharing.TestHistoryRequiresLoginSelenium method) test_share_workflow_with_login_redirect() (galaxy_test.selenium.test_workflow_sharing.TestWorkflowSharingRedirect method) test_shared_with_me() (galaxy_test.selenium.test_history_sharing.TestHistorySharing method) test_sharing() (galaxy_test.api.test_visualizations.TestVisualizationsApi method) test_sharing_access() (galaxy_test.api.sharable.SharingApiTests method) test_sharing_empty_not_allowed() (galaxy_test.api.test_histories.TestSharingHistory method) test_sharing_get_status() (galaxy_test.api.sharable.SharingApiTests method) test_sharing_private_history_makes_datasets_public() (galaxy_test.api.test_histories.TestSharingHistory method) test_sharing_publish() (galaxy_test.api.sharable.SharingApiTests method) test_sharing_valid() (galaxy_test.selenium.test_history_sharing.TestHistorySharing method) test_sharing_valid_by_id() (galaxy_test.selenium.test_history_sharing.TestHistorySharing method) test_sharing_with_duplicated_users() (galaxy_test.api.test_histories.TestSharingHistory method) test_sharing_with_invalid_user() (galaxy_test.api.sharable.SharingApiTests method) (galaxy_test.selenium.test_history_sharing.TestHistorySharing method) (galaxy_test.selenium.test_workflow_sharing.TestWorkflowSharing method) test_sharing_with_private_datasets() (galaxy_test.api.test_histories.TestSharingHistory method) test_sharing_with_self() (galaxy_test.selenium.test_history_sharing.TestHistorySharing method) (galaxy_test.selenium.test_workflow_sharing.TestWorkflowSharing method) test_sharing_with_user_email() (galaxy_test.api.sharable.SharingApiTests method) test_sharing_with_user_id() (galaxy_test.api.sharable.SharingApiTests method) test_sharing_without_manage_permissions() (galaxy_test.api.test_histories.TestSharingHistory method) test_sharing_without_user() (galaxy_test.api.sharable.SharingApiTests method) test_sharing_workflow_by_email() (galaxy_test.selenium.test_workflow_sharing.TestWorkflowSharing method) test_sharing_workflow_by_id() (galaxy_test.selenium.test_workflow_sharing.TestWorkflowSharing method) test_short_password() (galaxy_test.selenium.test_registration.TestRegistration method) test_show() (galaxy_test.api.test_datasets.TestDatasetsApi method) (galaxy_test.api.test_group_roles.TestGroupRolesApi method) (galaxy_test.api.test_group_users.TestGroupUsersApi method) (galaxy_test.api.test_groups.TestGroupsApi method) (galaxy_test.api.test_jobs.TestJobsApi method) (galaxy_test.api.test_pages.TestPagesApi method) (galaxy_test.api.test_tool_data.TestToolDataApi method) (galaxy_test.api.test_tours.TestToursApi method) (galaxy_test.api.test_users.TestUsersApi method) test_show_conditional() (galaxy_test.api.test_tools.TestToolsApi method) test_show_current() (galaxy_test.api.test_users.TestUsersApi method) test_show_dataset_collection() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_show_dataset_collection_contents() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_show_delete() (galaxy_test.api.test_users.TestUsersApi method) test_show_details() (galaxy_test.selenium.test_library_contents.TestLibraryContents method) test_show_dynamic_tools() (galaxy_test.api.test_tools.TestToolsApi method) test_show_error_codes() (galaxy_test.api.test_roles.TestRolesApi method) test_show_field() (galaxy_test.api.test_tool_data.TestToolDataApi method) test_show_hda() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_show_history() (galaxy_test.api.test_histories.TestHistoriesApi method) test_show_history_returns_expected_urls() (galaxy_test.api.test_histories.TestHistoriesApi method) test_show_invalid_key_is_400() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_show_most_recently_used() (galaxy_test.api.test_histories.TestHistoriesApi method) test_show_multi_data() (galaxy_test.api.test_tools.TestToolsApi method) test_show_only_admin() (galaxy_test.api.test_group_roles.TestGroupRolesApi method) (galaxy_test.api.test_group_users.TestGroupUsersApi method) (galaxy_test.api.test_groups.TestGroupsApi method) test_show_output_collection() (galaxy_test.api.test_tools.TestToolsApi method) test_show_permission_denied() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_show_private_dataset_permissions() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_show_repeat() (galaxy_test.api.test_tools.TestToolsApi method) test_show_respects_view() (galaxy_test.api.test_histories.TestHistoriesApi method) test_show_security() (galaxy_test.api.test_jobs.TestJobsApi method) test_show_subworkflow() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_show_tool_source_admin() (galaxy_test.api.test_tools.TestToolsApi method) test_show_tool_source_denied() (galaxy_test.api.test_tools.TestToolsApi method) test_show_unknown_field_raises_404() (galaxy_test.api.test_tool_data.TestToolDataApi method) test_show_unknown_raises_400() (galaxy_test.api.test_group_roles.TestGroupRolesApi method) (galaxy_test.api.test_group_users.TestGroupUsersApi method) (galaxy_test.api.test_groups.TestGroupsApi method) test_show_unknown_raises_404() (galaxy_test.api.test_tool_data.TestToolDataApi method) test_show_valid() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_show_with_wrong_tool_version_in_tool_id() (galaxy_test.api.test_tools.TestToolsApi method) test_sign_out() (galaxy_test.selenium.test_sign_out.TestSignOut method) test_simple_execution() (galaxy_test.selenium.test_workflow_run.TestWorkflowRun method) test_simple_mapping_connections() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_simple_output_actions() (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi method) test_simple_page_creation_edit_and_view() (galaxy_test.selenium.test_pages.TestPages method) test_simple_upload() (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi method) test_sizzle_loads() (galaxy_test.selenium.test_sizzle_loading.TestSizzleLoading method) test_sniffers() (galaxy_test.api.test_datatypes.TestDatatypesApi method) test_sort_by_name() (galaxy_test.selenium.test_histories_list.TestSavedHistories method) test_sorting() (galaxy_test.selenium.test_library_landing.TestLibraryLanding method) test_stage_fetch_decompress_false() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_stage_fetch_decompress_true() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_stage_object() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_stage_object_fetch() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_standard_search() (galaxy_test.selenium.test_histories_list.TestSavedHistories method) test_step_parameter_inputs() (galaxy_test.selenium.test_workflow_run.TestWorkflowRun method) test_storage_show() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_storage_show_on_deferred() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_storage_show_on_discarded() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_sub_folder() (galaxy_test.selenium.test_library_contents.TestLibraryContents method) test_subcollection_mapping() (galaxy_test.api.test_tools.TestToolsApi method) (galaxy_test.api.test_workflow_extraction.TestWorkflowExtractionApi method) test_subcollection_reduction() (galaxy_test.api.test_workflow_extraction.TestWorkflowExtractionApi method) test_subworkflow_duplicate() (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi method) test_subworkflow_import_order_maintained() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_subworkflow_inputs_optional_editor() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_subworkflow_map_over_data_column() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_subworkflow_output_as_output() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_subworkflow_recover_mapping_1() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_subworkflow_recover_mapping_2() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_subworkflow_runtime_parameters() (galaxy_test.selenium.test_workflow_run.TestWorkflowRun method) test_subworkflow_simple() (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi method) test_subworkflow_tags() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_subworkflows_expanded() (galaxy_test.selenium.test_workflow_run.TestWorkflowRun method) test_system_details_admin_only() (galaxy_test.api.test_jobs.TestJobsApi method) test_tabular_chunking_through_display_endpoint() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_tag_auto_propagation() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_tag_change() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_tag_filtering() (galaxy_test.selenium.test_workflow_management.TestWorkflowManagement method) test_tagging() (galaxy_test.selenium.test_workflow_management.TestWorkflowManagement method) test_tags() (galaxy_test.selenium.test_histories_list.TestSavedHistories method) test_test_by_versions() (galaxy_test.api.test_tools.TestToolsApi method) test_test_data_admin_security() (galaxy_test.api.test_tools.TestToolsApi method) test_test_data_collection_nested() (galaxy_test.api.test_tools.TestToolsApi method) test_test_data_collection_two_paired() (galaxy_test.api.test_tools.TestToolsApi method) test_test_data_composite_output() (galaxy_test.api.test_tools.TestToolsApi method) test_test_data_download() (galaxy_test.api.test_tools.TestToolsApi method) test_test_data_download_composite() (galaxy_test.api.test_tools.TestToolsApi method) test_test_data_downloads_security() (galaxy_test.api.test_tools.TestToolsApi method) test_test_data_filepath_security() (galaxy_test.api.test_tools.TestToolsApi method) test_test_data_null_boolean_inputs() (galaxy_test.api.test_tools.TestToolsApi method) test_test_data_yaml_tools() (galaxy_test.api.test_tools.TestToolsApi method) test_tool_deactivate() (galaxy_test.api.test_tools.TestToolsApi method) test_tool_runner_session_cookie_handling() (galaxy_test.api.test_authenticate.TestAuthenticateApi method) test_tools() (in module galaxy.tool_util.verify.script) test_trs_import() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_trs_import_from_dockstore_trs_url() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_trs_import_from_workflowhub_trs_url() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_types_and_mapping() (galaxy_test.api.test_datatypes.TestDatatypesApi method) test_ucsc_table_direct1_data_source() (galaxy_test.selenium.test_data_source_tools.TestDataSource method) test_undelete() (galaxy_test.api.test_folders.TestFoldersApi method) (galaxy_test.api.test_histories.TestHistoriesApi method) (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_undelete_user() (galaxy_test.api.test_users.TestUsersApi method) test_unhide_on_error() (galaxy_test.api.test_jobs.TestJobsApi method) test_unshared_history_inaccessible() (galaxy_test.selenium.test_history_sharing.TestHistorySharing method) test_unsharing() (galaxy_test.selenium.test_history_sharing.TestHistorySharing method) test_unsharing_workflow() (galaxy_test.selenium.test_workflow_sharing.TestWorkflowSharing method) test_unzip_collection() (galaxy_test.api.test_tools.TestToolsApi method) test_unzip_nested() (galaxy_test.api.test_tools.TestToolsApi method) test_update() (galaxy_test.api.test_folders.TestFoldersApi method) (galaxy_test.api.test_group_roles.TestGroupRolesApi method) (galaxy_test.api.test_group_users.TestGroupUsersApi method) (galaxy_test.api.test_groups.TestGroupsApi method) (galaxy_test.api.test_histories.TestHistoriesApi method) (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) (galaxy_test.api.test_libraries.TestLibrariesApi method) (galaxy_test.api.test_tours.TestToursApi method) (galaxy_test.api.test_users.TestUsersApi method) (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_update_batch() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_update_batch_collections() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_update_batch_dataset_collection() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_update_dataset_collection() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_update_dataset_in_folder() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_update_dataset_tags() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_update_datatype() (galaxy_test.api.test_datasets.TestDatasetsApi method) test_update_deleted_raise_403() (galaxy_test.api.test_folders.TestFoldersApi method) test_update_duplicating_name_raises_409() (galaxy_test.api.test_groups.TestGroupsApi method) test_update_invalid_attribute() (galaxy_test.api.test_histories.TestHistoriesApi method) test_update_invalid_types() (galaxy_test.api.test_histories.TestHistoriesApi method) test_update_missing_tool() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_update_name() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_update_name_empty() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_update_no_tool_id() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_update_non_admins_with_permission() (galaxy_test.api.test_libraries.TestLibrariesApi method) test_update_only_admin() (galaxy_test.api.test_group_roles.TestGroupRolesApi method) (galaxy_test.api.test_group_users.TestGroupUsersApi method) (galaxy_test.api.test_groups.TestGroupsApi method) test_update_sharing_with_users() (galaxy_test.api.sharable.SharingApiTests method) test_update_tags() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_update_title() (galaxy_test.api.test_visualizations.TestVisualizationsApi method) test_update_type_failures() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_upload() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_upload1_paste() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload1_paste_bad_datatype() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_and_validate_invalid() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_and_validate_valid() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_auto_decompress_off() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_bam_file() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_collection() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_upload_collection_deferred() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_upload_collection_failed_expansion_url() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_upload_collection_from_url() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_upload_composite_as_tar() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_composite_as_tar_fetch() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_composite_dataset_pasted_data() (galaxy_test.selenium.test_uploads.TestUploads method) test_upload_composite_from_bad_tar() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_dataset_resumable() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_dbkey() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_decompress_off_if_compressed_type_selected() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_decompress_off_with_auto_by_default() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_decompresses_if_uncompressed_type_selected() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_deferred() (galaxy_test.api.test_tools_upload.TestToolsUpload method) (galaxy_test.selenium.test_uploads.TestUploads method) test_upload_deprecated() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_upload_disable_posix_fix() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_file() (galaxy_test.selenium.test_uploads.TestUploads method) test_upload_force_composite() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_from_404_url() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_from_invalid_url() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_from_valid_url() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_from_valid_url_spaces() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_list() (galaxy_test.selenium.test_uploads.TestUploads method) test_upload_modal_retains_content() (galaxy_test.selenium.test_uploads.TestUploads method) test_upload_multiple_files_1() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_multiple_files_2() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_multiple_files_3() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_multiple_files_no_dbkey() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_multiple_files_space_to_tab() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_multiple_mixed_success() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_nested() (galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi method) test_upload_pair() (galaxy_test.selenium.test_uploads.TestUploads method) test_upload_pair_specify_extension() (galaxy_test.selenium.test_uploads.TestUploads method) test_upload_paired_list() (galaxy_test.selenium.test_uploads.TestUploads method) test_upload_pasted_content() (galaxy_test.selenium.test_uploads.TestUploads method) test_upload_pasted_url_content() (galaxy_test.selenium.test_uploads.TestUploads method) test_upload_posix_newline_fixes_by_default() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_simplest() (galaxy_test.selenium.test_uploads.TestUploads method) test_upload_specify_ext() (galaxy_test.selenium.test_uploads.TestUploads method) test_upload_specify_ext_all() (galaxy_test.selenium.test_uploads.TestUploads method) test_upload_specify_genome() (galaxy_test.selenium.test_uploads.TestUploads method) test_upload_specify_genome_all() (galaxy_test.selenium.test_uploads.TestUploads method) test_upload_tab_to_space() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_upload_tab_to_space_off_by_default() (galaxy_test.api.test_tools_upload.TestToolsUpload method) test_url_import() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_user_address() (galaxy_test.selenium.test_personal_information.TestManageInformation method) test_user_cannont_run_as() (galaxy_test.api.test_framework.TestApiFramework method) test_validated_post_job_action_invalid() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_validated_post_job_action_unvalidated_default() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_validated_post_job_action_validated() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_validation() (galaxy_test.api.test_tools.TestToolsApi method) test_validation_empty_dataset() (galaxy_test.api.test_tools.TestToolsApi method) test_validation_in_repeat() (galaxy_test.api.test_tools.TestToolsApi method) test_value_restriction_with_select_and_text_param() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_value_restriction_with_select_from_subworkflow_input() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_verify_dataset_details_tables() (galaxy_test.selenium.test_tool_form.TestToolForm method) test_version() (galaxy_test.api.test_configuration.TestConfigurationApi method) test_view() (galaxy_test.selenium.test_workflow_management.TestWorkflowManagement method) test_view_and_keys_parameters_for_collections() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_view_and_keys_parameters_for_datasets() (galaxy_test.api.test_history_contents.TestHistoryContentsApi method) test_whoami() (galaxy_test.api.test_configuration.TestConfigurationApi method) test_workflow_bookmarking() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_workflow_delete() (galaxy_test.selenium.test_workflow_management.TestWorkflowManagement method) test_workflow_embed_tool() (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi method) test_workflow_failed_input_not_ok() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_failed_output_not_found() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_failed_with_message_exception() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_flatten() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_flatten_with_mapped_over_execution() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_from_path_requires_admin() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_import_state_validation_1() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_import_tool() (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi method) test_workflow_index_accessibility() (galaxy_test.selenium.test_workflow_management.TestWorkflowManagement method) test_workflow_input_as_output() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_input_mapping() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_input_tags() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_invocation_report_1() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_invocation_report_custom() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_list_list_multi_data_map_over() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_map_reduce_pause() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_metadata_validation_0() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_new_autocreated_history() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_optional_input_filtering() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_optional_input_text_parameter_reevaluation() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_output_dataset() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_output_dataset_collection() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_output_handling() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) test_workflow_pause() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_pause_cancel() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_problem_display() (galaxy_test.selenium.test_pages.TestPages method) test_workflow_publishing() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_request() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_rerun_with_cached_job_consumes_implicit_hdca() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_rerun_with_use_cached_job() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_resume_from_failed_step() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_resume_from_failed_step_with_hdca_input() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_resume_with_mapped_over_collection_input() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_resume_with_mapped_over_input() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_run_apply_rules() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_run_button_disabled_when_required_input_missing() (galaxy_test.selenium.test_workflow_run.TestWorkflowRun method) test_workflow_run_dynamic_output_collections() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_run_dynamic_output_collections_2() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_run_dynamic_output_collections_3() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_run_form_with_broken_dataset() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_run_input_mapping_with_output_collections() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_run_input_mapping_with_subworkflows() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_run_output_collection_mapping() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_run_output_collections() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_run_tag_filter() (galaxy_test.selenium.test_workflow_run.TestWorkflowRun method) test_workflow_run_with_matching_lists() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_run_zip_collections() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_stability() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_workflow_warning_workflow_output_not_found() (galaxy_test.api.test_workflows.TestWorkflowsApi method) test_wrong_password() (galaxy_test.selenium.test_login.TestLogin method) test_zip_inputs() (galaxy_test.api.test_tools.TestToolsApi method) test_zip_list_inputs() (galaxy_test.api.test_tools.TestToolsApi method) TestAdminApp (class in galaxy_test.selenium.test_admin_app) TestAdminWorkflowsApi (class in galaxy_test.api.test_workflows) TestAnonymousHistories (class in galaxy_test.selenium.test_anon_history) TestApiFramework (class in galaxy_test.api.test_framework) TestArchivingHistoriesWithoutExportRecord (class in galaxy_test.api.test_histories) TestAuthenticateApi (class in galaxy_test.api.test_authenticate) TestAutomaticDependencyRevision (class in tool_shed.test.functional.test_0460_upload_to_repository) TestBasicRepositoryDependencies (class in tool_shed.test.functional.test_0020_basic_repository_dependencies) (class in tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies) (class in tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency) TestBasicRepositoryFeatures (class in tool_shed.test.functional.test_0000_basic_repository_features) TestBasicToolShedFeatures (class in tool_shed.test.functional.test_1000_install_basic_repository) TestBismarkRepository (class in tool_shed.test.functional.test_0070_invalid_tool) TestCaseGalaxyInteractor (class in galaxy_test.base.interactor) TestChangePassword (class in galaxy_test.selenium.test_change_password) TestCollectionBuilders (class in galaxy_test.selenium.test_collection_builders) TestCollectionDef (class in galaxy.tool_util.parser.interface) TestCollectionEdit (class in galaxy_test.selenium.test_collection_edit) TestCollectionOutputDef (class in galaxy.tool_util.parser.interface) TestComplexPriorInstallation (class in tool_shed.test.functional.test_0170_complex_prior_installation_required) (class in tool_shed.test.functional.test_1190_complex_prior_installation_required) TestComplexRepositoryDependencies (class in tool_shed.test.functional.test_0100_complex_repository_dependencies) TestConfig (class in galaxy.tool_util.verify.interactor) TestConfigurationApi (class in galaxy_test.api.test_configuration) TestConfiguredFileSources (class in galaxy.files.unittest_utils) TestCustomBuilds (class in galaxy_test.selenium.test_custom_builds) TestDataManagers (class in tool_shed.test.functional.test_1460_data_managers) TestDataNotFoundError TestDataResolver (class in galaxy.tool_util.verify.test_data) TestDatasetCollectionsApi (class in galaxy_test.api.test_dataset_collections) TestDatasetsApi (class in galaxy_test.api.test_datasets) TestDataSource (class in galaxy_test.selenium.test_data_source_tools) TestDatatypesApi (class in galaxy_test.api.test_datatypes) TestDeleteCurrentAccount (class in galaxy_test.selenium.test_personal_information) TestDeletedDependencies (class in tool_shed.test.functional.test_0440_deleting_dependency_definitions) TestDependencyDefinitionValidation (class in tool_shed.test.functional.test_0480_tool_dependency_xml_verification) TestDisplayApplicationsApi (class in galaxy_test.api.test_display_applications) TestDriver (class in galaxy_test.driver.driver_util) TestEnvironmentInheritance (class in tool_shed.test.functional.test_0470_tool_dependency_repository_type) TestException (class in galaxy.tool_util.verify.script) TestFolderContentsApi (class in galaxy_test.api.test_folder_contents) TestFoldersApi (class in galaxy_test.api.test_folders) TestFreebayesRepository (class in tool_shed.test.functional.test_0010_repository_with_tool_dependencies) (class in tool_shed.test.functional.test_1070_invalid_tool) TestGetUpdatedMetadata (class in tool_shed.test.functional.test_0550_metadata_updated_dependencies) TestGroupRolesApi (class in galaxy_test.api.test_group_roles) TestGroupsApi (class in galaxy_test.api.test_groups) TestGroupUsersApi (class in galaxy_test.api.test_group_users) TestHgWebFeatures (class in tool_shed.test.functional.test_0310_hg_api_features) TestHistoriesApi (class in galaxy_test.api.test_histories) TestHistoryContentsApi (class in galaxy_test.api.test_history_contents) TestHistoryContentsApiBulkOperation (class in galaxy_test.api.test_history_contents) TestHistoryCopyElements (class in galaxy_test.selenium.test_history_copy_elements) TestHistoryDatasetState (class in galaxy_test.selenium.test_dataset_metadata_download) (class in galaxy_test.selenium.test_history_dataset_state) TestHistoryMultiView (class in galaxy_test.selenium.test_history_multi_view) TestHistoryOptions (class in galaxy_test.selenium.test_history_options) TestHistoryPanel (class in galaxy_test.selenium.test_history_panel) TestHistoryPanelCollections (class in galaxy_test.selenium.test_history_panel_collections) TestHistoryRequiresLoginSelenium (class in galaxy_test.selenium.test_history_sharing) TestHistorySharing (class in galaxy_test.selenium.test_history_sharing) TestImportExportHistory (class in galaxy_test.api.test_histories) TestInstallingCircularDependencies (class in tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies) TestInstallingComplexRepositoryDependencies (class in tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies) TestInstallRepositoryCircularDependencies (class in tool_shed.test.functional.test_1050_circular_dependencies_4_levels) TestInstallRepositoryMultipleOwners (class in tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners) TestInvocationGridSelenium (class in galaxy_test.selenium.test_invocation_grid) TestJobsApi (class in galaxy_test.api.test_jobs) TestLibrariesApi (class in galaxy_test.api.test_libraries) TestLibraryContents (class in galaxy_test.selenium.test_library_contents) TestLibraryLanding (class in galaxy_test.selenium.test_library_landing) TestLibraryToCollections (class in galaxy_test.selenium.test_library_to_collections) TestLicensesApi (class in galaxy_test.api.test_licenses) TestLoggedInToolForm (class in galaxy_test.selenium.test_tool_form) TestLogin (class in galaxy_test.selenium.test_login) TestManageInformation (class in galaxy_test.selenium.test_personal_information) TestNavigatesGalaxySelenium (class in galaxy_test.selenium.test_navigates_galaxy) TestPageRevisionsApi (class in galaxy_test.api.test_page_revisions) TestPages (class in galaxy_test.selenium.test_pages) TestPagesApi (class in galaxy_test.api.test_pages) TestPosixConfiguredFileSources (class in galaxy.files.unittest_utils) TestProvenance (class in galaxy_test.api.test_history_contents_provenance) TestReference (class in galaxy.tool_util.verify.script) TestRegistration (class in galaxy_test.selenium.test_registration) TestRepairRepository (class in tool_shed.test.functional.test_1430_repair_installed_repository) TestRepositoryAdminRole (class in tool_shed.test.functional.test_0530_repository_admin_feature) TestRepositoryCircularDependencies (class in tool_shed.test.functional.test_0040_repository_circular_dependencies) (class in tool_shed.test.functional.test_0080_advanced_circular_dependencies) TestRepositoryCircularDependenciesAgain (class in tool_shed.test.functional.test_0090_tool_search) TestRepositoryCircularDependenciesToNLevels (class in tool_shed.test.functional.test_0050_circular_dependencies_4_levels) TestRepositoryCitableURLs (class in tool_shed.test.functional.test_0420_citable_urls_for_repositories) TestRepositoryDependencies (class in tool_shed.test.functional.test_1080_advanced_circular_dependency_installation) (class in tool_shed.test.functional.test_1090_repository_dependency_handling) (class in tool_shed.test.functional.test_1100_install_updated_repository_dependencies) TestRepositoryDependencyRevisions (class in tool_shed.test.functional.test_0030_repository_dependency_revisions) TestRepositoryMultipleOwners (class in tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners) TestRepositoryWithDependencyRevisions (class in tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions) TestResetAllRepositoryMetadata (class in tool_shed.test.functional.test_0300_reset_all_metadata) TestResetInstalledRepositoryMetadata (class in tool_shed.test.functional.test_1300_reset_all_metadata) TestRolesApi (class in galaxy_test.api.test_roles) tests (galaxy.tool_util.parser.interface.ToolSourceTests attribute) (galaxy.tools.Tool property) tests_summary() (galaxy.webapps.galaxy.api.tools.ToolsController method) TestsAssertsHasNQuant (class in galaxy.tool_util.linters.tests) TestsAssertsHasSizeOrValueQuant (class in galaxy.tool_util.linters.tests) TestsAssertsHasSizeQuant (class in galaxy.tool_util.linters.tests) TestsAssertsMultiple (class in galaxy.tool_util.linters.tests) TestSavedHistories (class in galaxy_test.selenium.test_histories_list) TestsExpectNumOutputs (class in galaxy.tool_util.linters.tests) TestsExpectNumOutputsFailing (class in galaxy.tool_util.linters.tests) TestSharingHistory (class in galaxy_test.api.test_histories) TestsHasExpectations (class in galaxy.tool_util.linters.tests) TestSignOut (class in galaxy_test.selenium.test_sign_out) TestSimplePriorInstallation (class in tool_shed.test.functional.test_0150_prior_installation_required) (class in tool_shed.test.functional.test_0160_circular_prior_installation_required) (class in tool_shed.test.functional.test_1170_prior_installation_required) (class in tool_shed.test.functional.test_1180_circular_prior_installation_required) TestSizzleLoading (class in galaxy_test.selenium.test_sizzle_loading) TestsMissing (class in galaxy.tool_util.linters.tests) TestsMissingDatasource (class in galaxy.tool_util.linters.tests) TestsNoValid (class in galaxy.tool_util.linters.tests) TestsOutputCheckDiscovered (class in galaxy.tool_util.linters.tests) TestsOutputCollectionCheckDiscovered (class in galaxy.tool_util.linters.tests) TestsOutputCollectionCheckDiscoveredNested (class in galaxy.tool_util.linters.tests) TestsOutputCollectionCorresponding (class in galaxy.tool_util.linters.tests) TestsOutputCompareAttrib (class in galaxy.tool_util.linters.tests) TestsOutputCorresponding (class in galaxy.tool_util.linters.tests) TestsOutputDefined (class in galaxy.tool_util.linters.tests) TestsOutputFailing (class in galaxy.tool_util.linters.tests) TestsOutputName (class in galaxy.tool_util.linters.tests) TestsParamInInputs (class in galaxy.tool_util.linters.tests) TestStockToursTestCase (class in galaxy_test.selenium.test_stock_tours) TestsTools (class in galaxy_test.api.test_tools) TestsValid (class in galaxy.tool_util.linters.tests) TestToolDataApi (class in galaxy_test.api.test_tool_data) TestToolDescribingTours (class in galaxy_test.selenium.test_tool_describing_tours) TestToolForm (class in galaxy_test.selenium.test_tool_form) TestToolHelpImages (class in tool_shed.test.functional.test_0140_tool_help_images) (class in tool_shed.test.functional.test_1160_tool_help_images) TestToolsApi (class in galaxy_test.api.test_tools) TestToolShedBrowseUtilities (class in tool_shed.test.functional.test_0430_browse_utilities) TestToolsUpload (class in galaxy_test.api.test_tools_upload) TestToolWithRepositoryDependencies (class in tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies) TestToolWithToolDependencies (class in tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies) TestToursApi (class in galaxy_test.api.test_tours) TestUninstallingAndReinstallingRepositories (class in tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository) (class in tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies) (class in tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions) TestUpdateInstalledRepository (class in tool_shed.test.functional.test_1470_updating_installed_repositories) TestUpdateManager (class in tool_shed.test.functional.test_1410_update_manager) TestUploads (class in galaxy_test.selenium.test_uploads) TestUsersApi (class in galaxy_test.api.test_users) TestVisualizationsApi (class in galaxy_test.api.test_visualizations) TestWebhooksApi (class in galaxy_test.api.test_webhooks) TestWorkflowEditor (class in galaxy_test.selenium.test_workflow_editor) TestWorkflowExtractionApi (class in galaxy_test.api.test_workflow_extraction) TestWorkflowFrameworkPerformance (class in galaxy_test.performance.test_workflow_framework_performance) TestWorkflowInvocationDetails (class in galaxy_test.selenium.test_workflow_invocation_details) TestWorkflowManagement (class in galaxy_test.selenium.test_workflow_management) TestWorkflowRun (class in galaxy_test.selenium.test_workflow_run) TestWorkflowsApi (class in galaxy_test.api.test_workflows) TestWorkflowsFromYamlApi (class in galaxy_test.api.test_workflows_from_yaml) TestWorkflowSharing (class in galaxy_test.selenium.test_workflow_sharing) TestWorkflowSharingApi (class in galaxy_test.api.test_workflows) TestWorkflowSharingRedirect (class in galaxy_test.selenium.test_workflow_sharing) Text (class in galaxy.datatypes.data) text (galaxy.schema.schema.CustomBuildLenType attribute) (galaxy.schema.schema.Hyperlink attribute) TEXT (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute) text (galaxy.tool_util.toolbox.views.definitions.Label attribute) text_column_filter() (in module galaxy.model.index_filter_util) text_data() (galaxy.managers.hdas.HDAManager method) text_io() (galaxy.datatypes.sniff.FilePrefix method) text_metrics (galaxy.model.Job attribute) (galaxy.model.Task attribute) TextArea (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) TextColumn (class in galaxy.web.legacy_framework.grids) TextField (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) TextGrid (class in galaxy.datatypes.speech) textinsert (galaxy.tours.TourStep attribute) TextToolParameter (class in galaxy.tools.parameters.basic) TFileClass (class in galaxy.files.sources) TGZ (galaxy.schema.schema.ModelStoreFormat attribute) themes (galaxy.config.GalaxyAppConfiguration attribute) themes_by_host (galaxy.config.GalaxyAppConfiguration attribute) ThermoRAW (class in galaxy.datatypes.proteomics) thread_is_sleeping() (galaxy.util.heartbeat.Heartbeat method) thread_local_log (galaxy.model.mapping.GalaxyModelMapping attribute) Tiff (class in galaxy.datatypes.images) time (galaxy.managers.metrics.Metric attribute) time_ago() (in module galaxy.web.framework.helpers) time_elapsed() (galaxy.webapps.reports.controllers.jobs.Timer method) timenow() (in module galaxy.datatypes.converters.lped_to_fped_converter) (in module galaxy.datatypes.converters.lped_to_pbed_converter) (in module galaxy.datatypes.converters.pbed_ldreduced_converter) (in module galaxy.datatypes.converters.pbed_to_lped_converter) timeout_for() (galaxy.selenium.has_driver.HasDriver method) (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) timeout_multiplier (galaxy.selenium.cli.DriverWrapper attribute) (galaxy.selenium.context.GalaxySeleniumContextImpl attribute) (galaxy.selenium.jupyter_context.JupyterContextImpl attribute) (galaxy.selenium.navigates_galaxy.NavigatesGalaxy attribute) (galaxy_test.selenium.jupyter_context.JupyterTestContextImpl attribute) TimeoutAssertionError Timer (class in galaxy.webapps.reports.controllers.jobs) times_downloaded (tool_shed.webapp.model.Repository attribute) timestamp (galaxy.model.PSANonce attribute) tip() (tool_shed.webapp.model.Repository method) tip_has_metadata() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) TipOnly (class in tool_shed.repository_types.metadata) title (galaxy.job_metrics.formatting.FormattedMetric attribute) (galaxy.model.Page attribute) (galaxy.model.PageRevision attribute) (galaxy.model.Visualization attribute) (galaxy.model.VisualizationRevision attribute) (galaxy.schema.schema.JobMetric attribute) (galaxy.schema.schema.PageSummaryBase attribute) (galaxy.schema.schema.SharingStatus attribute) (galaxy.tools.parameters.grouping.Repeat property) (galaxy.tours.TourStep attribute) (galaxy.web.legacy_framework.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.DatatypesGrid attribute) (tool_shed.grids.repository_grids.DeprecatedRepositoriesIOwnGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithInvalidToolsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesByUserGrid attribute) (tool_shed.grids.repository_grids.RepositoriesICanAdministerGrid attribute) (tool_shed.grids.repository_grids.RepositoriesInCategoryGrid attribute) (tool_shed.grids.repository_grids.RepositoriesIOwnGrid attribute) (tool_shed.grids.repository_grids.RepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithInvalidToolsGrid attribute) (tool_shed.grids.repository_grids.RepositoryDependenciesGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ToolDependenciesGrid attribute) (tool_shed.grids.repository_grids.ToolsGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_grids.ValidRepositoryGrid attribute) title_by_index() (galaxy.tools.parameters.grouping.UploadDataset method) title_default (galaxy.tours.TourDetails attribute) title_id (galaxy.webapps.galaxy.controllers.admin.GroupListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) title_plural (galaxy.tools.parameters.grouping.Repeat property) (galaxy.tools.parameters.grouping.Section property) (galaxy.tools.parameters.grouping.UploadDataset property) tmp_dir (galaxy.datatypes.metadata.MetadataTempFile attribute) (galaxy.model.metadata.MetadataTempFile attribute) tmp_directory() (galaxy.job_execution.compute_environment.ComputeEnvironment method) (galaxy.job_execution.compute_environment.SharedComputeEnvironment method) tmp_outdir_prefix (galaxy.tool_util.cwl.cwltool_deps.RuntimeContext attribute) tmpdir (galaxy.tool_util.cwl.cwltool_deps.RuntimeContext attribute) tmpdir_prefix (galaxy.tool_util.cwl.cwltool_deps.RuntimeContext attribute) to_archive() (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.data.Data method) (galaxy.tools.Tool method) to_basic_markdown() (in module galaxy.managers.markdown_util) to_bibtex() (galaxy.managers.citations.BibtexCitation method) (galaxy.managers.citations.DoiCitation method) to_bool() (in module galaxy.util.specs) to_bool_or_none() (in module galaxy.util.specs) to_cwl() (in module galaxy.workflow.modules) to_cwl_job() (in module galaxy.tool_util.cwl) (in module galaxy.tool_util.cwl.representation) to_dataset_instances() (galaxy.tools.wrappers.DatasetListWrapper static method) to_detailed_model() (in module tool_shed.managers.repositories) to_dict() (galaxy.files.ConfiguredFileSources method) (galaxy.files.ConfiguredFileSourcesConfig method) (galaxy.files.FileSourceDictifiable method) (galaxy.files.sources.BaseFilesSource method) (galaxy.files.sources.SingleFileSource method) (galaxy.job_execution.setup.JobIO method) (galaxy.managers.citations.BaseCitation method) (galaxy.model.HasTags method) (galaxy.model.History method) (galaxy.model.HistoryDatasetAssociation method) (galaxy.model.HistoryDatasetCollectionAssociation method) (galaxy.model.Job method) (galaxy.model.JobExportHistoryArchive method) (galaxy.model.Library method) (galaxy.model.LibraryDataset method) (galaxy.model.LibraryDatasetCollectionAssociation method) (galaxy.model.LibraryDatasetDatasetAssociation method) (galaxy.model.LibraryFolder method) (galaxy.model.Page method) (galaxy.model.PageRevision method) (galaxy.model.StoredWorkflow method) (galaxy.model.tool_shed_install.ToolShedRepository method) (galaxy.model.tool_shed_install.ToolVersion method) (galaxy.model.UserAddress method) (galaxy.model.Visualization method) (galaxy.model.Workflow method) (galaxy.model.WorkflowComment method) (galaxy.model.WorkflowInvocation method) (galaxy.model.WorkflowInvocationStep method) (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.cloud.Cloud method) (galaxy.objectstore.ConcreteObjectStore method) (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.DistributedObjectStore method) (galaxy.objectstore.HierarchicalObjectStore method) (galaxy.objectstore.irods.IRODSObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.objectstore.pithos.PithosObjectStore method) (galaxy.objectstore.s3.S3ObjectStore method) (galaxy.selenium.driver_factory.ConfiguredDriver method) (galaxy.tool_util.deps.dependencies.DependenciesDescription method) (galaxy.tool_util.deps.DependencyManager method) (galaxy.tool_util.deps.NullDependencyManager method) (galaxy.tool_util.deps.requirements.ContainerDescription method) (galaxy.tool_util.deps.requirements.RequirementSpecification method) (galaxy.tool_util.deps.requirements.ResourceRequirement method) (galaxy.tool_util.deps.requirements.ToolRequirement method) (galaxy.tool_util.deps.requirements.ToolRequirements method) (galaxy.tool_util.parser.interface.TestCollectionDef method) (galaxy.tool_util.parser.interface.TestCollectionOutputDef method) (galaxy.tool_util.parser.output_collection_def.DatasetCollectionDescription method) (galaxy.tool_util.parser.output_collection_def.FilePatternDatasetCollectionDescription method) (galaxy.tool_util.parser.output_objects.ToolOutput method) (galaxy.tool_util.parser.output_objects.ToolOutputBase method) (galaxy.tool_util.parser.output_objects.ToolOutputCollection method) (galaxy.tool_util.parser.output_objects.ToolOutputCollectionStructure method) (galaxy.tool_util.parser.stdio.ToolStdioExitCode method) (galaxy.tool_util.parser.stdio.ToolStdioRegex method) (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) (galaxy.tool_util.toolbox.lineages.interface.ToolLineage method) (galaxy.tool_util.toolbox.lineages.interface.ToolLineageVersion method) (galaxy.tool_util.toolbox.lineages.ToolLineage method) (galaxy.tool_util.toolbox.panel.ToolSection method) (galaxy.tool_util.toolbox.panel.ToolSectionLabel method) (galaxy.tool_util.toolbox.ToolSection method) (galaxy.tool_util.toolbox.ToolSectionLabel method) (galaxy.tool_util.verify.interactor.ToolTestDescription method) (galaxy.tools.data.TabularToolDataField method) (galaxy.tools.data.TabularToolDataTable method) (galaxy.tools.parameters.basic.BaseURLToolParameter method) (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.GenomeBuildParameter method) (galaxy.tools.parameters.basic.ParameterValueError method) (galaxy.tools.parameters.basic.RulesListToolParameter method) (galaxy.tools.parameters.basic.SelectTagParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.TextToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.DataCollectionToolParameter method) (galaxy.tools.parameters.DataToolParameter method) (galaxy.tools.parameters.grouping.Conditional method) (galaxy.tools.parameters.grouping.ConditionalWhen method) (galaxy.tools.parameters.grouping.Group method) (galaxy.tools.parameters.grouping.Repeat method) (galaxy.tools.parameters.grouping.Section method) (galaxy.tools.parameters.SelectToolParameter method) (galaxy.tools.Tool method) (galaxy.util.dictifiable.Dictifiable method) (galaxy.util.form_builder.AddressField method) (galaxy.util.form_builder.BaseField method) (galaxy.util.form_builder.CheckboxField method) (galaxy.util.form_builder.HistoryField method) (galaxy.util.form_builder.PasswordField method) (galaxy.util.form_builder.SelectField method) (galaxy.util.form_builder.TextArea method) (galaxy.util.form_builder.TextField method) (galaxy.util.form_builder.WorkflowField method) (galaxy.visualization.genomes.Genome method) (galaxy.visualization.plugins.plugin.VisualizationPlugin method) (galaxy.web.form_builder.AddressField method) (galaxy.web.form_builder.BaseField method) (galaxy.web.form_builder.CheckboxField method) (galaxy.web.form_builder.HistoryField method) (galaxy.web.form_builder.PasswordField method) (galaxy.web.form_builder.SelectField method) (galaxy.web.form_builder.TextArea method) (galaxy.web.form_builder.TextField method) (galaxy.web.form_builder.WorkflowField method) (galaxy.webhooks.Webhook method) (galaxy.workflow.modules.InputProxy method) (galaxy.workflow.refactor.schema.Position method) (tool_shed.webapp.model.Repository method) to_dict_time() (galaxy.files.sources.BaseFilesSource method) to_element_dict() (in module tool_shed.managers.repositories) to_external_value() (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.model.metadata.FileParameter method) (galaxy.model.metadata.MetadataParameter method) to_float_or_none() (in module galaxy.util.specs) to_galaxy_parameters() (in module galaxy.tool_util.cwl) (in module galaxy.tool_util.cwl.representation) to_hda_representative() (galaxy.model.HistoryDatasetCollectionAssociation method) to_history_dataset_association() (galaxy.model.LibraryDatasetDatasetAssociation method) to_html_string() (in module galaxy.tool_shed.util.basic_util) (in module tool_shed.util.basic_util) to_js_bool() (in module galaxy.web.framework.helpers) to_JSON() (galaxy.datatypes.metadata.MetadataTempFile method) to_json() (galaxy.job_execution.setup.JobIO method) to_JSON() (galaxy.model.metadata.MetadataTempFile method) to_json() (galaxy.tools.parameters.basic.BaseDataToolParameter method) (galaxy.tools.parameters.basic.BaseJsonToolParameter method) (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.FileToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.SimpleTextToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.SelectToolParameter method) (galaxy.tools.Tool method) to_JSON_dict() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataCollection method) to_library_dataset_dataset_association() (galaxy.model.HistoryDatasetAssociation method) to_list() (galaxy.tool_util.deps.requirements.ToolRequirements method) to_model() (galaxy.objectstore.ConcreteObjectStore method) (galaxy.tool_util.toolbox.views.edam.EdamToolPanelView method) (galaxy.tool_util.toolbox.views.interface.ToolPanelView method) (galaxy.tool_util.toolbox.views.static.StaticToolPanelView method) (in module tool_shed.managers.repositories) to_options_list() (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider method) to_panel_view() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) to_param_dict_string() (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.ColorToolParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.DataToolParameter method) (galaxy.tools.parameters.SelectToolParameter method) to_posix_lines (galaxy.schema.fetch_data.BaseDataElement attribute) (galaxy.tools.parameters.grouping.Dataset attribute) to_python() (galaxy.tools.parameters.basic.BaseDataToolParameter method) (galaxy.tools.parameters.basic.BaseJsonToolParameter method) (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.FileToolParameter method) (galaxy.tools.parameters.basic.FloatToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.IntegerToolParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.SelectToolParameter method) to_relative_path() (galaxy.files.sources.BaseFilesSource method) (galaxy.files.sources.posix.PosixFilesSource method) (galaxy.files.sources.SingleFileSource method) to_safe_string() (galaxy.datatypes.metadata.DictParameter method) (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.model.metadata.DictParameter method) (galaxy.model.metadata.FileParameter method) (galaxy.model.metadata.MetadataParameter method) to_statements() (galaxy.tool_util.deps.brew_exts.EnvAction method) to_str() (galaxy.app.StatsdStructuredExecutionTimer method) (galaxy.util.StructuredExecutionTimer method) to_str_or_none() (in module galaxy.util.specs) to_string() (galaxy.datatypes.metadata.ColumnTypesParameter method) (galaxy.datatypes.metadata.DictParameter method) (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.ListParameter method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.datatypes.metadata.PythonObjectParameter method) (galaxy.datatypes.metadata.SelectParameter method) (galaxy.model.metadata.ColumnTypesParameter method) (galaxy.model.metadata.DictParameter method) (galaxy.model.metadata.FileParameter method) (galaxy.model.metadata.ListParameter method) (galaxy.model.metadata.MetadataParameter method) (galaxy.model.metadata.PythonObjectParameter method) (galaxy.model.metadata.SelectParameter method) (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) to_test_assert_list() (in module galaxy.tool_util.parser.yaml) to_text() (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.RulesListToolParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.DataCollectionToolParameter method) (galaxy.tools.parameters.DataToolParameter method) (galaxy.tools.parameters.SelectToolParameter method) to_tool_path() (galaxy.tool_util.fetcher.ToolLocationFetcher method) to_unit() (galaxy.util.bytesize.ByteSize method) to_xml_file() (galaxy.datatypes.registry.Registry method) toJson() (galaxy.visualization.data_providers.phyloviz.baseparser.Base_Parser method) (galaxy.visualization.data_providers.phyloviz.baseparser.Node method) token (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.PasswordResetToken attribute) (galaxy.model.PSAPartial attribute) (tool_shed.webapp.model.PasswordResetToken attribute) token_endpoint (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute) TokenContainedEvaluator (class in galaxy.util.bool_expressions) TokenEvaluator (class in galaxy.util.bool_expressions) tokens (galaxy.model.CloudAuthz attribute) Tool (class in galaxy.tool_util.toolbox.views.definitions) (class in galaxy.tools) (class in galaxy.tools.data_manager.manager) tool (galaxy.tool_util.parser.output_actions.ToolOutputAction property) (galaxy.tool_util.parser.output_actions.ToolOutputActionConditional property) (galaxy.tool_util.parser.output_actions.ToolOutputActionGroup property) (galaxy.tool_util.parser.output_actions.ToolOutputActionOption property) (galaxy.tool_util.parser.output_actions.ToolOutputActionOptionFilter property) TOOL (galaxy.tool_util.toolbox.panel.panel_item_types attribute) (galaxy.tool_util.toolbox.panel_item_types attribute) tool (galaxy.tools.data_manager.manager.DataManager attribute) tool() (galaxy.tool_util.cwl.schema.SchemaLoader method) tool_action (galaxy.tools.ApplyRulesTool attribute) (galaxy.tools.AsyncDataSourceTool attribute) (galaxy.tools.BuildListCollectionTool attribute) (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.DataDestinationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.DuplicateFileToCollectionTool attribute) (galaxy.tools.ExportHistoryTool attribute) (galaxy.tools.ExpressionTool attribute) (galaxy.tools.ExtractDatasetCollectionTool attribute) (galaxy.tools.FilterDatasetsTool attribute) (galaxy.tools.FilterEmptyDatasetsTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) (galaxy.tools.FilterFromFileTool attribute) (galaxy.tools.FlattenTool attribute) (galaxy.tools.HarmonizeTool attribute) (galaxy.tools.ImportHistoryTool attribute) (galaxy.tools.InteractiveTool attribute) (galaxy.tools.KeepSuccessDatasetsTool attribute) (galaxy.tools.MergeCollectionTool attribute) (galaxy.tools.OutputParameterJSONTool attribute) (galaxy.tools.RelabelFromFileTool attribute) (galaxy.tools.SetMetadataTool attribute) (galaxy.tools.SortTool attribute) (galaxy.tools.TagFromFileTool attribute) (galaxy.tools.Tool attribute) (galaxy.tools.UnzipCollectionTool attribute) (galaxy.tools.ZipCollectionTool attribute) tool_cache (galaxy.app.MinimalGalaxyApplication attribute) (galaxy.app_unittest_utils.galaxy_mock.MockApp attribute) (galaxy.structured_app.StructuredApp attribute) tool_class (in module galaxy.tools) tool_classes (galaxy.jobs.JobConfiguration attribute) tool_config_paths (galaxy.config_watchers.ConfigWatchers property) tool_data_manager (galaxy.webapps.galaxy.api.tool_data.FastAPIToolData attribute) tool_data_path (galaxy.config.GalaxyAppConfiguration attribute) (galaxy.tools.remote_tool_eval.ToolAppConfig attribute) (galaxy.tools.repositories.ValidationContextConfig attribute) (tool_shed.test.base.twilltestcase.GalaxyInteractorToolShedInstallationClient property) (tool_shed.test.base.twilltestcase.ShedTwillTestCase property) (tool_shed.test.base.twilltestcase.StandaloneToolShedInstallationClient property) (tool_shed.test.base.twilltestcase.ToolShedInstallationClient property) tool_data_paths (galaxy.config_watchers.ConfigWatchers property) tool_data_table (galaxy.tools.parameters.dynamic_options.DynamicOptions property) tool_data_table_config (galaxy.tools.repositories.ValidationContextConfig attribute) tool_data_table_info() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) tool_data_table_info_1() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) tool_data_table_items() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) tool_data_table_types (galaxy.tools.data.ToolDataTableManager attribute) tool_data_tables (galaxy.managers.tool_data.ToolDataImportManager attribute) (galaxy.structured_app.MinimalManagerApp attribute) (galaxy.structured_app.MinimalToolApp attribute) (galaxy.structured_app.StructuredApp attribute) (galaxy.tools.remote_tool_eval.ToolApp attribute) tool_dependencies (galaxy.model.tool_shed_install.ToolShedRepository attribute) tool_dependencies_being_installed (galaxy.model.tool_shed_install.ToolShedRepository property) tool_dependencies_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) tool_dependencies_installed_or_in_error (galaxy.model.tool_shed_install.ToolShedRepository property) tool_dependencies_missing_or_being_installed (galaxy.model.tool_shed_install.ToolShedRepository property) tool_dependencies_with_installation_errors (galaxy.model.tool_shed_install.ToolShedRepository property) tool_dependency_dir (galaxy.app.MinimalGalaxyApplication property) (galaxy.config.GalaxyAppConfiguration attribute) (galaxy.model.tool_shed_install.HasToolBox property) (galaxy.structured_app.StructuredApp attribute) tool_directory (galaxy.model.DynamicTool attribute) tool_directory() (galaxy.job_execution.compute_environment.ComputeEnvironment method) (galaxy.job_execution.compute_environment.SharedComputeEnvironment method) tool_error_messages() (galaxy.webapps.reports.controllers.tools.Tools method) tool_errors (galaxy.model.WorkflowStep attribute) tool_execution_time() (galaxy.webapps.reports.controllers.tools.Tools method) tool_execution_time_per_month() (galaxy.webapps.reports.controllers.tools.Tools method) tool_fail() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) tool_filters (galaxy.config.GalaxyAppConfiguration attribute) tool_form_execute() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) tool_form_generate_tour() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) tool_format (galaxy.model.DynamicTool attribute) tool_id (galaxy.model.DynamicTool attribute) (galaxy.model.Event attribute) (galaxy.model.Job attribute) (galaxy.model.tool_shed_install.ToolVersion attribute) (galaxy.model.tool_shed_install.ToolVersionAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.WorkflowStep attribute) (galaxy.schema.schema.JobBaseModel attribute) (galaxy.schema.schema.WorkflowStepBase attribute) (galaxy.schema.schema.WorkflowStepToExportBase attribute) (galaxy.tool_util.toolbox.views.definitions.ExcludeTool attribute) (galaxy.tool_util.verify.interactor.InvalidToolTestDict attribute) (galaxy.tool_util.verify.interactor.ToolTestDescriptionDict attribute) (galaxy.tool_util.verify.interactor.ValidToolTestDict attribute) (galaxy.tool_util.verify.script.TestException attribute) (galaxy.tool_util.verify.script.TestReference attribute) tool_id_regex (galaxy.tool_util.toolbox.views.definitions.ExcludeToolRegex attribute) tool_ids (galaxy.schema.schema.JobIndexQueryPayload attribute) (galaxy.tool_util.toolbox.lineages.interface.ToolLineage property) (galaxy.tool_util.toolbox.lineages.ToolLineage property) tool_ids_by_requirements (galaxy.tool_util.deps.views.DependencyResolversView property) tool_ids_like (galaxy.schema.schema.JobIndexQueryPayload attribute) tool_info (galaxy.tool_util.deps.container_classes.ContainerProtocol property) tool_inputs (galaxy.model.WorkflowStep attribute) (galaxy.schema.schema.WorkflowStepBase attribute) tool_label_filters (galaxy.config.GalaxyAppConfiguration attribute) tool_lineages() (galaxy.managers.configuration.ConfigurationManager method) (galaxy.webapps.galaxy.api.configuration.FastAPIConfiguration method) tool_open() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) tool_output_to_structure() (in module galaxy.model.dataset_collections.structure) tool_panel_contents() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) tool_panel_section_id (galaxy.managers.workflows.WorkflowCreateOptions attribute) tool_panel_section_mapping (galaxy.managers.workflows.WorkflowCreateOptions attribute) tool_parameter_div() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) tool_parameter_edit_rules() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) tool_path (galaxy.config.GalaxyAppConfiguration attribute) (galaxy.model.DynamicTool attribute) tool_paths (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager property) tool_per_month() (galaxy.webapps.reports.controllers.jobs.Jobs method) tool_port (galaxy.model.InteractiveToolEntryPoint attribute) tool_provided_metadata (galaxy.job_execution.output_collect.BaseJobContext attribute) (galaxy.job_execution.output_collect.JobContext attribute) (galaxy.job_execution.output_collect.SessionlessJobContext attribute) tool_provided_metadata() (galaxy.tools.Tool method) tool_proxy (galaxy.tool_util.parser.cwl.CwlToolSource property) tool_proxy() (in module galaxy.tool_util.cwl) (in module galaxy.tool_util.cwl.parser) (in module galaxy.tool_util.parser.cwl) tool_proxy_from_persistent_representation() (in module galaxy.tool_util.cwl) tool_repository_long_description (in module tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners) (in module tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners) tool_requirements (galaxy.tools.Tool property) tool_requirements_status (galaxy.tools.Tool property) tool_response_to_output() (in module galaxy.tool_util.cwl.util) tool_section_filters (galaxy.config.GalaxyAppConfiguration attribute) tool_set_value() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) tool_shed module tool_shed (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.schema.schema.InstalledToolShedRepository attribute) (galaxy.schema.schema.ToolShedRepositorySummary attribute) (galaxy.tools.ApplyRulesTool attribute) (galaxy.tools.AsyncDataSourceTool attribute) (galaxy.tools.BuildListCollectionTool attribute) (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.DataDestinationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.DuplicateFileToCollectionTool attribute) (galaxy.tools.ExportHistoryTool attribute) (galaxy.tools.ExpressionTool attribute) (galaxy.tools.ExtractDatasetCollectionTool attribute) (galaxy.tools.FilterDatasetsTool attribute) (galaxy.tools.FilterEmptyDatasetsTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) (galaxy.tools.FilterFromFileTool attribute) (galaxy.tools.FlattenTool attribute) (galaxy.tools.HarmonizeTool attribute) (galaxy.tools.ImportHistoryTool attribute) (galaxy.tools.InteractiveTool attribute) (galaxy.tools.KeepSuccessDatasetsTool attribute) (galaxy.tools.MergeCollectionTool attribute) (galaxy.tools.OutputParameterJSONTool attribute) (galaxy.tools.RelabelFromFileTool attribute) (galaxy.tools.SortTool attribute) (galaxy.tools.TagFromFileTool attribute) (galaxy.tools.UnzipCollectionTool attribute) (galaxy.tools.ZipCollectionTool attribute) tool_shed.dependencies module tool_shed.dependencies.attribute_handlers module tool_shed.dependencies.repository module tool_shed.dependencies.repository.relation_builder module tool_shed.dependencies.tool module tool_shed.dependencies.tool.tag_attribute_handler module tool_shed.galaxy_install module tool_shed.grids module tool_shed.grids.admin_grids module tool_shed.grids.repository_grid_filter_manager module tool_shed.grids.repository_grids module tool_shed.grids.util module tool_shed.managers module tool_shed.managers.groups module tool_shed.managers.repositories module tool_shed.metadata module tool_shed.metadata.repository_metadata_manager module tool_shed.repository_registry module tool_shed.repository_types module tool_shed.repository_types.metadata module tool_shed.repository_types.registry module tool_shed.repository_types.repository_suite_definition module tool_shed.repository_types.tool_dependency_definition module tool_shed.repository_types.unrestricted module tool_shed.repository_types.util module tool_shed.test module tool_shed.test.base module tool_shed.test.base.common module tool_shed.test.base.test_db_util module tool_shed.test.base.twilltestcase module tool_shed.test.functional module tool_shed.test.functional.test_0000_basic_repository_features module tool_shed.test.functional.test_0010_repository_with_tool_dependencies module tool_shed.test.functional.test_0020_basic_repository_dependencies module tool_shed.test.functional.test_0030_repository_dependency_revisions module tool_shed.test.functional.test_0040_repository_circular_dependencies module tool_shed.test.functional.test_0050_circular_dependencies_4_levels module tool_shed.test.functional.test_0070_invalid_tool module tool_shed.test.functional.test_0080_advanced_circular_dependencies module tool_shed.test.functional.test_0090_tool_search module tool_shed.test.functional.test_0100_complex_repository_dependencies module tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies module tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners module tool_shed.test.functional.test_0140_tool_help_images module tool_shed.test.functional.test_0150_prior_installation_required module tool_shed.test.functional.test_0160_circular_prior_installation_required module tool_shed.test.functional.test_0170_complex_prior_installation_required module tool_shed.test.functional.test_0300_reset_all_metadata module tool_shed.test.functional.test_0310_hg_api_features module tool_shed.test.functional.test_0420_citable_urls_for_repositories module tool_shed.test.functional.test_0430_browse_utilities module tool_shed.test.functional.test_0440_deleting_dependency_definitions module tool_shed.test.functional.test_0460_upload_to_repository module tool_shed.test.functional.test_0470_tool_dependency_repository_type module tool_shed.test.functional.test_0480_tool_dependency_xml_verification module tool_shed.test.functional.test_0530_repository_admin_feature module tool_shed.test.functional.test_0550_metadata_updated_dependencies module tool_shed.test.functional.test_1000_install_basic_repository module tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies module tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies module tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions module tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies module tool_shed.test.functional.test_1050_circular_dependencies_4_levels module tool_shed.test.functional.test_1070_invalid_tool module tool_shed.test.functional.test_1080_advanced_circular_dependency_installation module tool_shed.test.functional.test_1090_repository_dependency_handling module tool_shed.test.functional.test_1100_install_updated_repository_dependencies module tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies module tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency module tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners module tool_shed.test.functional.test_1160_tool_help_images module tool_shed.test.functional.test_1170_prior_installation_required module tool_shed.test.functional.test_1180_circular_prior_installation_required module tool_shed.test.functional.test_1190_complex_prior_installation_required module tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository module tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies module tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions module tool_shed.test.functional.test_1300_reset_all_metadata module tool_shed.test.functional.test_1410_update_manager module tool_shed.test.functional.test_1430_repair_installed_repository module tool_shed.test.functional.test_1460_data_managers module tool_shed.test.functional.test_1470_updating_installed_repositories module tool_shed.tools module tool_shed.tools.data_table_manager module tool_shed.tools.tool_validator module tool_shed.tools.tool_version_manager module tool_shed.util module tool_shed.util.admin_util module tool_shed.util.basic_util module tool_shed.util.commit_util module tool_shed.util.common_util module tool_shed.util.container_util module tool_shed.util.encoding_util module tool_shed.util.hg_util module tool_shed.util.hgweb_config module tool_shed.util.metadata_util module tool_shed.util.readme_util module tool_shed.util.repository_content_util module tool_shed.util.repository_util module tool_shed.util.search_util module tool_shed.util.shed_index module tool_shed.util.shed_util_common module tool_shed.util.tool_dependency_util module tool_shed.util.tool_util module tool_shed.util.web_util module tool_shed.util.xml_util module tool_shed.utility_containers module tool_shed.utility_containers.utility_container_manager module tool_shed.webapp module tool_shed.webapp.api module tool_shed.webapp.api.authenticate module tool_shed.webapp.api.categories module tool_shed.webapp.api.configuration module tool_shed.webapp.api.groups module tool_shed.webapp.api.repositories module tool_shed.webapp.api.repository_revisions module tool_shed.webapp.api.tools module tool_shed.webapp.api.users module tool_shed.webapp.app module tool_shed.webapp.buildapp module tool_shed.webapp.config module tool_shed.webapp.controllers module tool_shed.webapp.controllers.admin module tool_shed.webapp.controllers.groups module tool_shed.webapp.controllers.hg module tool_shed.webapp.controllers.repository module tool_shed.webapp.controllers.user module tool_shed.webapp.fast_app module tool_shed.webapp.fast_factory module tool_shed.webapp.framework module tool_shed.webapp.framework.decorators module tool_shed.webapp.framework.middleware module tool_shed.webapp.framework.middleware.remoteuser module tool_shed.webapp.model module tool_shed.webapp.model.mapping module tool_shed.webapp.search module tool_shed.webapp.search.repo_search module tool_shed.webapp.search.tool_search module tool_shed.webapp.security module tool_shed.webapp.util module tool_shed.webapp.util.ratings_util module tool_shed.webapp.util.shed_statistics module tool_shed_decode() (in module galaxy.util.tool_shed.encoding_util) tool_shed_encode() (in module galaxy.util.tool_shed.encoding_util) tool_shed_from_repository_clone_url() (galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) tool_shed_is_this_tool_shed() (in module tool_shed.util.shed_util_common) tool_shed_path_name (galaxy.model.tool_shed_install.ToolShedRepository property) tool_shed_registry (galaxy.model.tool_shed_install.HasToolBox attribute) (galaxy.structured_app.MinimalManagerApp attribute) tool_shed_repository (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolVersion attribute) (galaxy.schema.schema.WorkflowToolStepToExport attribute) (galaxy.tools.Tool property) tool_shed_repository_cache (galaxy.structured_app.StructuredApp attribute) tool_shed_repository_id (galaxy.model.tool_shed_install.RepositoryDependency attribute) (galaxy.model.tool_shed_install.RepositoryRepositoryDependencyAssociation attribute) (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolVersion attribute) tool_shed_status (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.schema.schema.InstalledToolShedRepository attribute) tool_shed_url (galaxy.schema.schema.ToolShedRepository attribute) tool_state (galaxy.schema.schema.WorkflowStepToExport attribute) (galaxy.workflow.refactor.schema.AddStepAction attribute) tool_state_adjustment (galaxy.workflow.refactor.schema.RefactorActionExecutionMessageTypeEnum attribute) tool_stderr (galaxy.model.Job attribute) (galaxy.model.Task attribute) (galaxy.schema.schema.JobFullDetails attribute) tool_stdout (galaxy.model.Job attribute) (galaxy.model.Task attribute) (galaxy.schema.schema.JobFullDetails attribute) tool_tag_manager() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) (galaxy.tools.ToolBox method) tool_type (galaxy.tools.ApplyRulesTool attribute) (galaxy.tools.AsyncDataSourceTool attribute) (galaxy.tools.BuildListCollectionTool attribute) (galaxy.tools.DataDestinationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.DuplicateFileToCollectionTool attribute) (galaxy.tools.ExportHistoryTool attribute) (galaxy.tools.ExpressionTool attribute) (galaxy.tools.ExtractDatasetCollectionTool attribute) (galaxy.tools.FilterEmptyDatasetsTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) (galaxy.tools.FilterFromFileTool attribute) (galaxy.tools.FlattenTool attribute) (galaxy.tools.HarmonizeTool attribute) (galaxy.tools.ImportHistoryTool attribute) (galaxy.tools.InteractiveTool attribute) (galaxy.tools.KeepSuccessDatasetsTool attribute) (galaxy.tools.MergeCollectionTool attribute) (galaxy.tools.OutputParameterJSONTool attribute) (galaxy.tools.RelabelFromFileTool attribute) (galaxy.tools.SetMetadataTool attribute) (galaxy.tools.SortTool attribute) (galaxy.tools.TagFromFileTool attribute) (galaxy.tools.Tool attribute) (galaxy.tools.UnzipCollectionTool attribute) (galaxy.tools.ZipCollectionTool attribute) tool_type_local (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.ExpressionTool attribute) (galaxy.tools.Tool attribute) tool_uuid (galaxy.model.WorkflowStep property) tool_version (galaxy.model.DynamicTool attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.Job attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.WorkflowStep attribute) (galaxy.schema.schema.HDAExtended attribute) (galaxy.schema.schema.WorkflowStepBase attribute) (galaxy.schema.schema.WorkflowStepToExport attribute) (galaxy.tool_util.verify.interactor.InvalidToolTestDict attribute) (galaxy.tool_util.verify.interactor.ToolTestDescriptionDict attribute) (galaxy.tool_util.verify.interactor.ValidToolTestDict attribute) (galaxy.tool_util.verify.script.TestReference attribute) (galaxy.workflow.refactor.schema.UpgradeToolAction attribute) tool_version_change (galaxy.workflow.refactor.schema.RefactorActionExecutionMessageTypeEnum attribute) tool_versions (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.tools.Tool property) (tool_shed.webapp.model.RepositoryMetadata attribute) ToolAction (class in galaxy.tools.actions) ToolApp (class in galaxy.tools.remote_tool_eval) ToolAppConfig (class in galaxy.tools.remote_tool_eval) ToolBox (class in galaxy.tools) toolbox (galaxy.app.MinimalGalaxyApplication property) (galaxy.app_unittest_utils.galaxy_mock.MockApp property) (galaxy.model.tool_shed_install.HasToolBox property) (galaxy.structured_app.BasicSharedApp property) toolbox_filter_base_modules (galaxy.config.GalaxyAppConfiguration attribute) toolbox_install() (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) toolbox_requirements_status (galaxy.tool_util.deps.views.DependencyResolversView property) toolbox_search (galaxy.app.MinimalGalaxyApplication attribute) toolbox_uninstall() (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) ToolBoxRegistry (class in galaxy.tool_util.toolbox.views.interface) ToolBoxRegistryImpl (class in galaxy.tool_util.toolbox.base) ToolBoxSearch (class in galaxy.tools.search) ToolCache (class in galaxy.tools.cache) ToolConfRepository (class in galaxy.tool_util.toolbox.base) ToolConfWatcher (class in galaxy.tool_util.toolbox.watcher) ToolDataImportManager (class in galaxy.managers.tool_data) ToolDataManager (class in galaxy.managers.tool_data) ToolDataTable (class in galaxy.tools.data) ToolDataTableManager (class in galaxy.tools.data) (in module galaxy.tool_shed.tools.data_table_manager) (in module tool_shed.tools.data_table_manager) ToolDependenciesAPIController (class in galaxy.webapps.galaxy.api.tool_dependencies) ToolDependenciesGrid (class in tool_shed.grids.repository_grids) ToolDependenciesGrid.ToolDependencyColumn (class in tool_shed.grids.repository_grids) ToolDependency (class in galaxy.model.tool_shed_install) ToolDependency.states (class in galaxy.model.tool_shed_install) ToolDependencyAttributeHandler (class in tool_shed.dependencies.attribute_handlers) ToolDependencyDefinition (class in tool_shed.repository_types.tool_dependency_definition) ToolDependencyInstallationError (class in tool_shed.utility_containers) ToolDependencySuccessfulInstallation (class in tool_shed.utility_containers) ToolDocumentCache (class in galaxy.tools.cache) ToolEntryPointsAPIController (class in galaxy.webapps.galaxy.api.tool_entry_points) ToolErrorLog (class in galaxy.tools.evaluation) ToolEvaluator (class in galaxy.tools.evaluation) ToolExecutionCache (class in galaxy.tools.actions) ToolExecutionError ToolExpressionOutput (class in galaxy.tool_util.parser.output_objects) ToolFileEventHandler (class in galaxy.tool_util.toolbox.watcher) ToolFilterMixin (class in galaxy.managers.tools) ToolHash (class in galaxy.tools.cache) ToolIDMissing (class in galaxy.tool_util.linters.general) ToolIDValid (class in galaxy.tool_util.linters.general) ToolIDWhitespace (class in galaxy.tool_util.linters.general) ToolInfo (class in galaxy.tool_util.deps.dependencies) ToolInputsNotOKException ToolInputsNotReadyException ToolInputTranslator (class in galaxy.tools.parameters.input_translation) ToolLineage (class in galaxy.tool_util.toolbox.lineages) (class in galaxy.tool_util.toolbox.lineages.interface) ToolLineageVersion (class in galaxy.tool_util.toolbox.lineages.interface) ToolLocationFetcher (class in galaxy.tool_util.fetcher) ToolLocationResolver (class in galaxy.tool_util.locations) ToolMetadataDatasetCollector (class in galaxy.job_execution.output_collect) ToolMetaParameterException ToolMissingException ToolModule (class in galaxy.workflow.modules) ToolNameMissing (class in galaxy.tool_util.linters.general) ToolNameValid (class in galaxy.tool_util.linters.general) ToolNameWhitespace (class in galaxy.tool_util.linters.general) ToolNotFoundException ToolOutput (class in galaxy.tool_util.cwl.runnable) (class in galaxy.tool_util.parser.output_objects) ToolOutputAction (class in galaxy.tool_util.parser.output_actions) ToolOutputActionConditional (class in galaxy.tool_util.parser.output_actions) ToolOutputActionConditionalWhen (class in galaxy.tool_util.parser.output_actions) ToolOutputActionGroup (class in galaxy.tool_util.parser.output_actions) ToolOutputActionOption (class in galaxy.tool_util.parser.output_actions) ToolOutputActionOptionFilter (class in galaxy.tool_util.parser.output_actions) ToolOutputBase (class in galaxy.tool_util.parser.output_objects) ToolOutputCollection (class in galaxy.tool_util.parser.output_objects) ToolOutputCollectionPart (class in galaxy.tool_util.parser) (class in galaxy.tool_util.parser.output_objects) ToolOutputCollectionStructure (class in galaxy.tool_util.parser.output_objects) ToolPanelElements (class in galaxy.tool_util.toolbox.panel) ToolPanelManager (class in galaxy.tool_shed.galaxy_install.tools.tool_panel_manager) ToolPanelView (class in galaxy.tool_util.toolbox.views.interface) ToolPanelViewModel (class in galaxy.tool_util.toolbox.views.interface) ToolPanelViewModelType (class in galaxy.tool_util.toolbox.views.interface) ToolPanelViewSearch (class in galaxy.tools.search) ToolParameter (class in galaxy.tools.parameters.basic) ToolParameterSanitizer (class in galaxy.tools.parameters.sanitize) ToolParameterValueWrapper (class in galaxy.tools.wrappers) ToolProfileInvalid (class in galaxy.tool_util.linters.general) ToolProfileLegacy (class in galaxy.tool_util.linters.general) ToolProfileValid (class in galaxy.tool_util.linters.general) ToolProvidedMetadata (class in galaxy.tool_util.provided_metadata) ToolProvidedMetadataDatasetCollection (class in galaxy.tool_util.parser.output_collection_def) ToolRecommendations (class in galaxy.tools.recommendations) ToolRequirement (class in galaxy.tool_util.deps.requirements) ToolRequirements (class in galaxy.tool_util.deps.requirements) ToolRequirementsException ToolRunner (class in galaxy.webapps.galaxy.controllers.tool_runner) Tools (class in galaxy.webapps.reports.controllers.tools) tools (galaxy.jobs.JobConfiguration attribute) (galaxy.schema.schema.FavoriteObjectsSummary attribute) (galaxy.schema.schema.FavoriteObjectType attribute) tools() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) tools_and_job_state() (galaxy.webapps.reports.controllers.tools.Tools method) tools_and_job_state_per_month() (galaxy.webapps.reports.controllers.tools.Tools method) tools_by_id (galaxy.tools.ToolBox property) tools_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) tools_post() (galaxy_test.base.populators.BaseDatasetPopulator method) ToolsController (class in galaxy.webapps.galaxy.api.tools) (class in tool_shed.webapp.api.tools) ToolSearch (class in tool_shed.webapp.search.tool_search) ToolSection (class in galaxy.tool_util.toolbox) (class in galaxy.tool_util.toolbox.panel) ToolSectionLabel (class in galaxy.tool_util.toolbox) (class in galaxy.tool_util.toolbox.panel) ToolsGrid (class in tool_shed.grids.repository_grids) ToolsGrid.ToolsColumn (class in tool_shed.grids.repository_grids) ToolShedAppConfiguration (class in tool_shed.webapp.config) ToolShedAuthenticationController (class in tool_shed.webapp.api.authenticate) ToolShedController (class in galaxy.webapps.galaxy.api.toolshed) ToolShedDependency (class in galaxy.tool_util.deps.resolvers.galaxy_packages) ToolShedGalaxyWebTransaction (class in tool_shed.webapp.buildapp) ToolShedInstallationClient (class in tool_shed.test.base.twilltestcase) ToolShedMetadataGenerator (class in tool_shed.metadata.repository_metadata_manager) ToolShedModelMapping (class in tool_shed.webapp.model.mapping) ToolShedPackageDependencyResolver (class in galaxy.tool_util.deps.resolvers.tool_shed_packages) ToolShedRepositoriesController (class in galaxy.webapps.galaxy.api.tool_shed_repositories) ToolShedRepository (class in galaxy.model.tool_shed_install) (class in galaxy.schema.schema) ToolShedRepository.installation_status (class in galaxy.model.tool_shed_install) ToolShedRepository.states (class in galaxy.model.tool_shed_install) ToolShedRepositoryChangeset (class in galaxy.schema.schema) ToolShedRepositorySummary (class in galaxy.schema.schema) ToolShedUtilityContainerManager (class in tool_shed.utility_containers) ToolSource (class in galaxy.tool_util.parser) (class in galaxy.tool_util.parser.interface) ToolSourceTest (class in galaxy.tool_util.parser.interface) ToolSourceTests (class in galaxy.tool_util.parser.interface) ToolsService (class in galaxy.webapps.galaxy.services.tools) ToolStdioExitCode (class in galaxy.tool_util.parser.stdio) ToolStdioRegex (class in galaxy.tool_util.parser.stdio) ToolStep (class in galaxy.schema.schema) ToolTagAssociation (class in galaxy.model) ToolTestDescription (class in galaxy.tool_util.verify.interactor) ToolTestDescriptionDict (class in galaxy.tool_util.verify.interactor) ToolValidator (class in galaxy.tool_shed.tools.tool_validator) (class in tool_shed.tools.tool_validator) ToolVersion (class in galaxy.model.tool_shed_install) ToolVersionAssociation (class in galaxy.model.tool_shed_install) ToolVersionManager (class in tool_shed.tools.tool_version_manager) ToolVersionMissing (class in galaxy.tool_util.linters.general) ToolVersionPEP404 (class in galaxy.tool_util.linters.general) ToolVersionValid (class in galaxy.tool_util.linters.general) ToolVersionWhitespace (class in galaxy.tool_util.linters.general) ToolWatcher (class in galaxy.tool_util.toolbox.watcher) top (galaxy.schema.schema.WorkflowStepLayoutPosition attribute) (galaxy.workflow.refactor.schema.Position attribute) top_level_stored_workflow (galaxy.model.Workflow property) top_level_workflow (galaxy.model.Workflow property) topic (galaxy.tool_util.biotools.interface.BiotoolsEntry attribute) topics (galaxy.tool_util.toolbox.views.edam.EdamPanelMode attribute) topsort() (in module galaxy.util.topsort) topsort_levels() (in module galaxy.util.topsort) Torque (class in galaxy.jobs.runners.util.cli.job.torque) total (galaxy.schema.schema.LibraryAvailablePermissions attribute) total_disk_usage (galaxy.model.GalaxySession property) (galaxy.model.User property) (galaxy.model.UserQuotaBasicUsage attribute) (galaxy.schema.schema.DiskUsageUserModel attribute) (tool_shed.webapp.model.User property) total_disk_usage() (galaxy_test.base.populators.BaseDatasetPopulator method) total_matches (galaxy.schema.schema.HistoryContentStats attribute) total_rows (galaxy.schema.schema.LibraryFolderMetadata attribute) total_size (galaxy.model.Dataset attribute) (galaxy.model.store.DatasetAttributeImportModel attribute) (galaxy.schema.schema.DatasetSummary attribute) total_size() (in module galaxy.model.custom_types) touch() (galaxy.model.HistoryDatasetCollectionAssociation method) Tour (class in galaxy.tours) tour_contents() (galaxy.tours.ToursRegistry method) tour_wait_for_clickable_element() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) tour_wait_for_element_present() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) TourCallback (class in galaxy_test.selenium.test_stock_tours) TourCore (class in galaxy.tours) TourDetails (class in galaxy.tours) TourList (class in galaxy.tours) ToursRegistry (class in galaxy.tours) TourStep (class in galaxy.tours) tpm (galaxy.tool_shed.galaxy_install.install_manager.InstallRepositoryManager attribute) trace() (galaxy.web.framework.base.WebApplication method) (in module galaxy.util.custom_logging) traceback (galaxy.model.Job attribute) (galaxy.model.Task attribute) track_jobs_in_database (galaxy.config.GalaxyAppConfiguration attribute) track_started (galaxy.celery.GalaxyTask attribute) track_type (galaxy.datatypes.binary.Bam attribute) (galaxy.datatypes.binary.BigWig attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.interval.Bed attribute) (galaxy.datatypes.interval.BedGraph attribute) (galaxy.datatypes.interval.ChromatinInteractions attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Gff3 attribute) (galaxy.datatypes.interval.Gtf attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.interval.Wiggle attribute) (galaxy.datatypes.tabular.BaseVcf attribute) (galaxy.datatypes.tabular.Sam attribute) trackster() (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) TracksterConfig (class in galaxy.tools) TrafoXML (class in galaxy.datatypes.proteomics) training (galaxy.tool_util.toolbox.views.definitions.StaticToolBoxViewTypeEnum attribute) (galaxy.tool_util.toolbox.views.interface.ToolPanelViewModelType attribute) TraML (class in galaxy.datatypes.proteomics) trans (tool_shed.dependencies.attribute_handlers.RepositoryDependencyAttributeHandler attribute) (tool_shed.dependencies.attribute_handlers.ToolDependencyAttributeHandler attribute) transaction() (in module galaxy.model.base) (in module galaxy.model.migrations.util) transaction_chooser() (galaxy.webapps.base.webapp.WebApplication method) (tool_shed.webapp.buildapp.CommunityWebApplication method) transfer_part() (in module galaxy.objectstore.s3_multipart_upload) transform (galaxy.model.DatasetSource attribute) (galaxy.schema.schema.DatasetSource attribute) transform_publicname() (in module galaxy.security.validate_user_input) transient_paths_for() (galaxy.model.deferred.SimpleTransientPathMapper method) (galaxy.model.deferred.TransientPathMapper method) TransientDatasetPaths (class in galaxy.model.deferred) TransientPathMapper (class in galaxy.model.deferred) translate() (galaxy.tools.parameters.input_translation.ToolInputTranslator method) TransLogger (class in galaxy.web.framework.middleware.translogger) Traversable (class in galaxy.util.resources) Tree (class in galaxy.model.dataset_collections.structure) trim_module_name() (galaxy.celery.GalaxyCelery method) TrimmedString (class in galaxy.model.custom_types) Triples (class in galaxy.datatypes.triples) Trk (class in galaxy.datatypes.images) Trr (class in galaxy.datatypes.binary) trs_proxy (galaxy.structured_app.StructuredApp attribute) trs_server (galaxy.managers.workflows.WorkflowCreateOptions attribute) trs_tool_id (galaxy.managers.workflows.WorkflowCreateOptions attribute) trs_url (galaxy.managers.workflows.WorkflowCreateOptions attribute) trs_version_id (galaxy.managers.workflows.WorkflowCreateOptions attribute) TrsConsumeAPIController (class in galaxy.webapps.galaxy.api.trs_consumer) TrsProxy (class in galaxy.workflow.trs_proxy) TrsSearchAPIController (class in galaxy.webapps.galaxy.api.trs_search) TrsServer (class in galaxy.workflow.trs_proxy) truncate() (galaxy.datatypes.dataproviders.base.DataProvider method) (in module galaxy.web.framework.helpers) trust_hid() (galaxy.model.store.DirectoryImportModelStore1901 method) (galaxy.model.store.ModelImportStore method) trust_jupyter_notebook_conversion (galaxy.config.GalaxyAppConfiguration attribute) try_a_func() (in module galaxy.tool_util.deps.mulled.get_tests) try_get_authz_config() (galaxy.authnz.managers.AuthnzManager static method) try_get_request_body_as_json() (in module galaxy.webapps.galaxy.api) ts_repo_cache (galaxy.tools.error_reports.plugins.base_git.BaseGitPlugin attribute) ts_urls (galaxy.tools.error_reports.plugins.base_git.BaseGitPlugin attribute) TSV (class in galaxy.datatypes.tabular) tuples_of_repository_dependencies_needed_for_compiling_td (galaxy.model.tool_shed_install.ToolShedRepository property) Turtle (class in galaxy.datatypes.triples) tus_hooks() (galaxy.webapps.galaxy.api.job_files.JobFilesAPIController method) tus_patch() (galaxy.webapps.galaxy.api.job_files.JobFilesAPIController method) tus_upload_store (galaxy.config.GalaxyAppConfiguration attribute) tutorial_mode_activate() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) TwoBit (class in galaxy.datatypes.binary) TwoBitFastaDataProvider (class in galaxy.datatypes.dataproviders.dataset) type (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter attribute) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter attribute) (galaxy.datatypes.display_applications.parameters.DisplayApplicationTemplateParameter attribute) (galaxy.files.sources.FilesSourceProperties attribute) (galaxy.forms.forms.FormDefinitionAddressFieldFactory attribute) (galaxy.forms.forms.FormDefinitionFieldFactory attribute) (galaxy.forms.forms.FormDefinitionHistoryFieldFactory attribute) (galaxy.forms.forms.FormDefinitionPasswordFieldFactory attribute) (galaxy.forms.forms.FormDefinitionSelectFieldFactory attribute) (galaxy.forms.forms.FormDefinitionTextFieldFactory attribute) (galaxy.forms.forms.FormDefinitionWorkflowFieldFactory attribute) (galaxy.forms.forms.FormDefinitionWorkflowMappingFieldFactory attribute) (galaxy.model.DefaultQuotaAssociation attribute) (galaxy.model.FormDefinition attribute) (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) (galaxy.model.Role attribute) (galaxy.model.Tag attribute) (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.Visualization attribute) (galaxy.model.WorkflowComment attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.model.WorkflowStep attribute) (galaxy.schema.fetch_data.HdaDestination attribute) (galaxy.schema.fetch_data.HdcaDestination attribute) (galaxy.schema.fetch_data.LibraryDestination attribute) (galaxy.schema.fetch_data.LibraryFolderDestination attribute) (galaxy.schema.remote_files.FilesSourcePlugin attribute) (galaxy.schema.schema.BasicRoleModel attribute) (galaxy.schema.schema.BulkOperationParams attribute) (galaxy.schema.schema.ChangeDatatypeOperationParams attribute) (galaxy.schema.schema.ChangeDbkeyOperationParams attribute) (galaxy.schema.schema.FileLibraryFolderItem attribute) (galaxy.schema.schema.FolderLibraryFolderItem attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) (galaxy.schema.schema.HDCASummary attribute) (galaxy.schema.schema.HistoryItemCommon attribute) (galaxy.schema.schema.InputDataCollectionStep attribute) (galaxy.schema.schema.InputDataStep attribute) (galaxy.schema.schema.InputParameterStep attribute) (galaxy.schema.schema.LibraryFolderItemBase attribute) (galaxy.schema.schema.Output attribute) (galaxy.schema.schema.PauseStep attribute) (galaxy.schema.schema.SubworkflowStep attribute) (galaxy.schema.schema.TagOperationParams attribute) (galaxy.schema.schema.ToolStep attribute) (galaxy.schema.schema.WorkflowStepToExportBase attribute) (galaxy.tools.parameters.grouping.Conditional attribute) (galaxy.tools.parameters.grouping.Dataset attribute) (galaxy.tools.parameters.grouping.Group attribute) (galaxy.tools.parameters.grouping.Repeat attribute) (galaxy.tools.parameters.grouping.Section attribute) (galaxy.tools.parameters.grouping.UploadDataset attribute) (galaxy.util.plugin_config.PluginConfigSource attribute) (galaxy.workflow.modules.InputDataCollectionModule attribute) (galaxy.workflow.modules.InputDataModule attribute) (galaxy.workflow.modules.InputModule attribute) (galaxy.workflow.modules.InputParameterModule attribute) (galaxy.workflow.modules.PauseModule attribute) (galaxy.workflow.modules.SubWorkflowModule attribute) (galaxy.workflow.modules.ToolModule attribute) (galaxy.workflow.modules.WorkflowModule attribute) (galaxy.workflow.refactor.schema.AddInputAction attribute) (galaxy.workflow.refactor.schema.AddStepAction attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.Role attribute) (tool_shed.webapp.model.Tag attribute) type_descriptions_for_field_types() (in module galaxy.tool_util.cwl.representation) type_id (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HistoryItemCommon attribute) type_key (galaxy.tools.data.RefgenieToolDataTable attribute) (galaxy.tools.data.TabularToolDataTable attribute) (galaxy.tools.data.ToolDataTable attribute) type_map (galaxy.webapps.galaxy.services.sharable.SharedItemNotificationFactory attribute) type_representation_from_name() (in module galaxy.tool_util.cwl.representation) type_to_object_store_class() (in module galaxy.objectstore) TypeRepresentation (class in galaxy.tool_util.cwl.representation) types (galaxy.tool_util.toolbox.views.definitions.ExcludeTypes attribute) (tool_shed.webapp.model.Role attribute) types_and_mapping() (galaxy.webapps.galaxy.api.datatypes.FastAPIDatatypes method) typing (galaxy.celery.GalaxyTask attribute)

U

UCI (class in galaxy.model) ucsc_links() (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.interval.CustomTrack method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.Wiggle method) UCSCLimitException, [1] UCSCOutWrapper (class in galaxy.tools.exception_handling) (class in galaxy.util.ucsc) UCSCTrackHub (class in galaxy.datatypes.tracks) uid (galaxy.model.UserAuthnzToken attribute) umask_fix_perms() (in module galaxy.util) UnamePlugin (class in galaxy.job_metrics.instrumenters.uname) uncompress() (in module tool_shed.util.commit_util) uncompressed_datatype_instance (galaxy.datatypes.binary.Bz2DynamicCompressedArchive attribute) (galaxy.datatypes.binary.DynamicCompressedArchive attribute) (galaxy.datatypes.binary.GzDynamicCompressedArchive attribute) uncompressed_path (galaxy.datatypes.sniff.HandleCompressedFileResponse attribute) undeletable() (galaxy.model.DatasetInstance method) undelete (galaxy.schema.schema.DeleteLibraryPayload attribute) (galaxy.schema.schema.HistoryContentItemOperation attribute) undelete() (galaxy.managers.deletable.DeletableManagerMixin method) (galaxy.managers.groups.GroupsManager method) (galaxy.managers.roles.RoleManager method) (galaxy.managers.users.UserManager method) (galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController method) (galaxy.webapps.galaxy.api.forms.FastAPIForms method) (galaxy.webapps.galaxy.api.groups.FastAPIGroups method) (galaxy.webapps.galaxy.api.pages.FastAPIPages method) (galaxy.webapps.galaxy.api.quotas.FastAPIQuota method) (galaxy.webapps.galaxy.api.roles.FastAPIRoles method) (galaxy.webapps.galaxy.api.users.FastAPIUsers method) (galaxy.webapps.galaxy.services.histories.HistoriesService method) (galaxy.webapps.galaxy.services.pages.PagesService method) (galaxy.webapps.galaxy.services.quotas.QuotasService method) undelete_category() (tool_shed.webapp.controllers.admin.AdminController method) undelete_group() (tool_shed.util.admin_util.Admin method) undelete_operation (tool_shed.util.admin_util.Admin attribute) (tool_shed.webapp.controllers.admin.AdminController attribute) undelete_quota() (galaxy.managers.quotas.QuotaManager method) undelete_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) (tool_shed.webapp.controllers.admin.AdminController method) undelete_role() (tool_shed.util.admin_util.Admin method) undelete_user() (tool_shed.util.admin_util.Admin method) UNDERSCORED_OPS (galaxy.managers.base.ModelFilterParser attribute) unhide (galaxy.schema.schema.HistoryContentItemOperation attribute) unhide_datasets() (galaxy.model.History method) unicodify() (in module galaxy.util) UNINITIALIZED_ELEMENT (galaxy.model.DatasetCollectionElement attribute) UninitializedTree (class in galaxy.model.dataset_collections.structure) uninstall() (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method) uninstall_dependencies() (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tools.ToolsController method) uninstall_environments() (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method) uninstall_repository() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) (tool_shed.test.base.twilltestcase.GalaxyInteractorToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.StandaloneToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ToolShedInstallationClient method) uninstallable_resolvers (galaxy.tool_util.deps.views.DependencyResolversView property) UNINSTALLED (galaxy.model.tool_shed_install.ToolDependency.states attribute) uninstalled (galaxy.model.tool_shed_install.ToolShedRepository attribute) UNINSTALLED (galaxy.model.tool_shed_install.ToolShedRepository.installation_status attribute) (galaxy.model.tool_shed_install.ToolShedRepository.states attribute) uninstalled (galaxy.schema.schema.InstalledToolShedRepository attribute) uninstalled_repository_dependencies (galaxy.model.tool_shed_install.ToolShedRepository property) uninstalled_tool_dependencies (galaxy.model.tool_shed_install.ToolShedRepository property) UniProtXML (class in galaxy.datatypes.proteomics) unique_constraint_exists() (in module galaxy.model.migrations.util) unique_id() (in module galaxy.util) unique_workflow_outputs (galaxy.model.WorkflowStep property) UniqueValueFilter (class in galaxy.tools.parameters.dynamic_options) UnivaJobRunner (class in galaxy.jobs.runners.univa) UniverseApplication (class in galaxy.app) (class in galaxy.webapps.reports.app) (class in tool_shed.webapp.app) UNKNOWN (galaxy.schema.schema.DatasetValidatedState attribute) UnknownContentsType unlink() (in module galaxy.util) UnlinkedToolShedPackageDependencyResolver (class in galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages) unload_certified_level_one_repository_and_suite_tuple() (tool_shed.repository_registry.Registry method) unload_repository_and_suite_tuple() (tool_shed.repository_registry.Registry method) unpack_archive() (in module galaxy.tools.imp_exp.unpack_tar_gz_archive) unpause_dependent_jobs() (galaxy.model.HistoryDatasetAssociation method) unpublish() (galaxy.managers.sharable.SharableModelManager method) (galaxy.webapps.galaxy.api.pages.FastAPIPages method) (galaxy.webapps.galaxy.api.visualizations.FastAPIVisualizations method) (galaxy.webapps.galaxy.services.sharable.ShareableService method) UNREGISTERED (galaxy.model.DefaultQuotaAssociation.types attribute) Unrestricted (class in tool_shed.repository_types.unrestricted) UNSAFE (galaxy.job_metrics.Safety attribute) (galaxy.job_metrics.safety.Safety attribute) unsafe_walk() (in module galaxy.util.path) unset_dataset_matcher_factory() (in module galaxy.tools.parameters.dataset_matcher) unset_item_extended_metadata_obj() (galaxy.webapps.base.controller.UsesExtendedMetadataMixin method) unset_quota_default() (galaxy.managers.quotas.QuotaManager method) unset_request_id() (galaxy.model.base.ModelMapping method) unshare_with() (galaxy.managers.sharable.SharableModelManager method) UnspecifiedBuildValidator (class in galaxy.tools.parameters.validation) unstructured_path_rewrite() (galaxy.job_execution.compute_environment.ComputeEnvironment method) (galaxy.job_execution.compute_environment.SharedComputeEnvironment method) unused_dependency_paths (galaxy.tool_util.deps.views.DependencyResolversView property) unused_dependency_paths() (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) unused_port() (in module galaxy.util.sockets) UnusedMetadataSourceProvider (class in galaxy.model.store.discover) UnusedPermissionProvider (class in galaxy.model.store.discover) unvalidated() (galaxy.datatypes.data.DatatypeValidation static method) unversioned_install() (in module galaxy.tool_util.deps.brew_exts) unwrap() (galaxy.datatypes.metadata.MetadataElementSpec method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.model.metadata.MetadataElementSpec method) (galaxy.model.metadata.MetadataParameter method) UnzipCollectionTool (class in galaxy.tools) up_to_date (galaxy.model.JobExportHistoryArchive property) (galaxy.schema.schema.ObjectExportResponseBase attribute) update() (galaxy.managers.base.ModelManager method) (galaxy.managers.collections.DatasetCollectionManager method) (galaxy.managers.folders.FolderManager method) (galaxy.managers.group_roles.GroupRolesManager method) (galaxy.managers.group_users.GroupUsersManager method) (galaxy.managers.groups.GroupsManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.managers.library_datasets.LibraryDatasetsManager method) (galaxy.managers.tags.TagsManager method) (galaxy.model.custom_types.MutationDict method) (galaxy.model.History method) (galaxy.model.UsesCreateAndUpdateTime method) (galaxy.tool_util.cwl.cwltool_deps.CommentedMap method) (galaxy.util.odict.odict method) (galaxy.util.Params method) (galaxy.webapps.galaxy.api.cloudauthz.CloudAuthzController method) (galaxy.webapps.galaxy.api.folders.FastAPILibraryFolders method) (galaxy.webapps.galaxy.api.group_roles.FastAPIGroupRoles method) (galaxy.webapps.galaxy.api.group_users.FastAPIGroupUsers method) (galaxy.webapps.galaxy.api.groups.FastAPIGroups method) (galaxy.webapps.galaxy.api.libraries.FastAPILibraries method) (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method) (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method) (galaxy.webapps.galaxy.api.quotas.FastAPIQuota method) (galaxy.webapps.galaxy.api.tags.FastAPITags method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) (galaxy.webapps.galaxy.api.users.FastAPIUsers method) (galaxy.webapps.galaxy.api.visualizations.VisualizationsController method) (galaxy.webapps.galaxy.services.histories.HistoriesService method) (galaxy.webapps.galaxy.services.libraries.LibrariesService method) (galaxy.webapps.galaxy.services.library_folders.LibraryFoldersService method) (galaxy.webapps.galaxy.services.quotas.QuotasService method) (tool_shed.managers.groups.GroupManager method) (tool_shed.webapp.api.repositories.RepositoriesController method) (tool_shed.webapp.api.repository_revisions.RepositoryRevisionsController method) update_attributes() (galaxy.managers.hdcas.HDCAManager method) update_circular_repository_dependencies() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) update_current_sharing_with_users() (galaxy.managers.sharable.SharableModelManager method) update_from_file() (galaxy.model.MetadataFile method) (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) update_hdca_update_time_for_job() (galaxy.model.Job method) update_history() (galaxy_test.base.populators.BaseDatasetPopulator method) update_in_shed_tool_config() (galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) update_installed_repository() (tool_shed.test.base.twilltestcase.GalaxyInteractorToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) (tool_shed.test.base.twilltestcase.StandaloneToolShedInstallationClient method) (tool_shed.test.base.twilltestcase.ToolShedInstallationClient method) update_invocation_step() (galaxy.managers.workflows.WorkflowsManager method) update_job_lock() (galaxy.managers.jobs.JobManager method) (in module galaxy.webapps.galaxy.api.job_lock) update_key_value() (galaxy.tool_util.cwl.cwltool_deps.CommentedMap method) update_object_store_id() (galaxy.managers.datasets.DatasetManager method) (galaxy_test.base.populators.BaseDatasetPopulator method) update_object_store_with_datasets() (galaxy.model.store.discover.ModelPersistenceContext method) update_or_append() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) update_output_states() (galaxy.model.Job method) update_parent_folder_update_times() (galaxy.model.LibraryDatasetDatasetAssociation method) update_permissions() (galaxy.managers.datasets.DatasetAssociationManager method) (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method) update_permissions_raw() (galaxy_test.base.populators.BaseDatasetPopulator method) update_proxy() (galaxy.web.proxy.ProxyManager method) update_repository() (galaxy.tool_util.verify.test_data.GitDataResolver method) (in module galaxy.tool_shed.util.hg_util) (in module tool_shed.util.hg_util) (in module tool_shed.util.repository_util) update_repository_record() (galaxy.tool_shed.galaxy_install.update_repository_manager.UpdateRepositoryManager method) update_requests() (galaxy.web.proxy.JsonFileProxyIpc method) (galaxy.web.proxy.SqliteProxyIpc method) update_shed_config() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) update_stored_workflow_attributes (galaxy.managers.workflows.WorkflowUpdateOptions attribute) update_time (galaxy.model.DataManagerHistoryAssociation attribute) (galaxy.model.DataManagerJobAssociation attribute) (galaxy.model.Dataset attribute) (galaxy.model.DatasetCollection attribute) (galaxy.model.DatasetCollectionInstance attribute) (galaxy.model.DatasetPermissions attribute) (galaxy.model.DefaultQuotaAssociation attribute) (galaxy.model.DynamicTool attribute) (galaxy.model.Event attribute) (galaxy.model.FormDefinition attribute) (galaxy.model.FormDefinitionCurrent attribute) (galaxy.model.FormValues attribute) (galaxy.model.GalaxySession attribute) (galaxy.model.Group attribute) (galaxy.model.GroupQuotaAssociation attribute) (galaxy.model.GroupRoleAssociation attribute) (galaxy.model.History attribute) (galaxy.model.HistoryAudit attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization attribute) (galaxy.model.HistoryDatasetAssociationHistory attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) (galaxy.model.Job attribute) (galaxy.model.Library attribute) (galaxy.model.LibraryDataset attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationPermissions attribute) (galaxy.model.LibraryDatasetPermissions attribute) (galaxy.model.LibraryFolder attribute) (galaxy.model.LibraryFolderPermissions attribute) (galaxy.model.LibraryPermissions attribute) (galaxy.model.MetadataFile attribute) (galaxy.model.Notification attribute) (galaxy.model.Page attribute) (galaxy.model.PageRevision attribute) (galaxy.model.Quota attribute) (galaxy.model.Role attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.Task attribute) (galaxy.model.tool_shed_install.RepositoryDependency attribute) (galaxy.model.tool_shed_install.RepositoryRepositoryDependencyAssociation attribute) (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.model.tool_shed_install.ToolVersion attribute) (galaxy.model.User attribute) (galaxy.model.UserAddress attribute) (galaxy.model.UserGroupAssociation attribute) (galaxy.model.UserNotificationAssociation attribute) (galaxy.model.UserQuotaAssociation attribute) (galaxy.model.UserRoleAssociation attribute) (galaxy.model.UsesCreateAndUpdateTime attribute) (galaxy.model.Vault attribute) (galaxy.model.Visualization attribute) (galaxy.model.VisualizationRevision attribute) (galaxy.model.WorkerProcess attribute) (galaxy.model.Workflow attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowStep attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.ArchivedHistorySummary attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.DatasetSummary attribute) (galaxy.schema.schema.DCSummary attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HistoryItemCommon attribute) (galaxy.schema.schema.HistorySummary attribute) (galaxy.schema.schema.InvocationSortByEnum attribute) (galaxy.schema.schema.JobBaseModel attribute) (galaxy.schema.schema.JobIndexSortByEnum attribute) (galaxy.schema.schema.LibraryFolderDetails attribute) (galaxy.schema.schema.LibraryFolderItemBase attribute) (galaxy.schema.schema.PageSummary attribute) (galaxy.schema.schema.StoredWorkflowSummary attribute) (tool_shed.webapp.model.Category attribute) (tool_shed.webapp.model.GalaxySession attribute) (tool_shed.webapp.model.Group attribute) (tool_shed.webapp.model.GroupRoleAssociation attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) (tool_shed.webapp.model.RepositoryRatingAssociation attribute) (tool_shed.webapp.model.RepositoryRoleAssociation attribute) (tool_shed.webapp.model.Role attribute) (tool_shed.webapp.model.User attribute) (tool_shed.webapp.model.UserGroupAssociation attribute) (tool_shed.webapp.model.UserRoleAssociation attribute) update_tool_panel_dict() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) update_tool_shed_repository() (galaxy.tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) update_tool_shed_repository_status() (galaxy.tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) update_tour() (galaxy.webapps.galaxy.api.tours.FastAPITours method) update_user() (galaxy_test.base.populators.BaseDatasetPopulator method) update_user_raw() (galaxy_test.base.populators.BaseDatasetPopulator method) update_watch_data_table_paths() (galaxy.config_watchers.ConfigWatchers method) update_watcher_designation() (galaxy.model.database_heartbeat.DatabaseHeartbeat method) update_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method) update_workflow_from_raw_description() (galaxy.managers.workflows.WorkflowContentsManager method) UpdateAnnotationAction (class in galaxy.workflow.refactor.schema) UpdateContentItem (class in galaxy.schema.schema) UpdateCreatorAction (class in galaxy.workflow.refactor.schema) updated_changeset_revisions() (tool_shed.webapp.controllers.repository.RepositoryController method) UpdateDatasetPermissionsPayload (class in galaxy.schema.schema) UpdateHistoryContentsBatchPayload (class in galaxy.schema.schema) UpdateHistoryContentsPayload (class in galaxy.schema.schema) UpdateLibraryFolderPayload (class in galaxy.schema.schema) UpdateLibraryPayload (class in galaxy.schema.schema) UpdateLicenseAction (class in galaxy.workflow.refactor.schema) UpdateNameAction (class in galaxy.workflow.refactor.schema) UpdateOutputLabelAction (class in galaxy.workflow.refactor.schema) UpdateReportAction (class in galaxy.workflow.refactor.schema) UpdateRepositoryManager (class in galaxy.tool_shed.galaxy_install.update_repository_manager) updates() (tool_shed.webapp.api.repositories.RepositoriesController method) UpdatesRequest (class in tool_shed.managers.repositories) UpdateStepLabelAction (class in galaxy.workflow.refactor.schema) UpdateStepPositionAction (class in galaxy.workflow.refactor.schema) UpdateToChangeset (class in galaxy.tool_shed.galaxy_install.update_repository_manager) upgrade() (galaxy.model.migrations.AlembicManager method) upgrade_available (galaxy.model.tool_shed_install.ToolShedRepository property) upgrade_messages (galaxy.model.WorkflowStep attribute) UpgradeAllStepsAction (class in galaxy.workflow.refactor.schema) UpgradeSubworkflowAction (class in galaxy.workflow.refactor.schema) UpgradeToolAction (class in galaxy.workflow.refactor.schema) upload (galaxy.model.JobStateSummary attribute) UPLOAD (galaxy.schema.schema.DatasetState attribute) upload (galaxy.schema.schema.HDCJobStateSummary attribute) UPLOAD (galaxy.schema.schema.JobState attribute) upload_build() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_collection() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method) upload_list() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_options (galaxy.model.LibraryDataset attribute) upload_pair() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_paired_list() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_paste_data() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_payload() (galaxy_test.base.populators.BaseDatasetPopulator method) upload_queue_local_file() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_rule_build() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_rule_dataset_dialog() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_rule_set_data_type() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_rule_set_dataset() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_rule_start() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_set_collection_type() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_set_footer_extension() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_set_footer_genome() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_start() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_start_click() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_tab_click() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_tar() (in module tool_shed.util.repository_content_util) upload_tar_and_set_metadata() (in module tool_shed.managers.repositories) upload_warning (galaxy.managers.datatypes.DatatypeDetails attribute) upload_warning() (in module galaxy.datatypes.registry) upload_yaml_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method) UploadConfig (class in galaxy.tools.data_fetch) UploadDataset (class in galaxy.tools.parameters.grouping) UploadProblemException UploadsAPIController (class in galaxy.webapps.galaxy.api.uploads) UploadTarget (class in galaxy.tool_util.cwl.util) UploadToolAction (class in galaxy.tools.actions.upload) uri (galaxy.files.sources.Entry attribute) (galaxy.files.sources.RemoteDirectory attribute) (galaxy.files.sources.RemoteEntry attribute) (galaxy.files.sources.RemoteFile attribute) (galaxy.schema.remote_files.CreatedEntryResponse attribute) (galaxy.schema.remote_files.RemoteEntry attribute) (galaxy.schema.remote_files.RemoteFilesFormat attribute) (galaxy.schema.schema.ImportToolDataBundleUriSource attribute) (galaxy.tool_util.cwl.schema.RawProcessReference attribute) (galaxy.tool_util.cwl.schema.ResolvedProcessDefinition attribute) uri_from_path() (galaxy.files.sources.BaseFilesSource method) uri_join() (in module galaxy.files.sources) uri_root (galaxy.files.sources.FilesSourceProperties attribute) (galaxy.schema.remote_files.BrowsableFilesSourcePlugin attribute) url (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute) URL (galaxy.datatypes.binary.H5MLM attribute) url (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper property) (galaxy.managers.licenses.LicenseMetadataModel attribute) (galaxy.model.migrations.DatabaseConfig attribute) (galaxy.schema.fetch_data.ItemsFromModel attribute) (galaxy.schema.fetch_data.ItemsFromSrc attribute) (galaxy.schema.fetch_data.Src attribute) (galaxy.schema.fetch_data.UrlDataElement attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.ArchivedHistorySummary attribute) (galaxy.schema.schema.Creator attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.GroupRoleResponse attribute) (galaxy.schema.schema.GroupUserResponse attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HistoryImportArchiveSourceType attribute) (galaxy.schema.schema.HistoryItemCommon attribute) (galaxy.schema.schema.HistorySummary attribute) (galaxy.schema.schema.RoleModelResponse attribute) (galaxy.schema.schema.StoredWorkflowSummary attribute) (galaxy.selenium.context.GalaxySeleniumContext attribute) (galaxy.selenium.context.GalaxySeleniumContextImpl attribute) (galaxy.selenium.jupyter_context.JupyterContextImpl attribute) (galaxy_test.api.test_pages.TestPagesApi attribute) (galaxy_test.api.test_workflows.TestAdminWorkflowsApi attribute) (galaxy_test.api.test_workflows_cwl.BaseCwlWorkflowsApiTestCase attribute) (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi attribute) (galaxy_test.base.api.UsesApiTestCaseMixin attribute) (galaxy_test.base.testcase.FunctionalTestCase attribute) (galaxy_test.driver.integration_util.IntegrationTestCase attribute) (galaxy_test.driver.testcase.DrivenFunctionalTestCase attribute) (galaxy_test.selenium.jupyter_context.JupyterTestContextImpl attribute) (galaxy_test.selenium.test_admin_app.TestAdminApp attribute) (galaxy_test.selenium.test_anon_history.TestAnonymousHistories attribute) (galaxy_test.selenium.test_change_password.TestChangePassword attribute) (galaxy_test.selenium.test_collection_builders.TestCollectionBuilders attribute) (galaxy_test.selenium.test_collection_edit.TestCollectionEdit attribute) (galaxy_test.selenium.test_data_source_tools.TestDataSource attribute) (galaxy_test.selenium.test_dataset_metadata_download.TestHistoryDatasetState attribute) (galaxy_test.selenium.test_histories_list.TestSavedHistories attribute) (galaxy_test.selenium.test_history_copy_elements.TestHistoryCopyElements attribute) (galaxy_test.selenium.test_history_dataset_state.TestHistoryDatasetState attribute) (galaxy_test.selenium.test_history_multi_view.TestHistoryMultiView attribute) (galaxy_test.selenium.test_history_options.TestHistoryOptions attribute) (galaxy_test.selenium.test_history_panel.TestHistoryPanel attribute) (galaxy_test.selenium.test_history_panel_collections.TestHistoryPanelCollections attribute) (galaxy_test.selenium.test_history_sharing.TestHistoryRequiresLoginSelenium attribute) (galaxy_test.selenium.test_history_sharing.TestHistorySharing attribute) (galaxy_test.selenium.test_invocation_grid.TestInvocationGridSelenium attribute) (galaxy_test.selenium.test_library_contents.TestLibraryContents attribute) (galaxy_test.selenium.test_library_landing.TestLibraryLanding attribute) (galaxy_test.selenium.test_library_to_collections.TestLibraryToCollections attribute) (galaxy_test.selenium.test_login.TestLogin attribute) (galaxy_test.selenium.test_navigates_galaxy.TestNavigatesGalaxySelenium attribute) (galaxy_test.selenium.test_pages.TestPages attribute) (galaxy_test.selenium.test_personal_information.TestDeleteCurrentAccount attribute) (galaxy_test.selenium.test_personal_information.TestManageInformation attribute) (galaxy_test.selenium.test_registration.TestRegistration attribute) (galaxy_test.selenium.test_sign_out.TestSignOut attribute) (galaxy_test.selenium.test_sizzle_loading.TestSizzleLoading attribute) (galaxy_test.selenium.test_stock_tours.TestStockToursTestCase attribute) (galaxy_test.selenium.test_tool_describing_tours.TestToolDescribingTours attribute) (galaxy_test.selenium.test_tool_form.TestLoggedInToolForm attribute) (galaxy_test.selenium.test_tool_form.TestToolForm attribute) (galaxy_test.selenium.test_uploads.TestUploads attribute) (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor attribute) (galaxy_test.selenium.test_workflow_invocation_details.TestWorkflowInvocationDetails attribute) (galaxy_test.selenium.test_workflow_management.TestWorkflowManagement attribute) (galaxy_test.selenium.test_workflow_run.TestWorkflowRun attribute) (galaxy_test.selenium.test_workflow_sharing.TestWorkflowSharing attribute) (galaxy_test.selenium.test_workflow_sharing.TestWorkflowSharingRedirect attribute) (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures attribute) (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository attribute) (tool_shed.test.functional.test_0020_basic_repository_dependencies.TestBasicRepositoryDependencies attribute) (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions attribute) (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies attribute) (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels attribute) (tool_shed.test.functional.test_0070_invalid_tool.TestBismarkRepository attribute) (tool_shed.test.functional.test_0080_advanced_circular_dependencies.TestRepositoryCircularDependencies attribute) (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain attribute) (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies attribute) (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies attribute) (tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners.TestRepositoryMultipleOwners attribute) (tool_shed.test.functional.test_0140_tool_help_images.TestToolHelpImages attribute) (tool_shed.test.functional.test_0150_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_0160_circular_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_0170_complex_prior_installation_required.TestComplexPriorInstallation attribute) (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata attribute) (tool_shed.test.functional.test_0310_hg_api_features.TestHgWebFeatures attribute) (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs attribute) (tool_shed.test.functional.test_0430_browse_utilities.TestToolShedBrowseUtilities attribute) (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies attribute) (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision attribute) (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance attribute) (tool_shed.test.functional.test_0480_tool_dependency_xml_verification.TestDependencyDefinitionValidation attribute) (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole attribute) (tool_shed.test.functional.test_0550_metadata_updated_dependencies.TestGetUpdatedMetadata attribute) (tool_shed.test.functional.test_1000_install_basic_repository.TestBasicToolShedFeatures attribute) (tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies.TestToolWithToolDependencies attribute) (tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies.TestToolWithRepositoryDependencies attribute) (tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions.TestRepositoryWithDependencyRevisions attribute) (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies attribute) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies attribute) (tool_shed.test.functional.test_1070_invalid_tool.TestFreebayesRepository attribute) (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies attribute) (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies attribute) (tool_shed.test.functional.test_1100_install_updated_repository_dependencies.TestRepositoryDependencies attribute) (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies attribute) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies attribute) (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners attribute) (tool_shed.test.functional.test_1160_tool_help_images.TestToolHelpImages attribute) (tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation attribute) (tool_shed.test.functional.test_1190_complex_prior_installation_required.TestComplexPriorInstallation attribute) (tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository.TestUninstallingAndReinstallingRepositories attribute) (tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies.TestUninstallingAndReinstallingRepositories attribute) (tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions.TestUninstallingAndReinstallingRepositories attribute) (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata attribute) (tool_shed.test.functional.test_1410_update_manager.TestUpdateManager attribute) (tool_shed.test.functional.test_1430_repair_installed_repository.TestRepairRepository attribute) (tool_shed.test.functional.test_1460_data_managers.TestDataManagers attribute) (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository attribute)

url_builder (galaxy.managers.context.ProvidesAppContext property) (galaxy.managers.model_stores.ModelStoreUserContext property) (galaxy.webapps.base.webapp.GalaxyWebTransaction property) (galaxy.work.context.WorkRequestContext property) url_builder() (in module galaxy.webapps.base.webapp) url_for() (galaxy.managers.base.ModelSerializer static method) (in module galaxy.web) (in module galaxy.web.framework) (in module galaxy.webapps.base.controller) (in module galaxy.webapps.reports) (in module tool_shed.webapp) url_for_not_available() (in module galaxy.managers.base) url_get() (in module galaxy.util) url_path (galaxy.webapps.galaxy.api.GalaxyASGIRequest property) url_to_destination() (galaxy.jobs.handler.DefaultJobDispatcher method) (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) (galaxy.jobs.runners.pbs.PBSJobRunner method) UrlBuilder (class in galaxy.webapps.galaxy.api) UrlDataElement (class in galaxy.schema.fetch_data) URLDataProvider (class in galaxy.datatypes.dataproviders.external) usage() (galaxy.webapps.galaxy.api.users.FastAPIUsers method) usage_for() (galaxy.webapps.galaxy.api.users.FastAPIUsers method) use (galaxy.objectstore.QuotaSourceInfo attribute) use() (galaxy.model.PSANonce class method) use_api (galaxy.tool_util.biotools.BiotoolsMetadataSourceConfig attribute) (galaxy.tool_util.biotools.source.BiotoolsMetadataSourceConfig attribute) use_async (galaxy.web.legacy_framework.grids.Grid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) use_bootstrap_dropdown() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) use_fetch_api (galaxy.tool_util.client.staging.InteractorStaging property) (galaxy.tool_util.client.staging.StagingInterface property) use_final (tool_shed.webapp.search.repo_search.RepoWeighting attribute) use_hide_message (galaxy.web.legacy_framework.grids.Grid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) use_mq (galaxy.jobs.runners.pulsar.PulsarMQJobRunner attribute) use_paging (galaxy.web.legacy_framework.grids.Grid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) use_pbkdf2 (galaxy.model.User attribute) use_remote_user (galaxy.config.GalaxyAppConfiguration attribute) User (class in galaxy.model) (class in galaxy.webapps.galaxy.controllers.user) (class in tool_shed.webapp.controllers.user) (class in tool_shed.webapp.model) user (galaxy.app_unittest_utils.galaxy_mock.MockTrans property) (galaxy.authnz.psa_authnz.Storage attribute) (galaxy.job_execution.output_collect.JobContext property) (galaxy.managers.context.ProvidesUserContext property) (galaxy.managers.model_stores.ModelStoreUserContext property) (galaxy.model.APIKeys attribute) User (galaxy.model.base.SharedModelMapping attribute) user (galaxy.model.CloudAuthz attribute) (galaxy.model.CustosAuthnzToken attribute) (galaxy.model.DataManagerHistoryAssociation attribute) (galaxy.model.DefaultUserPermissions attribute) (galaxy.model.Event attribute) (galaxy.model.GalaxySession attribute) (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.History attribute) (galaxy.model.HistoryAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociation property) (galaxy.model.HistoryDatasetAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization attribute) (galaxy.model.HistoryDatasetAssociationRatingAssociation attribute) (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetCollectionRatingAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryRatingAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.HistoryUserShareAssociation attribute) (galaxy.model.Job attribute) (galaxy.model.LibraryDatasetCollectionAnnotationAssociation attribute) (galaxy.model.LibraryDatasetCollectionRatingAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) User (galaxy.model.mapping.GalaxyModelMapping attribute) user (galaxy.model.Page attribute) (galaxy.model.PageAnnotationAssociation attribute) (galaxy.model.PageRatingAssociation attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.PageUserShareAssociation attribute) (galaxy.model.PasswordResetToken attribute) USER (galaxy.model.Role.types attribute) user (galaxy.model.store.discover.ModelPersistenceContext property) (galaxy.model.store.discover.SessionlessModelPersistenceContext property) (galaxy.model.StoredWorkflow attribute) (galaxy.model.StoredWorkflowAnnotationAssociation attribute) (galaxy.model.StoredWorkflowMenuEntry attribute) (galaxy.model.StoredWorkflowRatingAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.StoredWorkflowUserShareAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.UserAction attribute) (galaxy.model.UserAddress attribute) (galaxy.model.UserAuthnzToken attribute) (galaxy.model.UserGroupAssociation attribute) (galaxy.model.UserNotificationAssociation attribute) (galaxy.model.UserQuotaAssociation attribute) (galaxy.model.UserQuotaSourceUsage attribute) (galaxy.model.UserRoleAssociation attribute) (galaxy.model.UserShareAssociation attribute) (galaxy.model.Visualization attribute) (galaxy.model.VisualizationAnnotationAssociation attribute) (galaxy.model.VisualizationRatingAssociation attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.VisualizationUserShareAssociation attribute) (galaxy.model.WorkflowStepAnnotationAssociation attribute) (galaxy.model.WorkflowStepTagAssociation attribute) (galaxy.schema.tasks.ComputeDatasetHashTaskRequest attribute) (galaxy.schema.tasks.GenerateHistoryContentDownload attribute) (galaxy.schema.tasks.GenerateHistoryDownload attribute) (galaxy.schema.tasks.GenerateInvocationDownload attribute) (galaxy.schema.tasks.ImportModelStoreTaskRequest attribute) (galaxy.schema.tasks.MaterializeDatasetInstanceTaskRequest attribute) (galaxy.schema.tasks.WriteHistoryContentTo attribute) (galaxy.schema.tasks.WriteHistoryTo attribute) (galaxy.schema.tasks.WriteInvocationTo attribute) (galaxy.webapps.base.webapp.GalaxyWebTransaction property) (galaxy.work.context.WorkRequestContext property) (tool_shed.webapp.model.APIKeys attribute) (tool_shed.webapp.model.GalaxySession attribute) (tool_shed.webapp.model.PasswordResetToken attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.RepositoryRatingAssociation attribute) (tool_shed.webapp.model.UserGroupAssociation attribute) (tool_shed.webapp.model.UserRoleAssociation attribute) user_api_interactor() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) user_assoc (galaxy.managers.roles.RoleManager attribute) user_can_administer_repository() (tool_shed.webapp.security.CommunityRBACAgent method) user_can_do_run_as (galaxy.managers.context.ProvidesUserContext property) user_can_do_run_as() (galaxy.managers.users.UserManager method) user_can_import_repository_archive() (tool_shed.webapp.security.CommunityRBACAgent method) user_can_purge (galaxy.model.Dataset property) user_checks() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) user_context_required (galaxy.files.sources.BaseFilesSource property) user_details (galaxy.schema.schema.JobIndexQueryPayload attribute) user_disk_usage() (galaxy.webapps.reports.controllers.users.Users method) user_email (galaxy.schema.schema.JobSummary attribute) (galaxy_test.selenium.test_custom_builds.TestCustomBuilds attribute) user_email() (galaxy_test.base.populators.BaseDatasetPopulator method) (galaxy_test.base.populators.LibraryPopulator method) user_exists() (galaxy.model.UserAuthnzToken class method) user_ftp_dir (galaxy.managers.context.ProvidesUserContext property) user_get_default_permissions() (galaxy.model.security.GalaxyRBACAgent method) user_has_access() (galaxy.files.sources.BaseFilesSource method) (galaxy.files.sources.SingleFileSource method) user_id (galaxy.model.APIKeys attribute) (galaxy.model.CeleryUserRateLimit attribute) (galaxy.model.CloudAuthz attribute) (galaxy.model.CustosAuthnzToken attribute) (galaxy.model.DataManagerHistoryAssociation attribute) (galaxy.model.DefaultUserPermissions attribute) (galaxy.model.Event attribute) (galaxy.model.GalaxySession attribute) (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.History attribute) (galaxy.model.HistoryAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization attribute) (galaxy.model.HistoryDatasetAssociationRatingAssociation attribute) (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetCollectionRatingAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryRatingAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.HistoryUserShareAssociation attribute) (galaxy.model.Job attribute) (galaxy.model.LibraryDatasetCollectionAnnotationAssociation attribute) (galaxy.model.LibraryDatasetCollectionRatingAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.Page attribute) (galaxy.model.PageAnnotationAssociation attribute) (galaxy.model.PageRatingAssociation attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.PageUserShareAssociation attribute) (galaxy.model.PasswordResetToken attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.StoredWorkflowAnnotationAssociation attribute) (galaxy.model.StoredWorkflowMenuEntry attribute) (galaxy.model.StoredWorkflowRatingAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.StoredWorkflowUserShareAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.UserAction attribute) (galaxy.model.UserAddress attribute) (galaxy.model.UserAuthnzToken attribute) (galaxy.model.UserGroupAssociation attribute) (galaxy.model.UserNotificationAssociation attribute) (galaxy.model.UserPreference attribute) (galaxy.model.UserQuotaAssociation attribute) (galaxy.model.UserQuotaSourceUsage attribute) (galaxy.model.UserRoleAssociation attribute) (galaxy.model.Visualization attribute) (galaxy.model.VisualizationAnnotationAssociation attribute) (galaxy.model.VisualizationRatingAssociation attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.VisualizationUserShareAssociation attribute) (galaxy.model.WorkflowStepAnnotationAssociation attribute) (galaxy.model.WorkflowStepTagAssociation attribute) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.ExportObjectRequestMetadata attribute) (galaxy.schema.schema.HistoryDetailed attribute) (galaxy.schema.schema.InvocationIndexQueryPayload attribute) (galaxy.schema.schema.JobIndexQueryPayload attribute) (galaxy.schema.schema.PageIndexQueryPayload attribute) (galaxy.schema.tasks.RequestUser attribute) (tool_shed.webapp.model.APIKeys attribute) (tool_shed.webapp.model.GalaxySession attribute) (tool_shed.webapp.model.PasswordResetToken attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.RepositoryRatingAssociation attribute) (tool_shed.webapp.model.UserGroupAssociation attribute) (tool_shed.webapp.model.UserRoleAssociation attribute) user_id() (galaxy_test.base.populators.BaseDatasetPopulator method) user_ids (galaxy.schema.schema.RoleDefinitionModel attribute) (galaxy.schema.schema.ShareWithPayload attribute) USER_INFO (galaxy.model.FormDefinition.types attribute) user_is_active (galaxy.managers.context.ProvidesUserContext property) user_is_admin (galaxy.managers.context.ProvidesUserContext property) user_is_bootstrap_admin (galaxy.managers.context.ProvidesUserContext property) user_library_import_dir_auto_creation (galaxy.config.GalaxyAppConfiguration attribute) user_library_import_symlink_allowlist (galaxy.config.GalaxyAppConfiguration attribute) user_list_grid (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) (tool_shed.util.admin_util.Admin attribute) (tool_shed.webapp.controllers.admin.AdminController attribute) user_manager (galaxy.structured_app.MinimalManagerApp attribute) (galaxy.webapps.galaxy.api.users.UserAPIController attribute) (galaxy.webapps.galaxy.controllers.user.User attribute) user_model() (galaxy.model.UserAuthnzToken class method) user_notification_associations (galaxy.model.Notification attribute) user_per_month() (galaxy.webapps.reports.controllers.jobs.Jobs method) (galaxy.webapps.reports.controllers.workflows.Workflows method) user_populator() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) user_private_role_id() (galaxy_test.base.populators.BaseDatasetPopulator method) (galaxy_test.base.populators.LibraryPopulator method) user_role_ids (galaxy.managers.folders.SecurityParams attribute) user_serializer (galaxy.webapps.galaxy.api.users.FastAPIUsers attribute) user_set_default_permissions() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) user_share_model (galaxy.managers.cloud.CloudManager attribute) (galaxy.managers.cloudauthzs.CloudAuthzManager attribute) (galaxy.managers.histories.HistoryManager attribute) (galaxy.managers.pages.PageManager attribute) (galaxy.managers.sharable.SharableModelManager attribute) (galaxy.managers.visualizations.VisualizationManager attribute) (galaxy.managers.workflows.WorkflowsManager attribute) user_template_environment() (galaxy.model.User static method) user_tname (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.ItemTagAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.WorkflowStepTagAssociation attribute) user_to_detailed_model() (galaxy.webapps.galaxy.services.users.UsersService method) user_tool_filters (galaxy.config.GalaxyAppConfiguration attribute) user_tool_label_filters (galaxy.config.GalaxyAppConfiguration attribute) user_tool_section_filters (galaxy.config.GalaxyAppConfiguration attribute) user_value (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.ItemTagAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.WorkflowStepTagAssociation attribute) user_vault (galaxy.files.DictFileSourcesUserContext property) (galaxy.files.ProvidesUserFileSourcesUserContext property) (galaxy.managers.context.ProvidesUserContext property) UserAction (class in galaxy.model) UserActivationRequiredException UserAddress (class in galaxy.model) UserAPIController (class in galaxy.webapps.galaxy.api.users) UserAuthnzToken (class in galaxy.model) UserBeaconSetting (class in galaxy.schema.schema) UserCannotRunAsException UserCreationPayload (class in galaxy.schema.schema) UserDeletionPayload (class in galaxy.schema.schema) UserDeserializer (class in galaxy.managers.users) userdir (galaxy.schema.remote_files.RemoteFilesTarget attribute) UserEmail (class in galaxy.schema.schema) UserFolderPermissions (class in galaxy.webapps.galaxy.services.library_folder_contents) UserFtpFilesSource (class in galaxy.files.sources.galaxy) UserGrid (class in tool_shed.grids.admin_grids) UserGrid.EmailColumn (class in tool_shed.grids.admin_grids) UserGrid.ExternalColumn (class in tool_shed.grids.admin_grids) UserGrid.GroupsColumn (class in tool_shed.grids.admin_grids) UserGrid.LastLoginColumn (class in tool_shed.grids.admin_grids) UserGrid.RolesColumn (class in tool_shed.grids.admin_grids) UserGrid.StatusColumn (class in tool_shed.grids.admin_grids) UserGrid.UserLoginColumn (class in tool_shed.grids.admin_grids) UserGrid.UserNameColumn (class in tool_shed.grids.admin_grids) UserGroupAssociation (class in galaxy.model) (class in tool_shed.webapp.model) userinfo_endpoint (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute) UserInvalidRunAsException userless_histories() (galaxy.webapps.reports.controllers.system.System method) UserLibraryImportFilesSource (class in galaxy.files.sources.galaxy) UserListGrid (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.DiskUsageColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.GroupsColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.LastLoginColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.RolesColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.StatusColumn (class in galaxy.webapps.galaxy.controllers.admin) UserManager (class in galaxy.managers.users) UserModel (class in galaxy.schema.schema) username (galaxy.files.DictFileSourcesUserContext property) (galaxy.files.ProvidesUserFileSourcesUserContext property) (galaxy.model.History property) (galaxy.model.Page property) (galaxy.model.User attribute) (galaxy.model.Visualization property) (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.BaseUserModel attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.HistoryDetailed attribute) (galaxy.schema.schema.LimitedUserModel attribute) (galaxy.schema.schema.PageSummary attribute) (galaxy.schema.schema.SharingStatus attribute) (galaxy.schema.schema.UserCreationPayload attribute) (tool_shed.webapp.model.User attribute) username_and_slug (galaxy.schema.schema.ArchivedHistoryDetailed attribute) (galaxy.schema.schema.CustomHistoryView attribute) (galaxy.schema.schema.HistoryDetailed attribute) (galaxy.schema.schema.SharingStatus attribute) username_contains() (galaxy.managers.histories.HistoryFilters method) username_eq() (galaxy.managers.histories.HistoryFilters method) username_max_length() (galaxy.model.UserAuthnzToken class method) usernames_that_can_push() (tool_shed.webapp.security.CommunityRBACAgent method) UserNotificationAssociation (class in galaxy.model) UserPreference (class in galaxy.model) UserQuotaAssociation (class in galaxy.model) UserQuotaBasicUsage (class in galaxy.model) UserQuotaSourceUsage (class in galaxy.model) UserQuotaUsage (class in galaxy.model) UserRoleAssociation (class in galaxy.model) (class in tool_shed.webapp.model) Users (class in galaxy.webapps.reports.controllers.users) users (galaxy.model.Group attribute) (galaxy.model.Quota attribute) (galaxy.model.Role attribute) (tool_shed.webapp.model.Group attribute) (tool_shed.webapp.model.Role attribute) users() (tool_shed.util.admin_util.Admin method) users_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) users_shared_with (galaxy.model.History attribute) (galaxy.model.Page attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.Visualization attribute) (galaxy.schema.schema.SharingStatus attribute) users_shared_with_count (galaxy.model.History attribute) users_shared_with_dot_users (galaxy.model.History attribute) (galaxy.model.Page attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.Visualization attribute) UsersController (class in tool_shed.webapp.api.users) UserSerializer (class in galaxy.managers.users) UserShareAssociation (class in galaxy.model) UsersService (class in galaxy.webapps.galaxy.services.users) UserVaultWrapper (class in galaxy.security.vault) uses_param (galaxy.tool_util.cwl.representation.TypeRepresentation property) uses_tool_shed_dependencies() (galaxy.tool_util.deps.DependencyManager method) (galaxy.tool_util.deps.NullDependencyManager method) UsesAnnotations (class in galaxy.model.item_attrs) UsesApiTestCaseMixin (class in galaxy_test.base.api) UsesApp (class in galaxy.app_unittest_utils.tools_support) UsesCeleryTasks (class in galaxy_test.base.api) UsesCreateAndUpdateTime (class in galaxy.model) UsesExtendedMetadataMixin (class in galaxy.webapps.base.controller) UsesFormDefinitionsMixin (class in galaxy.webapps.base.controller) UsesHomebrewMixin (class in galaxy.tool_util.deps.resolvers.resolver_mixins) UsesInstalledRepositoriesMixin (class in galaxy.tool_util.deps.resolvers.resolver_mixins) UsesItemRatings (class in galaxy.model.item_attrs) UsesTagsMixin (class in galaxy.webapps.base.controller) UsesToolDependencyDirMixin (class in galaxy.tool_util.deps.resolvers.resolver_mixins) uuid (galaxy.model.Dataset attribute) (galaxy.model.DynamicTool attribute) (galaxy.model.MetadataFile attribute) (galaxy.model.store.DatasetAttributeImportModel attribute) (galaxy.model.Workflow attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowOutput attribute) (galaxy.model.WorkflowStep attribute) (galaxy.schema.schema.DatasetJobInfo attribute) (galaxy.schema.schema.DatasetSummary attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) (galaxy.schema.schema.WorkflowInput attribute) (galaxy.schema.schema.WorkflowOutput attribute) (galaxy.schema.schema.WorkflowStepToExportBase attribute) (galaxy.schema.schema.WorkflowToExport attribute) (galaxy.tools.parameters.grouping.Dataset attribute) UUIDType (class in galaxy.model.custom_types) UX_POPUP (galaxy.selenium.navigates_galaxy.WAIT_TYPES attribute) UX_RENDER (galaxy.selenium.navigates_galaxy.WAIT_TYPES attribute) UX_TRANSITION (galaxy.selenium.navigates_galaxy.WAIT_TYPES attribute)

V

v1_image_name() (in module galaxy.tool_util.deps.mulled.util) v2_image_name() (in module galaxy.tool_util.deps.mulled.util) VALID (galaxy.tool_util.lint.LintLevel attribute) valid() (galaxy.tool_util.lint.LintContext method) valid_category_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) valid_chroms() (galaxy.visualization.data_providers.genome.BBIDataProvider method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) VALID_FLAGS (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider attribute) valid_gff3_phase (galaxy.datatypes.interval.Gff3 attribute) valid_gff3_strand (galaxy.datatypes.interval.Gff3 attribute) valid_gff_frame (galaxy.datatypes.interval.Gff attribute) valid_input_states (galaxy.model.Dataset attribute) (galaxy.tools.DatabaseOperationTool property) (galaxy.tools.Tool property) valid_messages (galaxy.tool_util.lint.LintContext property) VALID_METHODS (galaxy.datatypes.dataproviders.external.URLDataProvider attribute) valid_modes (galaxy.tool_util.deps.container_volumes.ContainerVolume attribute) valid_operations (galaxy.model.Quota attribute) valid_ops (galaxy.managers.genomes.GenomeFilterMixin attribute) (galaxy.managers.taggable.TaggableFilterMixin attribute) VALID_PRESET (galaxy.tools.parameters.sanitize.ToolParameterSanitizer attribute) VALID_RENDER_TARGETS (galaxy.visualization.plugins.config_parser.VisualizationsConfigParser attribute) valid_repository_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) valid_update_keys (galaxy.web.proxy.ProxyManager attribute) validate (galaxy.managers.base.ModelDeserializer attribute) (galaxy.managers.taggable.TaggableDeserializerMixin attribute) validate() (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.datatypes.sequence.BaseFastq method) (galaxy.datatypes.tabular.BaseVcf method) (galaxy.model.DatasetCollection method) (galaxy.model.metadata.MetadataParameter method) (galaxy.tools.parameters.basic.BaseDataToolParameter method) (galaxy.tools.parameters.basic.DirectoryUriToolParameter method) (galaxy.tools.parameters.basic.RulesListToolParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.TextToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.SelectToolParameter method) (galaxy.tools.parameters.validation.DatasetEmptyValidator method) (galaxy.tools.parameters.validation.DatasetExtraFilesPathEmptyValidator method) (galaxy.tools.parameters.validation.DatasetOkValidator method) (galaxy.tools.parameters.validation.EmptyTextfieldValidator method) (galaxy.tools.parameters.validation.ExpressionValidator method) (galaxy.tools.parameters.validation.LengthValidator method) (galaxy.tools.parameters.validation.MetadataEqualValidator method) (galaxy.tools.parameters.validation.MetadataInDataTableColumnValidator method) (galaxy.tools.parameters.validation.MetadataInFileColumnValidator method) (galaxy.tools.parameters.validation.MetadataInRangeValidator method) (galaxy.tools.parameters.validation.MetadataNotInDataTableColumnValidator method) (galaxy.tools.parameters.validation.MetadataValidator method) (galaxy.tools.parameters.validation.NoOptionsValidator method) (galaxy.tools.parameters.validation.RegexValidator method) (galaxy.tools.parameters.validation.UnspecifiedBuildValidator method) (galaxy.tools.parameters.validation.Validator method) (galaxy.tools.parameters.validation.ValueInDataTableColumnValidator method) (galaxy.tools.parameters.validation.ValueNotInDataTableColumnValidator method) (galaxy.web_stack.message.ApplicationStackMessage method) (galaxy.web_stack.message.ParamMessage method) (in module galaxy.datatypes.data) validate_and_load_datatypes_config() (in module galaxy.metadata.set_metadata) validate_and_normalize_target() (in module galaxy.model.store.discover) validate_and_sanitize_basestring() (in module galaxy.util.validation) validate_and_sanitize_basestring_list() (in module galaxy.util.validation) validate_biocompute_object() (galaxy_test.base.populators.BaseWorkflowPopulator method) validate_boolean() (in module galaxy.util.validation) validate_by_group_workflow_parameters_mapper() (in module galaxy.workflow.resources) validate_changeset_revision() (tool_shed.webapp.controllers.repository.RepositoryController method) validate_config() (in module galaxy.jobs.dynamic_tool_destination) validate_dataset() (galaxy_test.base.populators.BaseDatasetPopulator method) validate_dataset_and_wait() (galaxy_test.base.populators.BaseDatasetPopulator method) validate_datatype_extension() (in module galaxy.tools.actions.upload_common) validate_destination() (in module galaxy.jobs.dynamic_tool_destination) validate_email() (in module galaxy.security.validate_user_input) validate_email_domain_name() (in module galaxy.security.validate_user_input) validate_email_str() (in module galaxy.security.validate_user_input) validate_galaxy_markdown() (in module galaxy.managers.markdown_parse) validate_in_users_and_groups() (galaxy.webapps.galaxy.services.quotas.QuotasService method) validate_invocation_crate_directory() (galaxy_test.base.populators.BaseWorkflowPopulator method) validate_jsonrpc_request() (in module galaxy.util.json) validate_jsonrpc_response() (in module galaxy.util.json) validate_key() (galaxy.security.vault.VaultKeyValidationWrapper static method) validate_non_local() (in module galaxy.files.uris) validate_password() (in module galaxy.security.validate_user_input) validate_password_str() (in module galaxy.security.validate_user_input) validate_path_resolution_graph() (galaxy.config.schema.AppSchema method) validate_path_upload() (in module galaxy.actions.library) validate_preferred_object_store_id() (in module galaxy.security.validate_user_input) validate_publicname() (in module galaxy.security.validate_user_input) validate_publicname_str() (in module galaxy.security.validate_user_input) validate_repository_name() (in module tool_shed.util.repository_util) validate_rule() (galaxy.jobs.dynamic_tool_destination.RuleValidator class method) (galaxy.util.rules_dsl.AddColumnBasenameRuleDefinition method) (galaxy.util.rules_dsl.AddColumnConcatenateRuleDefinition method) (galaxy.util.rules_dsl.AddColumnGroupTagValueRuleDefinition method) (galaxy.util.rules_dsl.AddColumnMetadataRuleDefinition method) (galaxy.util.rules_dsl.AddColumnRegexRuleDefinition method) (galaxy.util.rules_dsl.AddColumnRownumRuleDefinition method) (galaxy.util.rules_dsl.AddColumnSubstrRuleDefinition method) (galaxy.util.rules_dsl.AddColumnValueRuleDefinition method) (galaxy.util.rules_dsl.AddFilterCompareRuleDefinition method) (galaxy.util.rules_dsl.AddFilterCountRuleDefinition method) (galaxy.util.rules_dsl.AddFilterEmptyRuleDefinition method) (galaxy.util.rules_dsl.AddFilterMatchesRuleDefinition method) (galaxy.util.rules_dsl.AddFilterRegexRuleDefinition method) (galaxy.util.rules_dsl.BaseRuleDefinition method) (galaxy.util.rules_dsl.RemoveColumnsRuleDefinition method) (galaxy.util.rules_dsl.SortRuleDefinition method) (galaxy.util.rules_dsl.SplitColumnsRuleDefinition method) (galaxy.util.rules_dsl.SwapColumnsRuleDefinition method) validate_server_directory_upload() (in module galaxy.actions.library) validate_source() (galaxy.datatypes.dataproviders.base.DataProvider method) (galaxy.datatypes.dataproviders.chunk.ChunkDataProvider method) validate_tabular() (in module galaxy.datatypes.sniff) validate_uri_access() (in module galaxy.files.uris) validate_uri_root() (galaxy.files.ConfiguredFileSources method) validated() (galaxy.datatypes.data.DatatypeValidation static method) validated_state (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) validated_state_message (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HDADetailed attribute) validated_states (galaxy.model.DatasetInstance attribute) ValidateOutputsAction (class in galaxy.job_execution.actions.post) validation_error_to_message_exception() (in module galaxy.web.framework.decorators) ValidationContext (class in galaxy.tools.repositories) ValidationContextConfig (class in galaxy.tools.repositories) ValidationOnlyTokenEvaluator (class in galaxy.util.bool_expressions) Validator (class in galaxy.tools.parameters.validation) ValidatorAttribIncompatible (class in galaxy.tool_util.linters.inputs) ValidatorDatasetMetadataEqualValue (class in galaxy.tool_util.linters.inputs) ValidatorDatasetMetadataEqualValueOrJson (class in galaxy.tool_util.linters.inputs) ValidatorExpression (class in galaxy.tool_util.linters.inputs) ValidatorExpressionFuture (class in galaxy.tool_util.linters.inputs) ValidatorHasNoText (class in galaxy.tool_util.linters.inputs) ValidatorHasText (class in galaxy.tool_util.linters.inputs) ValidatorMetadataCheckSkip (class in galaxy.tool_util.linters.inputs) ValidatorMetadataName (class in galaxy.tool_util.linters.inputs) ValidatorMinMax (class in galaxy.tool_util.linters.inputs) ValidatorParamIncompatible (class in galaxy.tool_util.linters.inputs) ValidatorTableName (class in galaxy.tool_util.linters.inputs) ValidCategoryGrid (class in tool_shed.grids.repository_grids) ValidCategoryGrid.RepositoriesColumn (class in tool_shed.grids.repository_grids) ValidRepositoryGrid (class in tool_shed.grids.repository_grids) ValidRepositoryGrid.CategoryColumn (class in tool_shed.grids.repository_grids) ValidRepositoryGrid.InstallableRevisionColumn (class in tool_shed.grids.repository_grids) ValidRepositoryGrid.RepositoryCategoryColumn (class in tool_shed.grids.repository_grids) ValidToolTestDict (class in galaxy.tool_util.verify.interactor) value (galaxy.config.config_manage.OptionValue attribute) (galaxy.job_metrics.formatting.FormattedMetric attribute) (galaxy.model.DynamicTool attribute) (galaxy.model.ExtendedMetadataIndex attribute) (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.JobParameter attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.UserPreference attribute) (galaxy.model.Vault attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.WorkflowInvocationOutputValue attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.model.WorkflowRequestStepState attribute) (galaxy.model.WorkflowStepTagAssociation attribute) (galaxy.schema.schema.JobMetric attribute) (galaxy.schema.schema.LabelValuePair attribute) (galaxy.schema.schema.WorkflowInput attribute) (galaxy.tool_util.parser.output_objects.ChangeFormatModel attribute) (galaxy.tools.wrappers.DatasetListWrapper attribute) (galaxy.tools.wrappers.InputValueWrapper attribute) (galaxy.tools.wrappers.RawObjectWrapper attribute) (galaxy.tools.wrappers.ToolParameterValueWrapper attribute) value_from (galaxy.model.WorkflowStepInput attribute) (galaxy.tools.parameters.grouping.Conditional attribute) value_from_basic() (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.grouping.Conditional method) (galaxy.tools.parameters.grouping.Group method) (galaxy.tools.parameters.grouping.Repeat method) (galaxy.tools.parameters.grouping.Section method) (galaxy.tools.parameters.grouping.UploadDataset method) value_from_type (galaxy.model.WorkflowStepInput attribute) value_label (galaxy.tools.parameters.basic.ColumnListParameter attribute) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter attribute) (galaxy.tools.parameters.basic.GenomeBuildParameter attribute) (galaxy.tools.parameters.basic.SelectTagParameter attribute) (galaxy.tools.parameters.basic.SelectToolParameter attribute) (galaxy.tools.parameters.SelectToolParameter attribute)

value_to_basic() (galaxy.tools.parameters.basic.BaseJsonToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.grouping.Conditional method) (galaxy.tools.parameters.grouping.Group method) (galaxy.tools.parameters.grouping.Repeat method) (galaxy.tools.parameters.grouping.Section method) (galaxy.tools.parameters.grouping.UploadDataset method) value_to_display_text() (galaxy.tools.parameters.basic.ToolParameter method) ValueFilterQueryParams (class in galaxy.schema) ValueInDataTableColumnValidator (class in galaxy.tools.parameters.validation) ValueNotInDataTableColumnValidator (class in galaxy.tools.parameters.validation) values (galaxy.model.User attribute) values() (galaxy.schema.schema.DatasetState class method) (galaxy.tool_util.cwl.cwltool_deps.CommentedMap method) (galaxy.util.bunch.Bunch method) (galaxy.util.odict.odict method) ValueToolOutputActionConditionalWhen (class in galaxy.tool_util.parser.output_actions) variables (galaxy.job_metrics.instrumenters.env.EnvPlugin attribute) variant (galaxy.model.Notification attribute) Vault (class in galaxy.model) (class in galaxy.security.vault) vault (galaxy.structured_app.StructuredApp attribute) VaultFactory (class in galaxy.security.vault) VaultKeyPrefixWrapper (class in galaxy.security.vault) VaultKeyValidationWrapper (class in galaxy.security.vault) Vcf (class in galaxy.datatypes.tabular) VcfDataProvider (class in galaxy.visualization.data_providers.genome) VcfGz (class in galaxy.datatypes.tabular) VcfTabixDataProvider (class in galaxy.visualization.data_providers.genome) Vel (class in galaxy.datatypes.binary) Velvet (class in galaxy.datatypes.assembly) verbose (in module galaxy.jobs.dynamic_tool_destination) verbose_name (galaxy.job_execution.actions.post.ChangeDatatypeAction attribute) (galaxy.job_execution.actions.post.ColumnSetAction attribute) (galaxy.job_execution.actions.post.DefaultJobAction attribute) (galaxy.job_execution.actions.post.DeleteDatasetAction attribute) (galaxy.job_execution.actions.post.DeleteIntermediatesAction attribute) (galaxy.job_execution.actions.post.EmailAction attribute) (galaxy.job_execution.actions.post.HideDatasetAction attribute) (galaxy.job_execution.actions.post.RemoveTagDatasetAction attribute) (galaxy.job_execution.actions.post.RenameDatasetAction attribute) (galaxy.job_execution.actions.post.TagDatasetAction attribute) (galaxy.job_execution.actions.post.ValidateOutputsAction attribute) verify() (in module galaxy.authnz.psa_authnz) (in module galaxy.tool_util.verify) verify_assertion() (in module galaxy.tool_util.verify.asserts) verify_assertions() (in module galaxy.tool_util.verify.asserts) verify_collection() (in module galaxy.tool_util.verify.interactor) verify_database_is_initialized() (in module galaxy.model.migrations.scripts) verify_databases() (in module galaxy.model.migrations) verify_databases_via_script() (in module galaxy.model.migrations) verify_hid() (in module galaxy.tool_util.verify.interactor) verify_installed_repositories() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) verify_installed_repository_data_table_entries() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) verify_installed_repository_metadata_unchanged() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) verify_installed_repository_no_tool_panel_section() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) verify_output() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) verify_output_collection() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) verify_output_dataset() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) verify_ssl (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute) verify_tool() (in module galaxy.tool_util.verify.interactor) verify_unchanged_repository_metadata() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) version (galaxy.managers.display_applications.DisplayApplication attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetAssociationHistory attribute) (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.Workflow property) (galaxy.schema.schema.WorkflowToExport attribute) (galaxy.tool_util.deps.resolvers.ContainerDependency property) (galaxy.tools.ApplyRulesTool attribute) (galaxy.tools.AsyncDataSourceTool attribute) (galaxy.tools.BuildListCollectionTool attribute) (galaxy.tools.data_manager.manager.Tool attribute) (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.DataDestinationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.DuplicateFileToCollectionTool attribute) (galaxy.tools.ExportHistoryTool attribute) (galaxy.tools.ExpressionTool attribute) (galaxy.tools.ExtractDatasetCollectionTool attribute) (galaxy.tools.FilterDatasetsTool attribute) (galaxy.tools.FilterEmptyDatasetsTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) (galaxy.tools.FilterFromFileTool attribute) (galaxy.tools.FlattenTool attribute) (galaxy.tools.HarmonizeTool attribute) (galaxy.tools.ImportHistoryTool attribute) (galaxy.tools.InteractiveTool attribute) (galaxy.tools.KeepSuccessDatasetsTool attribute) (galaxy.tools.MergeCollectionTool attribute) (galaxy.tools.OutputParameterJSONTool attribute) (galaxy.tools.RelabelFromFileTool attribute) (galaxy.tools.SortTool attribute) (galaxy.tools.TagFromFileTool attribute) (galaxy.tools.Tool attribute) (galaxy.tools.UnzipCollectionTool attribute) (galaxy.tools.ZipCollectionTool attribute) version() (galaxy.managers.configuration.ConfigurationManager method) (galaxy.webapps.galaxy.api.configuration.FastAPIConfiguration method) (tool_shed.webapp.api.configuration.ConfigurationController method) VERSION_2_PREFIX (galaxy.datatypes.binary.RData attribute) VERSION_3_PREFIX (galaxy.datatypes.binary.RData attribute) version_changes (galaxy.workflow.modules.SubWorkflowModule property) version_command_line (galaxy.tools.evaluation.PartialToolEvaluator attribute) (galaxy.tools.evaluation.RemoteToolEvaluator attribute) version_object (galaxy.tools.Tool property) version_of() (galaxy.model.StoredWorkflow method) version_path() (galaxy.job_execution.compute_environment.ComputeEnvironment method) (galaxy.job_execution.compute_environment.SharedComputeEnvironment method) version_sorted() (in module galaxy.tool_util.deps.mulled.util) versioned_install() (in module galaxy.tool_util.deps.brew_exts) versioned_objects() (in module galaxy.model.base) versioned_objects_strict() (in module galaxy.model.base) versioned_session() (in module galaxy.model.base) Video (class in galaxy.datatypes.media) view (galaxy.schema.SerializationParams attribute) view() (galaxy.webapps.galaxy.controllers.history.HistoryController method) view_changelog() (tool_shed.webapp.controllers.repository.RepositoryController method) view_changeset() (tool_shed.webapp.controllers.repository.RepositoryController method) view_converters() (in module galaxy.managers.datatypes) view_dicts (galaxy.tool_util.toolbox.views.sources.StaticToolBoxViewSources attribute) view_directories (galaxy.tool_util.toolbox.views.sources.StaticToolBoxViewSources attribute) view_index() (in module galaxy.managers.datatypes) view_mapping() (in module galaxy.managers.datatypes) view_or_manage_repository() (tool_shed.webapp.controllers.repository.RepositoryController method) view_repository() (tool_shed.webapp.controllers.repository.RepositoryController method) view_show_job() (in module galaxy.managers.jobs) view_sniffers() (in module galaxy.managers.datatypes) view_tool_metadata() (tool_shed.webapp.controllers.repository.RepositoryController method) view_type (galaxy.tool_util.toolbox.views.definitions.StaticToolBoxView attribute) (galaxy.tool_util.toolbox.views.interface.ToolPanelViewModel attribute) view_types_and_mapping() (in module galaxy.managers.datatypes) views (galaxy.managers.base.ModelSerializer attribute) (galaxy.managers.cloudauthzs.CloudAuthzsSerializer attribute) (galaxy.managers.configuration.AdminConfigSerializer attribute) (galaxy.managers.configuration.ConfigSerializer attribute) (galaxy.managers.datasets.DatasetAssociationSerializer attribute) (galaxy.managers.datasets.DatasetSerializer attribute) (galaxy.managers.hdcas.DCESerializer attribute) (galaxy.managers.hdcas.DCSerializer attribute) (galaxy.managers.hdcas.HDCASerializer attribute) (galaxy.managers.history_contents.HistoryContentsSerializer attribute) (galaxy.managers.users.CurrentUserSerializer attribute) (galaxy.managers.users.UserSerializer attribute) (galaxy.managers.visualizations.VisualizationSerializer attribute) (galaxy.managers.workflows.WorkflowSerializer attribute) virtual_display_if_enabled() (in module galaxy.selenium.driver_factory) visible (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.store.discover.JsonCollectedDatasetMatch property) (galaxy.schema.schema.HDACustom attribute) (galaxy.schema.schema.HistoryItemBase attribute) (galaxy.schema.schema.UpdateHistoryContentsPayload attribute) (galaxy.tools.parameters.basic.FTPFileToolParameter property) (galaxy.tools.parameters.basic.ToolParameter property) (galaxy.tools.parameters.grouping.Group property) visible_dataset_collections (galaxy.model.History attribute) visible_datasets (galaxy.model.History attribute) visit_class() (in module galaxy.tool_util.cwl.cwltool_deps) visit_inputs() (galaxy.tools.Tool method) visit_url() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) Visium (class in galaxy.datatypes.binary) Visualization (class in galaxy.model) (class in galaxy.schema.schema) (galaxy.managers.tags.TaggableItemClass attribute) visualization (galaxy.model.VisualizationAnnotationAssociation attribute) (galaxy.model.VisualizationRatingAssociation attribute) (galaxy.model.VisualizationRevision attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.VisualizationUserShareAssociation attribute) visualization_id (galaxy.model.VisualizationAnnotationAssociation attribute) (galaxy.model.VisualizationRatingAssociation attribute) (galaxy.model.VisualizationRevision attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.VisualizationUserShareAssociation attribute) visualization_plugins_directory (galaxy.config.GalaxyAppConfiguration attribute) VisualizationAnnotationAssociation (class in galaxy.model) VisualizationController (class in galaxy.webapps.galaxy.controllers.visualization) VisualizationDeserializer (class in galaxy.managers.visualizations) VisualizationManager (class in galaxy.managers.visualizations) VisualizationPlugin (class in galaxy.visualization.plugins.plugin) VisualizationRatingAssociation (class in galaxy.model) VisualizationRevision (class in galaxy.model) visualizations (galaxy.schema.schema.HDACustom attribute) visualizations_registry (galaxy.structured_app.StructuredApp attribute) VisualizationsConfigParser (class in galaxy.visualization.plugins.config_parser) VisualizationsController (class in galaxy.webapps.galaxy.api.visualizations) VisualizationSerializer (class in galaxy.managers.visualizations) VisualizationsRegistry (class in galaxy.visualization.plugins.registry) VisualizationsService (class in galaxy.webapps.galaxy.services.visualizations) VisualizationTagAssociation (class in galaxy.model) VisualizationUserShareAssociation (class in galaxy.model) Volume (class in galaxy.tool_util.deps.container_classes) Vtk (class in galaxy.datatypes.constructive_solid_geometry) VtkAscii (class in galaxy.datatypes.constructive_solid_geometry) VtkBinary (class in galaxy.datatypes.constructive_solid_geometry)

W

wait() (galaxy.selenium.has_driver.HasDriver method) (galaxy_test.base.populators.CwlRun method) (galaxy_test.base.populators.CwlToolRun method) (galaxy_test.base.populators.CwlWorkflowRun method) wait_for() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) wait_for_absent() (galaxy.selenium.has_driver.HasDriver method) (galaxy.selenium.smart_components.SmartTarget method) wait_for_absent_or_hidden() (galaxy.selenium.has_driver.HasDriver method) (galaxy.selenium.smart_components.SmartTarget method) wait_for_and_clear_and_send_keys() (galaxy.selenium.smart_components.SmartTarget method) wait_for_and_click() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) (galaxy.selenium.smart_components.SmartTarget method) wait_for_and_click_selector() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) wait_for_and_send_keys() (galaxy.selenium.smart_components.SmartTarget method) wait_for_clickable() (galaxy.selenium.has_driver.HasDriver method) (galaxy.selenium.smart_components.SmartTarget method) wait_for_dataset() (galaxy_test.base.populators.BaseDatasetPopulator method) wait_for_dataset_collection() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method) wait_for_download_ready() (galaxy_test.base.populators.BaseDatasetPopulator method) wait_for_element_count_of_at_least() (galaxy.selenium.has_driver.HasDriver method) (galaxy.selenium.smart_components.SmartTarget method) wait_for_export_task_on_record() (galaxy_test.base.populators.BaseDatasetPopulator method) wait_for_fetched_collection() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method) wait_for_hid_ok_and_open_details() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) wait_for_history() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) (galaxy_test.base.populators.BaseDatasetPopulator method) wait_for_history_jobs() (galaxy_test.base.populators.BaseDatasetPopulator method) wait_for_history_to_have_hid() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) wait_for_history_with_name() (galaxy_test.base.populators.BaseDatasetPopulator method) wait_for_history_workflows() (galaxy_test.base.populators.BaseWorkflowPopulator method) wait_for_http_server() (in module galaxy_test.driver.driver_util) wait_for_id() (galaxy.selenium.has_driver.HasDriver method) wait_for_invocation() (galaxy_test.base.populators.BaseWorkflowPopulator method) wait_for_invocation_and_jobs() (galaxy_test.base.populators.BaseWorkflowPopulator method) wait_for_job() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) (galaxy_test.base.populators.BaseDatasetPopulator method) wait_for_jobs() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) (galaxy_test.base.populators.BaseDatasetPopulator method) wait_for_logged_in() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) wait_for_overlays_cleared() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) wait_for_present() (galaxy.selenium.has_driver.HasDriver method) (galaxy.selenium.smart_components.SmartTarget method) wait_for_purge() (galaxy_test.base.populators.BaseDatasetPopulator method) wait_for_select() (galaxy.selenium.smart_components.SmartTarget method) wait_for_selector() (galaxy.selenium.has_driver.HasDriver method) wait_for_selector_absent() (galaxy.selenium.has_driver.HasDriver method) wait_for_selector_absent_or_hidden() (galaxy.selenium.has_driver.HasDriver method) wait_for_selector_clickable() (galaxy.selenium.has_driver.HasDriver method) wait_for_selector_visible() (galaxy.selenium.has_driver.HasDriver method) wait_for_sizzle_selector_clickable() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) wait_for_text() (galaxy.selenium.smart_components.SmartTarget method) wait_for_tool_run() (galaxy_test.base.populators.BaseDatasetPopulator method) wait_for_toolbox_reload() (galaxy.app.MinimalGalaxyApplication method) (galaxy.app_unittest_utils.galaxy_mock.MockApp method) (galaxy.structured_app.MinimalManagerApp method) wait_for_value() (galaxy.selenium.smart_components.SmartTarget method) wait_for_visible() (galaxy.selenium.has_driver.HasDriver method) (galaxy.selenium.smart_components.SmartTarget method) wait_for_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method) wait_for_xpath() (galaxy.selenium.has_driver.HasDriver method) wait_for_xpath_visible() (galaxy.selenium.has_driver.HasDriver method) wait_length() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) wait_on() (in module galaxy.tool_util.verify.wait) (in module galaxy_test.base.populators) wait_on_assertion() (in module galaxy_test.base.populators) wait_on_download() (galaxy_test.base.populators.BaseDatasetPopulator method) wait_on_download_request() (galaxy_test.base.populators.BaseDatasetPopulator method) wait_on_history_length() (galaxy_test.base.populators.BaseDatasetPopulator method) wait_on_library_dataset() (galaxy_test.base.populators.LibraryPopulator method) wait_on_state() (in module galaxy_test.base.populators) wait_on_task() (galaxy_test.base.populators.BaseDatasetPopulator method) wait_on_task_id() (galaxy_test.base.populators.BaseDatasetPopulator method) WAIT_TYPES (class in galaxy.selenium.navigates_galaxy) wait_types (galaxy.selenium.navigates_galaxy.NavigatesGalaxy attribute) waiting (galaxy.model.JobStateSummary attribute) WAITING (galaxy.model.Task.states attribute) waiting (galaxy.schema.schema.HDCJobStateSummary attribute) WAITING (galaxy.schema.schema.JobState attribute) waiting_for_elements (galaxy.model.DatasetCollection property) (galaxy.model.HistoryDatasetCollectionAssociation property) WaitType (class in galaxy.selenium.navigates_galaxy) wake() (galaxy.util.sleeper.Sleeper method) walk_collections() (galaxy.model.dataset_collections.structure.Tree method) walk_controller_modules() (in module galaxy.web.framework.base) walk_loaded_tools() (in module galaxy.tool_util.toolbox.views.interface) walk_over_extra_files() (in module galaxy.job_execution.output_collect) walk_over_file_collectors() (in module galaxy.job_execution.output_collect) walk_sections() (galaxy.tool_util.toolbox.panel.ToolPanelElements method) wants_params_cleaned (galaxy.tools.DataSourceTool property) WARN (galaxy.tool_util.lint.LintLevel attribute) warn() (galaxy.tool_util.lint.LintContext method) (in module galaxy.tools.util.galaxyops) warn_messages (galaxy.tool_util.lint.LintContext property) WARNING (galaxy.model.tool_shed_install.ToolDependency.states attribute) (galaxy.model.tool_shed_install.ToolShedRepository.states attribute) (galaxy.tool_util.parser.stdio.StdioErrorLevel attribute) warnings (galaxy.tools.parameters.grouping.Dataset attribute) was_recorded (galaxy.tool_util.verify.script.TestException attribute) watch_directory() (galaxy.tool_util.toolbox.watcher.ToolWatcher method) (galaxy.util.watcher.NullWatcher method) (galaxy.util.watcher.Watcher method) watch_file() (galaxy.tool_util.toolbox.watcher.ToolConfWatcher method) (galaxy.tool_util.toolbox.watcher.ToolWatcher method) (galaxy.util.watcher.NullWatcher method) (galaxy.util.watcher.Watcher method) watch_tool() (galaxy.tool_util.toolbox.AbstractToolBox method) (galaxy.tool_util.toolbox.base.AbstractToolBox method) Watcher (class in galaxy.util.watcher) watchers (galaxy.app_unittest_utils.galaxy_mock.MockApp attribute) (galaxy.config_watchers.ConfigWatchers property) (galaxy.structured_app.StructuredApp attribute) Wav (class in galaxy.datatypes.media) WebappConfig (class in galaxy.main_config) WebappConfigResolver (class in galaxy.main_config) WebApplication (class in galaxy.web.framework.base) (class in galaxy.webapps.base.webapp) WebApplicationStack (class in galaxy.web_stack) WebappSetupProps (class in galaxy.main_config) WebDavFilesSource (class in galaxy.files.sources.webdav) Webhook (class in galaxy.webhooks) webhook_data() (galaxy.webapps.galaxy.api.webhooks.WebhooksController method) webhooks_registry (galaxy.structured_app.StructuredApp attribute) WebhooksController (class in galaxy.webapps.galaxy.api.webhooks) WebhooksRegistry (class in galaxy.webhooks) WeblessApplicationStack (class in galaxy.web_stack) welcome() (galaxy.webapps.galaxy.controllers.root.RootController method) well_known_oidc_config_uri (galaxy.authnz.custos_authnz.CustosAuthnzConfiguration attribute) when (galaxy.schema.schema.WorkflowStepBase attribute) when_expression (galaxy.model.WorkflowStep attribute) when_ready() (in module galaxy.web_stack.gunicorn_config) which() (in module galaxy.tool_util.deps.brew_exts) (in module galaxy.util) (in module galaxy.util.commands) whoami() (galaxy.webapps.galaxy.api.configuration.FastAPIConfiguration method) width (galaxy.schema.schema.WorkflowStepLayoutPosition attribute) Wiff (class in galaxy.datatypes.proteomics) Wiff2 (class in galaxy.datatypes.proteomics) Wiff2Tar (class in galaxy.datatypes.binary) WiffTar (class in galaxy.datatypes.binary) Wiggle (class in galaxy.datatypes.interval) wiggle_dataprovider() (galaxy.datatypes.interval.Wiggle method) wiggle_dict_dataprovider() (galaxy.datatypes.interval.Wiggle method) WiggleDataProvider (class in galaxy.datatypes.dataproviders.dataset) with_path_for_job() (galaxy.job_execution.datasets.DatasetPath method) WithModelClass (class in galaxy.schema.schema) work_context (galaxy.job_execution.output_collect.JobContext property) WorkerProcess (class in galaxy.model) workers() (galaxy.web_stack.ApplicationStack method) Workflow (class in galaxy.model) (class in galaxy.tool_util.toolbox.views.definitions) workflow (galaxy.managers.workflows.CreatedWorkflow attribute) (galaxy.managers.workflows.RefactorResponse attribute) (galaxy.model.WorkflowComment attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowStep attribute) WORKFLOW (galaxy.tool_util.toolbox.panel.panel_item_types attribute) (galaxy.tool_util.toolbox.panel_item_types attribute) workflow_card_element() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_card_elements() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_contents_manager (galaxy.model.store.StoreAppProtocol attribute) (galaxy.structured_app.MinimalManagerApp attribute) workflow_create_new() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_delete_by_name() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_editor_add_input() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) workflow_editor_click_option() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_editor_click_options() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_editor_click_run() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_editor_click_save() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_editor_connect() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) workflow_editor_destroy_connection() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) workflow_editor_maximize_center_pane() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) workflow_editor_options_menu_element() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_editor_set_license() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_editor_source_sink_terminal_ids() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) workflow_id (galaxy.model.WorkflowComment attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowStep attribute) (galaxy.schema.schema.InvocationIndexQueryPayload attribute) (galaxy.schema.schema.JobIndexQueryPayload attribute) (galaxy.schema.schema.SubworkflowStep attribute) (galaxy_test.api.test_workflow_extraction.RunJobsSummary attribute) (galaxy_test.base.populators.RunJobsSummary attribute) workflow_import_submit_url() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_add_tag() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_click_import() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_click_search() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_click_tag() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_click_tag_display() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_column_text() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_get_current_filter() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_name() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_open() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_open_with_name() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) workflow_index_search_for() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_tag_elements() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_tags() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_view_external_link() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_inputs() (galaxy_test.base.populators.BaseWorkflowPopulator method) workflow_invocation (galaxy.model.WorkflowInvocationMessage attribute) (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationOutputValue attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.model.WorkflowRequestInputStepParameter attribute) (galaxy.model.WorkflowRequestStepState attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) workflow_invocation_id (galaxy.model.WorkflowInvocationMessage attribute) (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationOutputValue attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.model.WorkflowRequestInputStepParameter attribute) (galaxy.model.WorkflowRequestStepState attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) workflow_invocation_step (galaxy.model.Job attribute) (galaxy.model.WorkflowInvocationOutputValue attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation attribute)

workflow_invocation_step_id (galaxy.model.WorkflowInvocationStepOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation attribute) workflow_invocations (galaxy.model.History attribute) workflow_invocations() (galaxy_test.base.populators.BaseWorkflowPopulator method) workflow_manager (galaxy.app_unittest_utils.galaxy_mock.MockApp attribute) (galaxy.structured_app.MinimalManagerApp attribute) (galaxy.webapps.galaxy.controllers.page.PageController attribute) workflow_output (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationOutputValue attribute) workflow_output_drop_forced (galaxy.workflow.refactor.schema.RefactorActionExecutionMessageTypeEnum attribute) workflow_output_for() (galaxy.model.Workflow method) (galaxy.model.WorkflowStep method) workflow_output_id (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationOutputValue attribute) workflow_output_labels (galaxy.model.Workflow property) workflow_outputs (galaxy.model.Workflow property) (galaxy.model.WorkflowStep attribute) (galaxy.schema.schema.WorkflowStepToExportBase attribute) workflow_paths() (galaxy.model.store.BaseDirectoryImportModelStore method) (galaxy.model.store.DictImportModelStore method) (galaxy.model.store.ModelImportStore method) workflow_populator (galaxy_test.api.test_workflows.ChangeDatatypeTests attribute) (galaxy_test.api.test_workflows.RunsWorkflowFixtures attribute) (galaxy_test.api.test_workflows.TestAdminWorkflowsApi attribute) (galaxy_test.api.test_workflows_cwl.BaseCwlWorkflowsApiTestCase attribute) (galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi attribute) workflow_proxy() (in module galaxy.tool_util.cwl) workflow_rename() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_report_json() (galaxy_test.base.populators.BaseWorkflowPopulator method) workflow_report_pdf() (galaxy_test.base.populators.BaseWorkflowPopulator method) workflow_request (galaxy_test.base.populators.RunJobsSummary attribute) workflow_request_to_run_config() (in module galaxy.workflow.run_request) workflow_resource_params_mapper (galaxy.config.GalaxyAppConfiguration attribute) workflow_run_config_to_request() (in module galaxy.workflow.run_request) workflow_run_ensure_expanded() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_run_specify_inputs() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_run_submit() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_run_with_name() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_scheduling_manager (galaxy.structured_app.StructuredApp attribute) workflow_share_click() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_shared_with_me_open() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_sharing_click_publish() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_step (galaxy.model.PostJobAction attribute) (galaxy.model.WorkflowInvocationMessage attribute) (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationOutputValue attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute) (galaxy.model.WorkflowOutput attribute) (galaxy.model.WorkflowRequestInputStepParameter attribute) (galaxy.model.WorkflowRequestStepState attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowStepAnnotationAssociation attribute) (galaxy.model.WorkflowStepInput attribute) (galaxy.model.WorkflowStepTagAssociation attribute) workflow_step_id (galaxy.model.PostJobAction attribute) (galaxy.model.WorkflowInvocationMessage attribute) (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationOutputValue attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute) (galaxy.model.WorkflowOutput attribute) (galaxy.model.WorkflowRequestInputStepParameter attribute) (galaxy.model.WorkflowRequestStepState attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowStepAnnotationAssociation attribute) (galaxy.model.WorkflowStepInput attribute) (galaxy.model.WorkflowStepTagAssociation attribute) workflow_step_index (galaxy.model.WorkflowInvocationMessage property) workflow_to_dict() (galaxy.managers.workflows.WorkflowContentsManager method) workflow_upload_yaml_with_random_name() (galaxy_test.selenium.test_workflow_editor.TestWorkflowEditor method) WorkflowAnnotationsController (class in galaxy.webapps.galaxy.api.annotations) WorkflowCanvas (class in galaxy.workflow.render) WorkflowComment (class in galaxy.model) WorkflowContentsManager (class in galaxy.managers.workflows) WorkflowController (class in galaxy.webapps.galaxy.controllers.workflow) WorkflowCreateOptions (class in galaxy.managers.workflows) WorkflowField (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) WorkflowIndexQueryPayload (class in galaxy.schema.schema) WorkflowInput (class in galaxy.schema.schema) WorkflowInvocation (class in galaxy.model) (galaxy.schema.schema.JobSourceType attribute) WorkflowInvocationMessage (class in galaxy.model) WorkflowInvocationOnlyExportStore (class in galaxy.model.store) WorkflowInvocationOutputDatasetAssociation (class in galaxy.model) WorkflowInvocationOutputDatasetCollectionAssociation (class in galaxy.model) WorkflowInvocationOutputValue (class in galaxy.model) WorkflowInvocationStateSummary (class in galaxy.schema.schema) WorkflowInvocationStep (class in galaxy.model) WorkflowInvocationStepObjectStores (class in galaxy.model) WorkflowInvocationStepOutputDatasetAssociation (class in galaxy.model) WorkflowInvocationStepOutputDatasetCollectionAssociation (class in galaxy.model) WorkflowInvocationToSubworkflowInvocationAssociation (class in galaxy.model) WorkflowMappingField (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) WorkflowMarkdownGeneratorPlugin (class in galaxy.workflow.reports.generators) WorkflowModule (class in galaxy.workflow.modules) WorkflowModuleFactory (class in galaxy.workflow.modules) WorkflowModuleInjector (class in galaxy.workflow.modules) WorkflowOutput (class in galaxy.model) (class in galaxy.schema.schema) WorkflowParameterExpansion (class in galaxy.tools.parameters.meta) WorkflowPopulator (class in galaxy_test.base.populators) WorkflowRefactorExecutor (class in galaxy.workflow.refactor.execute) WorkflowReportGeneratorPlugin (class in galaxy.workflow.reports.generators) WorkflowRequestInputParameter (class in galaxy.model) WorkflowRequestInputParameter.types (class in galaxy.model) WorkflowRequestInputStepParameter (class in galaxy.model) WorkflowRequestMonitor (class in galaxy.workflow.scheduling_manager) WorkflowRequestStepState (class in galaxy.model) WorkflowRequestToInputDatasetAssociation (class in galaxy.model) WorkflowRequestToInputDatasetCollectionAssociation (class in galaxy.model) WorkflowRunConfig (class in galaxy.workflow.run) (class in galaxy.workflow.run_request) Workflows (class in galaxy.webapps.reports.controllers.workflows) workflows (galaxy.model.StoredWorkflow attribute) workflows_directory (galaxy.model.store.DirectoryModelExportStore property) (galaxy.model.store.WriteCrates property) WorkflowSchedulingManager (class in galaxy.workflow.scheduling_manager) WorkflowSchedulingMessage (class in galaxy.web_stack.message) WorkflowSchedulingPlugin (class in galaxy.workflow.schedulers) WorkflowSerializer (class in galaxy.managers.workflows) WorkflowsManager (class in galaxy.managers.workflows) WorkflowStateResolutionOptions (class in galaxy.managers.workflows) WorkflowStep (class in galaxy.model) WorkflowStepAnnotationAssociation (class in galaxy.model) WorkflowStepBase (class in galaxy.schema.schema) WorkflowStepConnection (class in galaxy.model) WorkflowStepInput (class in galaxy.model) WorkflowStepLayoutPosition (class in galaxy.schema.schema) WorkflowStepTagAssociation (class in galaxy.model) WorkflowStepToExport (class in galaxy.schema.schema) WorkflowStepToExportBase (class in galaxy.schema.schema) WorkflowToExport (class in galaxy.schema.schema) WorkflowToolStepToExport (class in galaxy.schema.schema) WorkflowUpdateOptions (class in galaxy.managers.workflows) working_directory (galaxy.model.Task attribute) working_directory() (galaxy.job_execution.compute_environment.ComputeEnvironment method) (galaxy.job_execution.compute_environment.SharedComputeEnvironment method) WorkRequestContext (class in galaxy.work.context) wrap() (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.MetadataElementSpec method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.datatypes.metadata.SelectParameter method) (galaxy.model.metadata.FileParameter method) (galaxy.model.metadata.MetadataElementSpec method) (galaxy.model.metadata.MetadataParameter method) (galaxy.model.metadata.SelectParameter method) wrap_if_allowed() (in module galaxy.webapps.util) wrap_if_allowed_or_fail() (in module galaxy.webapps.util) wrap_in_middleware() (in module galaxy.webapps.galaxy.buildapp) (in module galaxy.webapps.reports.buildapp) (in module tool_shed.webapp.buildapp) wrap_values() (galaxy.tools.parameters.wrapped.WrappedParameters method) wrap_with_alias() (galaxy.webapps.galaxy.api.FrameworkRouter method) wrap_with_safe_string() (in module galaxy.security.object_wrapper) WrappedParameters (class in galaxy.tools.parameters.wrapped) writable (galaxy.files.sources.FilesSourceProperties attribute) (galaxy.schema.remote_files.FilesSourcePlugin attribute) writable_files (galaxy.datatypes.data.Data property) write() (galaxy.datatypes.dataproviders.base.DataProvider method) (galaxy.objectstore.unittest_utils.Config method) (galaxy.tool_util.verify.script.Results method) (galaxy.util.zipstream.ZipstreamWrapper method) write_bundle() (galaxy.tools.data_manager.manager.DataManager method) write_command() (galaxy.jobs.runners.chronos.ChronosJobRunner method) write_config() (tool_shed.util.hgweb_config.HgWebConfigManager method) write_data_to_file() (galaxy.visualization.data_providers.basic.BaseDataProvider method) (galaxy.visualization.data_providers.genome.BamDataProvider method) (galaxy.visualization.data_providers.genome.BedDataProvider method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) (galaxy.visualization.data_providers.genome.IntervalDataProvider method) (galaxy.visualization.data_providers.genome.IntervalIndexDataProvider method) (galaxy.visualization.data_providers.genome.TabixDataProvider method) (galaxy.visualization.data_providers.genome.VcfDataProvider method) write_dataset_collection() (galaxy.managers.collections.DatasetCollectionManager method) (in module galaxy.managers.hdcas) write_evalute_script() (in module galaxy.tools.expressions) (in module galaxy.tools.expressions.script) write_executable_script() (galaxy.jobs.runners.BaseJobRunner method) write_file_fixtures() (in module galaxy.files.unittest_utils) write_from() (galaxy.files.sources.BaseFilesSource method) (galaxy.files.sources.SingleFileSource method) write_history_content_to() (galaxy.managers.model_stores.ModelStoreManager method) write_history_to() (galaxy.managers.model_stores.ModelStoreManager method) write_invocation_to() (galaxy.managers.model_stores.ModelStoreManager method) write_job_metadata() (in module galaxy.metadata.set_metadata) write_log() (galaxy.web.framework.middleware.translogger.TransLogger method) write_object_store_conf (galaxy.metadata.ExtendedDirectoryMetadataGenerator attribute) (galaxy.metadata.PortableDirectoryMetadataGenerator attribute) write_script() (in module galaxy.jobs.runners.util.job_script) write_secret() (galaxy.security.vault.CustosVault method) (galaxy.security.vault.DatabaseVault method) (galaxy.security.vault.HashicorpVault method) (galaxy.security.vault.NullVault method) (galaxy.security.vault.UserVaultWrapper method) (galaxy.security.vault.Vault method) (galaxy.security.vault.VaultKeyPrefixWrapper method) (galaxy.security.vault.VaultKeyValidationWrapper method) write_split_files() (galaxy.datatypes.sequence.Sequence class method) write_store() (galaxy.webapps.galaxy.services.histories.HistoriesService method) write_temp_file() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) write_to_file() (galaxy.datatypes.dataproviders.external.TempfileDataProvider method) writeable (galaxy.files.sources.FilesSourceOptions attribute) WriteCrates (class in galaxy.model.store) WriteHistoryContentTo (class in galaxy.schema.tasks) WriteHistoryTo (class in galaxy.schema.tasks) WriteInvocationTo (class in galaxy.schema.tasks) writelines() (galaxy.datatypes.dataproviders.base.DataProvider method) WriteStoreToPayload (class in galaxy.schema.schema) wsgi_preflight (galaxy.main_config.WebappConfig attribute)

X

x (galaxy.schema.schema.WorkflowStepLayoutPosition attribute) Xbm (class in galaxy.datatypes.images) XForwardedHostMiddleware (class in galaxy.web.framework.middleware.xforwardedhost) Xgmml (class in galaxy.datatypes.graph) XGMMLGraphDataProvider (class in galaxy.datatypes.graph) XHunterAslFormat (class in galaxy.datatypes.proteomics) Xlsx (class in galaxy.datatypes.binary) XML() (in module galaxy.util) xml_dataprovider() (galaxy.datatypes.xml.GenericXml method) xml_element_compare() (in module galaxy.util) xml_element_list_compare() (in module galaxy.util) xml_element_to_dict() (in module galaxy.util) xml_string (galaxy.tools.data.TabularToolDataTable property) xml_text() (in module galaxy.util) xml_to_dict() (galaxy.web_stack.handlers.ConfiguresHandlers static method)

xml_to_string() (in module galaxy.util) XMLDataProvider (class in galaxy.datatypes.dataproviders.hierarchy) XmlInputSource (class in galaxy.tool_util.parser.xml) XMLLintMessageLine (class in galaxy.tool_util.lint) XMLLintMessageXPath (class in galaxy.tool_util.lint) XMLOrder (class in galaxy.tool_util.linters.xml_order) XmlPageSource (class in galaxy.tool_util.parser.xml) XmlPagesSource (class in galaxy.tool_util.parser.xml) XmlToolSource (class in galaxy.tool_util.parser.xml) Xpm (class in galaxy.datatypes.images) XquestSpecXML (class in galaxy.datatypes.proteomics) XquestXML (class in galaxy.datatypes.proteomics) xrefs (galaxy.tool_util.ontologies.ontology_data.OntologyData attribute) xrefs() (galaxy.webapps.galaxy.api.tools.ToolsController method) Xtc (class in galaxy.datatypes.binary) XYZ (class in galaxy.datatypes.molecules)

Y

y (galaxy.schema.schema.WorkflowStepLayoutPosition attribute) Yaml (class in galaxy.datatypes.text) yaml_constructors (galaxy.util.yaml_util.OrderedLoader attribute) yaml_no_ts() (in module galaxy.tool_util.cwl.cwltool_deps)

YamlInputSource (class in galaxy.tool_util.parser.yaml) YamlPageSource (class in galaxy.tool_util.parser.yaml) YamlToolSource (class in galaxy.tool_util.parser.yaml) YepTar (class in galaxy.datatypes.binary)

Z

zip_single_fileobj() (in module galaxy.datatypes.sniff) ZipCollectionTool (class in galaxy.tools)

zipfile_ok() (galaxy.util.compression_utils.CompressedFile method) ZipstreamWrapper (class in galaxy.util.zipstream) ZsetGeof (class in galaxy.datatypes.constructive_solid_geometry)