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.authnz.custos_authnz.CustosAuthnz method) (galaxy.authnz.IdentityProvider method) (galaxy.authnz.managers.AuthnzManager method) (galaxy.authnz.psa_authnz.PSAAuthnz method) (galaxy.authnz.psa_authnz.Strategy method) (galaxy.config.BaseAppConfiguration method) (galaxy.config.config_manage.GzipFilter method) (galaxy.config.config_manage.PrefixFilter 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.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.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.registry.Registry method) (galaxy.datatypes.sniff.ConvertFunction method) (galaxy.datatypes.sniff.Decompress 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.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.ActionInputError method) (galaxy.exceptions.error_codes.ErrorCode method) (galaxy.exceptions.HandlerAssignmentError method) (galaxy.exceptions.MessageException method) (galaxy.exceptions.ToolExecutionError 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.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_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.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.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.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.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.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.HistoryExportView method) (galaxy.managers.histories.HistoryManager method) (galaxy.managers.histories.HistorySerializer 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.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.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.AlembicManager method) (galaxy.model.migrations.DatabaseStateCache method) (galaxy.model.migrations.DatabaseStateVerifier method) (galaxy.model.migrations.IncorrectVersionError method) (galaxy.model.migrations.InvalidModelIdError method) (galaxy.model.migrations.NoVersionTableError method) (galaxy.model.migrations.OutdatedDatabaseError method) (galaxy.model.migrations.RevisionNotFoundError method) (galaxy.model.migrations.scripts.DatabaseDoesNotExistError method) (galaxy.model.migrations.scripts.DatabaseNotInitializedError method) (galaxy.model.migrations.scripts.LegacyManageDb method) (galaxy.model.migrations.scripts.LegacyScriptsException method) (galaxy.model.NoConverterException method) (galaxy.model.none_like.NoneDataset 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.search.GalaxyQuery method) (galaxy.model.search.GalaxyQueryAnd method) (galaxy.model.search.GalaxyQueryComparison method) (galaxy.model.search.GalaxySearchEngine method) (galaxy.model.search.SearchQuery method) (galaxy.model.search.ViewField method) (galaxy.model.search.ViewQueryBaseClass 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.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.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.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.UserPreference method) (galaxy.model.UserQuotaAssociation method) (galaxy.model.UserRoleAssociation method) (galaxy.model.Vault method) (galaxy.model.view.HistoryDatasetCollectionJobStateSummary method) (galaxy.model.view.utils.CreateView method) (galaxy.model.view.utils.DropView 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.WorkflowInvocation 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.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.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.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.components.Component method) (galaxy.selenium.components.Label method) (galaxy.selenium.components.SelectorTemplate method) (galaxy.selenium.components.Text method) (galaxy.selenium.context.GalaxySeleniumContextImpl method) (galaxy.selenium.driver_factory.ConfiguredDriver 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.tool_shed.galaxy_install.datatypes.custom_datatype_manager.CustomDatatypeLoader 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.Sleeper method) (galaxy.tool_shed.galaxy_install.update_repository_manager.UpdateRepositoryManager method) (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (galaxy.tool_shed.tool_shed_registry.Registry 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.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.NullContainer 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.CachedMulledSingularityContainerResolver 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.BaseGalaxyToolBox method) (galaxy.tool_util.toolbox.base.ToolBoxRegistryImpl method) (galaxy.tool_util.toolbox.BaseGalaxyToolBox 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.tags.PersistentToolTagManager 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.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.cache.ToolShedRepositoryCache method) (galaxy.tools.data.RefgenieToolDataTable method) (galaxy.tools.data.TabularToolDataField method) (galaxy.tools.data.TabularToolDataTable method) (galaxy.tools.data.ToolDataPathFiles method) (galaxy.tools.data.ToolDataTable method) (galaxy.tools.data.ToolDataTableManager method) (galaxy.tools.data_fetch.UploadConfig method) (galaxy.tools.data_manager.manager.DataManager method) (galaxy.tools.data_manager.manager.DataManagers 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.LibraryDatasetToolParameter 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.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.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.WrappedParameters 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.dbkeys.GenomeBuilds 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.properties.NicerConfigParser.InterpolateWrapper method) (galaxy.util.renamed_temporary_file.RenamedTemporaryFile 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.CommunityTagsColumn method) (galaxy.web.framework.helpers.grids.Grid method) (galaxy.web.framework.helpers.grids.GridAction method) (galaxy.web.framework.helpers.grids.GridColumn method) (galaxy.web.framework.helpers.grids.GridColumnFilter method) (galaxy.web.framework.helpers.grids.GridOperation method) (galaxy.web.framework.helpers.grids.MulticolFilterColumn method) (galaxy.web.framework.helpers.grids.OwnerAnnotationColumn method) (galaxy.web.framework.helpers.grids.SharingStatusColumn 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.short_term_storage.ShortTermStorageConfiguration method) (galaxy.web.short_term_storage.ShortTermStorageManager method) (galaxy.web.short_term_storage.ShortTermStorageServeCancelledInformation method) (galaxy.web.short_term_storage.ShortTermStorageServeCompletedInformation method) (galaxy.web.short_term_storage.ShortTermStorageTarget method) (galaxy.web.short_term_storage.ShortTermStorageTargetSecurity 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.BaseGalaxyAPIController method) (galaxy.webapps.galaxy.api.cloud.CloudController 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.dataset_collections.FastAPIDatasetCollections method) (galaxy.webapps.galaxy.api.datasets.FastAPIDatasets method) (galaxy.webapps.galaxy.api.datatypes.FastAPIDatatypes method) (galaxy.webapps.galaxy.api.folders.FastAPILibraryFolders 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.histories.FastAPIHistories method) (galaxy.webapps.galaxy.api.history_contents.FastAPIHistoryContents method) (galaxy.webapps.galaxy.api.job_ports.JobPortsAPIController method) (galaxy.webapps.galaxy.api.jobs.FastAPIJobs 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.tools.FetchTools method) (galaxy.webapps.galaxy.api.tours.FastAPITours method) (galaxy.webapps.galaxy.api.UrlBuilder method) (galaxy.webapps.galaxy.api.users.FastAPIHistories method) (galaxy.webapps.galaxy.api.visualizations.FastAPIVisualizations method) (galaxy.webapps.galaxy.api.workflows.FastAPIWorkflows method) (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface 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.dataset_collections.DatasetCollectionsService method) (galaxy.webapps.galaxy.services.datasets.DatasetsService method) (galaxy.webapps.galaxy.services.histories.HistoriesService method) (galaxy.webapps.galaxy.services.history_contents.HistoriesContentsService method) (galaxy.webapps.galaxy.services.history_contents.HistoryItemOperator method) (galaxy.webapps.galaxy.services.history_contents.ItemOperation method) (galaxy.webapps.galaxy.services.invocations.InvocationsService method) (galaxy.webapps.galaxy.services.jobs.JobsService 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.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.galaxy.services.workflows.WorkflowsService 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.DelayedWorkflowEvaluation 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_test.base.api.ApiTestInteractor 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) (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.galaxy_install.dependency_display.DependencyDisplayer method) (tool_shed.galaxy_install.utility_containers.GalaxyUtilityContainerManager 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.managers.repositories.RepoManager method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager 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.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.utility_containers.utility_container_manager.DataManager method) (tool_shed.utility_containers.utility_container_manager.Datatype method) (tool_shed.utility_containers.utility_container_manager.Folder method) (tool_shed.utility_containers.utility_container_manager.InvalidDataManager method) (tool_shed.utility_containers.utility_container_manager.InvalidTool method) (tool_shed.utility_containers.utility_container_manager.ReadMe method) (tool_shed.utility_containers.utility_container_manager.RepositoryDependency method) (tool_shed.utility_containers.utility_container_manager.Tool method) (tool_shed.utility_containers.utility_container_manager.ToolDependency method) (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) (tool_shed.utility_containers.utility_container_manager.Workflow method) (tool_shed.webapp.api.configuration.ConfigurationController 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.Component method) (tool_shed.webapp.model.ComponentReview 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.RepositoryReview 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.tags) accept_alert() (galaxy.selenium.has_driver.HasDriver method) accept_matches() (galaxy.webapps.galaxy.api.APIContentTypeRoute method) access (galaxy.schema.schema.DatasetPermissions 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.HDADetailed attribute) (galaxy.schema.schema.HDAInaccessible attribute) accessible_count (galaxy.schema.schema.ShareHistoryExtra attribute) AccessibleManagerMixin (class in galaxy.managers.secured) 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.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.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.ImportHistoryTool attribute) (galaxy.tools.InteractiveTool 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_operation (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) 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_and_roles_query (galaxy.model.History property) 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.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_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.CustomBuildsTestcase method) add_custom_builds() (galaxy.webapps.galaxy.api.users.UserAPIController 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_empty_response_middleware() (in module galaxy.webapps.base.api) 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_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_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_installation_directories_to_tool_dependencies() (tool_shed.galaxy_install.dependency_display.DependencyDisplayer 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_local_repository() (galaxy.tools.cache.ToolShedRepositoryCache method) add_manager() (galaxy.tools.data_manager.manager.DataManagers method) add_metric() (galaxy.model.JobLike method) add_new_entries_from_config_file() (galaxy.tools.data.ToolDataTableManager 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_repository_registry_entry() (tool_shed.webapp.api.repositories.RepositoriesController method) add_repository_review_component() (tool_shed.test.base.twilltestcase.ShedTwillTestCase 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_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_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_tool_versions() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager 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) 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) 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) addError() (galaxy_test.base.instrument.StructuredTestDataPlugin method) addFailure() (galaxy_test.base.instrument.StructuredTestDataPlugin method) 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) addSuccess() (galaxy_test.base.instrument.StructuredTestDataPlugin method) adjust_hidden() (galaxy.webapps.galaxy.controllers.history.HistoryController method) adjust_total_disk_usage() (galaxy.model.User method) Admin (class in tool_shed.util.admin_util) ADMIN (galaxy.model.Role.types attribute) admin_api_keys() (galaxy.webapps.galaxy.controllers.userskeys.User method) admin_job_list (galaxy.webapps.galaxy.services.jobs.JobIndexViewEnum attribute) admin_job_lock() (in module galaxy.queue_worker) admin_only (galaxy.webapps.galaxy.api.IndexQueryTag property) admin_open() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) admin_role (tool_shed.webapp.model.Repository property) admin_users (galaxy.config.CommonConfigurationMixin property) (galaxy.tools.remote_tool_eval.ToolAppConfig property) AdminAppTestCase (class in galaxy_test.selenium.test_admin_app) 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) AdminWorkflowsApiTestCase (class in galaxy_test.api.test_workflows) Affybatch (class in galaxy.datatypes.genetics) after (galaxy.webapps.galaxy.services.history_contents.DirectionOptions attribute) AFTER (galaxy_test.api.test_history_contents.HistoryContentsApiNearTestCase attribute) after_setting_metadata() (galaxy.datatypes.data.Data method) aggregate_state_query (galaxy.model.view.HistoryDatasetCollectionJobStateSummary attribute) 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 property) 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) (galaxy.webapps.galaxy.api.histories.CreateHistoryFormData attribute) all_entry_points_configured (galaxy.model.Job property) all_jobs (galaxy.model.view.HistoryDatasetCollectionJobStateSummary attribute) (galaxy.schema.schema.HDCJobStateSummary attribute) all_metadata_files (galaxy.tools.wrappers.DatasetCollectionWrapper property) (galaxy.tools.wrappers.DatasetFilenameWrapper property) 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_users() (galaxy.webapps.galaxy.controllers.userskeys.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.BaseCwlWorkflowTestCase attribute) allow_population_by_field_name (galaxy.schema.fetch_data.FetchBaseModel.Config attribute) (galaxy.schema.schema.Model.Config attribute) (galaxy.tool_util.toolbox.views.definitions.Label.Config attribute) (galaxy.tool_util.toolbox.views.definitions.Section.Config attribute) (galaxy.tool_util.toolbox.views.definitions.StaticToolBoxView.Config attribute) (galaxy.tool_util.toolbox.views.definitions.Tool.Config attribute) (galaxy.tool_util.toolbox.views.definitions.Workflow.Config attribute) allow_push() (tool_shed.webapp.model.Repository method) allow_user_access() (galaxy.tools.DataManagerTool method) (galaxy.tools.Tool method) allowed() (galaxy.web.framework.helpers.grids.GridOperation method) (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_config_and_load_proprietary_datatypes() (galaxy.tool_shed.galaxy_install.datatypes.custom_datatype_manager.CustomDatatypeLoader method) 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.app.UniverseApplication attribute) (galaxy.structured_app.StructuredApp 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.dataset.DatasetInterface method) (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.VisualizationAnnotationAssociation attribute) (galaxy.model.WorkflowStepAnnotationAssociation attribute) (galaxy.schema.schema.CreatePagePayload attribute) (galaxy.schema.schema.HDADetailed attribute) (galaxy.schema.schema.HistoryBeta attribute) (galaxy.schema.schema.HistorySummary attribute) (galaxy.schema.schema.StoredWorkflowDetailed 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) anon_user_api_value() (galaxy.webapps.galaxy.api.users.UserAPIController method) anonymous (galaxy.managers.context.ProvidesUserContext property) AnonymousHistoriesTestCase (class in galaxy_test.selenium.test_anon_history) 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_error_message() (in module galaxy.web.framework.decorators) api_get() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) api_key (galaxy.webapps.galaxy.services.authenticate.APIKeyResponse attribute) api_key() (galaxy.webapps.galaxy.api.users.UserAPIController method) api_key_header() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) api_key_manager (galaxy.webapps.galaxy.api.users.UserAPIController attribute) 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.app.UniverseApplication attribute) (galaxy.structured_app.StructuredApp attribute) api_name (galaxy_test.api.sharable.SharingApiTests attribute) (galaxy_test.api.test_histories.SharingHistoryTestCase attribute) (galaxy_test.api.test_pages.PageApiTestCase attribute) (galaxy_test.api.test_visualizations.VisualizationsApiTestCase attribute) (galaxy_test.api.test_workflows.WorkflowsSharingApiTestCase 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.HDADetailed attribute) ApiBiotoolsMetadataSource (class in galaxy.tool_util.biotools.source) APIContentTypeRoute (class in galaxy.webapps.galaxy.api) ApiFrameworkTestCase (class in galaxy_test.api.test_framework) ApiKeyManager (class in galaxy.managers.api_keys) 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.BagArchiveModelExportStore attribute) (galaxy.model.store.BagDirectoryModelExportStore attribute) (galaxy.model.store.BaseDirectoryImportModelStore 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.TarModelExportStore 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) app_factory() (in module galaxy.webapps.galaxy.buildapp) (in module galaxy.webapps.reports.buildapp) (in module tool_shed.webapp.buildapp) app_kwds() (galaxy.main.GalaxyConfigBuilder method) app_loop() (in module galaxy.main) app_name (galaxy.config.config_manage.App property) (galaxy.main_config.WebappSetupProps property) 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.MinimalGalaxyApplication attribute) (galaxy.structured_app.BasicSharedApp attribute) (galaxy.webapps.reports.app.UniverseApplication attribute) (tool_shed.webapp.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) (galaxy.webapps.galaxy.services.history_contents.HistoryItemOperator 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.framework.helpers.grids.Grid method) (galaxy.web.legacy_framework.grids.Grid method) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid method) (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid method) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid method) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid method) (galaxy.webapps.galaxy.controllers.page.HistoryDatasetAssociationSelectionGrid method) (galaxy.webapps.galaxy.controllers.page.HistorySelectionGrid method) (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid method) (galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid method) (galaxy.webapps.galaxy.controllers.page.PageListGrid method) (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid method) (galaxy.webapps.galaxy.controllers.visualization.LibraryDatasetsSelectionGrid method) (galaxy.webapps.galaxy.controllers.visualization.TracksterSelectionGrid method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationAllPublishedGrid method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationListGrid method) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid method) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid 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) approve_repository_review() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method) approved (tool_shed.webapp.model.ComponentReview attribute) (tool_shed.webapp.model.RepositoryReview attribute) approved_states (tool_shed.webapp.model.ComponentReview attribute) (tool_shed.webapp.model.RepositoryReview attribute) AppSchema (class in galaxy.config.schema) archive (galaxy.schema.fetch_data.ElementsFromType attribute) (galaxy.util.compression_utils.CompressedFile attribute) archive() (galaxy.webapps.galaxy.api.history_contents.FastAPIHistoryContents method) (galaxy.webapps.galaxy.services.history_contents.HistoriesContentsService method) archive_dir (galaxy.model.JobImportHistoryArchive attribute) archive_download() (galaxy.webapps.galaxy.api.histories.FastAPIHistories method) archive_export() (galaxy.webapps.galaxy.api.histories.FastAPIHistories method) (galaxy.webapps.galaxy.services.histories.HistoriesService method) archive_file (galaxy.schema.schema.CreateHistoryPayload attribute) (galaxy.webapps.galaxy.api.histories.CreateHistoryFormData attribute) archive_repository_revision() (in module tool_shed.util.hg_util) archive_source (galaxy.managers.workflows.WorkflowCreateOptions attribute) (galaxy.schema.schema.CreateHistoryPayload attribute) (galaxy.webapps.galaxy.api.histories.CreateHistoryFormData attribute) archive_type (galaxy.schema.schema.CreateHistoryPayload attribute) (galaxy.webapps.galaxy.api.histories.CreateHistoryFormData attribute) 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_css_class (galaxy.selenium.components.SelectorTemplate property) 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_form() (galaxy.webapps.galaxy.api.histories.CreateHistoryFormData method) (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) as_xml() (galaxy.webapps.galaxy.controllers.history.HistoryController method) asbool() (in module galaxy.util) 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.WorkflowEditorTestCase method) assert_custom_builds_in_grid() (galaxy_test.selenium.test_custom_builds.CustomBuildsTestcase 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_finalized() (galaxy.tools.Tool method) assert_grid_histories_are() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase method) assert_grid_histories_sorted_by_owner() (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase 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_hashes_initialized() (galaxy.tools.cache.ToolCache method) assert_histories_in_grid() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase method) assert_history() (galaxy_test.selenium.test_history_multi_view.HistoryMultiViewTestCase method) assert_input_mapped() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) assert_input_not_mapped() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase 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.WorkflowEditorTestCase method) assert_name_changed() (galaxy_test.selenium.test_history_panel.HistoryPanelTestCase method) assert_no_error_message() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) assert_not_connected() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase 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_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.WorkflowEditorTestCase method) assert_wf_name_is() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) assert_xml_element() (in module galaxy.tool_util.verify.asserts.xml) assert_xpath() (galaxy.selenium.has_driver.HasDriver method) 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) associated_item_names (galaxy.model.ItemTagAssociation attribute) 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) attach_identifier() (galaxy.model.SerializationOptions 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.webapps.galaxy.api.dataset_collections.FastAPIDatasetCollections method) (galaxy.webapps.galaxy.services.dataset_collections.DatasetCollectionsService method) 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.app.MinimalGalaxyApplication attribute) (galaxy.structured_app.BasicSharedApp attribute) (galaxy.webapps.reports.app.UniverseApplication attribute) (tool_shed.webapp.app.UniverseApplication attribute) AUTH_TUPLE (class in galaxy.tool_shed.tool_shed_registry) 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.CustosAuthnz 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) AuthenticationApiTestCase (class in galaxy_test.api.test_authenticate) 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) AuthProvider (class in galaxy.auth.providers) Auto (galaxy.webapps.galaxy.services.datasets.DataMode attribute) 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) available_tracks (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.LibraryDatasetsSelectionGrid attribute) average_rating (galaxy.model.History attribute) (galaxy.model.Page attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.Visualization 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) 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) BamDataResult (class in galaxy.webapps.galaxy.services.datasets) 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) 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) BaseCwlWorkflowTestCase (class in galaxy_test.api.test_workflows_cwl) BaseDatabaseIdField (class in galaxy.schema.fields) BaseDataElement (class in galaxy.schema.fetch_data) BaseDataElement.Config (class in galaxy.schema.fetch_data) BaseDataPayload (class in galaxy.schema.fetch_data) BaseDataPayload.Config (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) BaseGalaxyToolBox (class in galaxy.tool_util.toolbox) (class in galaxy.tool_util.toolbox.base) BaseGitPlugin (class in galaxy.tools.error_reports.plugins.base_git) BaseHistories (class in galaxy_test.api.test_histories) BaseItemTagsController (class in galaxy.webapps.galaxy.api.item_tags) BaseJobContext (class in galaxy.job_execution.output_collect) BaseJobExec (class in galaxy.jobs.runners.util.cli.job) BaseJobMetric (class in galaxy.model) BaseJobRunner (class in galaxy.jobs.runners) BaseJsonToolParameter (class in galaxy.tools.parameters.basic) basename (galaxy.tool_util.cwl.util.OutputPropertiesType attribute) BaseObjectStore (class in galaxy.objectstore) BasePageApiTestCase (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) 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) 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) BasicApp (class in galaxy.structured_app) BasicRoleModel (class in galaxy.schema.schema) BasicSharedApp (class in galaxy.structured_app) BasicToolShedFeatures (class in tool_shed.test.functional.test_1000_install_basic_repository) BBIDataProvider (class in galaxy.visualization.data_providers.genome) Bcf (class in galaxy.datatypes.binary) BcfUncompressed (class in galaxy.datatypes.binary) 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 (galaxy.webapps.galaxy.services.history_contents.DirectionOptions attribute) BEFORE (galaxy_test.api.test_history_contents.HistoryContentsApiNearTestCase attribute) before_get() (galaxy.util.properties.NicerConfigParser.InterpolateWrapper method) before_setting_metadata() (galaxy.datatypes.data.Data method) beta_history_element() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy 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) boolean_false() (in module tool_shed.webapp.model.migrate.versions.0013_add_review_tables) (in module tool_shed.webapp.model.migrate.versions.0022_add_repository_admin_roles) BooleanColumn (class in galaxy.web.framework.helpers.grids) (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) (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) browse_categories() (tool_shed.webapp.controllers.repository.RepositoryController method) browse_category() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) browse_component_review() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) browse_components() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method) browse_custom_datatypes() (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() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (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_review() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController 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.tool_util.deps.mulled.util.Target property) 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_approved_select_field() (in module tool_shed.grids.util) 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.LibraryToCollectionsTestCase 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_data_managers_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) build_datatypes_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager 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_for_rerun() (galaxy.webapps.galaxy.api.jobs.JobController 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.framework.helpers.grids.Grid method) (galaxy.web.legacy_framework.grids.Grid method) (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid method) (galaxy.webapps.galaxy.controllers.forms.FormsGrid method) (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid method) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid method) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid method) (galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid method) (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid method) (galaxy.webapps.galaxy.controllers.visualization.LibraryDatasetsSelectionGrid method) (galaxy.webapps.galaxy.controllers.visualization.TracksterSelectionGrid method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationAllPublishedGrid method) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid 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) (tool_shed.grids.repository_review_grids.RepositoriesReadyForReviewGrid method) (tool_shed.grids.repository_review_grids.RepositoriesReviewedByMeGrid method) (tool_shed.grids.repository_review_grids.RepositoriesWithNoToolTestsGrid method) (tool_shed.grids.repository_review_grids.RepositoriesWithoutReviewsGrid method) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid method) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid method) (tool_shed.grids.repository_review_grids.ReviewedRepositoriesIOwnGrid method) build_invalid_data_managers_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager 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_invalid_tools_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) build_invocations_query() (galaxy.managers.workflows.WorkflowsManager method) 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_module() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) build_mulled_singularity_pull_command() (galaxy.tool_util.deps.container_classes.SingularityContainer 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_readme_files_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) build_redirect_url_params() (galaxy.tools.Tool method) build_repository_containers() (tool_shed.galaxy_install.utility_containers.GalaxyUtilityContainerManager method) (tool_shed.utility_containers.ToolShedUtilityContainerManager method) build_repository_dependencies_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager 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_select_input() (in module galaxy.webapps.galaxy.controllers.admin) build_shed_tool_conf_select_field() (in module galaxy.tool_shed.util.tool_util) (in module 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_tests() (galaxy_test.driver.driver_util.TestDriver method) build_timestamp_trigger() (in module galaxy.model.triggers.history_update_time_field) build_tool_dependencies_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) build_tool_panel_section_select_field() (in module galaxy.tool_shed.util.tool_util) (in module tool_shed.util.tool_util) build_tool_state() (galaxy_test.base.populators.BaseDatasetPopulator method) build_tools_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager 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) build_workflows_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) 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 property) 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) bulk_operation() (galaxy.webapps.galaxy.api.history_contents.FastAPIHistoryContents method) (galaxy.webapps.galaxy.services.history_contents.HistoriesContentsService method) 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 (class in galaxy.selenium.components) 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_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

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_ok (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_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() (galaxy.model.User method) call_hook() (galaxy.tools.Tool method) CallableSafeStringWrapper (class in galaxy.security.object_wrapper) callback() (galaxy.authnz.custos_authnz.CustosAuthnz 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_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.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_add_to_key_rd_dicts() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) can_browse_repository_reviews() (in module tool_shed.util.review_util) can_change (galaxy.schema.schema.ShareHistoryExtra attribute) 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) (in module 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_dataset() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_manage_library_item() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) 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_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_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) (galaxy.web.short_term_storage.ShortTermStorageManager method) (galaxy.web.short_term_storage.ShortTermStorageMonitor method) cancel_history_jobs() (galaxy_test.base.populators.BaseDatasetPopulator method) cancel_invocation() (galaxy.managers.workflows.WorkflowsManager method) (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) cancel_job() (galaxy_test.base.populators.BaseDatasetPopulator method) CANCELLED (galaxy.model.WorkflowInvocation.states attribute) CancelWorkflowEvaluation cannot_change (galaxy.schema.schema.ShareHistoryExtra attribute) CascadingBiotoolsMetadataSource (class in galaxy.tool_util.biotools.source) case_insensitive (galaxy.managers.base.ParsedFilter property) 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 (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_0130_datatype_converters) (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_0540_get_all_metadata_from_api) (in module tool_shed.test.functional.test_0550_metadata_updated_dependencies) (in module tool_shed.test.functional.test_1150_datatype_converters) (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_1450_installing_datatypes_sniffers) (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) 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.Router property) Cel (class in galaxy.datatypes.binary) celery_config() (in module galaxy_test.base.api) celery_includes() (in module galaxy_test.conftest) (in module galaxy_test.selenium.conftest) celery_parameters() (galaxy_test.base.api.UsesCeleryTasks method) celery_worker_parameters() (galaxy_test.base.api.UsesCeleryTasks method) 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_dbkey (galaxy.schema.schema.HistoryContentItemOperation attribute) change_dbkey_value_and_click_submit() (galaxy_test.selenium.test_collection_edit.CollectionEditTestCase 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) ChangeDatatypeTestCase (class in galaxy_test.api.test_workflows) ChangeDbkeyOperationParams (class in galaxy.schema.schema) ChangePasswordTestCase (class in galaxy_test.selenium.test_change_password) changeset2rev() (in module tool_shed.util.hg_util) changeset_revision (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.schema.schema.ToolShedRepositorySummary attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) (tool_shed.webapp.model.RepositoryReview attribute) changeset_revision_reviewed_by_user() (in module tool_shed.util.review_util) 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_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_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_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_dbkey_value() (galaxy_test.selenium.test_collection_edit.CollectionEditTestCase method) check_custos_sdk() (galaxy.dependencies.ConditionalDependencies method) 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_exported_repository_dependency() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) 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_missing_tools() (in module galaxy.util.tool_shed.common_util) (in module tool_shed.util.common_util) check_for_strings() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) check_for_updates() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) (tool_shed.webapp.controllers.repository.RepositoryController method) 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_onedatafs() (galaxy.dependencies.ConditionalDependencies method) check_fs_s3fs() (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.ShedTwillTestCase method) check_galaxy_root (galaxy.main_config.WebappSetupProps property) check_galaxycloudrunner() (galaxy.dependencies.ConditionalDependencies method) check_gzip() (in module galaxy.datatypes.checkers) (in module galaxy.util.checkers) check_histories() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) 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_keras() (galaxy.dependencies.ConditionalDependencies method) check_limits() (galaxy.jobs.runners.AsynchronousJobState method) check_manageable() (galaxy.managers.folders.FolderManager method) check_master_api_key() (galaxy.managers.users.UserManager method) check_modifiable() (galaxy.managers.library_datasets.LibraryDatasetsManager method) check_modifyable() (galaxy.managers.folders.FolderManager method) check_mysqlclient() (galaxy.dependencies.ConditionalDependencies method) check_or_update_tool_shed_status_for_installed_repository() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) 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_pygithub() (galaxy.dependencies.ConditionalDependencies method) check_pykube() (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.RolesApiTestCase static method) check_run() (galaxy_test.base.populators.BaseDatasetPopulator method) check_s3fs() (galaxy.dependencies.ConditionalDependencies 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_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_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) 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_tool_association (galaxy.model.tool_shed_install.ToolVersion attribute) children (galaxy.model.ExtendedMetadata attribute) (galaxy.model.Tag attribute) (galaxy.model.Vault 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) circster() (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) CisML (class in galaxy.datatypes.xml) CitationCollection (class in galaxy.managers.citations) citations() (galaxy.webapps.galaxy.api.histories.FastAPIHistories method) (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) CitationsManager (class in galaxy.managers.citations) city (galaxy.model.UserAddress attribute) class (galaxy.tool_util.cwl.util.OutputPropertiesType attribute) class_ (galaxy.schema.schema.Creator attribute) (galaxy.schema.schema.Organization attribute) (galaxy.schema.schema.Person attribute) (galaxy.webapps.galaxy.services.datasets.ExtraFileEntry attribute) CLASS_NAME (galaxy.selenium.components.By attribute) 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) (in module tool_shed.util.shed_util_common) clean_multiline_string() (in module galaxy.util) clean_repository_metadata() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) 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) (galaxy.web.short_term_storage.ShortTermStorageManager method) (galaxy.web.short_term_storage.ShortTermStorageMonitor 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_external_metadata() (galaxy.metadata.MetadataCollectionStrategy method) cleanup_from_JSON_dict_filename() (galaxy.datatypes.metadata.MetadataTempFile class method) (galaxy.model.metadata.MetadataTempFile class 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_history() (galaxy.webapps.galaxy.controllers.root.RootController method) clear_input_field_and_write() (galaxy_test.selenium.test_personal_information.ManageInformationTestCase method) clear_module_extras() (galaxy.model.WorkflowStep method) clear_tags() (galaxy_test.selenium.test_history_panel.HistoryPanelTestCase 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_grid_popup_option() (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_shared_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.ToolFormTestCase 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() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) 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) 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) CloudController (class in galaxy.webapps.galaxy.api.cloud) CloudManager (class in galaxy.managers.cloud) cluster_files_directory (galaxy.config.GalaxyAppConfiguration attribute) 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) (galaxy.webapps.galaxy.services.invocations.InvocationSerializationView attribute) (galaxy.webapps.galaxy.services.jobs.JobIndexViewEnum 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.BagArchiveModelExportStore attribute) (galaxy.model.store.BagDirectoryModelExportStore attribute) (galaxy.model.store.TarModelExportStore attribute) collection_export() (galaxy_test.selenium.test_library_to_collections.LibraryToCollectionsTestCase 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.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 property) (galaxy.util.rules_dsl.RuleSet property) (galaxy.webapps.galaxy.services.history_contents.CollectionElementIdentifier attribute) (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) CollectionBuildersTestCase (class in galaxy_test.selenium.test_collection_builders) CollectionEditTestCase (class in galaxy_test.selenium.test_collection_edit) CollectionElementIdentifier (class in galaxy.schema.schema) (class in galaxy.webapps.galaxy.services.history_contents) collections_attrs (galaxy.model.store.BagArchiveModelExportStore attribute) (galaxy.model.store.BagDirectoryModelExportStore attribute) (galaxy.model.store.TarModelExportStore 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 property) (galaxy.model.store.discover.DiscoveredFile property) (galaxy.model.store.discover.DiscoveredFileError property) ColletionSourceType (class in galaxy.schema.schema) ColorToolParameter (class in galaxy.tools.parameters.basic) column (galaxy.model.InnerCollectionFilter property) 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.Grid 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.ToolVersionListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.page.HistoryDatasetAssociationSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.HistorySelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageListGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.VisualizationSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.WorkflowSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.LibraryDatasetsSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.TracksterSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationListGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid 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) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesReadyForReviewGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesReviewedByMeGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithNoToolTestsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithoutReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) (tool_shed.grids.repository_review_grids.ReviewedRepositoriesIOwnGrid 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) commaify() (in module galaxy.util) command_line (galaxy.model.Job attribute) (galaxy.model.Task attribute) (galaxy.schema.schema.JobSummary 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) CommandLineException, [1] comment (tool_shed.webapp.model.ComponentReview attribute) (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) 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) common_columns (galaxy.managers.history_contents.HistoryContentsManager attribute) common_prefix_dir (galaxy.util.compression_utils.CompressedFile property) common_problems() (galaxy.webapps.galaxy.api.jobs.JobController method) CommonConfigurationMixin (class in galaxy.config) CommunityRatingColumn (class in galaxy.web.framework.helpers.grids) (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.framework.helpers.grids) (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_datatypes() (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_readme_files() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) 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) compare_workflows() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) compile_create_view() (in module galaxy.model.view.utils) compile_drop_view() (in module galaxy.model.view.utils) complete() (galaxy.authnz.psa_authnz.Strategy method) Component (class in galaxy.selenium.components) (class in tool_shed.webapp.model) component (tool_shed.webapp.model.ComponentReview attribute) component_grid (tool_shed.webapp.controllers.repository_review.RepositoryReviewController attribute) component_id (tool_shed.webapp.model.ComponentReview attribute) component_overlaps_region() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) component_reviews (tool_shed.webapp.model.RepositoryReview attribute) ComponentGrid (class in tool_shed.grids.repository_review_grids) ComponentGrid.DescriptionColumn (class in tool_shed.grids.repository_review_grids) ComponentGrid.NameColumn (class in tool_shed.grids.repository_review_grids) ComponentReview (class in tool_shed.webapp.model) 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.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 property) (galaxy.datatypes.sniff.HandleUploadedDatasetFileInternalResponse property) 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_outputs() (galaxy.job_execution.setup.JobIO method) compute_runtime_state() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) ComputeEnvironment (class in galaxy.job_execution.compute_environment) concat_messages() (tool_shed.tools.tool_validator.ToolValidator method) ConcreteObjectStore (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_tmp_prefix (galaxy_test.base.uses_shed.UsesShed attribute) 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) ConditionalWhen (class in galaxy.tools.parameters.grouping) 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.ConfiguresGalaxyMixin attribute) (galaxy.app_unittest_utils.galaxy_mock.MockApp attribute) (galaxy.model.CloudAuthz attribute) (galaxy.model.VisualizationRevision attribute) (galaxy.model.WorkflowStep attribute) (galaxy.structured_app.BasicApp attribute) (galaxy.tools.remote_tool_eval.ToolApp attribute) (galaxy.webapps.reports.app.UniverseApplication attribute) (tool_shed.webapp.app.UniverseApplication attribute) config_allows_origin() (in module galaxy.webapps.base.webapp) 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 property) 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) ConfigurationApiTestCase (class in galaxy_test.api.test_configuration) ConfigurationController (class in tool_shed.webapp.api.configuration) ConfigurationError, [1], [2] ConfigurationManager (class in galaxy.managers.configuration) configure() (galaxy_test.base.instrument.StructuredTestDataPlugin method) 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) configure_shed() (galaxy_test.base.uses_shed.UsesShed class method) configure_shed_and_conda() (galaxy_test.base.uses_shed.UsesShed class method) configured (galaxy.model.InteractiveToolEntryPoint 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) ConfiguresGalaxyMixin (class in galaxy.app) ConfiguresHandlers (class in galaxy.web_stack.handlers) 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) ConnectedValue (class in galaxy.tools.parameters.basic) 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.Router static method) ConsumesModelStores (class in galaxy.webapps.galaxy.services.base) contact_owner() (tool_shed.webapp.controllers.repository.RepositoryController method) contained() (galaxy.managers.history_contents.HistoryContentsManager method) 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 property) container_finder (galaxy.app.ConfiguresGalaxyMixin attribute) container_from_element() (in module galaxy.tool_util.deps.requirements) container_ids (galaxy.web.proxy.ProxyMapping property) container_info (galaxy.model.JobContainerAssociation attribute) container_interface (galaxy.web.proxy.ProxyMapping property) container_name (galaxy.model.JobContainerAssociation attribute) container_resolver (galaxy.tool_util.deps.containers.ResolvedContainerDescription property) 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.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) 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_folder() (tool_shed.utility_containers.utility_container_manager.Folder method) contains_non_orm_filter() (galaxy.managers.base.ModelFilterParser method) contains_only_kombu_tables() (galaxy.model.migrations.DatabaseStateCache method) contains_repository_dependency() (tool_shed.utility_containers.utility_container_manager.Folder 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.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) (galaxy.webapps.galaxy.services.history_contents.CreateHistoryContentPayload attribute) (galaxy.webapps.galaxy.services.history_contents.CreateHistoryContentPayloadFromCopy 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.Label attribute) (galaxy.tool_util.toolbox.views.definitions.Section attribute) (galaxy.tool_util.toolbox.views.definitions.Tool attribute) (galaxy.tool_util.toolbox.views.definitions.Workflow attribute) contents (galaxy.schema.schema.ContentsNearResult attribute) (galaxy.schema.schema.HistoryContentsWithStatsResult attribute) contents() (galaxy.managers.history_contents.HistoryContentsManager method) (galaxy.webapps.galaxy.api.dataset_collections.FastAPIDatasetCollections method) (galaxy.webapps.galaxy.services.dataset_collections.DatasetCollectionsService method) contents_active (galaxy.schema.schema.HistoryBeta attribute) contents_count() (galaxy.managers.history_contents.HistoryContentsManager method) contents_iter() (galaxy.model.History method) contents_near() (galaxy.webapps.galaxy.api.history_contents.FastAPIHistoryContents method) (galaxy.webapps.galaxy.services.history_contents.HistoriesContentsService method) contents_query() (galaxy.managers.history_contents.HistoryContentsManager method) contents_url (galaxy.schema.schema.DCObject attribute) (galaxy.schema.schema.HDCASummary attribute) (galaxy.schema.schema.HistoryDetailed attribute) ContentsNearResult (class in galaxy.schema.schema) ContentsNearStats (class in galaxy.schema.schema) 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.item_tags.HistoryContentTagsController attribute) (galaxy.webapps.galaxy.api.item_tags.HistoryTagsController attribute) (galaxy.webapps.galaxy.api.item_tags.WorkflowTagsController 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_bytes() (in module galaxy.objectstore) 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() (galaxy.webapps.galaxy.api.datasets.FastAPIDatasets method) (galaxy.webapps.galaxy.services.datasets.DatasetsService method) converted_datasets_state (galaxy.webapps.galaxy.services.datasets.RequestDataType attribute) converted_ext() (galaxy.webapps.galaxy.api.datasets.FastAPIDatasets method) (galaxy.webapps.galaxy.services.datasets.DatasetsService method) converted_newlines (galaxy.datatypes.sniff.ConvertResult property) (galaxy.datatypes.sniff.HandleUploadedDatasetFileInternalResponse property) (galaxy.datatypes.upload_util.HandleUploadResponse property) converted_path (galaxy.datatypes.sniff.ConvertResult property) (galaxy.datatypes.sniff.HandleUploadedDatasetFileInternalResponse property) (galaxy.datatypes.upload_util.HandleUploadResponse property) converted_regex (galaxy.datatypes.sniff.ConvertResult property) converted_spaces (galaxy.datatypes.sniff.HandleUploadedDatasetFileInternalResponse property) (galaxy.datatypes.upload_util.HandleUploadResponse property) ConvertedDatasetDataProvider (class in galaxy.datatypes.dataproviders.dataset) ConvertedDatasetsMap (class in galaxy.webapps.galaxy.services.datasets) ConvertedDatasetsMap.Config (class in galaxy.webapps.galaxy.services.datasets) 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) Cool (class in galaxy.datatypes.binary) copied_from_history_dataset_association (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_library_dataset_dataset_association (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.WorkflowOutput method) (galaxy.model.WorkflowStepConnection method) (galaxy.model.WorkflowStepInput 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.api.dataset_collections.FastAPIDatasetCollections method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) (galaxy.webapps.galaxy.services.dataset_collections.DatasetCollectionsService method) copy_attributes() (galaxy.model.DatasetInstance method) (galaxy.model.HistoryDatasetAssociation method) copy_database_template() (in module galaxy_test.driver.driver_util) 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_datasets() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) copy_disk_sample_files_to_dir() (tool_shed.tools.tool_validator.ToolValidator method) copy_elements (galaxy.schema.schema.CreateNewCollectionPayload attribute) (galaxy.webapps.galaxy.services.history_contents.CreateHistoryContentPayload attribute) (galaxy.webapps.galaxy.services.history_contents.CreateHistoryContentPayloadFromCollection 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_history() (galaxy_test.base.populators.BaseDatasetPopulator method) (galaxy_test.selenium.test_history_multi_view.HistoryMultiViewTestCase method) copy_item_annotation() (galaxy.model.item_attrs.UsesAnnotations method) copy_ldda() (galaxy.managers.hdas.HDAManager method) copy_library_permissions() (galaxy.model.security.GalaxyRBACAgent method) copy_list() (in module galaxy.model) copy_review() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method) copy_safe_peek (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.images.Gmaj attribute) (galaxy.datatypes.images.Laj attribute) 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_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) country (galaxy.model.UserAddress attribute) CountTable (class in galaxy.datatypes.mothur) Coverage (galaxy.webapps.galaxy.services.datasets.DataMode attribute) 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.pages.PageManager 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.dataset_collections.FastAPIDatasetCollections method) (galaxy.webapps.galaxy.api.dynamic_tools.DynamicToolsController method) (galaxy.webapps.galaxy.api.extended_metadata.BaseExtendedMetadataController method) (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method) (galaxy.webapps.galaxy.api.folders.FastAPILibraryFolders method) (galaxy.webapps.galaxy.api.forms.FormDefinitionAPIController method) (galaxy.webapps.galaxy.api.groups.GroupAPIController method) (galaxy.webapps.galaxy.api.histories.FastAPIHistories method) (galaxy.webapps.galaxy.api.history_contents.FastAPIHistoryContents method) (galaxy.webapps.galaxy.api.item_tags.BaseItemTagsController method) (galaxy.webapps.galaxy.api.job_files.JobFilesAPIController method) (galaxy.webapps.galaxy.api.job_ports.JobPortsAPIController method) (galaxy.webapps.galaxy.api.jobs.JobController 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.search.SearchController method) (galaxy.webapps.galaxy.api.tools.ToolsController method) (galaxy.webapps.galaxy.api.uploads.UploadsAPIController method) (galaxy.webapps.galaxy.api.users.UserAPIController method) (galaxy.webapps.galaxy.api.visualizations.VisualizationsController method) (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController 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.dataset_collections.DatasetCollectionsService method) (galaxy.webapps.galaxy.services.histories.HistoriesService method) (galaxy.webapps.galaxy.services.history_contents.HistoriesContentsService 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.SharingHistoryTestCase method) (galaxy_test.api.test_pages.PageApiTestCase method) (galaxy_test.api.test_visualizations.VisualizationsApiTestCase method) (galaxy_test.api.test_workflows.WorkflowsSharingApiTestCase method) (tool_shed.managers.groups.GroupManager method) (tool_shed.managers.repositories.RepoManager 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.managers.users.UserManager method) create_applet_tag_peek() (in module galaxy.datatypes.images) 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_component() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method) 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_element() (in module galaxy.util.tool_shed.xml_util) (in module tool_shed.util.xml_util) create_entry_points() (galaxy.managers.interactivetool.InteractiveToolManager 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_form() (galaxy.webapps.galaxy.controllers.forms.Forms method) create_from_store() (galaxy.webapps.galaxy.api.histories.FastAPIHistories method) (galaxy.webapps.galaxy.api.history_contents.FastAPIHistoryContents method) (galaxy.webapps.galaxy.api.libraries.FastAPILibraries method) (galaxy.webapps.galaxy.services.histories.HistoriesService method) (galaxy.webapps.galaxy.services.history_contents.HistoriesContentsService 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.api.histories.FastAPIHistories method) (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_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.SavedHistoriesTestCase method) (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase method) 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_invocations_from_store() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController 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_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_or_verify_database() (in module tool_shed.webapp.model.migrate.check) create_outdir() (galaxy.tool_util.cwl.cwltool_deps.RuntimeContext method) create_page() (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.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.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_repository_dict_for_proprietary_datatypes() (galaxy.tool_shed.galaxy_install.datatypes.custom_datatype_manager.CustomDatatypeLoader method) create_repository_review() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) create_review() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController 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_simple_list_collection() (galaxy_test.selenium.test_collection_edit.CollectionEditTestCase 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_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.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.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.schema.DCSummary 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.LibraryLegacySummary attribute) (galaxy.schema.schema.PageSortByEnum attribute) (galaxy.schema.schema.StoredWorkflowSummary attribute) (galaxy.schema.schema.WorkflowSortByEnum attribute) (tool_shed.webapp.model.APIKeys attribute) (tool_shed.webapp.model.Category attribute) (tool_shed.webapp.model.ComponentReview 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.RepositoryReview 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_unique_slug() (galaxy.managers.sharable.SharableModelManager method) create_user() (galaxy.authnz.custos_authnz.CustosAuthnz method) (galaxy.authnz.managers.AuthnzManager method) (galaxy.model.UserAuthnzToken class method) (galaxy.webapps.galaxy.controllers.authnz.OIDC method) create_user_in_galaxy() (tool_shed.test.base.twilltestcase.ShedTwillTestCase 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.discover.JsonCollectedDatasetMatch property) (galaxy.schema.fetch_data.BaseDataElement attribute) (galaxy.schema.schema.HDADetailed attribute) created_time (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.JobContainerAssociation attribute) CreatedWorkflow (class in galaxy.managers.workflows) CreateHistoryContentFromStore (class in galaxy.webapps.galaxy.services.history_contents) CreateHistoryContentPayload (class in galaxy.webapps.galaxy.services.history_contents) CreateHistoryContentPayload.Config (class in galaxy.webapps.galaxy.services.history_contents) CreateHistoryContentPayloadBase (class in galaxy.webapps.galaxy.services.history_contents) CreateHistoryContentPayloadFromCollection (class in galaxy.webapps.galaxy.services.history_contents) CreateHistoryContentPayloadFromCopy (class in galaxy.webapps.galaxy.services.history_contents) CreateHistoryFormData (class in galaxy.webapps.galaxy.api.histories) CreateHistoryFromStore (class in galaxy.schema.schema) CreateHistoryPayload (class in galaxy.schema.schema) CreateInvocationFromStore (class in galaxy.webapps.galaxy.api.workflows) CreateInvocationFromStore.Config (class in galaxy.webapps.galaxy.api.workflows) CreateLibrariesFromStore (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) CreatePagePayload.Config (class in galaxy.schema.schema) CreateView (class in galaxy.model.view.utils) creating_job (galaxy.model.DatasetInstance property) (galaxy.schema.schema.HDADetailed attribute) creating_job() (galaxy.managers.datasets.DatasetAssociationManager method) creating_job_associations (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) Creator (class in galaxy.schema.schema) creator (galaxy.schema.schema.StoredWorkflowDetailed attribute) (galaxy.schema.schema.WorkflowToExport attribute) (galaxy.workflow.refactor.schema.UpdateCreatorAction attribute) creator_metadata (galaxy.model.Workflow attribute) csFasta (class in galaxy.datatypes.sequence) css() (galaxy.app_unittest_utils.galaxy_mock.MockTemplateHelpers method) (in module galaxy.web.framework.helpers) CSS_SELECTOR (galaxy.selenium.components.By attribute) CSV (class in galaxy.datatypes.tabular) ctx_rev (galaxy.model.tool_shed_install.ToolShedRepository attribute) CuffDiffSQlite (class in galaxy.datatypes.binary) cur_filter_pref_name (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.web.legacy_framework.grids.Grid attribute) cur_sort_key_pref_name (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.web.legacy_framework.grids.Grid attribute) current (galaxy.schema.schema.LibraryPermissionScope attribute) 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_user() (galaxy.managers.users.UserManager method) current_version (galaxy.tools.safe_update property) CurrentUserSerializer (class in galaxy.managers.users) CustomBuildsMetadataResponse (class in galaxy.schema.schema) CustomBuildsTestcase (class in galaxy_test.selenium.test_custom_builds) CustomDatatypeLoader (class in galaxy.tool_shed.galaxy_install.datatypes.custom_datatype_manager) CustomHistoryItem (class in galaxy.schema.schema) CustomHistoryItem.Config (class in galaxy.schema.schema) CustomTrack (class in galaxy.datatypes.interval) custos_auth (galaxy.model.User attribute) CustosAuthnz (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) 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) 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) DATA (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute) data (galaxy.webapps.galaxy.services.datasets.DataResult attribute) (galaxy.webapps.galaxy.services.datasets.RequestDataType attribute) data_collection_input (galaxy.schema.schema.WorkflowModuleType attribute) DATA_COLLECTON (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_input (galaxy.schema.schema.WorkflowModuleType attribute) data_line_offset (galaxy.datatypes.tabular.SraManifest attribute) (galaxy.datatypes.tabular.TabularData attribute) data_manager_association (galaxy.model.Job attribute) data_manager_config_elems_to_xml_file() (galaxy.tool_shed.galaxy_install.tools.data_manager.DataManagerHandler method) 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.app.UniverseApplication attribute) (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.Sam attribute) data_tables (galaxy.managers.tool_data.ToolDataManager property) data_tables_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) data_type (galaxy.schema.schema.HDADetailed attribute) data_types_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy 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.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) DatabaseDoesNotExistError DatabaseHeartbeat (class in galaxy.model.database_heartbeat) DatabaseManager (class in galaxy.model.database_utils) DatabaseNotInitializedError DatabaseOperationTool (class in galaxy.tools) DatabaseStateCache (class in galaxy.model.migrations) 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) DataManager (class in galaxy.tools.data_manager.manager) (class in galaxy.webapps.galaxy.controllers.data_manager) (class in tool_shed.utility_containers.utility_container_manager) DataManagerHandler (class in galaxy.tool_shed.galaxy_install.tools.data_manager) DataManagerHistoryAssociation (class in galaxy.model) DataManagerJobAssociation (class in galaxy.model) 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) DataMode (class in galaxy.webapps.galaxy.services.datasets) 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) DataResult (class in galaxy.webapps.galaxy.services.datasets) Dataset (class in galaxy.model) (class in galaxy.tools.parameters.grouping) dataset (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) (galaxy.webapps.galaxy.services.datasets.DatasetErrorMessage attribute) Dataset.conversion_messages (class in galaxy.model) Dataset.states (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.GalaxyManagerApplication 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_details (galaxy.webapps.galaxy.services.history_contents.HistoryContentsIndexParams attribute) (galaxy.webapps.galaxy.services.history_contents.LegacyHistoryContentsIndexParams attribute) 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.HDASummary attribute) dataset_id_to_path (galaxy.model.store.BagArchiveModelExportStore attribute) (galaxy.model.store.BagDirectoryModelExportStore attribute) (galaxy.model.store.TarModelExportStore 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_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_manager_by_type (galaxy.webapps.galaxy.services.datasets.DatasetsService property) dataset_path_rewriter (galaxy.job_execution.setup.JobIO property) dataset_path_rewrites() (in module galaxy.job_execution.datasets) dataset_permission_map_for_access() (galaxy.model.security.GalaxyRBACAgent method) dataset_populator (galaxy_test.api.test_tools.TestsTools attribute) (galaxy_test.api.test_workflows.ChangeDatatypeTestCase attribute) (galaxy_test.base.populators.BaseDatasetCollectionPopulator attribute) (galaxy_test.base.populators.BaseWorkflowPopulator attribute) (galaxy_test.base.populators.DatasetCollectionPopulator attribute) dataset_source_id (galaxy.model.DatasetSourceHash attribute) dataset_state (galaxy.webapps.galaxy.services.datasets.DatasetStorageDetails 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) (galaxy.webapps.galaxy.services.datasets.DataResult 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) DatasetCollection (class in galaxy.model) DatasetCollection.populated_states (class in galaxy.model) DatasetCollectionApiTestCase (class in galaxy_test.api.test_dataset_collections) DatasetCollectionAttributesResult (class in galaxy.webapps.galaxy.services.dataset_collections) DatasetCollectionContentElements (class in galaxy.webapps.galaxy.services.dataset_collections) DatasetCollectionDescription (class in galaxy.tool_util.parser.output_collection_def) DatasetCollectionElement (class in galaxy.model) DatasetCollectionInstance (class in galaxy.model) DatasetCollectionInstanceType (class in galaxy.schema.schema) DatasetCollectionManager (class in galaxy.managers.collections) DatasetCollectionPopulator (class in galaxy_test.base.populators) DatasetCollectionsService (class in galaxy.webapps.galaxy.services.dataset_collections) 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) DatasetErrorMessage (class in galaxy.webapps.galaxy.services.datasets) 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) DatasetInheritanceChain (class in galaxy.webapps.galaxy.services.datasets) DatasetInheritanceChainEntry (class in galaxy.webapps.galaxy.services.datasets) DatasetInstance (class in galaxy.model) DatasetInstance.conversion_messages (class in galaxy.model) DatasetInstance.states (class in galaxy.model) DatasetInstance.validated_states (class in galaxy.model) DatasetInstanceMaterializer (class in galaxy.model.deferred) DatasetInterface (class in galaxy.webapps.galaxy.controllers.dataset) DatasetJobInfo (class in galaxy.schema.schema) 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) (galaxy.webapps.galaxy.services.datasets.DeleteDatasetBatchPayload 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) DatasetsApiTestCase (class in galaxy_test.api.test_datasets) DatasetSerializer (class in galaxy.managers.datasets) DatasetSource (class in galaxy.model) DatasetSourceHash (class in galaxy.model) DatasetSourceId (class in galaxy.schema.schema) DatasetSourceType (class in galaxy.schema.schema) DatasetsService (class in galaxy.webapps.galaxy.services.datasets) DatasetStorageDetails (class in galaxy.webapps.galaxy.services.datasets) DatasetSubprocessDataProvider (class in galaxy.datatypes.dataproviders.dataset) DatasetTextContentDetails (class in galaxy.webapps.galaxy.services.datasets) datasource_tool_open() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) DataSourceParser (class in galaxy.visualization.plugins.config_parser) DataSourceTestCase (class in galaxy_test.selenium.test_data_source_tools) 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 (class in tool_shed.utility_containers.utility_container_manager) datatype (galaxy.datatypes.upload_util.HandleUploadResponse property) (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.managers.display_applications.DisplayApplicationsManager property) (galaxy.model.store.StoreAppProtocol attribute) (galaxy.structured_app.BasicApp 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) (tool_shed.webapp.app.UniverseApplication attribute) DatatypesApiTestCase (class in galaxy_test.api.test_datatypes) DatatypesCombinedMap (class in galaxy.managers.datatypes) 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) datetime_to_iso8601() (in module galaxy.managers.metrics) DateTimeColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.web.legacy_framework.grids) db_builds (galaxy.managers.context.ProvidesHistoryContext property) db_dataset_for() (galaxy.managers.context.ProvidesHistoryContext method) db_heads (galaxy.model.migrations.AlembicManager property) 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.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) (galaxy.webapps.galaxy.services.dataset_collections.DatasetCollectionAttributesResult attribute) (galaxy.webapps.galaxy.services.dataset_collections.UpdateCollectionAttributePayload attribute) (galaxy.webapps.galaxy.services.history_contents.CreateHistoryContentPayload attribute) (galaxy.webapps.galaxy.services.history_contents.CreateHistoryContentPayloadFromCollection attribute) DBKeyParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) dbkeys (galaxy.webapps.galaxy.services.dataset_collections.DatasetCollectionAttributesResult attribute) DCASerializer (class in galaxy.managers.hdcas) Dcd (class in galaxy.datatypes.binary) DCDetailed (class in galaxy.schema.schema) 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) 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.ShedTwillTestCase 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.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_query_ids() (galaxy.model.search.SearchQuery method) (galaxy.model.search.ViewQueryBaseClass method) decode_runtime_state() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) decode_type_id() (galaxy.managers.history_contents.HistoryContentsFilters method) decode_with_security() (in module galaxy.managers.base) DecodedDatabaseIdField (class in galaxy.schema.fields) decoder() (in module galaxy.tools.cache) Decompress (class in galaxy.datatypes.sniff) deep_dict_operation_merge() (in module galaxy.webapps.openapi.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.dataset.DatasetInterface 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.framework.helpers.grids.Grid attribute) (galaxy.web.legacy_framework.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageListGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.LibraryDatasetsSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationListGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid 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 property) 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) (galaxy.util.dbkeys.GenomeBuilds 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 property) 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 property) 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.framework.helpers.grids.Grid 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.ToolVersionListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageListGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.LibraryDatasetsSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.TracksterSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationListGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid 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) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) DEFAULT_SPECS (galaxy.jobs.runners.BaseJobRunner attribute) default_storage_duration (galaxy.web.short_term_storage.ShortTermStorageConfiguration 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_value (galaxy.model.WorkflowStepInput attribute) (galaxy.util.dbkeys.GenomeBuilds 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.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.model.Dataset.states attribute) (galaxy.model.DatasetInstance.states attribute) deferred (galaxy.schema.fetch_data.BaseDataElement 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.libraries.LibraryManager 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.group_roles.FastAPIGroupRoles method) (galaxy.webapps.galaxy.api.group_users.FastAPIGroupUsers method) (galaxy.webapps.galaxy.api.histories.FastAPIHistories method) (galaxy.webapps.galaxy.api.history_contents.FastAPIHistoryContents method) (galaxy.webapps.galaxy.api.item_tags.BaseItemTagsController method) (galaxy.webapps.galaxy.api.jobs.JobController 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.Router method) (galaxy.webapps.galaxy.api.sanitize_allow.SanitizeAllowController method) (galaxy.webapps.galaxy.api.tool_data.FastAPIToolData method) (galaxy.webapps.galaxy.api.users.UserAPIController method) (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) (galaxy.webapps.galaxy.services.histories.HistoriesService method) (galaxy.webapps.galaxy.services.history_contents.HistoriesContentsService 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) (tool_shed.managers.repositories.RepoManager method) delete_async() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) delete_batch() (galaxy.webapps.galaxy.api.datasets.FastAPIDatasets method) (galaxy.webapps.galaxy.services.datasets.DatasetsService method) delete_custom_build() (galaxy_test.selenium.test_custom_builds.CustomBuildsTestcase method) delete_custom_builds() (galaxy.webapps.galaxy.api.users.UserAPIController 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_obj() (in module tool_shed.test.base.test_db_util) delete_operation (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) (tool_shed.util.admin_util.Admin attribute) (tool_shed.webapp.controllers.admin.AdminController attribute) delete_quota() (galaxy.managers.quotas.QuotaManager method) delete_repo_request() (galaxy_test.base.uses_shed.UsesShed 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) delete_user_roles() (in module tool_shed.test.base.test_db_util) DeleteCurrentAccountTestCase (class in galaxy_test.selenium.test_personal_information) deleted (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) DELETED (galaxy.model.Job.states attribute) deleted (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.view.HistoryDatasetCollectionJobStateSummary attribute) (galaxy.model.Visualization attribute) (galaxy.schema.schema.DeleteHistoryContentResult attribute) (galaxy.schema.schema.HDCJobStateSummary attribute) (galaxy.schema.schema.HistoryActiveContentCounts attribute) (galaxy.schema.schema.HistoryItemBase attribute) (galaxy.schema.schema.HistorySummary attribute) (galaxy.schema.schema.LibraryFolderDetails attribute) (galaxy.schema.schema.LibraryLegacySummary attribute) (galaxy.schema.schema.PageIndexQueryPayload attribute) (galaxy.schema.schema.PageSummary attribute) (galaxy.schema.schema.StoredWorkflowSummary attribute) (galaxy.schema.schema.UserModel attribute) (galaxy.webapps.galaxy.services.history_contents.LegacyHistoryContentsIndexParams attribute) (tool_shed.webapp.model.Category attribute) (tool_shed.webapp.model.ComponentReview attribute) (tool_shed.webapp.model.Group attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.RepositoryReview 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.model.Job.states attribute) deleted_new (galaxy.model.view.HistoryDatasetCollectionJobStateSummary attribute) (galaxy.schema.schema.HDCJobStateSummary attribute) DeleteDatasetAction (class in galaxy.job_execution.actions.post) DeleteDatasetBatchPayload (class in galaxy.webapps.galaxy.services.datasets) DeleteDatasetBatchResult (class in galaxy.webapps.galaxy.services.datasets) DeletedColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.web.legacy_framework.grids) DeleteHistoryContentPayload (class in galaxy.schema.schema) DeleteHistoryContentResult (class in galaxy.schema.schema) DeleteHistoryPayload (class in galaxy.webapps.galaxy.api.histories) DeleteIntermediatesAction (class in galaxy.job_execution.actions.post) DeleteLibraryPayload (class in galaxy.schema.schema) DELETING (galaxy.model.Job.states attribute) delimiter (galaxy.datatypes.tabular.BaseCSV attribute) dep (galaxy.webapps.galaxy.services.datasets.DatasetInheritanceChainEntry attribute) dependencies (galaxy.model.Job attribute) DependenciesDescription (class in galaxy.tool_util.deps.dependencies) Dependency (class in galaxy.tool_util.deps.resolvers) dependency_resolvers_view (galaxy.app.UniverseApplication attribute) (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) DependencyDisplayer (class in tool_shed.galaxy_install.dependency_display) 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_jobs (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) 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) descendant() (galaxy.selenium.components.SelectorTemplate 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.schema.fetch_data.LibraryDestination attribute) (galaxy.schema.schema.CreateLibraryFolderPayload attribute) (galaxy.schema.schema.CreateLibraryPayload attribute) (galaxy.schema.schema.Input attribute) (galaxy.schema.schema.LibraryFolderDetails attribute) (galaxy.schema.schema.LibraryLegacySummary attribute) (galaxy.schema.schema.RoleDefinitionModel attribute) (galaxy.schema.schema.RoleModel attribute) (galaxy.schema.schema.UpdateLibraryFolderPayload attribute) (galaxy.schema.schema.UpdateLibraryPayload attribute) (galaxy.selenium.components.Label property) (galaxy.selenium.components.SelectorTemplate property) (galaxy.selenium.components.Target property) (galaxy.selenium.components.Text property) (galaxy.tool_util.toolbox.views.definitions.StaticToolBoxView attribute) (galaxy.tool_util.toolbox.views.interface.ToolPanelViewModel attribute) (galaxy.tours.TourCore attribute) (galaxy.webapps.galaxy.api.IndexQueryTag property) (galaxy.webapps.galaxy.services.datasets.DatasetStorageDetails attribute) (tool_shed.webapp.model.Category attribute) (tool_shed.webapp.model.Component 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_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 property) (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() (galaxy.webapps.galaxy.api.jobs.JobController method) 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) 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) diagnostics() (galaxy.webapps.galaxy.api.tools.ToolsController method) dialect (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.ComponentReview attribute) (tool_shed.webapp.model.Group attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) (tool_shed.webapp.model.RepositoryReview 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.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.ComponentReview attribute) (tool_shed.webapp.model.Group attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) (tool_shed.webapp.model.RepositoryReview 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) 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) DirectionOptions (class in galaxy.webapps.galaxy.services.history_contents) Directory (class in galaxy.datatypes.data) directory (galaxy.schema.fetch_data.ElementsFromType attribute) Directory (galaxy.webapps.galaxy.services.datasets.ExtraFilesEntryClass 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.histories.FastAPIHistories method) (galaxy.webapps.galaxy.api.pages.FastAPIPages method) (galaxy.webapps.galaxy.api.visualizations.FastAPIVisualizations method) (galaxy.webapps.galaxy.api.workflows.FastAPIWorkflows 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) DISABLED (galaxy.tools.parameters.basic.workflow_building_modes attribute) discard() (galaxy.util.oset.OrderedSet method) DISCARDED (galaxy.model.Dataset.states attribute) (galaxy.model.DatasetInstance.states attribute) discarded_data (galaxy.model.store.ImportOptions attribute) disconnect() (galaxy.authnz.custos_authnz.CustosAuthnz 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) disk_usage() (galaxy.webapps.reports.controllers.system.System method) DiskObjectStore (class in galaxy.objectstore) dispatch() (galaxy.web_stack.message.ApplicationStackMessageDispatcher method) (galaxy.webapps.base.api.SuppressNoResponseReturnedMiddleware method) display (galaxy.util.rules_dsl.RuleSet property) display() (galaxy.webapps.galaxy.api.datasets.FastAPIDatasets method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.services.datasets.DatasetsService method) display_amount (galaxy.model.Quota property) display_application() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) display_apps (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_at() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) display_by_id() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) display_by_username_and_slug() (galaxy.webapps.base.controller.SharableMixin method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface 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_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_galaxy_browse_repositories_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase 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.ShedTwillTestCase method) display_installed_repository_manage_page() (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.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.NcbiTaxonomySQlite method) (galaxy.datatypes.binary.NetCDF method) (galaxy.datatypes.binary.Npz 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.images.Gmaj method) (galaxy.datatypes.images.Laj 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_repository_reviews_by_user() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) display_reviewed_repositories_owned_by_user() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) display_structured() (galaxy.webapps.galaxy.controllers.history.HistoryController method) display_tool() (tool_shed.webapp.controllers.repository.RepositoryController method) display_types (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) DisplayApplicationDataParameter (class in galaxy.datatypes.display_applications.parameters) DisplayApplicationLink (class in galaxy.datatypes.display_applications.application) DisplayApplicationParameter (class in galaxy.datatypes.display_applications.parameters) DisplayApplicationsApiTestCase (class in galaxy_test.api.test_display_applications) DisplayApplicationsController (class in galaxy.webapps.galaxy.api.display_applications) DisplayApplicationsManager (class in galaxy.managers.display_applications) DisplayApplicationTemplateParameter (class in galaxy.datatypes.display_applications.parameters) DisplayByUsernameAndSlugGridOperation (class in galaxy.web.framework.helpers.grids) (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) 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_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.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) DOMAIN (galaxy.model.search.HistoryDatasetView attribute) (galaxy.model.search.HistoryView attribute) (galaxy.model.search.JobView attribute) (galaxy.model.search.PageRevisionView attribute) (galaxy.model.search.PageView attribute) (galaxy.model.search.WorkflowView attribute) DotBracket (class in galaxy.datatypes.sequence) downgrade() (in module tool_shed.webapp.model.migrate.versions.0001_initial_tables) (in module tool_shed.webapp.model.migrate.versions.0002_add_tool_suite_column) (in module tool_shed.webapp.model.migrate.versions.0003_review_and_review_association_tables) (in module tool_shed.webapp.model.migrate.versions.0004_repository_tables) (in module tool_shed.webapp.model.migrate.versions.0005_drop_tool_related_tables) (in module tool_shed.webapp.model.migrate.versions.0006_add_email_alerts_column) (in module tool_shed.webapp.model.migrate.versions.0007_add_long_description_times_downloaded_columns) (in module tool_shed.webapp.model.migrate.versions.0008_add_repository_metadata_table) (in module tool_shed.webapp.model.migrate.versions.0009_add_malicious_column) (in module tool_shed.webapp.model.migrate.versions.0010_add_new_repo_alert_column) (in module tool_shed.webapp.model.migrate.versions.0011_add_tool_versions_column) (in module tool_shed.webapp.model.migrate.versions.0012_add_downloadable_column) (in module tool_shed.webapp.model.migrate.versions.0013_add_review_tables) (in module tool_shed.webapp.model.migrate.versions.0014_add_deprecated_column) (in module tool_shed.webapp.model.migrate.versions.0015_add_api_keys_table) (in module tool_shed.webapp.model.migrate.versions.0016_add_do_not_test_tools_functionally_correct_errors_columns) (in module tool_shed.webapp.model.migrate.versions.0017_add_galaxy_utility_columns_to_repository_metadata_table) (in module tool_shed.webapp.model.migrate.versions.0018_add_repository_metadata_flag_columns) (in module tool_shed.webapp.model.migrate.versions.0019_add_skip_tool_test_table_and_test_install_error_column) (in module tool_shed.webapp.model.migrate.versions.0020_add_repository_type_column) (in module tool_shed.webapp.model.migrate.versions.0021_change_repository_type_value) (in module tool_shed.webapp.model.migrate.versions.0022_add_repository_admin_roles) (in module tool_shed.webapp.model.migrate.versions.0023_add_repository_url_and_hompeage_url) (in module tool_shed.webapp.model.migrate.versions.0024_password_reset) (in module tool_shed.webapp.model.migrate.versions.0025_session_timeout) (in module tool_shed.webapp.model.migrate.versions.0026_add_numeric_revision_column) 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_collection() (galaxy.webapps.galaxy.api.history_contents.FastAPIHistoryContents method) download_dataset_from_library() (galaxy_test.selenium.test_library_contents.LibraryContentsTestCase method) download_field_file() (galaxy.webapps.galaxy.api.tool_data.FastAPIToolData method) download_invocation_bco() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController 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.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) DriverWrapper (class in galaxy.selenium.cli) DRMAAJobRunner (class in galaxy.jobs.runners.drmaa) drop_column() (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) DropView (class in galaxy.model.view.utils) 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 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.app.UniverseApplication attribute) (galaxy.structured_app.StructuredApp 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.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_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.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.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.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_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 property) edam_topics (galaxy.tool_util.biotools.interface.ParsedBiotoolsEntry attribute) (galaxy.tool_util.biotools.ParsedBiotoolsEntry attribute) (galaxy.tool_util.ontologies.ontology_data.OntologyData property) 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_component() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method) edit_content() (galaxy.webapps.galaxy.controllers.page.PageController 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_review() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController 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) 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 (galaxy.tours.TourStep attribute) (galaxy.webapps.galaxy.services.invocations.InvocationSerializationView 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) (galaxy.webapps.galaxy.services.history_contents.CollectionElementIdentifier attribute) element_identifiers_extensions_and_paths (galaxy.model.DatasetCollection property) 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.FilterEmptyDatasetsTool method) (galaxy.tools.FilterFailedDatasetsTool method) element_locator (galaxy.selenium.components.Label property) (galaxy.selenium.components.SelectorTemplate property) (galaxy.selenium.components.Target property) (galaxy.selenium.components.Text property) 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) 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.Creator attribute) (galaxy.schema.schema.GroupUserModel attribute) (galaxy.schema.schema.UserEmail attribute) (galaxy.schema.schema.UserModel 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) 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) emboss_repository_long_description (in module tool_shed.test.functional.test_0470_tool_dependency_repository_type) EMPTY (galaxy.model.Dataset.states attribute) (galaxy.model.DatasetInstance.states attribute) empty (galaxy.model.History property) (galaxy.schema.schema.HistoryBeta attribute) empty() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) EmptyTextfieldValidator (class in galaxy.tools.parameters.validation) enable_email_alerts() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) enable_link_access() (galaxy.webapps.galaxy.api.histories.FastAPIHistories method) (galaxy.webapps.galaxy.api.pages.FastAPIPages method) (galaxy.webapps.galaxy.api.visualizations.FastAPIVisualizations method) (galaxy.webapps.galaxy.api.workflows.FastAPIWorkflows method) (galaxy.webapps.galaxy.services.sharable.ShareableService method) ENABLED (galaxy.tools.parameters.basic.workflow_building_modes 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.security.idencoding.IdEncodingHelper method) (galaxy.webapps.galaxy.services.base.ServiceBase method) encode_runtime_state() (galaxy.workflow.modules.WorkflowModule method) encode_with_security() (in module galaxy.managers.base) EncodedDatabaseIdField (class in galaxy.schema.fields) 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 property) end (galaxy.datatypes.util.maf_utilities.SplicedAlignment property) (galaxy.tools.util.maf_utilities.SplicedAlignment property) engine (galaxy.model.Dataset attribute) enqueue() (galaxy.jobs.manager.JobManager method) (galaxy.jobs.manager.NoopManager 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_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_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.CollectionBuildersTestCase attribute) (galaxy_test.selenium.test_collection_edit.CollectionEditTestCase attribute) (galaxy_test.selenium.test_data_source_tools.DataSourceTestCase attribute) <