Index

_

__init__() (galaxy.app.ExecutionTimerFactory method) (galaxy.app.StatsdStructuredExecutionTimer method) (galaxy.app.UniverseApplication 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.containers.Container method) (galaxy.containers.ContainerInterface method) (galaxy.containers.ContainerVolume method) (galaxy.containers.docker.DockerAPIClient method) (galaxy.containers.docker_model.DockerAttributeContainer method) (galaxy.containers.docker_model.DockerContainer method) (galaxy.containers.docker_model.DockerNode method) (galaxy.containers.docker_model.DockerNodeLabel method) (galaxy.containers.docker_model.DockerService method) (galaxy.containers.docker_model.DockerServiceConstraint method) (galaxy.containers.docker_model.DockerTask 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.DAA method) (galaxy.datatypes.binary.Dcd method) (galaxy.datatypes.binary.DMND method) (galaxy.datatypes.binary.H5 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.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.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.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.ContainerCLIError method) (galaxy.exceptions.ContainerImageNotFound method) (galaxy.exceptions.ContainerNotFound method) (galaxy.exceptions.ContainerRunError 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.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.forms.forms.FormDefinitionFactory 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_metrics.collectl.cli.CollectlCli method) (galaxy.job_metrics.collectl.stats.StatisticsTracker method) (galaxy.job_metrics.instrumenters.cgroup.CgroupPlugin method) (galaxy.job_metrics.instrumenters.collectl.CollectlPlugin 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.job_metrics.JobMetrics 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.condor.CondorJobRunner 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.job.lsf.LSF method) (galaxy.jobs.runners.util.cli.job.slurm.Slurm method) (galaxy.jobs.runners.util.cli.job.torque.Torque 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.SharedComputeEnvironment method) (galaxy.jobs.TaskWrapper method) (galaxy.jobs.transfer_manager.TransferManager method) (galaxy.main.GalaxyConfigBuilder method) (galaxy.managers.api_keys.ApiKeyManager 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.ModelValidator 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.cloud.CloudManager method) (galaxy.managers.cloudauthzs.CloudAuthzsSerializer method) (galaxy.managers.collections.DatasetCollectionManager method) (galaxy.managers.configuration.ConfigSerializer method) (galaxy.managers.datasets.DatasetAssociationManager method) (galaxy.managers.datasets.DatasetManager method) (galaxy.managers.datasets.DatasetRBACPermissions method) (galaxy.managers.datasets.DatasetSerializer 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.libraries.LibraryManager method) (galaxy.managers.library_datasets.LibraryDatasetsManager method) (galaxy.managers.licenses.LicensesManager method) (galaxy.managers.pages.PageContentProcessor method) (galaxy.managers.pages.PageDeserializer method) (galaxy.managers.pages.PageManager method) (galaxy.managers.pages.PageSerializer method) (galaxy.managers.rbac_secured.RBACPermission method) (galaxy.managers.roles.RoleManager method) (galaxy.managers.session.GalaxySessionManager method) (galaxy.managers.sharable.SharableModelManager method) (galaxy.managers.sharable.SharableModelSerializer method) (galaxy.managers.tools.DynamicToolManager method) (galaxy.managers.users.UserManager method) (galaxy.managers.users.UserSerializer method) (galaxy.managers.visualizations.VisualizationDeserializer method) (galaxy.managers.visualizations.VisualizationManager method) (galaxy.managers.visualizations.VisualizationSerializer method) (galaxy.managers.workflows.MissingToolsException method) (galaxy.managers.workflows.RawWorkflowDescription method) (galaxy.managers.workflows.WorkflowContentsManager method) (galaxy.managers.workflows.WorkflowsManager method) (galaxy.metadata.ExtendedDirectoryMetadataGenerator method) (galaxy.metadata.PortableDirectoryMetadataGenerator method) (galaxy.model.APIKeys method) (galaxy.model.base.ModelMapping method) (galaxy.model.BaseJobMetric method) (galaxy.model.CloudAuthz method) (galaxy.model.ConverterDependencyException method) (galaxy.model.CustosAuthnzToken method) (galaxy.model.database_heartbeat.DatabaseHeartbeat 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.DatasetCollectionInstance 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.DeferredJob 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.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.ItemTagAssociation 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.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.StorableObject method) (galaxy.model.store.BagArchiveImportModelStore method) (galaxy.model.store.BagArchiveModelExportStore method) (galaxy.model.store.BagDirectoryModelExportStore 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.ImportOptions method) (galaxy.model.store.ModelImportStore method) (galaxy.model.store.ObjectImportTracker method) (galaxy.model.store.SessionlessContext 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.MigrateTools 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.TransferJob method) (galaxy.model.UCI 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.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.openid.openid_manager.OpenIDManager method) (galaxy.openid.providers.OpenIDProvider method) (galaxy.openid.providers.OpenIDProviders 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.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.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.InstallToolDependencyManager 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.migrate.common.MigrateToolsApplication method) (galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) (galaxy.tool_shed.galaxy_install.tool_dependencies.env_manager.EnvManager method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader.AsynchronousReader method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder.EnvFileBuilder method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager.StepManager method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager.TagManager method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertDirectoryExecutable method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertDirectoryExists method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertFileExecutable method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertFileExists method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.Autoconf method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.ChangeDirectory method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.Chmod method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadBinary method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadByUrl method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadFile method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MakeDirectory method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MakeInstall method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MoveDirectoryFiles method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MoveFile method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.RegexReplace method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetEnvironment method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetEnvironmentForInstall method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupPerlEnvironment method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupPythonEnvironment method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupREnvironment method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupRubyEnvironment method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupVirtualEnv method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.ShellCommand method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.TemplateCommand method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Install method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Package method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.ReadMe method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Repository method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.SetEnvironment method) (galaxy.tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager 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.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.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.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.mulled.mulled_search.CondaSearch method) (galaxy.tool_util.deps.mulled.mulled_search.QuaySearch 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.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.locations.http.HttpToolResolver method) (galaxy.tool_util.parser.cwl.CwlPageSource method) (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.PagesSource 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.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.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.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.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.DatasetEmptyValidator method) (galaxy.tools.parameters.validation.DatasetExtraFilesPathEmptyValidator method) (galaxy.tools.parameters.validation.DatasetOkValidator method) (galaxy.tools.parameters.validation.EmptyTextfieldValidator method) (galaxy.tools.parameters.validation.ExpressionValidator method) (galaxy.tools.parameters.validation.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.NoOptionsValidator method) (galaxy.tools.parameters.validation.RegexValidator method) (galaxy.tools.parameters.validation.UnspecifiedBuildValidator 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.repositories.ValidationContext method) (galaxy.tools.search.ToolBoxSearch 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.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) (galaxy.tools.toolbox.base.BaseGalaxyToolBox method) (galaxy.tools.toolbox.BaseGalaxyToolBox method) (galaxy.tools.toolbox.filters.FilterFactory method) (galaxy.tools.toolbox.lineages.factory.LineageMap method) (galaxy.tools.toolbox.lineages.interface.ToolLineage method) (galaxy.tools.toolbox.lineages.interface.ToolLineageVersion method) (galaxy.tools.toolbox.lineages.LineageMap method) (galaxy.tools.toolbox.lineages.ToolLineage method) (galaxy.tools.toolbox.panel.ToolSection method) (galaxy.tools.toolbox.panel.ToolSectionLabel method) (galaxy.tools.toolbox.tags.PersistentToolTagManager method) (galaxy.tools.toolbox.ToolSection method) (galaxy.tools.toolbox.ToolSectionLabel method) (galaxy.tools.toolbox.watcher.ToolConfWatcher method) (galaxy.tools.toolbox.watcher.ToolFileEventHandler method) (galaxy.tools.toolbox.watcher.ToolWatcher method) (galaxy.tools.ToolErrorLog 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.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.custom_logging.TraceLogger 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.object_wrapper.SafeStringWrapper method) (galaxy.util.odict.odict method) (galaxy.util.oset.OrderedSet method) (galaxy.util.Params method) (galaxy.util.ParamsWithSpecs method) (galaxy.util.pastescript.serve.BadCommand method) (galaxy.util.pastescript.serve.Command method) (galaxy.util.pastescript.serve.Command.BadCommand method) (galaxy.util.pastescript.serve.LazyWriter 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.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.interactive_environments.InteractiveEnvironmentRequest method) (galaxy.visualization.plugins.plugin.InteractiveEnvironmentPlugin 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.LazyProperty method) (galaxy.web.framework.base.Request method) (galaxy.web.framework.base.Response method) (galaxy.web.framework.base.WebApplication method) (galaxy.web.framework.base.WSGIEnvironmentProperty 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.batch.BatchMiddleware 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.sentry.Sentry 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.statsd_client.GalaxyStatsdClient 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.MessageApplicationStack method) (galaxy.web_stack.transport.ApplicationStackTransport method) (galaxy.web_stack.transport.UWSGIFarmMessageTransport method) (galaxy.web_stack.UWSGIApplicationStack method) (galaxy.web_stack.WeblessApplicationStack method) (galaxy.webapps.base.controller.BaseController method) (galaxy.webapps.base.controller.Datatype method) (galaxy.webapps.base.controller.JSAppLauncher method) (galaxy.webapps.base.webapp.GalaxyWebTransaction method) (galaxy.webapps.base.webapp.WebApplication method) (galaxy.webapps.galaxy.api.annotations.HistoryAnnotationsController method) (galaxy.webapps.galaxy.api.annotations.HistoryContentAnnotationsController method) (galaxy.webapps.galaxy.api.authenticate.AuthenticationController method) (galaxy.webapps.galaxy.api.cloud.CloudController method) (galaxy.webapps.galaxy.api.cloudauthz.CloudAuthzController method) (galaxy.webapps.galaxy.api.configuration.ConfigurationController method) (galaxy.webapps.galaxy.api.container_resolution.ContainerResolutionAPIController method) (galaxy.webapps.galaxy.api.dataset_collections.DatasetCollectionsController method) (galaxy.webapps.galaxy.api.datasets.DatasetsController method) (galaxy.webapps.galaxy.api.dynamic_tools.DynamicToolsController method) (galaxy.webapps.galaxy.api.extended_metadata.HistoryDatasetExtendMetadataController method) (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method) (galaxy.webapps.galaxy.api.folders.FoldersController method) (galaxy.webapps.galaxy.api.histories.HistoriesController method) (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method) (galaxy.webapps.galaxy.api.job_ports.JobPortsAPIController method) (galaxy.webapps.galaxy.api.jobs.FastAPIJobs method) (galaxy.webapps.galaxy.api.jobs.JobController method) (galaxy.webapps.galaxy.api.libraries.LibrariesController 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.licenses.LicensesController method) (galaxy.webapps.galaxy.api.metrics.MetricsController method) (galaxy.webapps.galaxy.api.page_revisions.PageRevisionsController method) (galaxy.webapps.galaxy.api.pages.PagesController method) (galaxy.webapps.galaxy.api.plugins.PluginsController method) (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method) (galaxy.webapps.galaxy.api.roles.FastAPIRoles method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) (galaxy.webapps.galaxy.api.tool_entry_points.ToolEntryPointsAPIController method) (galaxy.webapps.galaxy.api.tools.ToolsController method) (galaxy.webapps.galaxy.api.tours.FastAPITours method) (galaxy.webapps.galaxy.api.tours.ToursController method) (galaxy.webapps.galaxy.api.trs_consumer.TrsConsumeAPIController method) (galaxy.webapps.galaxy.api.trs_search.TrsSearchAPIController method) (galaxy.webapps.galaxy.api.users.UserAPIController method) (galaxy.webapps.galaxy.api.visualizations.VisualizationsController method) (galaxy.webapps.galaxy.api.webhooks.WebhooksController method) (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.openid.OpenID 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.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.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.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.framework.SeleniumSessionDatasetCollectionPopulator method) (galaxy_test.selenium.framework.SeleniumSessionDatasetPopulator method) (galaxy_test.selenium.framework.SeleniumSessionWorkflowPopulator method) (galaxy_test.selenium.framework.TestSnapshot 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.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.framework.middleware.remoteuser.RemoteUser method) (tool_shed.webapp.model.APIKeys 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.ItemTagAssociation method) (tool_shed.webapp.model.PasswordResetToken method) (tool_shed.webapp.model.PostJobAction 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.model.Workflow method) (tool_shed.webapp.model.WorkflowStep method) (tool_shed.webapp.model.WorkflowStepConnection method) (tool_shed.webapp.model.WorkflowStepInput method) (tool_shed.webapp.security.Action method) (tool_shed.webapp.security.CommunityRBACAgent method) (tool_shed.webapp.util.shed_statistics.ShedCounter method)

A

Ab1 (class in galaxy.datatypes.binary) 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) AbstractToolBox (class in galaxy.tools.toolbox) (class in galaxy.tools.toolbox.base) AbstractToolTagManager (class in galaxy.tools.toolbox.tags) access_entry_point() (galaxy.webapps.galaxy.api.tool_entry_points.ToolEntryPointsAPIController method) access_entry_point_target() (galaxy.managers.interactivetool.InteractiveToolManager method) access_token (galaxy.model.CustosAuthnzToken attribute) AccessDatasetRBACPermission (class in galaxy.managers.rbac_secured) AccessibleManagerMixin (class in galaxy.managers.secured) AccNos (class in galaxy.datatypes.mothur) accumulate_tool_dependencies() (in module galaxy.util.tool_shed.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.jobs.actions.post.RemoveTagDatasetAction attribute) (galaxy.jobs.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.workflow.refactor.schema.RefactorActionExecution attribute) action_arguments (galaxy.model.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) (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper attribute) action_name (galaxy.managers.rbac_secured.AccessDatasetRBACPermission attribute) (galaxy.managers.rbac_secured.DatasetRBACPermission attribute) (galaxy.managers.rbac_secured.ManageDatasetRBACPermission attribute) action_name() (galaxy.datatypes.display_applications.parameters.DisplayDataValueWrapper property) (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper property) action_type (galaxy.model.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.UpgradeSubworkflowAction attribute) (galaxy.workflow.refactor.schema.UpgradeToolAction attribute) (in module galaxy.tool_util.parser.output_actions) ActionBox (class in galaxy.jobs.actions.post) ActionInputError actions (galaxy.jobs.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.managers.users.UserManager method) (galaxy.tool_util.deps.conda_util.CondaContext property) (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.User attribute) active() (galaxy.model.InteractiveToolEntryPoint property) (galaxy.model.WorkflowInvocation property) 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) add() (galaxy.managers.citations.CitationCollection method) (galaxy.model.dataset_collections.matching.CollectionsToMatch method) (galaxy.model.store.SessionlessContext method) (galaxy.util.oset.OrderedSet method) add_api_controller() (galaxy.web.framework.base.WebApplication method) add_api_controllers() (galaxy.webapps.base.webapp.WebApplication method) add_boxes() (galaxy.workflow.render.WorkflowCanvas method) add_category_entry() (tool_shed.repository_registry.Registry method) add_change_callback() (galaxy.model.database_heartbeat.DatabaseHeartbeat method) add_changeset() (in module tool_shed.util.hg_util) add_client_route() (galaxy.web.framework.base.WebApplication method) add_column() (in module galaxy.model.migrate.versions.util) add_composite_file() (galaxy.datatypes.data.Data method) add_connection() (galaxy.model.WorkflowStep method) (galaxy.workflow.render.WorkflowCanvas method) add_custom_build() (galaxy_test.selenium.test_custom_builds.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_deserializers() (galaxy.managers.annotatable.AnnotatableDeserializerMixin method) (galaxy.managers.base.ModelDeserializer method) (galaxy.managers.cloudauthzs.CloudAuthzsDeserializer method) (galaxy.managers.datasets.DatasetAssociationDeserializer method) (galaxy.managers.deletable.DeletableDeserializerMixin method) (galaxy.managers.deletable.PurgableDeserializerMixin method) (galaxy.managers.hdas.HDADeserializer method) (galaxy.managers.histories.HistoryDeserializer method) (galaxy.managers.pages.PageDeserializer method) (galaxy.managers.ratable.RatableDeserializerMixin method) (galaxy.managers.sharable.SharableModelDeserializer method) (galaxy.managers.taggable.TaggableDeserializerMixin method) (galaxy.managers.users.UserDeserializer method) (galaxy.managers.visualizations.VisualizationDeserializer method) add_display_app() (galaxy.datatypes.data.Data method) add_display_application() (galaxy.datatypes.data.Data method) add_dummy_datasets() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) add_edge() (galaxy.util.simplegraph.SimpleGraph method) add_entries() (galaxy.tools.data.ToolDataTable method) add_entry() (galaxy.tools.data.ToolDataTable method) (tool_shed.repository_registry.Registry method) (tool_shed.util.hgweb_config.HgWebConfigManager method) add_entry_to_installed_repository_dependencies_of_installed_repositories() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) add_entry_to_installed_tool_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_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) add_entry_to_tool_dependencies_of_installed_repositories() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) add_env_shell_file_paths() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method) add_error() (galaxy.tools.ToolErrorLog method) add_exception_handler() (in module galaxy.webapps.galaxy.fast_app) add_folder() (galaxy.model.LibraryFolder method) add_galaxy_session() (galaxy.model.History method) add_handler() (galaxy.web_stack.handlers.ConfiguresHandlers method) add_history() (galaxy.model.GalaxySession method) add_implicit_input_collection() (galaxy.model.HistoryDatasetCollectionAssociation method) add_implicit_output_dataset_collection() (galaxy.model.Job method) add_index() (in module galaxy.model.migrate.versions.util) 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_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_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_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_sequencer() (in module galaxy.model.migrate.versions.0067_populate_sequencer_table) 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) add_species() (galaxy.datatypes.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.RegionAlignment method) add_sreg() (galaxy.openid.openid_manager.OpenIDManager method) add_steps() (galaxy.workflow.render.WorkflowCanvas method) add_tag_async() (galaxy.webapps.galaxy.controllers.tag.TagsController method) add_tags_from_list() (galaxy.model.tags.TagHandler method) add_tags_to_datasets() (galaxy.model.store.discover.ModelPersistenceContext 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.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox 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) add_visualization_revision() (galaxy.webapps.base.controller.UsesVisualizationMixin 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) address() (galaxy.containers.Container property) (galaxy.containers.docker_model.DockerContainer property) (galaxy.containers.docker_model.DockerService property) 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_lock() (in module galaxy.queue_worker) admin_login() (galaxy_test.selenium.framework.TestWithSeleniumMixin method) admin_open() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) admin_role() (tool_shed.webapp.model.Repository property) admin_users() (galaxy.config.CommonConfigurationMixin property) AdminActions (class in galaxy.actions.admin) 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_setting_metadata() (galaxy.datatypes.data.Data method) aggressive_error_checks() (in module galaxy.tool_util.parser.stdio) 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.selenium.smart_components.SmartTarget method) all_control_queues_for_declare() (in module galaxy.queues) all_entry_points_configured() (galaxy.model.Job property) all_jobs (galaxy.model.view.HistoryDatasetCollectionJobStateSummary attribute) all_requirements() (galaxy.tools.ToolBox property) (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_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_datatype_change (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.interval.BedStrict 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_missing_tools (galaxy.managers.workflows.WorkflowUpdateOptions 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_DATA_SOURCE_ATTRIBUTES (galaxy.visualization.plugins.config_parser.DataSourceParser attribute) ALLOWED_ENTRY_POINT_TYPES (galaxy.visualization.plugins.config_parser.VisualizationsConfigParser attribute) allowed_middleware() (galaxy.web_stack.ApplicationStack method) ALLOWED_MODEL_CLASSES (galaxy.visualization.plugins.config_parser.DataSourceParser attribute) allowed_to_disconnect() (in module galaxy.authnz.psa_authnz) already_executed() (galaxy.tool_util.verify.script.Results method) already_successful() (galaxy.tool_util.verify.script.Results method) alter_column() (in module galaxy.model.migrate.versions.util) alter_config_and_load_prorietary_datatypes() (galaxy.tool_shed.galaxy_install.datatypes.custom_datatype_manager.CustomDatatypeLoader method) AlwaysReject (class in galaxy.auth.providers.alwaysreject) Amos (class in galaxy.datatypes.assembly) amount() (galaxy.model.Quota property) 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.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) annotation_mapping() (in module galaxy.model.mapping) 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) 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) 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) 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_interactor_for_logged_in_user() (galaxy_test.selenium.framework.TestWithSeleniumMixin method) api_key() (galaxy.webapps.galaxy.api.users.UserAPIController method) api_key_header() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) api_keys (galaxy.model.User attribute) (tool_shed.webapp.model.User attribute) api_keys() (tool_shed.webapp.controllers.user.User method) api_payload_to_create_params() (in module galaxy.managers.collections_util) api_post() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) ApiBatchTestCase (class in galaxy_test.api.test_api_batch) ApiFrameworkTestCase (class in galaxy_test.api.test_framework) ApiKeyManager (class in galaxy.managers.api_keys) APIKeys (class in galaxy.model) (class in tool_shed.webapp.model) ApiTestInteractor (class in galaxy_test.base.api) App (class in galaxy.config.config_manage) app_factory() (in module galaxy.web.buildapp) (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) app_properties_from_args() (in module galaxy.util.script) appconfig() (in module galaxy.util.pastescript.loadwsgi) 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_line() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder.EnvFileBuilder method) append_section() (galaxy.tools.toolbox.panel.ToolPanelElements method) append_tool() (galaxy.tools.toolbox.panel.ToolPanelElements method) AppInfo (class in galaxy.tool_util.deps.dependencies) application (galaxy.web.framework.middleware.batch.BatchMiddleware attribute) (galaxy.web.framework.middleware.sqldebug.SQLDebugMiddleware attribute) application_stack_class() (in module galaxy.web_stack) application_stack_instance() (in module galaxy.web_stack) application_stack_log_filter() (in module galaxy.web_stack) application_stack_log_formatter() (in module galaxy.web_stack) ApplicationStack (class in galaxy.web_stack) ApplicationStackLogFilter (class in galaxy.web_stack) ApplicationStackMessage (class in galaxy.web_stack.message) ApplicationStackMessageDispatcher (class in galaxy.web_stack.message) ApplicationStackTransport (class in galaxy.web_stack.transport) apply() (galaxy.tool_util.deps.resolvers.RequirementMapping method) (galaxy.util.rules_dsl.AddColumnBasenameRuleDefinition method) (galaxy.util.rules_dsl.AddColumnConcatenateRuleDefinition method) (galaxy.util.rules_dsl.AddColumnGroupTagValueRuleDefinition method) (galaxy.util.rules_dsl.AddColumnMetadataRuleDefinition method) (galaxy.util.rules_dsl.AddColumnRegexRuleDefinition method) (galaxy.util.rules_dsl.AddColumnRownumRuleDefinition method) (galaxy.util.rules_dsl.AddColumnSubstrRuleDefinition method) (galaxy.util.rules_dsl.AddColumnValueRuleDefinition method) (galaxy.util.rules_dsl.AddFilterCompareRuleDefinition method) (galaxy.util.rules_dsl.AddFilterCountRuleDefinition method) (galaxy.util.rules_dsl.AddFilterEmptyRuleDefinition method) (galaxy.util.rules_dsl.AddFilterMatchesRuleDefinition method) (galaxy.util.rules_dsl.AddFilterRegexRuleDefinition method) (galaxy.util.rules_dsl.BaseRuleDefinition method) (galaxy.util.rules_dsl.RemoveColumnsRuleDefinition method) (galaxy.util.rules_dsl.RuleSet method) (galaxy.util.rules_dsl.SortRuleDefinition method) (galaxy.util.rules_dsl.SplitColumnsRuleDefinition method) (galaxy.util.rules_dsl.SwapColumnsRuleDefinition method) apply_action() (galaxy.tool_util.parser.output_actions.FormatToolOutputAction method) (galaxy.tool_util.parser.output_actions.MetadataToolOutputAction method) (galaxy.tool_util.parser.output_actions.ToolOutputAction method) (galaxy.tool_util.parser.output_actions.ToolOutputActionConditional method) (galaxy.tool_util.parser.output_actions.ToolOutputActionConditionalWhen method) (galaxy.tool_util.parser.output_actions.ToolOutputActionGroup method) apply_item_tag() (galaxy.model.tags.TagHandler method) apply_item_tags() (galaxy.model.tags.TagHandler method) apply_preferences() (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController 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) 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.webapps.galaxy.api.history_contents.HistoryContentsController method) archive_dir (galaxy.model.JobImportHistoryArchive attribute) archive_download() (galaxy.webapps.galaxy.api.histories.HistoriesController method) archive_export() (galaxy.webapps.galaxy.api.histories.HistoriesController method) archive_repository_revision() (in module tool_shed.util.hg_util) Arff (class in galaxy.datatypes.text) arg_parser() (in module galaxy.tool_util.verify.script) 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_gbrowse_display_file() (galaxy.datatypes.tabular.Tabular 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_directory_executable() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertDirectoryExecutable method) assert_directory_exists() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertDirectoryExists 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_file_executable() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertFileExecutable method) assert_file_exists() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertFileExists method) 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_changes_and_save() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) 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_initial_history_panel_state_correct() (galaxy_test.selenium.framework.TestWithSeleniumMixin 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_item_dbkey_displayed_as() (galaxy_test.selenium.framework.UsesHistoryItemAssertions method) assert_item_hid_text() (galaxy_test.selenium.framework.UsesHistoryItemAssertions method) assert_item_info_includes() (galaxy_test.selenium.framework.UsesHistoryItemAssertions method) assert_item_name() (galaxy_test.selenium.framework.UsesHistoryItemAssertions method) assert_item_peek_includes() (galaxy_test.selenium.framework.UsesHistoryItemAssertions method) assert_item_summary_includes() (galaxy_test.selenium.framework.UsesHistoryItemAssertions method) assert_message() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) assert_modal_has_text() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase 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_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_xpath() (galaxy.selenium.has_driver.HasDriver method) AssertDirectoryExecutable (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) AssertDirectoryExists (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) AssertFileExecutable (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) AssertFileExists (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) assign_admin_role() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) assign_handler() (galaxy.web_stack.handlers.ConfiguresHandlers method) assoc_type (galaxy.model.PSAAssociation attribute) (galaxy.model.UserAuthnzToken attribute) associate() (galaxy.managers.base.ModelManager method) associate_action_dataset_role() (galaxy.model.security.GalaxyRBACAgent method) associate_components() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) (tool_shed.webapp.security.RBACAgent method) associate_group_role() (galaxy.model.security.GalaxyRBACAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) associate_repository_category() (tool_shed.webapp.security.CommunityRBACAgent method) associate_user_group() (galaxy.model.security.GalaxyRBACAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) associate_user_role() (galaxy.model.security.GalaxyRBACAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) (tool_shed.webapp.security.RBACAgent method) association (galaxy.authnz.psa_authnz.Storage attribute) ASync (class in galaxy.webapps.galaxy.controllers.async) async_template (galaxy.web.legacy_framework.grids.Grid attribute) AsyncDataSourceTool (class in galaxy.tools) AsynchronousJobRunner (class in galaxy.jobs.runners) AsynchronousJobState (class in galaxy.jobs.runners) AsynchronousReader (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader) 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) 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_TUPLE (in module 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) AuthenticationApiTestCase (class in galaxy_test.api.test_authenticate) AuthenticationController (class in galaxy.webapps.galaxy.api.authenticate) AuthenticationFailed AuthenticationRequired 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_propagated_tags() (galaxy.model.HasTags property) Autoconf (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) 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) avg() (galaxy.job_metrics.collectl.stats.StatisticsTracker property) Axes (class in galaxy.datatypes.mothur) Axt (class in galaxy.datatypes.sequence) AzureBlobObjectStore (class in galaxy.objectstore.azure_blob)

B

backdrop (galaxy.tours.TourStep attribute) backend (galaxy.model.PSAPartial attribute) BadCommand BadValue (class in galaxy.tools) BafTar (class in galaxy.datatypes.binary) BagArchiveImportModelStore (class in galaxy.model.store) BagArchiveModelExportStore (class in galaxy.model.store) BagDirectoryModelExportStore (class in galaxy.model.store) Bam (class in galaxy.datatypes.binary) BamDataProvider (class in galaxy.visualization.data_providers.genome) BamInputSorted (class in galaxy.datatypes.binary) BamNative (class in galaxy.datatypes.binary) BamQuerynameSorted (class in galaxy.datatypes.binary) bare_ampersand (galaxy.managers.pages.PageContentProcessor attribute) base (galaxy.web.framework.base.Request attribute) Base64ChunkDataProvider (class in galaxy.datatypes.dataproviders.chunk) base_dataprovider() (galaxy.datatypes.data.Data method) base_docker_cmd() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest 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) BaseAPIController (class in galaxy.webapps.base.controller) BaseAppConfiguration (class in galaxy.config) BaseBcf (class in galaxy.datatypes.binary) BaseCitation (class in galaxy.managers.citations) BaseController (class in galaxy.webapps.base.controller) BaseCSV (class in galaxy.datatypes.tabular) 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) 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) BaseField (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) BaseFilesSource (class in galaxy.files.sources) BaseGalaxyToolBox (class in galaxy.tools.toolbox) (class in galaxy.tools.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) BaseObjectStore (class in galaxy.objectstore) BasePageApiTestCase (class in galaxy_test.api.test_pages) BaseParamParser (class in galaxy.web.params) 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) basestring() (galaxy.managers.base.ModelValidator method) basestring_list() (galaxy.managers.base.ModelValidator method) BaseToolProvidedMetadata (class in galaxy.tool_util.provided_metadata) BaseTree (class in galaxy.model.dataset_collections.structure) BaseUIController (class in galaxy.webapps.base.controller) 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) BasicToolShedFeatures (class in tool_shed.test.functional.test_1000_install_basic_repository) BatchMiddleware (class in galaxy.web.framework.middleware.batch) 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) BedTabixDataProvider (class in galaxy.visualization.data_providers.genome) before_get() (galaxy.util.properties.NicerConfigParser.InterpolateWrapper method) before_setting_metadata() (galaxy.datatypes.data.Data 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) bind_all_addrs (galaxy.web_stack.UWSGIApplicationStack attribute) 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) 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) body_renderer() (galaxy.web.framework.middleware.batch.BatchMiddleware method) bookmarks_from_dataset() (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) bool() (galaxy.managers.base.ModelValidator method) 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) BooleanFilter (class in galaxy.tool_util.parser.output_actions) BooleanToolParameter (class in galaxy.tools.parameters.basic) BoolOptionParser (class in galaxy.util.pastescript.serve) bootstrap_admin_user (galaxy.model.User attribute) (tool_shed.webapp.model.User attribute) BootstrapAdminUser (class in galaxy.schema) 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) 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) browser_url (galaxy.web.framework.base.Request attribute) bucket_proxy() (galaxy.webapps.galaxy.controllers.root.RootController method) build() (galaxy.model.dataset_collections.builder.CollectionBuilder method) (galaxy.tool_util.deps.mulled.util.Target property) (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_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_command() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method) (in module galaxy.jobs.command_factory) (in module galaxy.tool_util.deps.docker_util) build_command_line() (galaxy.job_metrics.collectl.cli.CollectlCli method) (galaxy.jobs.runners.BaseJobRunner method) build_command_list() (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider method) build_container_interfaces() (in module galaxy.containers) 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) 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_function() (galaxy.tools.toolbox.filters.FilterFactory method) build_filters() (galaxy.tools.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.tool_util.deps.mulled.mulled_search.QuaySearch method) (galaxy.tools.search.ToolBoxSearch 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_native_uwsgi_app() (in module galaxy.webapps.base.webapp) build_object_store_from_config() (in module galaxy.objectstore) build_param_dict() (galaxy.tools.evaluation.ToolEvaluator method) build_parameter_dict() (galaxy.datatypes.display_applications.application.DisplayApplicationLink method) build_path() (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method) build_pg_timestamp_fn() (in module galaxy.model.triggers) build_pg_trigger() (in module galaxy.model.triggers) 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) 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.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) build_tool_dependencies_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) build_tool_dependencies_select_field() (in module galaxy.tool_shed.util.tool_dependency_util) build_tool_panel_section_select_field() (in module galaxy.tool_shed.util.tool_util) 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) (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) BuildMulledDockerContainerResolver (class in galaxy.tool_util.deps.container_resolvers.mulled) BuildMulledSingularityContainerResolver (class in galaxy.tool_util.deps.container_resolvers.mulled) 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.visualization.plugins.registry.VisualizationsRegistry attribute) 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_api_key() (galaxy.managers.users.UserManager method) by_dataset() (galaxy.managers.rbac_secured.DatasetRBACPermission method) by_email() (galaxy.managers.users.UserManager method) by_email_like() (galaxy.managers.users.UserManager method) by_id() (galaxy.managers.base.ModelManager 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_file_is_writeable() (galaxy.tools.cache.ToolDocumentCache property) cache_job_destination() (galaxy.jobs.mapper.JobRunnerMapper method) cache_tool() (galaxy.tools.cache.ToolCache method) cacheable (galaxy.tool_util.deps.resolvers.Dependency attribute) CacheableStaticURLParser (class in galaxy.web.framework.middleware.static) cached (galaxy.tool_util.deps.CachedDependencyManager attribute) (galaxy.tool_util.deps.DependencyManager attribute) (galaxy.tool_util.deps.NullDependencyManager attribute) cached_container_description() (galaxy.tool_util.deps.container_resolvers.mulled.MulledDockerContainerResolver method) (galaxy.tool_util.deps.container_resolvers.mulled.MulledSingularityContainerResolver method) cached_id() (in module galaxy.model) CachedDependencyManager (class in galaxy.tool_util.deps) 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) calculate_pagination() (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method) call_hook() (galaxy.tools.Tool method) CallableSafeStringWrapper (class in galaxy.util.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_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_current_user_add_to_library_item() (galaxy.webapps.base.controller.UsesLibraryMixinItems 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_eliminate_tool_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) (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.tools.ToolBox method) (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox 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_split() (galaxy.jobs.JobWrapper method) (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) can_uninstall_dependencies() (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_assume_authn() (galaxy.authnz.managers.AuthnzManager static method) CANCEL (galaxy.openid.openid_manager.OpenIDManager attribute) cancel() (galaxy.model.WorkflowInvocation 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 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) Cel (class in galaxy.datatypes.binary) 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.datatypes.registry.Registry method) (galaxy.model.DatasetInstance method) change_entry() (tool_shed.util.hgweb_config.HgWebConfigManager method) change_ownership_for_run() (galaxy.jobs.JobWrapper 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.JobWrapper method) (galaxy.jobs.TaskWrapper method) change_user_group() (galaxy.util.pastescript.serve.ServeCommand method) changed() (galaxy.model.UserAuthnzToken class method) ChangeDatatypeAction (class in galaxy.jobs.actions.post) ChangeDatatypeTestCase (class in galaxy_test.api.test_workflows) ChangeDirectory (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) 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) (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.tools.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.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.webapps.base.webapp.GalaxyWebTransaction method) check_docker() (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_entry_points() (galaxy.jobs.JobWrapper method) check_for_missing_tools() (in module galaxy.util.tool_shed.common_util) check_for_strings() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) check_for_tool_dependencies() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy 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_dropboxfs() (galaxy.dependencies.ConditionalDependencies method) check_fs_s3fs() (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_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_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_installed_repository_tool_dependencies() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) check_interval() (galaxy.model.DeferredJob property) check_kamaki() (galaxy.dependencies.ConditionalDependencies method) check_keras() (galaxy.dependencies.ConditionalDependencies method) check_limits() (galaxy.jobs.JobWrapper method) (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_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_raven() (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_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_script_integrity() (in module galaxy.jobs.runners.util.job_script) check_security() (galaxy.managers.workflows.WorkflowsManager 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_output() (galaxy.jobs.JobWrapper method) check_tool_tag_set() (in module galaxy.util.tool_shed.common_util) check_user_activation() (galaxy.managers.context.ProvidesUserContext method) check_user_can_add_to_library_item() (galaxy.webapps.base.controller.UsesLibraryMixinItems 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_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) 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) (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) Chmod (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) 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) CHUNKABLE (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.tabular.TabularData attribute) ChunkDataProvider (class in galaxy.datatypes.dataproviders.chunk) 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.HistoriesController method) (galaxy.webapps.galaxy.api.tools.ToolsController 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) 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.JobWrapper method) (galaxy.jobs.runners.JobState method) (galaxy.jobs.TaskWrapper method) (galaxy.tools.cache.ToolCache method) cleanup_after_job() (galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper method) cleanup_external_metadata() (galaxy.metadata.MetadataCollectionStrategy method) cleanup_from_JSON_dict_filename() (galaxy.datatypes.metadata.MetadataTempFile class method) (galaxy.model.metadata.MetadataTempFile class method) cleanup_job() (galaxy.jobs.JobWrapper property) 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_tooltips() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) clear_working_directory() (galaxy.jobs.JobWrapper method) 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_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_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.base.controller.JSAppLauncher method) (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_file_descriptor() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method) close_logs() (galaxy.util.heartbeat.Heartbeat method) Cloud (class in galaxy.objectstore.cloud) CloudAuthz (class in galaxy.model) cloudauthz (galaxy.model.User attribute) (galaxy.model.UserAuthnzToken attribute) CloudAuthzController (class in galaxy.webapps.galaxy.api.cloudauthz) CloudAuthzManager (class in galaxy.managers.cloudauthzs) cloudauthzs (galaxy.model.User attribute) 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) CloudImage_table (in module galaxy.model.migrate.versions.0026_cloud_tables) (in module galaxy.model.migrate.versions.0050_drop_cloud_tables) CloudManager (class in galaxy.managers.cloud) CMAP (class in galaxy.datatypes.tabular) CML (class in galaxy.datatypes.molecules) cmp() (in module galaxy.util.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.util.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) (galaxy.job_metrics.JobMetrics method) (galaxy.job_metrics.NullJobInstrumenter method) collection (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetCollectionAssociation 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_id (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetCollectionAssociation 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.workflow.modules.InputDataCollectionModule attribute) (galaxy.workflow.refactor.schema.AddInputAction attribute) collection_type() (galaxy.tool_util.cwl.representation.TypeRepresentation property) (galaxy.util.rules_dsl.RuleSet property) 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) collections_properties() (galaxy.model.store.BaseDirectoryImportModelStore 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) CollectlCli (class in galaxy.job_metrics.collectl.cli) CollectlPlugin (class in galaxy.job_metrics.instrumenters.collectl) collector() (galaxy.model.store.discover.DiscoveredFile property) (galaxy.model.store.discover.DiscoveredFileError property) ColorToolParameter (class in galaxy.tools.parameters.basic) column_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.TabularData method) 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.jobs.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 (class in galaxy.util.pastescript.serve) command() (galaxy.util.pastescript.serve.ServeCommand method) Command.BadCommand command_line (galaxy.model.Job attribute) (galaxy.model.Task 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) CommandLineException, [1] commands_in_new_shell() (galaxy.jobs.JobWrapper property) 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_drop_materialized_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_files (galaxy.datatypes.data.Data attribute) composite_type (galaxy.datatypes.anvio.AnvioComposite attribute) (galaxy.datatypes.assembly.Velvet 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.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)

compressed (galaxy.datatypes.annotation.Augustus attribute) (galaxy.datatypes.binary.CompressedArchive attribute) (galaxy.datatypes.binary.Xlsx 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.GzDynamicCompressedArchive attribute) (galaxy.datatypes.tabular.Eland attribute) (galaxy.datatypes.tabular.VcfGz attribute) CompressedArchive (class in galaxy.datatypes.binary) CompressedFile (class in galaxy.util.compression_utils) CompressedZipArchive (class in galaxy.datatypes.binary) compute_collection_info() (galaxy.workflow.modules.WorkflowModule method) compute_fasta_length() (in module galaxy.datatypes.converters.fasta_to_len) compute_outputs() (galaxy.jobs.JobWrapper method) compute_runtime_state() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) ComputeEnvironment (class in galaxy.jobs) 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_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) CondaSearch (class in galaxy.tool_util.deps.mulled.mulled_search) 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) conf_defaults (galaxy.containers.ContainerInterface attribute) (galaxy.containers.docker.DockerCLIInterface attribute) (galaxy.containers.docker.DockerInterface attribute) (galaxy.containers.docker_swarm.DockerSwarmInterface attribute) conf_run_kwopts (galaxy.containers.docker.DockerInterface attribute) config (galaxy.model.CloudAuthz attribute) (galaxy.model.VisualizationRevision attribute) (galaxy.model.WorkflowStep attribute) config_directories_from_setting() (in module galaxy.util) config_directory() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SimpleComputeEnvironment method) config_elems_to_xml_file() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) config_exception() (in module galaxy.jobs) config_file_from_args() (in module galaxy.util.script) config_is_ini() (galaxy.main.GalaxyConfigBuilder property) 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) ConfigDoesNotAllowException ConfigSerializer (class in galaxy.managers.configuration) Configuration (class in galaxy.webapps.reports.config) (in module galaxy.config) (in module tool_shed.webapp.config) ConfigurationApiTestCase (class in galaxy_test.api.test_configuration) ConfigurationController (class in galaxy.webapps.galaxy.api.configuration) (class in tool_shed.webapp.api.configuration) ConfigurationError, [1], [2] 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.UniverseApplication method) configure_logging() (in module galaxy.config) configure_provider() (galaxy.managers.cloud.CloudManager static method) configured (galaxy.model.InteractiveToolEntryPoint attribute) configured_pools() (galaxy.web_stack.ApplicationStack property) (galaxy.web_stack.UWSGIApplicationStack property) (galaxy.web_stack.WeblessApplicationStack property) ConfiguredFileSources (class in galaxy.files) ConfiguredFileSourcesConfig (class in galaxy.files) ConfiguresGalaxyMixin (class in galaxy.config) ConfiguresHandlers (class in galaxy.web_stack.handlers) ConfigWatchers (class in galaxy.config_watchers) Conflict 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) constraint() (galaxy.containers.docker_model.DockerNodeLabel property) constraint_add() (galaxy.containers.docker_model.DockerService method) constraint_string() (galaxy.containers.docker_model.DockerNodeLabel property) constraints() (galaxy.containers.docker_model.DockerNodeLabels property) (galaxy.containers.docker_model.DockerService property) contact_owner() (tool_shed.webapp.controllers.repository.RepositoryController method) contained() (galaxy.managers.containers.ContainerManagerMixin method) (galaxy.managers.history_contents.HistoryContentsManager method) contained_class (galaxy.managers.containers.ContainerManagerMixin attribute) (galaxy.managers.containers.DatasetCollectionAsContainerManagerMixin attribute) (galaxy.managers.containers.LibraryFolderAsContainerManagerMixin attribute) (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.containers) (class in galaxy.tool_util.deps.container_classes) container (galaxy.model.Job attribute) container_class (galaxy.containers.ContainerInterface attribute) (galaxy.containers.docker.DockerInterface attribute) (galaxy.containers.docker_swarm.DockerSwarmInterface attribute) container_description() (galaxy.tool_util.deps.containers.ResolvedContainerDescription property) 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_monitor_command() (galaxy.jobs.JobWrapper method) container_name (galaxy.model.JobContainerAssociation attribute) container_resolver() (galaxy.tool_util.deps.containers.ResolvedContainerDescription property) container_run_args() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) container_spec_option_map (galaxy.containers.docker_swarm.DockerSwarmAPIInterface attribute) container_testing() (in module galaxy.tool_util.deps.mulled.mulled_update_singularity_containers) container_type (galaxy.containers.ContainerInterface attribute) (galaxy.containers.docker.DockerAPIInterface attribute) (galaxy.containers.docker.DockerCLIInterface attribute) (galaxy.containers.docker_swarm.DockerSwarmAPIInterface attribute) (galaxy.containers.docker_swarm.DockerSwarmCLIInterface attribute) (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.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) ContainerCLIError ContainerDependency (class in galaxy.tool_util.deps.resolvers) ContainerDescription (class in galaxy.tool_util.deps.requirements) ContainerFinder (class in galaxy.tool_util.deps.containers) ContainerImageNotFound ContainerInterface (class in galaxy.containers) ContainerInterfaceConfig (class in galaxy.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) ContainerManagerMixin (class in galaxy.managers.containers) ContainerNotFound ContainerPort (class in galaxy.containers) 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) ContainerRunError containers_config_file() (galaxy.containers.ContainerInterface property) ContainerVolume (class in galaxy.containers) contains_collection() (galaxy.model.HistoryDatasetCollectionAssociation method) contains_folder() (tool_shed.utility_containers.utility_container_manager.Folder 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.tours.TourStep attribute) content_format (galaxy.model.PageRevision attribute) content_id (galaxy.workflow.refactor.schema.UpgradeSubworkflowAction attribute) content_id() (galaxy.model.WorkflowStep property) content_type (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) contents() (galaxy.managers.containers.ContainerManagerMixin method) (galaxy.managers.history_contents.HistoryContentsManager method) (galaxy.webapps.galaxy.api.dataset_collections.DatasetCollectionsController method) contents_count() (galaxy.managers.history_contents.HistoryContentsManager method) contents_iter() (galaxy.model.History method) contents_near() (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method) contents_query() (galaxy.managers.history_contents.HistoryContentsManager method) context (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) ControllerUnavailable ControlTask (class in galaxy.queue_worker) 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_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_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.DatasetsController method) ConvertedDatasetDataProvider (class in galaxy.datatypes.dataproviders.dataset) converter_safe() (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.DataToolParameter method) ConverterDependencyException converters() (galaxy.webapps.galaxy.api.datatypes.DatatypesController method) cookie_path() (galaxy.webapps.base.webapp.GalaxyWebTransaction property) cookies (galaxy.web.framework.base.Request attribute) 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_associations (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.managers.pages.PageManager method) (galaxy.model.DatasetCollection 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.tools.DefaultToolState method) (galaxy.tools.toolbox.panel.ToolSection method) (galaxy.tools.toolbox.ToolSection method) (galaxy.util.odict.odict method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController 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_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_hda_to_library_folder() (galaxy.webapps.base.controller.UsesLibraryMixinItems method) copy_history() (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) copy_sample_files() (in module galaxy.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) Cpt (class in galaxy.datatypes.binary) CpuInfoPlugin (class in galaxy.job_metrics.instrumenters.cpuinfo) cpus() (galaxy.containers.docker_model.DockerNode property) (galaxy.containers.docker_model.DockerService property) (galaxy.containers.docker_model.DockerTask property) 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.hdas.HDAManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.managers.pages.PageManager method) (galaxy.managers.roles.RoleManager method) (galaxy.managers.users.UserManager 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.DatasetCollectionsController 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.FoldersController method) (galaxy.webapps.galaxy.api.forms.FormDefinitionAPIController method) (galaxy.webapps.galaxy.api.groups.GroupAPIController method) (galaxy.webapps.galaxy.api.histories.HistoriesController method) (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController 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.LibrariesController method) (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method) (galaxy.webapps.galaxy.api.metrics.MetricsController method) (galaxy.webapps.galaxy.api.page_revisions.PageRevisionsController method) (galaxy.webapps.galaxy.api.pages.PagesController method) (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method) (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method) (galaxy.webapps.galaxy.api.roles.FastAPIRoles method) (galaxy.webapps.galaxy.api.roles.RoleAPIController 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) (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_and_write_tmp_file() (in module galaxy.util.tool_shed.xml_util) create_api_key() (galaxy.managers.api_keys.ApiKeyManager method) (galaxy.managers.users.UserManager method) (galaxy.webapps.base.controller.CreatesApiKeysMixin 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_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_dynamic_tool() (galaxy.tools.ToolBox method) (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) create_element() (in module galaxy.util.tool_shed.xml_util) create_entry_points() (galaxy.managers.interactivetool.InteractiveToolManager method) create_env_var_dict() (galaxy.tool_shed.galaxy_install.tool_dependencies.env_manager.EnvManager method) create_extended_metadata() (galaxy.webapps.base.controller.UsesExtendedMetadataMixin method) create_extra_files_path() (galaxy.model.Dataset method) create_file() (galaxy.datatypes.dataproviders.external.TempfileDataProvider method) create_for_history() (galaxy.model.JobExportHistoryArchive static method) create_form() (galaxy.webapps.galaxy.controllers.forms.Forms 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_item_slug() (galaxy.webapps.base.controller.SharableMixin 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_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_or_update_env_shell_file() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder.EnvFileBuilder static method) create_or_update_repository_metadata() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) create_or_update_tool_dependency() (in module galaxy.tool_shed.util.tool_dependency_util) create_or_update_tool_shed_repository() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) create_or_update_tool_shed_repository_record() (galaxy.tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager method) create_or_update_tool_shed_repository_records() (galaxy.tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager method) create_or_update_workflow_output() (galaxy.model.WorkflowStep method) create_or_verify_database() (in module galaxy.model.migrate.check) (in module galaxy.model.tool_shed_install.migrate.check) (in module tool_shed.webapp.model.migrate.check) 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.webapps.galaxy.controllers.admin.AdminGalaxy method) (galaxy_test.base.populators.BaseDatasetPopulator method) create_random_port_spec() (galaxy.containers.docker_swarm.DockerSwarmAPIInterface static 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.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_section() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) create_sequencer_form_definition() (in module galaxy.model.migrate.versions.0067_populate_sequencer_table) create_social_auth() (galaxy.model.UserAuthnzToken class method) create_string_filter() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) create_subworkflow_invocation_for_step() (galaxy.model.WorkflowInvocation method) create_table() (in module galaxy.model.migrate.versions.util) create_tag_filter() (galaxy.managers.taggable.TaggableFilterMixin method) create_tag_handler_session() (galaxy.model.tags.TagHandler method) create_temporary_tool_dependencies_config() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Repository method) create_time (galaxy.model.APIKeys 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.DeferredJob 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.TransferJob 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.Visualization attribute) (galaxy.model.VisualizationRevision attribute) (galaxy.model.Workflow attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowStep 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_timestamps() (in module galaxy.model.migrate.versions.0165_add_content_update_time) create_tool() (galaxy.managers.tools.DynamicToolManager method) (galaxy.tools.ToolBox method) (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) (galaxy_test.base.populators.BaseDatasetPopulator method) create_tool_dependency_objects() (in module galaxy.tool_shed.util.tool_dependency_util) create_tool_dependency_with_initialized_env_sh_file() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Repository method) create_tool_filter() (galaxy.managers.tools.ToolFilterMixin method) create_tool_from_path() (galaxy_test.base.populators.BaseDatasetPopulator method) 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_visualization() (galaxy.webapps.base.controller.UsesVisualizationMixin 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) created_from_basename() (galaxy.model.DatasetInstance property) (galaxy.model.store.discover.JsonCollectedDatasetMatch property) created_time (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.JobContainerAssociation attribute) created_with_galaxy_version() (galaxy.jobs.JobWrapper property) CreatedWorkflow (class in galaxy.managers.workflows) CreatesApiKeysMixin (class in galaxy.webapps.base.controller) CreateView (class in galaxy.model.view.utils) creating_job() (galaxy.managers.datasets.DatasetAssociationManager method) (galaxy.model.DatasetInstance property) creating_job_associations (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) creator (galaxy.workflow.refactor.schema.UpdateCreatorAction attribute) creator_metadata (galaxy.model.Workflow attribute) csFasta (class in galaxy.datatypes.sequence) css() (in module galaxy.web.framework.helpers) 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.model.FormDefinition 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_state() (galaxy.containers.docker_model.DockerTask property) current_state_time() (galaxy.containers.docker_model.DockerTask property) current_user() (galaxy.managers.users.UserManager method) CurrentUserSerializer (class in galaxy.managers.users) CustomBuildsTestcase (class in galaxy_test.selenium.test_custom_builds) CustomDatatypeLoader (class in galaxy.tool_shed.galaxy_install.datatypes.custom_datatype_manager) CustomTrack (class in galaxy.datatypes.interval) custos_auth (galaxy.model.User attribute) CustosAuthnz (class in galaxy.authnz.custos_authnz) CustosAuthnzToken (class in galaxy.model) cut_and_decode() (galaxy.managers.folders.FolderManager method) cut_the_prefix() (galaxy.managers.folders.FolderManager method) CwlPageSource (class in galaxy.tool_util.parser.cwl) CwlToolSource (class in galaxy.tool_util.parser.cwl) CwlWorkflowOutput (class in galaxy.tool_util.cwl.runnable) CycleError

D

DAA (class in galaxy.datatypes.binary) daemonize() (galaxy.util.pastescript.serve.ServeCommand method) DaemonizeException 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_COLLECTON (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute) data_conversion_status() (galaxy.managers.hdas.HDAManager method) 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_list() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) data_managers_path() (galaxy.tool_shed.galaxy_install.tools.data_manager.DataManagerHandler property) 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_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) data_types_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) database_conf() (in module galaxy_test.driver.driver_util) DATABASE_OPERATION (galaxy.selenium.navigates_galaxy.WAIT_TYPES attribute) DatabaseHeartbeat (class in galaxy.model.database_heartbeat) DatabaseOperationTool (class in galaxy.tools) DataCollectionToolParameter (class in galaxy.tools.parameters) (class in galaxy.tools.parameters.basic) DataDestinationTool (class in galaxy.tools) 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) DataProvider (class in galaxy.datatypes.dataproviders.base) dataprovider() (galaxy.datatypes.data.Data method) dataprovider_factory() (in module galaxy.datatypes.dataproviders.decorators) DataProviderRegistry (class in galaxy.visualization.data_providers.registry) dataproviders (galaxy.datatypes.binary.Bam attribute) (galaxy.datatypes.binary.SQlite attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.data.Text attribute) (galaxy.datatypes.graph.Sif attribute) (galaxy.datatypes.graph.Xgmml attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.interval.Wiggle attribute) (galaxy.datatypes.tabular.BaseCSV attribute) (galaxy.datatypes.tabular.BaseVcf attribute) (galaxy.datatypes.tabular.CSV attribute) (galaxy.datatypes.tabular.Pileup attribute) (galaxy.datatypes.tabular.Sam attribute) (galaxy.datatypes.tabular.Tabular attribute) (galaxy.datatypes.tabular.TabularData attribute) (galaxy.datatypes.tabular.TSV attribute) (galaxy.datatypes.xml.GenericXml attribute) Dataset (class in galaxy.model) dataset (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.JobToInputDatasetAssociation attribute) (galaxy.model.JobToInputLibraryDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetAssociation attribute) (galaxy.model.JobToOutputLibraryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) dataset() (galaxy.model.DatasetCollectionElement property) (galaxy.model.JobExternalOutputMetadata property) 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.ImplicitlyCreatedDatasetCollectionInput attribute) (galaxy.model.JobToImplicitOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation 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_populator() (galaxy_test.selenium.framework.TestWithSeleniumMixin property) dataset_collections (galaxy.model.History attribute) (galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetCollectionRatingAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetCollectionAnnotationAssociation attribute) (galaxy.model.LibraryDatasetCollectionRatingAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryFolder 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_dict_dataprovider() (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.TabularData method) dataset_elements() (galaxy.model.DatasetCollection property) dataset_id (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) 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_make_primary() (galaxy.webapps.galaxy.controllers.root.RootController method) dataset_path_rewriter() (galaxy.jobs.JobWrapper property) (galaxy.jobs.TaskWrapper property) dataset_path_rewrites() (in module galaxy.job_execution.datasets) dataset_permission_map_for_access() (galaxy.model.security.GalaxyRBACAgent method) dataset_populator() (galaxy_test.selenium.framework.TestWithSeleniumMixin property) dataset_source_id (galaxy.model.DatasetSourceHash attribute) dataset_states_and_extensions_summary() (galaxy.model.DatasetCollection property) dataset_storage_info() (galaxy_test.base.populators.BaseDatasetPopulator method) dataset_to_param() (in module galaxy_test.api.test_tools) dataset_type (galaxy.visualization.data_providers.genome.BamDataProvider attribute) (galaxy.visualization.data_providers.genome.BBIDataProvider attribute) (galaxy.visualization.data_providers.genome.BedDataProvider attribute) (galaxy.visualization.data_providers.genome.ChromatinInteractionsDataProvider attribute) (galaxy.visualization.data_providers.genome.ENCODEPeakDataProvider attribute) (galaxy.visualization.data_providers.genome.GenomeDataProvider attribute) (galaxy.visualization.data_providers.genome.IntervalDataProvider attribute) (galaxy.visualization.data_providers.genome.IntervalIndexDataProvider attribute) (galaxy.visualization.data_providers.genome.RawGFFDataProvider attribute) (galaxy.visualization.data_providers.genome.SamDataProvider attribute) (galaxy.visualization.data_providers.genome.TabixDataProvider attribute) (galaxy.visualization.data_providers.genome.VcfDataProvider attribute) (galaxy.visualization.data_providers.genome.VcfTabixDataProvider attribute) (galaxy.visualization.data_providers.phyloviz.PhylovizDataProvider attribute) dataset_version (galaxy.model.JobToInputDatasetAssociation attribute) dataset_wrapper_to_directory_json() (in module galaxy.tool_util.cwl.representation) dataset_wrapper_to_file_json() (in module galaxy.tool_util.cwl.representation) DatasetAccessPermissionFailedException DatasetAssociationDeserializer (class in galaxy.managers.datasets) DatasetAssociationFilterParser (class in galaxy.managers.datasets) DatasetAssociationManager (class in galaxy.managers.datasets) 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) DatasetCollectionAsContainerManagerMixin (class in galaxy.managers.containers) DatasetCollectionDescription (class in galaxy.tool_util.parser.output_collection_def) DatasetCollectionElement (class in galaxy.model) DatasetCollectionInstance (class in galaxy.model) DatasetCollectionManager (class in galaxy.managers.collections) DatasetCollectionPopulator (class in galaxy_test.base.populators) DatasetCollectionsController (class in galaxy.webapps.galaxy.api.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) 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) 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) DatasetInterface (class in galaxy.webapps.galaxy.controllers.dataset) 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) DatasetPermissions (class in galaxy.model) DatasetPopulator (class in galaxy_test.base.populators) DatasetRBACPermission (class in galaxy.managers.rbac_secured) DatasetRBACPermissions (class in galaxy.managers.datasets) datasets (galaxy.model.History attribute) (galaxy.model.LibraryFolder attribute) datasets_are_public() (galaxy.model.security.GalaxyRBACAgent method) datasets_properties() (galaxy.model.store.BaseDirectoryImportModelStore method) (galaxy.model.store.ModelImportStore method) DatasetsApiTestCase (class in galaxy_test.api.test_datasets) DatasetsController (class in galaxy.webapps.galaxy.api.datasets) DatasetSerializer (class in galaxy.managers.datasets) DatasetSource (class in galaxy.model) DatasetSourceHash (class in galaxy.model) DatasetSubprocessDataProvider (class in galaxy.datatypes.dataproviders.dataset) DataSourceParser (class in galaxy.visualization.plugins.config_parser) DataSourceTool (class in galaxy.tools) DataSourceToolAction (class in galaxy.tools.actions.data_source) DataToolParameter (class in galaxy.tools.parameters) (class in galaxy.tools.parameters.basic) Datatype (class in galaxy.webapps.base.controller) (class in tool_shed.utility_containers.utility_container_manager) datatype() (galaxy.model.DatasetInstance property) datatype_for_extension() (in module galaxy.model) DatatypeIsInstanceToolOutputActionConditionalWhen (class in galaxy.tool_util.parser.output_actions) datatypes_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) DatatypesApiTestCase (class in galaxy_test.api.test_datatypes) DatatypesController (class in galaxy.webapps.galaxy.api.datatypes) DatatypesGrid (class in tool_shed.grids.repository_grids) DatatypesGrid.DatatypesColumn (class in tool_shed.grids.repository_grids) DatatypeValidation (class in galaxy.datatypes.data) date_string_re (galaxy.managers.base.ModelFilterParser attribute) 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_next_hid() (in module galaxy.model.mapping) 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_TRANSACTION_ISOLATION (galaxy.web_stack.handlers.HANDLER_ASSIGNMENT_METHODS attribute) dbkey (galaxy.model.Visualization attribute) (galaxy.model.VisualizationRevision attribute) dbkey() (galaxy.model.DatasetInstance property) (galaxy.model.store.discover.JsonCollectedDatasetMatch property) DBKeyParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) DCASerializer (class in galaxy.managers.hdcas) Dcd (class in galaxy.datatypes.binary) DCESerializer (class in galaxy.managers.hdcas) DCSerializer (class in galaxy.managers.hdcas) deactivate() (galaxy.managers.tools.DynamicToolManager method) (galaxy.tool_util.deps.conda_util.CondaContext property) 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.webapps.galaxy.api.metrics.MetricsController 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.security.idencoding.IdEncodingHelper method) (galaxy.webapps.base.controller.BaseController method) (galaxy.webapps.galaxy.api.configuration.ConfigurationController method) (in module galaxy.managers.base) 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) decoder() (in module galaxy.tools.cache) 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_compute_environment() (galaxy.jobs.JobWrapper method) DEFAULT_CONFIG (galaxy.web.framework.middleware.batch.BatchMiddleware 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_ENTRY_FN (galaxy.webapps.base.controller.JSAppLauncher attribute) 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_TAG (galaxy.web_stack.handlers.ConfiguresHandlers attribute) default_interactive (galaxy.util.pastescript.serve.Command attribute) DEFAULT_INVALID_CHAR (galaxy.tools.parameters.sanitize.ToolParameterSanitizer attribute) default_is_multi_byte (galaxy.tool_util.parser.interface.ToolSource attribute) (galaxy.tool_util.parser.ToolSource 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_merge_type (galaxy.model.WorkflowStepInput 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.containers.ContainerManagerMixin attribute) (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_scatter_type (galaxy.model.WorkflowStepInput attribute) default_serializer() (galaxy.managers.base.ModelSerializer method) (galaxy.managers.configuration.ConfigSerializer method) default_shed_tool_conf_dict() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.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_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_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_verbosity (galaxy.util.pastescript.serve.Command attribute) (galaxy.util.pastescript.serve.ServeCommand attribute) DEFAULT_VERSION (galaxy.tools.data_manager.manager.DataManager attribute) default_web_host (galaxy_test.selenium.framework.TestWithSeleniumMixin attribute) default_web_host_for_selenium_tests() (in module galaxy_test.selenium.framework) DefaultHistoryPermissions (class in galaxy.model) DefaultJobAction (class in galaxy.jobs.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) (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.GenomeIndexToolData attribute) deferred_job (galaxy.model.DeferredJob attribute) deferred_job_id (galaxy.model.GenomeIndexToolData attribute) DeferredJob (class in galaxy.model) DeferredJob.states (class in galaxy.model) defines_new_history() (galaxy.model.store.BaseDirectoryImportModelStore 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.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.deletable.DeletableManagerMixin method) (galaxy.managers.folders.FolderManager method) (galaxy.managers.libraries.LibraryManager 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.extended_metadata.BaseExtendedMetadataController method) (galaxy.webapps.galaxy.api.folders.FoldersController method) (galaxy.webapps.galaxy.api.group_roles.GroupRolesAPIController method) (galaxy.webapps.galaxy.api.group_users.GroupUsersAPIController method) (galaxy.webapps.galaxy.api.histories.HistoriesController method) (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method) (galaxy.webapps.galaxy.api.item_tags.BaseItemTagsController method) (galaxy.webapps.galaxy.api.jobs.JobController method) (galaxy.webapps.galaxy.api.libraries.LibrariesController method) (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method) (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method) (galaxy.webapps.galaxy.api.pages.PagesController method) (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method) (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method) (galaxy.webapps.galaxy.api.tool_data.ToolData 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_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_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_item_annotation() (galaxy.model.item_attrs.UsesAnnotations method) delete_item_tags() (galaxy.model.tags.TagHandler method) 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_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_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) 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) (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) DeleteDatasetAction (class in galaxy.jobs.actions.post) DeletedColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.web.legacy_framework.grids) DeleteIntermediatesAction (class in galaxy.jobs.actions.post) DELETING (galaxy.model.Job.states attribute) delimiter (galaxy.datatypes.tabular.BaseCSV attribute) dependencies (galaxy.model.Job attribute) DependenciesDescription (class in galaxy.tool_util.deps.dependencies) Dependency (class in galaxy.tool_util.deps.resolvers) dependency_shell_commands() (galaxy.jobs.JobWrapper property) (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) 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) deps_error_message() (in module galaxy.tool_util.deps.mulled.mulled_search) deregister_func() (galaxy.web_stack.message.ApplicationStackMessageDispatcher method) deregister_message_handler() (galaxy.web_stack.ApplicationStack method) (galaxy.web_stack.MessageApplicationStack 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.roles.RoleDefinitionModel attribute) (galaxy.managers.roles.RoleModel 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.tours.TourCore attribute) (galaxy.util.pastescript.serve.Command attribute) (galaxy.util.pastescript.serve.ServeCommand 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() (galaxy.selenium.components.Label property) (galaxy.selenium.components.SelectorTemplate property) (galaxy.selenium.components.Target property) (galaxy.selenium.components.Text property) description_from_tool_object() (in module galaxy.tools.test) descs (galaxy.tool_util.parser.stdio.StdioErrorLevel 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) designation (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) designation() (galaxy.model.store.discover.JsonCollectedDatasetMatch property) desired_state() (galaxy.containers.docker_model.DockerTask property) destination() (galaxy.config.config_manage.App property) 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) destroy() (galaxy.model.PSAPartial class method) destroyable() (galaxy.containers.docker_model.DockerNode method) detailsUrl (galaxy.managers.licenses.LicenseMetadataModel attribute) detect_datatype() (galaxy.managers.datasets.DatasetAssociationManager method) 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.model.DatasetCollection attribute) (galaxy.model.DatasetCollectionElement 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.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) (galaxy.tools.toolbox.panel.ToolSection attribute) (galaxy.tools.toolbox.panel.ToolSectionLabel attribute) (galaxy.tools.toolbox.ToolSection attribute) (galaxy.tools.toolbox.ToolSectionLabel 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_element_visible_keys (galaxy.model.DatasetCollection attribute) (galaxy.model.DatasetCollectionElement 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) (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_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) 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) difflib (in module galaxy.util.pastescript.serve) dimension() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription property) direct_match() (galaxy.tools.parameters.history_query.HistoryQuery method) direction (galaxy.jobs.actions.post.RemoveTagDatasetAction attribute) (galaxy.jobs.actions.post.TagDatasetAction attribute) Directory (class in galaxy.datatypes.data) directory_hash_id() (in module galaxy.util) 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_commands_in_new_shell() (galaxy.jobs.JobWrapper method) disable_parent_class_sniffing() (in module galaxy.datatypes.sniff) disabled (galaxy.tool_util.deps.resolvers.DependencyResolver attribute) discard() (galaxy.util.oset.OrderedSet method) DISCARDED (galaxy.model.Dataset.states attribute) (galaxy.model.DatasetInstance.states 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.jobs.JobWrapper method) (galaxy.tools.Tool method) 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_for_element() (in module galaxy.model.store.discover) DiscoveredFile (class in galaxy.model.store.discover) DiscoveredFileError (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) display() (galaxy.util.rules_dsl.RuleSet property) (galaxy.webapps.galaxy.api.datasets.DatasetsController method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.root.RootController method) display_amount() (galaxy.model.Quota property) display_application() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) 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.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_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.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.H5 method) (galaxy.datatypes.binary.IdpDB method) (galaxy.datatypes.binary.Loom method) (galaxy.datatypes.binary.MCool method) (galaxy.datatypes.binary.NcbiTaxonomySQlite method) (galaxy.datatypes.binary.NetCDF method) (galaxy.datatypes.binary.PostgresqlArchive 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.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_url() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) displayable() (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.tabular.TabularData method) 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) DisplayApplicationsController (class in galaxy.webapps.galaxy.api.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_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_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) docker_cache_path() (in module galaxy.tool_util.deps.container_classes) docker_cmd() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) docker_columns() (in module galaxy.containers.docker_decorators) docker_compatible_realpath() (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method) 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_json() (in module galaxy.containers.docker_decorators) docker_to_singularity() (in module galaxy.tool_util.deps.mulled.mulled_update_singularity_containers) DockerAPIClient (class in galaxy.containers.docker) DockerAPIInterface (class in galaxy.containers.docker) DockerAttributeContainer (class in galaxy.containers.docker_model) DockerCLIInterface (class in galaxy.containers.docker) DockerContainer (class in galaxy.containers.docker_model) (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) DockerInterface (class in galaxy.containers.docker) DockerNode (class in galaxy.containers.docker_model) DockerNodeLabel (class in galaxy.containers.docker_model) DockerNodeLabels (class in galaxy.containers.docker_model) DockerService (class in galaxy.containers.docker_model) DockerServiceConstraint (class in galaxy.containers.docker_model) DockerServiceConstraints (class in galaxy.containers.docker_model) DockerSwarmAPIInterface (class in galaxy.containers.docker_swarm) DockerSwarmCLIInterface (class in galaxy.containers.docker_swarm) DockerSwarmInterface (class in galaxy.containers.docker_swarm) DockerTask (class in galaxy.containers.docker_model) DockerVolume (class in galaxy.containers.docker_model) DockStoreResolver (class in galaxy.tool_util.locations.dockstore) docstring_trim() (in module galaxy.util) 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) DONE (galaxy.model.TransferJob.states attribute) DotBracket (class in galaxy.datatypes.sequence) downgrade() (in module galaxy.model.migrate.versions.0002_metadata_file_table) (in module galaxy.model.migrate.versions.0003_security_and_libraries) (in module galaxy.model.migrate.versions.0004_indexes_and_defaults) (in module galaxy.model.migrate.versions.0005_cleanup_datasets_fix) (in module galaxy.model.migrate.versions.0006_change_qual_datatype) (in module galaxy.model.migrate.versions.0007_sharing_histories) (in module galaxy.model.migrate.versions.0008_galaxy_forms) (in module galaxy.model.migrate.versions.0009_request_table) (in module galaxy.model.migrate.versions.0010_hda_display_at_authz_table) (in module galaxy.model.migrate.versions.0011_v0010_mysql_index_fix) (in module galaxy.model.migrate.versions.0012_user_address) (in module galaxy.model.migrate.versions.0013_change_lib_item_templates_to_forms) (in module galaxy.model.migrate.versions.0014_pages) (in module galaxy.model.migrate.versions.0015_tagging) (in module galaxy.model.migrate.versions.0016_v0015_mysql_index_fix) (in module galaxy.model.migrate.versions.0017_library_item_indexes) (in module galaxy.model.migrate.versions.0018_ordered_tags_and_page_tags) (in module galaxy.model.migrate.versions.0019_request_library_folder) (in module galaxy.model.migrate.versions.0020_library_upload_job) (in module galaxy.model.migrate.versions.0021_user_prefs) (in module galaxy.model.migrate.versions.0022_visualization_tables) (in module galaxy.model.migrate.versions.0023_page_published_and_deleted_columns) (in module galaxy.model.migrate.versions.0024_page_slug_unique_constraint) (in module galaxy.model.migrate.versions.0025_user_info) (in module galaxy.model.migrate.versions.0026_cloud_tables) (in module galaxy.model.migrate.versions.0027_request_events) (in module galaxy.model.migrate.versions.0028_external_metadata_file_override) (in module galaxy.model.migrate.versions.0029_user_actions) (in module galaxy.model.migrate.versions.0030_history_slug_column) (in module galaxy.model.migrate.versions.0031_community_and_workflow_tags) (in module galaxy.model.migrate.versions.0032_stored_workflow_slug_column) (in module galaxy.model.migrate.versions.0033_published_cols_for_histories_and_workflows) (in module galaxy.model.migrate.versions.0034_page_user_share_association) (in module galaxy.model.migrate.versions.0035_item_annotations_and_workflow_step_tags) (in module galaxy.model.migrate.versions.0036_add_deleted_column_to_library_template_assoc_tables) (in module galaxy.model.migrate.versions.0037_samples_library) (in module galaxy.model.migrate.versions.0038_add_inheritable_column_to_library_template_assoc_tables) (in module galaxy.model.migrate.versions.0039_add_synopsis_column_to_library_table) (in module galaxy.model.migrate.versions.0040_page_annotations) (in module galaxy.model.migrate.versions.0041_workflow_invocation) (in module galaxy.model.migrate.versions.0042_workflow_invocation_fix) (in module galaxy.model.migrate.versions.0043_visualization_sharing_tagging_annotating) (in module galaxy.model.migrate.versions.0044_add_notify_column_to_request_table) (in module galaxy.model.migrate.versions.0045_request_type_permissions_table) (in module galaxy.model.migrate.versions.0046_post_job_actions) (in module galaxy.model.migrate.versions.0047_job_table_user_id_column) (in module galaxy.model.migrate.versions.0048_dataset_instance_state_column) (in module galaxy.model.migrate.versions.0049_api_keys_table) (in module galaxy.model.migrate.versions.0050_drop_cloud_tables) (in module galaxy.model.migrate.versions.0051_imported_col_for_jobs_table) (in module galaxy.model.migrate.versions.0052_sample_dataset_table) (in module galaxy.model.migrate.versions.0053_item_ratings) (in module galaxy.model.migrate.versions.0054_visualization_dbkey) (in module galaxy.model.migrate.versions.0055_add_pja_assoc_for_jobs) (in module galaxy.model.migrate.versions.0056_workflow_outputs) (in module galaxy.model.migrate.versions.0057_request_notify) (in module galaxy.model.migrate.versions.0058_history_import_export) (in module galaxy.model.migrate.versions.0059_sample_dataset_file_path) (in module galaxy.model.migrate.versions.0060_history_archive_import) (in module galaxy.model.migrate.versions.0061_tasks) (in module galaxy.model.migrate.versions.0062_user_openid_table) (in module galaxy.model.migrate.versions.0063_sequencer_table) (in module galaxy.model.migrate.versions.0064_add_run_and_sample_run_association_tables) (in module galaxy.model.migrate.versions.0065_add_name_to_form_fields_and_values) (in module galaxy.model.migrate.versions.0066_deferred_job_and_transfer_job_tables) (in module galaxy.model.migrate.versions.0067_populate_sequencer_table) (in module galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services) (in module galaxy.model.migrate.versions.0069_rename_sequencer_form_type) (in module galaxy.model.migrate.versions.0070_add_info_column_to_deferred_job_table) (in module galaxy.model.migrate.versions.0071_add_history_and_workflow_to_sample) (in module galaxy.model.migrate.versions.0072_add_pid_and_socket_columns_to_transfer_job_table) (in module galaxy.model.migrate.versions.0073_add_ldda_to_implicit_conversion_table) (in module galaxy.model.migrate.versions.0074_add_purged_column_to_library_dataset_table) (in module galaxy.model.migrate.versions.0075_add_subindex_column_to_run_table) (in module galaxy.model.migrate.versions.0076_fix_form_values_data_corruption) (in module galaxy.model.migrate.versions.0077_create_tool_tag_association_table) (in module galaxy.model.migrate.versions.0078_add_columns_for_disk_usage_accounting) (in module galaxy.model.migrate.versions.0079_input_library_to_job_table) (in module galaxy.model.migrate.versions.0080_quota_tables) (in module galaxy.model.migrate.versions.0081_add_tool_version_to_hda_ldda) (in module galaxy.model.migrate.versions.0082_add_tool_shed_repository_table) (in module galaxy.model.migrate.versions.0083_add_prepare_files_to_task) (in module galaxy.model.migrate.versions.0084_add_ldda_id_to_implicit_conversion_table) (in module galaxy.model.migrate.versions.0085_add_task_info) (in module galaxy.model.migrate.versions.0086_add_tool_shed_repository_table_columns) (in module galaxy.model.migrate.versions.0087_tool_id_guid_map_table) (in module galaxy.model.migrate.versions.0088_add_installed_changeset_revison_column) (in module galaxy.model.migrate.versions.0089_add_object_store_id_columns) (in module galaxy.model.migrate.versions.0090_add_tool_shed_repository_table_columns) (in module galaxy.model.migrate.versions.0091_add_tool_version_tables) (in module galaxy.model.migrate.versions.0092_add_migrate_tools_table) (in module galaxy.model.migrate.versions.0093_add_job_params_col) (in module galaxy.model.migrate.versions.0094_add_job_handler_col) (in module galaxy.model.migrate.versions.0095_hda_subsets) (in module galaxy.model.migrate.versions.0096_openid_provider) (in module galaxy.model.migrate.versions.0097_add_ctx_rev_column) (in module galaxy.model.migrate.versions.0098_genome_index_tool_data_table) (in module galaxy.model.migrate.versions.0099_add_tool_dependency_table) (in module galaxy.model.migrate.versions.0100_alter_tool_dependency_table_version_column) (in module galaxy.model.migrate.versions.0101_drop_installed_changeset_revision_column) (in module galaxy.model.migrate.versions.0102_add_tool_dependency_status_columns) (in module galaxy.model.migrate.versions.0103_add_tool_shed_repository_status_columns) (in module galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters) (in module galaxy.model.migrate.versions.0105_add_cleanup_event_table) (in module galaxy.model.migrate.versions.0106_add_missing_indexes) (in module galaxy.model.migrate.versions.0107_add_exit_code_to_job_and_task) (in module galaxy.model.migrate.versions.0108_add_extended_metadata) (in module galaxy.model.migrate.versions.0109_add_repository_dependency_tables) (in module galaxy.model.migrate.versions.0110_add_dataset_uuid) (in module galaxy.model.migrate.versions.0111_add_job_destinations) (in module galaxy.model.migrate.versions.0112_add_data_manager_history_association_and_data_manager_job_association_tables) (in module galaxy.model.migrate.versions.0113_update_migrate_tools_table) (in module galaxy.model.migrate.versions.0114_update_migrate_tools_table_again) (in module galaxy.model.migrate.versions.0115_longer_user_password_field) (in module galaxy.model.migrate.versions.0116_drop_update_available_col_add_tool_shed_status_col) (in module galaxy.model.migrate.versions.0117_add_user_activation) (in module galaxy.model.migrate.versions.0118_add_hda_extended_metadata) (in module galaxy.model.migrate.versions.0119_job_metrics) (in module galaxy.model.migrate.versions.0120_dataset_collections) (in module galaxy.model.migrate.versions.0121_workflow_uuids) (in module galaxy.model.migrate.versions.0122_grow_mysql_blobs) (in module galaxy.model.migrate.versions.0123_add_workflow_request_tables) (in module galaxy.model.migrate.versions.0124_job_state_history) (in module galaxy.model.migrate.versions.0125_workflow_step_tracking) (in module galaxy.model.migrate.versions.0126_password_reset) (in module galaxy.model.migrate.versions.0127_output_collection_adjustments) (in module galaxy.model.migrate.versions.0128_session_timeout) (in module galaxy.model.migrate.versions.0129_job_external_output_metadata_validity) (in module galaxy.model.migrate.versions.0130_change_pref_datatype) (in module galaxy.model.migrate.versions.0131_subworkflow_and_input_parameter_modules) (in module galaxy.model.migrate.versions.0132_add_lastpasswordchange_to_user) (in module galaxy.model.migrate.versions.0133_add_dependency_column_to_job) (in module galaxy.model.migrate.versions.0134_hda_set_deleted_if_purged) (in module galaxy.model.migrate.versions.0135_add_library_tags) (in module galaxy.model.migrate.versions.0136_collection_and_workflow_state) (in module galaxy.model.migrate.versions.0137_add_copied_from_job_id_column) (in module galaxy.model.migrate.versions.0138_add_hda_version) (in module galaxy.model.migrate.versions.0139_add_history_dataset_association_history_table) (in module galaxy.model.migrate.versions.0140_add_dataset_version_to_job_to_input_dataset_association_table) (in module galaxy.model.migrate.versions.0141_add_oidc_tables) (in module galaxy.model.migrate.versions.0142_change_numeric_metric_precision) (in module galaxy.model.migrate.versions.0143_add_cloudauthz_tables) (in module galaxy.model.migrate.versions.0144_add_cleanup_event_user_table) (in module galaxy.model.migrate.versions.0145_add_workflow_step_input) (in module galaxy.model.migrate.versions.0146_workflow_paths) (in module galaxy.model.migrate.versions.0147_job_messages) (in module galaxy.model.migrate.versions.0148_add_checksum_table) (in module galaxy.model.migrate.versions.0149_dynamic_tools) (in module galaxy.model.migrate.versions.0150_add_create_time_field_for_cloudauthz) (in module galaxy.model.migrate.versions.0151_add_worker_process) (in module galaxy.model.migrate.versions.0152_add_metadata_file_uuid) (in module galaxy.model.migrate.versions.0153_add_custos_authnz_token_table) (in module galaxy.model.migrate.versions.0154_created_from_basename) (in module galaxy.model.migrate.versions.0155_job_galaxy_version) (in module galaxy.model.migrate.versions.0156_add_interactivetools) (in module galaxy.model.migrate.versions.0157_rework_dataset_validation) (in module galaxy.model.migrate.versions.0158_workflow_reports) (in module galaxy.model.migrate.versions.0159_add_job_external_id_index) (in module galaxy.model.migrate.versions.0160_hda_set_deleted_if_purged_again) (in module galaxy.model.migrate.versions.0161_add_workflow_invocation_output_table) (in module galaxy.model.migrate.versions.0162_job_only_pjas) (in module galaxy.model.migrate.versions.0163_worker_process_pid) (in module galaxy.model.migrate.versions.0164_page_format) (in module galaxy.model.migrate.versions.0165_add_content_update_time) (in module galaxy.model.migrate.versions.0166_job_state_summary_view) (in module galaxy.model.migrate.versions.0167_add_job_to_input_dataset_collection_element_association) (in module galaxy.model.migrate.versions.0168_stored_workflow_hidden_col) (in module galaxy.model.migrate.versions.0169_add_missing_indexes) (in module galaxy.model.migrate.versions.0170_add_more_missing_indexes) (in module galaxy.model.migrate.versions.0171_schemaorg_metadata) (in module galaxy.model.migrate.versions.0172_it_entrypoint_requires_domain) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0001_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0002_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0003_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0004_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0005_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0006_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0007_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0008_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0009_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0010_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0011_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0012_tools) (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 (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) download() (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method) (galaxy.webapps.galaxy.api.tools.ToolsController method) (tool_shed.webapp.controllers.repository.RepositoryController method) download_binary() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadBinary method) download_command() (in module galaxy.util.commands) download_dataset_collection() (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method) download_dataset_from_library() (galaxy_test.selenium.test_library_contents.LibraryContentsTestCase method) download_field_file() (galaxy.webapps.galaxy.api.tool_data.ToolData method) download_invocation_bco() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) download_output() (in module galaxy.tool_util.cwl.util) download_to_file() (in module galaxy.util) download_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method) downloadable (tool_shed.webapp.model.RepositoryMetadata attribute) downloadable_revisions (tool_shed.webapp.model.Repository attribute) DownloadBinary (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) DownloadByUrl (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) DownloadFile (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) drain() (galaxy.containers.docker_model.DockerNode method) 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.context.GalaxySeleniumContext property) DriverWrapper (class in galaxy.selenium.cli) DRMAAJobRunner (class in galaxy.jobs.runners.drmaa) drop_column() (in module galaxy.model.migrate.versions.util) drop_index() (in module galaxy.model.migrate.versions.util) drop_table() (in module galaxy.model.migrate.versions.util) drop_timestamp_triggers() (in module galaxy.model.triggers) drop_timestamps() (in module galaxy.model.migrate.versions.0165_add_content_update_time) 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_test_information() (in module galaxy_test.selenium.framework) 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.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) dynamic_confs() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) dynamic_structure() (galaxy.tool_util.parser.output_objects.ToolOutputCollection property) dynamic_tool (galaxy.model.WorkflowStep attribute) dynamic_tool_confs() (galaxy.webapps.galaxy.api.configuration.ConfigurationController method) dynamic_tool_id (galaxy.model.Job attribute) (galaxy.model.WorkflowStep 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

echo() (galaxy.webapps.galaxy.controllers.root.RootController method) echo_json() (galaxy.webapps.galaxy.controllers.root.RootController method) 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.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.datatypes.registry.Registry property) (galaxy.webapps.galaxy.api.datatypes.DatatypesController 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.H5 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.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.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) (galaxy.webapps.galaxy.api.datatypes.DatatypesController method) 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_form() (galaxy.webapps.galaxy.controllers.forms.Forms method) edit_info() (tool_shed.webapp.controllers.user.User method) edit_quota() (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) 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) element_as_dict() (galaxy.datatypes.dataproviders.hierarchy.XMLDataProvider method) element_count (galaxy.model.DatasetCollection attribute) element_identifier (galaxy.model.DatasetCollectionElement attribute) element_identifier() (galaxy.tools.wrappers.DatasetCollectionWrapper property) (galaxy.tools.wrappers.DatasetFilenameWrapper property) element_identifiers() (galaxy.model.store.discover.JsonCollectedDatasetMatch property) element_index (galaxy.model.DatasetCollectionElement 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_type() (galaxy.model.DatasetCollectionElement property) ElementIdentifierMapper (class in galaxy.tools.wrappers) elements (galaxy.model.DatasetCollection 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) ElibSQlite (class in galaxy.datatypes.binary) email (galaxy.model.PSACode attribute) (galaxy.model.User attribute) (galaxy.schema.BootstrapAdminUser attribute) (tool_shed.webapp.model.User attribute) email() (galaxy.files.DictFileSourcesUserContext property) (galaxy.files.ProvidesUserFileSourcesUserContext property) email_alerts (tool_shed.webapp.model.Repository attribute) email_alerts_repository_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) EmailAction (class in galaxy.jobs.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.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) EmptyTextfieldValidator (class in galaxy.tools.parameters.validation) enable_email_alerts() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) 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.base.controller.BaseController 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) encode_runtime_state() (galaxy.workflow.modules.WorkflowModule method) encode_type_id() (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method) 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) end() (galaxy.datatypes.util.maf_utilities.SplicedAlignment property) (galaxy.tools.util.maf_utilities.SplicedAlignment property) endpoint_spec_option_map (galaxy.containers.docker_swarm.DockerSwarmAPIInterface attribute) engine (galaxy.model.Dataset attribute) engine_false() (in module galaxy.model.migrate.versions.util) engine_true() (in module galaxy.model.migrate.versions.util) enqueue() (galaxy.jobs.JobWrapper method) (galaxy.jobs.manager.JobManager method) (galaxy.jobs.manager.NoopManager method) enqueue_output() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method) ensure_brew_on_path() (in module galaxy.tool_util.deps.brew_exts) 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_port_cleanup() (in module galaxy.util.pastescript.serve) ensure_pykube() (in module galaxy.jobs.runners.util.pykube_util) ensure_raw_description() (galaxy.managers.workflows.WorkflowContentsManager method) ensure_registered (galaxy_test.selenium.framework.TestWithSeleniumMixin attribute) (galaxy_test.selenium.test_collection_builders.CollectionBuildersTestCase attribute) (galaxy_test.selenium.test_history_copy_elements.HistoryCopyElementsTestCase attribute) (galaxy_test.selenium.test_history_multi_view.HistoryMultiViewTestCase attribute) (galaxy_test.selenium.test_history_panel.HistoryPanelTestCase attribute) (galaxy_test.selenium.test_history_panel_collections.HistoryPanelCollectionsTestCase attribute) (galaxy_test.selenium.test_history_panel_pagination.HistoryPanelPaginationTestCase attribute) (galaxy_test.selenium.test_history_structure.HistoryStructureTestCase attribute) (galaxy_test.selenium.test_jupyter.JupyterTestCase attribute) (galaxy_test.selenium.test_pages.PagesTestCase attribute) (galaxy_test.selenium.test_tool_form.LoggedInToolFormTestCase attribute) (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase attribute) (galaxy_test.selenium.test_workflow_management.WorkflowManagementTestCase attribute) (galaxy_test.selenium.test_workflow_run.WorkflowRunTestCase attribute)

ensure_tempdir() (galaxy.config.GalaxyAppConfiguration method) ensure_tool_conf_item() (in module galaxy.tools.toolbox.parser) ensure_tool_run_response_okay() (in module galaxy.tool_util.verify.interactor) ensure_user_with_email() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) ensure_visualization_available() (galaxy_test.selenium.framework.TestWithSeleniumMixin method) entry_url (galaxy.model.InteractiveToolEntryPoint attribute) env() (galaxy.containers.docker_model.DockerService property) env_config_directory() (galaxy.jobs.SharedComputeEnvironment method) env_path() (galaxy.tool_util.deps.conda_util.CondaContext method) env_to_statement() (in module galaxy.jobs.runners.util.env) EnvAction (class in galaxy.tool_util.deps.brew_exts) EnvFileBuilder (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder) environment_commands() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method) environment_dict() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method) EnvManager (class in galaxy.tool_shed.galaxy_install.tool_dependencies.env_manager) EnvPlugin (class in galaxy.job_metrics.instrumenters.env) envs_path() (galaxy.tool_util.deps.conda_util.CondaContext property) Eps (class in galaxy.datatypes.images) eq_datatype() (galaxy.managers.datasets.DatasetAssociationFilterParser method) equals() (galaxy.managers.citations.BaseCitation method) (galaxy.model.CloudAuthz method) err_code (galaxy.exceptions.ActionInputError attribute) (galaxy.exceptions.AdminRequiredException attribute) (galaxy.exceptions.AuthenticationFailed attribute) (galaxy.exceptions.AuthenticationRequired attribute) (galaxy.exceptions.ConfigDoesNotAllowException attribute) (galaxy.exceptions.ConfigurationError attribute) (galaxy.exceptions.Conflict attribute) (galaxy.exceptions.DeprecatedMethod attribute) (galaxy.exceptions.DuplicatedIdentifierException attribute) (galaxy.exceptions.DuplicatedSlugException attribute) (galaxy.exceptions.InconsistentDatabase attribute) (galaxy.exceptions.InsufficientPermissionsException attribute) (galaxy.exceptions.InternalServerError attribute) (galaxy.exceptions.InvalidFileFormatError attribute) (galaxy.exceptions.ItemAccessibilityException attribute) (galaxy.exceptions.ItemOwnershipException attribute) (galaxy.exceptions.MalformedContents attribute) (galaxy.exceptions.MalformedId attribute) (galaxy.exceptions.MessageException attribute) (galaxy.exceptions.NotImplemented attribute) (galaxy.exceptions.ObjectAttributeInvalidException attribute) (galaxy.exceptions.ObjectAttributeMissingException attribute) (galaxy.exceptions.ObjectNotFound attribute) (galaxy.exceptions.RequestParameterInvalidException attribute) (galaxy.exceptions.RequestParameterMissingException attribute) (galaxy.exceptions.ToolExecutionError attribute) (galaxy.exceptions.ToolMetaParameterException attribute) (galaxy.exceptions.ToolMissingException attribute) (galaxy.exceptions.UnknownContentsType attribute) (galaxy.exceptions.UserActivationRequiredException attribute) Error (class in galaxy.webapps.galaxy.controllers.error) ERROR (galaxy.model.Dataset.conversion_messages attribute) (galaxy.model.Dataset.states attribute) (galaxy.model.DatasetInstance.conversion_messages attribute) (galaxy.model.DatasetInstance.states attribute) (galaxy.model.DeferredJob.states attribute) (galaxy.model.Job.states attribute) (galaxy.model.Task.states attribute) (galaxy.model.tool_shed_install.ToolDependency.states attribute) (galaxy.model.tool_shed_install.ToolShedRepository.installation_status attribute) (galaxy.model.tool_shed_install.ToolShedRepository.states attribute) (galaxy.model.TransferJob.states attribute) error (galaxy.model.view.HistoryDatasetCollectionJobStateSummary attribute) error() (galaxy.tool_util.lint.LintContext method) (galaxy.web.framework.middleware.remoteuser.RemoteUser method) (galaxy.webapps.galaxy.api.jobs.JobController method) (in module galaxy.web) (in module galaxy.web.framework.decorators) (tool_shed.webapp.framework.middleware.remoteuser.RemoteUser method) error_code (galaxy.exceptions.ToolInputsNotReadyException attribute) error_count() (galaxy.tool_util.verify.script.Results property) error_if_anonymous() (galaxy.managers.users.UserManager method) error_if_uploading() (galaxy.managers.hdas.HDAManager method) error_message (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) error_message() (galaxy.model.store.discover.DiscoveredFileError property) error_on_exit_code() (in module galaxy.tool_util.parser.stdio) error_stack() (galaxy.webapps.galaxy.api.tools.ToolsController method) error_unless_accessible() (galaxy.managers.secured.AccessibleManagerMixin method) error_unless_admin() (galaxy.managers.users.UserManager method) error_unless_dataset_purge_allowed() (galaxy.managers.datasets.DatasetManager method) error_unless_owner() (galaxy.managers.secured.OwnableManagerMixin method) error_unless_permitted() (galaxy.managers.rbac_secured.RBACPermission method) ErrorCode (class in galaxy.exceptions.error_codes) ErrorMiddleware (class in galaxy.web.framework.middleware.error) ErrorPlugin (class in galaxy.tools.error_reports) (class in galaxy.tools.error_reports.plugins) ErrorReporter (class in galaxy.tools.errors) ErrorReports (class in galaxy.tools.error_reports) errors() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) errors_per_tool() (galaxy.webapps.reports.controllers.jobs.Jobs method) escape() (in module tool_shed.util.web_util) escape_html() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) Eset (class in galaxy.datatypes.genetics) estimate_file_lines() (galaxy.datatypes.data.Text method) evaluate() (in module galaxy.tools.expressions) (in module galaxy.tools.expressions.evaluation) evaluate_template() (in module galaxy.tool_shed.util.basic_util) Event (class in galaxy.model) EventHandler (class in galaxy.util.watcher) exact (galaxy.tool_util.deps.resolvers.NullDependency attribute) exact() (galaxy.tool_util.deps.resolvers.ContainerDependency property) (galaxy.tool_util.deps.resolvers.Dependency property) (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependency property) (galaxy.tool_util.deps.resolvers.resolver_mixins.HomebrewDependency property) exact_tools (galaxy.managers.workflows.WorkflowStateResolutionOptions attribute) example_datatype_registry_for_sample() (in module galaxy.datatypes.registry) ExcelXls (class in galaxy.datatypes.binary) exception() (galaxy.tool_util.verify.script.TestException property) exception_handler() (galaxy.web.framework.middleware.error.ErrorMiddleware method) exception_indicates_not_clickable() (in module galaxy.selenium.has_driver) exception_indicates_stale_element() (in module galaxy.selenium.has_driver) exception_seems_to_indicate_transition() (in module galaxy.selenium.navigates_galaxy) exchange() (galaxy.queue_worker.ControlTask property) exec_after_process() (galaxy.tools.DataManagerTool method) (galaxy.tools.ExpressionTool method) (galaxy.tools.ImportHistoryTool method) (galaxy.tools.InteractiveTool method) (galaxy.tools.SetMetadataTool method) (galaxy.tools.Tool method) exec_before_job() (galaxy.tools.DataSourceTool method) (galaxy.tools.ExpressionTool method) (galaxy.tools.OutputParameterJSONTool method) (galaxy.tools.Tool method) exec_clean() (galaxy.tool_util.deps.conda_util.CondaContext method) exec_command() (galaxy.tool_util.deps.conda_util.CondaContext method) exec_create() (galaxy.tool_util.deps.conda_util.CondaContext method) exec_install() (galaxy.tool_util.deps.conda_util.CondaContext method) exec_remove() (galaxy.tool_util.deps.conda_util.CondaContext method) execute() (galaxy.jobs.actions.post.ActionBox class method) (galaxy.jobs.actions.post.ChangeDatatypeAction class method) (galaxy.jobs.actions.post.ColumnSetAction class method) (galaxy.jobs.actions.post.DefaultJobAction class method) (galaxy.jobs.actions.post.DeleteDatasetAction class method) (galaxy.jobs.actions.post.DeleteIntermediatesAction class method) (galaxy.jobs.actions.post.EmailAction class method) (galaxy.jobs.actions.post.HideDatasetAction class method) (galaxy.jobs.actions.post.RenameDatasetAction class method) (galaxy.jobs.actions.post.SetMetadataAction class method) (galaxy.jobs.actions.post.TagDatasetAction class method) (galaxy.jobs.actions.post.ValidateOutputsAction class method) (galaxy.jobs.runners.util.cli.shell.BaseShellExec method) (galaxy.jobs.runners.util.cli.shell.local.LocalShell method) (galaxy.jobs.runners.util.cli.shell.rsh.ParamikoShell method) (galaxy.jobs.runners.util.cli.shell.rsh.RemoteShell method) (galaxy.tool_util.verify.test_data.GitDataResolver method) (galaxy.tools.actions.data_manager.DataManagerToolAction method) (galaxy.tools.actions.DefaultToolAction method) (galaxy.tools.actions.history_imp_exp.ExportHistoryToolAction method) (galaxy.tools.actions.history_imp_exp.ImportHistoryToolAction method) (galaxy.tools.actions.metadata.SetMetadataToolAction method) (galaxy.tools.actions.model_operations.ModelOperationToolAction method) (galaxy.tools.actions.ToolAction method) (galaxy.tools.actions.upload.BaseUploadToolAction method) (galaxy.tools.Tool method) (galaxy.workflow.modules.InputModule method) (galaxy.workflow.modules.InputParameterModule method) (galaxy.workflow.modules.PauseModule method) (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) (in module galaxy.tool_util.deps.brew_exts) (in module galaxy.tools.execute) (in module galaxy.util.commands) execute_on_mapped_over() (galaxy.jobs.actions.post.ActionBox class method) (galaxy.jobs.actions.post.DeleteDatasetAction class method) (galaxy.jobs.actions.post.HideDatasetAction class method) (galaxy.jobs.actions.post.RenameDatasetAction class method) (galaxy.jobs.actions.post.TagDatasetAction class method) execute_statements() (in module galaxy.model.triggers) execute_step() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager.StepManager method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertDirectoryExecutable method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertDirectoryExists method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertFileExecutable method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertFileExists method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.Autoconf method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.ChangeDirectory method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.Chmod method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadBinary method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadByUrl method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadFile method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MakeDirectory method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MakeInstall method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MoveDirectoryFiles method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MoveFile method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.RecipeStep method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.RegexReplace method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetEnvironment method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetEnvironmentForInstall method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupPerlEnvironment method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupPythonEnvironment method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupREnvironment method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupRubyEnvironment method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupVirtualEnv method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.ShellCommand method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.TemplateCommand method) execute_via_app() (galaxy.tools.actions.metadata.SetMetadataToolAction method) execution_time (galaxy.model.Task attribute) ExecutionTimer (class in galaxy.util) ExecutionTimerFactory (class in galaxy.app) exists() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method) (galaxy.tool_util.verify.test_data.FileDataResolver method) (galaxy.tool_util.verify.test_data.GitDataResolver method) (galaxy.tools.data.ToolDataPathFiles method) exit_code (galaxy.model.Job attribute) (galaxy.model.Task attribute) exit_code() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) exmeta_item_id (galaxy.webapps.galaxy.api.extended_metadata.HistoryDatasetExtendMetadataController attribute) (galaxy.webapps.galaxy.api.extended_metadata.LibraryDatasetExtendMetadataController attribute) expand_here_template() (in module galaxy.tools.data) expand_incoming() (galaxy.tools.Tool method) expand_json_keys() (in module galaxy.webapps.galaxy.api.roles) expand_meta_parameters() (in module galaxy.tools.parameters.meta) expand_multi_inputs() (in module galaxy.util.permutations) expand_pretty_datetime_format() (in module galaxy.web.formatting) expand_user_properties() (galaxy.model.User static method) expand_workflow_inputs() (in module galaxy.tools.parameters.meta) expect_repo_created_strings() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) expected_app_factories() (galaxy.config.config_manage.App property) expiration_time (galaxy.model.CustosAuthnzToken attribute) (galaxy.model.PasswordResetToken attribute) (tool_shed.webapp.model.PasswordResetToken attribute) expire_tool() (galaxy.tools.cache.ToolCache method) expired_datasets (galaxy.model.LibraryDataset attribute) ExplicitContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit) ExplicitSingularityContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit) export_archive() (galaxy.webapps.galaxy.controllers.history.HistoryController method) export_for_update() (galaxy_test.base.populators.BaseWorkflowPopulator method) export_history() (galaxy.model.store.DirectoryModelExportStore method) (galaxy.model.store.ModelExportStore method) export_invocation_bco() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) export_library() (galaxy.model.store.DirectoryModelExportStore method) export_list() (galaxy.tool_util.deps.conda_util.CondaContext method) export_name() (galaxy.model.JobExportHistoryArchive property) export_to_file() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) export_to_myexp() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) export_url() (galaxy_test.base.populators.BaseDatasetPopulator method) export_via_api() (tool_shed.webapp.controllers.repository.RepositoryController method) exported_key() (galaxy.model.store.DirectoryModelExportStore method) ExportHistoryTool (class in galaxy.tools) ExportHistoryToolAction (class in galaxy.tools.actions.history_imp_exp) exports (galaxy.model.History attribute) ExportsHistoryMixin (class in galaxy.webapps.base.controller) expose() (in module galaxy.web) (in module galaxy.web.framework.decorators) (in module galaxy.webapps.reports) (in module tool_shed.webapp) expose_api() (in module galaxy.web) (in module galaxy.web.framework.decorators) expose_api_anonymous() (in module galaxy.web) (in module galaxy.web.framework.decorators) expose_api_anonymous_and_sessionless() (in module galaxy.web) (in module galaxy.web.framework.decorators) expose_api_raw() (in module galaxy.web) (in module galaxy.web.framework.decorators) expose_api_raw_anonymous() (in module galaxy.web) (in module galaxy.web.framework.decorators) expose_api_raw_anonymous_and_sessionless() (in module galaxy.web) (in module galaxy.web.framework.decorators) EXPRESSION_INPUTS_NAME (galaxy.tools.ExpressionTool attribute) ExpressionContext (class in galaxy.util.expressions) ExpressionJson (class in galaxy.datatypes.text) ExpressionTool (class in galaxy.tools) ExpressionValidator (class in galaxy.tools.parameters.validation) expunge_all() (galaxy.managers.context.ProvidesAppContext method) ext (galaxy.datatypes.tabular.SraManifest attribute) ext() (galaxy.model.DatasetInstance property) (galaxy.model.store.discover.JsonCollectedDatasetMatch property) extend() (galaxy.model.custom_types.MutationList method) extend_data_with() (galaxy.tools.data.TabularToolDataTable method) extend_validation_errors() (galaxy.model.DatasetInstance method) extended (galaxy.metadata.ExtendedDirectoryMetadataGenerator attribute) (galaxy.metadata.MetadataCollectionStrategy attribute) extended_brew_info() (in module galaxy.tool_util.deps.brew_exts) extended_metadata (galaxy.model.ExtendedMetadataIndex attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) extended_metadata_id (galaxy.model.ExtendedMetadataIndex attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetAssociationHistory attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) ExtendedDirectoryMetadataGenerator (class in galaxy.metadata) ExtendedMetadata (class in galaxy.model) ExtendedMetadataIndex (class in galaxy.model) extension (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetAssociationHistory attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) external (galaxy.model.User attribute) (tool_shed.webapp.model.User attribute) external_filename (galaxy.model.Dataset attribute) external_metadata_set_successfully() (galaxy.metadata.MetadataCollectionStrategy method) (galaxy.metadata.PortableDirectoryMetadataGenerator method) external_output_metadata (galaxy.model.Job attribute) external_output_metadata() (galaxy.jobs.JobWrapper property) external_runjob() (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) external_user_id (galaxy.model.CustosAuthnzToken attribute) extra_data (galaxy.model.UserAuthnzToken attribute) extra_files() (galaxy.managers.datasets.DatasetAssociationManager method) (galaxy.model.store.discover.JsonCollectedDatasetMatch property) (galaxy.webapps.galaxy.api.datasets.DatasetsController method) extra_files_path (galaxy.model.DatasetHash attribute) (galaxy.model.DatasetSource attribute) extra_files_path() (galaxy.model.Dataset property) (galaxy.model.DatasetInstance property) extra_files_path_exists() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) extra_files_path_name() (galaxy.model.Dataset property) extra_files_path_name_from() (galaxy.model.Dataset method) extra_preferences() (galaxy.model.User property) extract() (galaxy.util.compression_utils.CompressedFile method) extract_components_from_tuple() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) extract_domain() (in module galaxy.security.validate_user_input) extract_options_from_dict() (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider class method) extract_value() (galaxy.tools.test.ParamContext method) extract_workflow() (in module galaxy.workflow.extract) ExtractDatasetCollectionTool (class in galaxy.tools) ExtractInputAction (class in galaxy.workflow.refactor.schema) ExtractUntypedParameter (class in galaxy.workflow.refactor.schema)

F

Facts (class in galaxy.util.facts) facts() (galaxy.web_stack.ApplicationStack property) (galaxy.web_stack.UWSGIApplicationStack property) fail() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.model.WorkflowInvocation method) (in module galaxy.tools.util.galaxyops) fail_job() (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.pbs.PBSJobRunner method) FAILED (galaxy.model.DatasetCollection.populated_states attribute) (galaxy.model.ImplicitCollectionJobs.populated_states attribute) (galaxy.model.Job.states attribute) failed (galaxy.model.view.HistoryDatasetCollectionJobStateSummary attribute) FAILED (galaxy.model.WorkflowInvocation.states attribute) failed() (galaxy.tool_util.lint.LintContext method) FAILED_METADATA (galaxy.model.Dataset.states attribute) (galaxy.model.DatasetInstance.states attribute) FailedTest (class in tool_shed.utility_containers) FAILURE (galaxy.openid.openid_manager.OpenIDManager attribute) failure() (in module galaxy.jobs.runners.state_handlers.resubmit) failure_count() (galaxy.tool_util.verify.script.Results property) fake_dataset_association (galaxy.model.FakeDatasetAssociation attribute) FakeDatasetAssociation (class in galaxy.model) FallbackContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit) FallbackNoRequirementsContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit) FallbackNoRequirementsSingularityContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit) FallbackSingularityContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit) Fast5Archive (class in galaxy.datatypes.binary) Fast5ArchiveBz2 (class in galaxy.datatypes.binary) Fast5ArchiveGz (class in galaxy.datatypes.binary) Fasta (class in galaxy.datatypes.sequence) fasta_path (galaxy.model.GenomeIndexToolData attribute) FastaDataProvider (class in galaxy.datatypes.dataproviders.dataset) FastAPIJobs (class in galaxy.webapps.galaxy.api.jobs) FastAPILicenses (class in galaxy.webapps.galaxy.api.licenses) FastAPIRoles (class in galaxy.webapps.galaxy.api.roles) FastAPITours (class in galaxy.webapps.galaxy.api.tours) Fastg (class in galaxy.datatypes.sequence) Fastq (class in galaxy.datatypes.sequence) FastqCSSanger (class in galaxy.datatypes.sequence) FastqIllumina (class in galaxy.datatypes.sequence) FastqSanger (class in galaxy.datatypes.sequence) FastqSolexa (class in galaxy.datatypes.sequence) FATAL (galaxy.tool_util.parser.stdio.StdioErrorLevel attribute) FATAL_OOM (galaxy.tool_util.parser.stdio.StdioErrorLevel attribute) fda() (galaxy.model.JobExportHistoryArchive property) FeatureLocationIndex (class in galaxy.datatypes.tabular) FeatureLocationIndexDataProvider (class in galaxy.visualization.data_providers.genome) FeatureXML (class in galaxy.datatypes.proteomics) feed() (galaxy.managers.pages.PageContentProcessor method) fetch() (galaxy.webapps.galaxy.api.tools.ToolsController method) (galaxy_test.base.populators.BaseDatasetPopulator method) fetch_job_data() (in module galaxy_test.base.instrument) fetch_job_states() (in module galaxy.managers.jobs) fetch_repository_metadata() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) fetch_requests() (galaxy.web.proxy.JsonFileProxyIpc method) (galaxy.web.proxy.ProxyIpc method) (galaxy.web.proxy.SqliteProxyIpc method) FetchUploadToolAction (class in galaxy.tools.actions.upload) ffprobe() (in module galaxy.datatypes.media) FIELD (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute) field_to_field_type() (in module galaxy.tool_util.cwl.representation) fields (galaxy.model.FormDefinition attribute) FIELDS (galaxy.model.search.HistoryDatasetView attribute) (galaxy.model.search.HistoryView attribute) (galaxy.model.search.JobView attribute) (galaxy.model.search.LibraryDatasetDatasetView attribute) (galaxy.model.search.LibraryDatasetView attribute) (galaxy.model.search.LibraryFolderView attribute) (galaxy.model.search.LibraryView attribute) (galaxy.model.search.PageRevisionView attribute) (galaxy.model.search.PageView attribute) (galaxy.model.search.ToolView attribute) (galaxy.model.search.ViewQueryBaseClass attribute) (galaxy.model.search.WorkflowView attribute) fields() (galaxy.util.form_builder.AddressField static method) (galaxy.web.form_builder.AddressField static method) file_append() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder.EnvFileBuilder method) file_ext (galaxy.datatypes.annotation.Augustus attribute) (galaxy.datatypes.annotation.SnapHmm attribute) (galaxy.datatypes.anvio.AnvioComposite attribute) (galaxy.datatypes.anvio.AnvioContigsDB attribute) (galaxy.datatypes.anvio.AnvioDB attribute) (galaxy.datatypes.anvio.AnvioGenomesDB attribute) (galaxy.datatypes.anvio.AnvioPanDB attribute) (galaxy.datatypes.anvio.AnvioProfileDB attribute) (galaxy.datatypes.anvio.AnvioSamplesDB attribute) (galaxy.datatypes.anvio.AnvioStructureDB attribute) (galaxy.datatypes.assembly.Amos attribute) (galaxy.datatypes.assembly.Roadmaps attribute) (galaxy.datatypes.assembly.Sequences attribute) (galaxy.datatypes.assembly.Velvet attribute) (galaxy.datatypes.binary.Ab1 attribute) (galaxy.datatypes.binary.Anndata attribute) (galaxy.datatypes.binary.BafTar attribute) (galaxy.datatypes.binary.Bam attribute) (galaxy.datatypes.binary.BamInputSorted attribute) (galaxy.datatypes.binary.BamNative attribute) (galaxy.datatypes.binary.BamQuerynameSorted attribute) (galaxy.datatypes.binary.Bcf attribute) (galaxy.datatypes.binary.BcfUncompressed attribute) (galaxy.datatypes.binary.BigBed attribute) (galaxy.datatypes.binary.BigWig attribute) (galaxy.datatypes.binary.Biom2 attribute) (galaxy.datatypes.binary.BlibSQlite attribute) (galaxy.datatypes.binary.Cel attribute) (galaxy.datatypes.binary.ChiraSQLite attribute) (galaxy.datatypes.binary.CompressedArchive attribute) (galaxy.datatypes.binary.CompressedZipArchive attribute) (galaxy.datatypes.binary.Cool attribute) (galaxy.datatypes.binary.Cpt attribute) (galaxy.datatypes.binary.CRAM attribute) (galaxy.datatypes.binary.CuffDiffSQlite attribute) (galaxy.datatypes.binary.DAA attribute) (galaxy.datatypes.binary.Dcd attribute) (galaxy.datatypes.binary.DlibSQlite attribute) (galaxy.datatypes.binary.DMND attribute) (galaxy.datatypes.binary.Edr attribute) (galaxy.datatypes.binary.ElibSQlite attribute) (galaxy.datatypes.binary.ExcelXls attribute) (galaxy.datatypes.binary.Fast5Archive attribute) (galaxy.datatypes.binary.Fast5ArchiveBz2 attribute) (galaxy.datatypes.binary.Fast5ArchiveGz attribute) (galaxy.datatypes.binary.GAFASQLite attribute) (galaxy.datatypes.binary.GeminiSQLite attribute) (galaxy.datatypes.binary.GenericAsn1Binary attribute) (galaxy.datatypes.binary.GmxBinary attribute) (galaxy.datatypes.binary.H5 attribute) (galaxy.datatypes.binary.ICM attribute) (galaxy.datatypes.binary.Idat attribute) (galaxy.datatypes.binary.IdpDB attribute) (galaxy.datatypes.binary.Loom attribute) (galaxy.datatypes.binary.MashSketch attribute) (galaxy.datatypes.binary.MassHunterTar attribute) (galaxy.datatypes.binary.MassLynxTar attribute) (galaxy.datatypes.binary.MCool attribute) (galaxy.datatypes.binary.Meryldb attribute) (galaxy.datatypes.binary.MzSQlite attribute) (galaxy.datatypes.binary.NcbiTaxonomySQlite attribute) (galaxy.datatypes.binary.NetCDF attribute) (galaxy.datatypes.binary.OSW attribute) (galaxy.datatypes.binary.OxliCountGraph attribute) (galaxy.datatypes.binary.OxliGraphLabels attribute) (galaxy.datatypes.binary.OxliNodeGraph attribute) (galaxy.datatypes.binary.OxliStopTags attribute) (galaxy.datatypes.binary.OxliSubset attribute) (galaxy.datatypes.binary.OxliTagSet attribute) (galaxy.datatypes.binary.Parquet attribute) (galaxy.datatypes.binary.PostgresqlArchive attribute) (galaxy.datatypes.binary.PQP attribute) (galaxy.datatypes.binary.ProBam attribute) (galaxy.datatypes.binary.RData attribute) (galaxy.datatypes.binary.RMA6 attribute) (galaxy.datatypes.binary.Scf attribute) (galaxy.datatypes.binary.SearchGuiArchive attribute) (galaxy.datatypes.binary.Sff attribute) (galaxy.datatypes.binary.SQlite attribute) (galaxy.datatypes.binary.SQmass attribute) (galaxy.datatypes.binary.Sra attribute) (galaxy.datatypes.binary.TdfTar attribute) (galaxy.datatypes.binary.Trr attribute) (galaxy.datatypes.binary.TwoBit attribute) (galaxy.datatypes.binary.Vel attribute) (galaxy.datatypes.binary.WiffTar attribute) (galaxy.datatypes.binary.Xlsx attribute) (galaxy.datatypes.binary.Xtc attribute) (galaxy.datatypes.binary.YepTar attribute) (galaxy.datatypes.blast.BlastDomainDb attribute) (galaxy.datatypes.blast.BlastDomainDb5 attribute) (galaxy.datatypes.blast.BlastNucDb attribute) (galaxy.datatypes.blast.BlastNucDb5 attribute) (galaxy.datatypes.blast.BlastProtDb attribute) (galaxy.datatypes.blast.BlastProtDb5 attribute) (galaxy.datatypes.blast.BlastXml attribute) (galaxy.datatypes.blast.LastDb attribute) (galaxy.datatypes.chrominfo.ChromInfo attribute) (galaxy.datatypes.constructive_solid_geometry.PlyAscii attribute) (galaxy.datatypes.constructive_solid_geometry.PlyBinary attribute) (galaxy.datatypes.constructive_solid_geometry.STL attribute) (galaxy.datatypes.constructive_solid_geometry.VtkAscii attribute) (galaxy.datatypes.constructive_solid_geometry.VtkBinary attribute) (galaxy.datatypes.coverage.LastzCoverage attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.data.GenericAsn1 attribute) (galaxy.datatypes.data.Newick attribute) (galaxy.datatypes.data.Nexus attribute) (galaxy.datatypes.data.Text attribute) (galaxy.datatypes.genetics.Affybatch attribute) (galaxy.datatypes.genetics.AllegroLOD attribute) (galaxy.datatypes.genetics.DataIn attribute) (galaxy.datatypes.genetics.Eigenstratgeno attribute) (galaxy.datatypes.genetics.Eigenstratpca attribute) (galaxy.datatypes.genetics.Eset attribute) (galaxy.datatypes.genetics.Fped attribute) (galaxy.datatypes.genetics.Fphe attribute) (galaxy.datatypes.genetics.GenomeGraphs attribute) (galaxy.datatypes.genetics.GenotypeMatrix attribute) (galaxy.datatypes.genetics.IdeasPre attribute) (galaxy.datatypes.genetics.ldIndep attribute) (galaxy.datatypes.genetics.Lped attribute) (galaxy.datatypes.genetics.MAlist attribute) (galaxy.datatypes.genetics.MarkerMap attribute) (galaxy.datatypes.genetics.Pbed attribute) (galaxy.datatypes.genetics.Phe attribute) (galaxy.datatypes.genetics.Pheno attribute) (galaxy.datatypes.genetics.Pphe attribute) (galaxy.datatypes.genetics.RexpBase attribute) (galaxy.datatypes.genetics.Rgenetics attribute) (galaxy.datatypes.genetics.rgFeatureList attribute) (galaxy.datatypes.genetics.rgSampleList attribute) (galaxy.datatypes.genetics.rgTabList attribute) (galaxy.datatypes.genetics.SNPMatrix attribute) (galaxy.datatypes.genetics.Snptest attribute) (galaxy.datatypes.gis.Shapefile attribute) (galaxy.datatypes.graph.Sif attribute) (galaxy.datatypes.graph.Xgmml attribute) (galaxy.datatypes.images.Analyze75 attribute) (galaxy.datatypes.images.Bmp attribute) (galaxy.datatypes.images.Eps attribute) (galaxy.datatypes.images.Gif attribute) (galaxy.datatypes.images.Gifti attribute) (galaxy.datatypes.images.Gmaj attribute) (galaxy.datatypes.images.Hamamatsu attribute) (galaxy.datatypes.images.Im attribute) (galaxy.datatypes.images.Image attribute) (galaxy.datatypes.images.Jpg attribute) (galaxy.datatypes.images.Laj attribute) (galaxy.datatypes.images.Mirax attribute) (galaxy.datatypes.images.Nifti1 attribute) (galaxy.datatypes.images.Nifti2 attribute) (galaxy.datatypes.images.Nrrd attribute) (galaxy.datatypes.images.Pbm attribute) (galaxy.datatypes.images.Pcd attribute) (galaxy.datatypes.images.Pcx attribute) (galaxy.datatypes.images.Pdf attribute) (galaxy.datatypes.images.Pgm attribute) (galaxy.datatypes.images.Png attribute) (galaxy.datatypes.images.Ppm attribute) (galaxy.datatypes.images.Psd attribute) (galaxy.datatypes.images.Rast attribute) (galaxy.datatypes.images.Rgb attribute) (galaxy.datatypes.images.Sakura attribute) (galaxy.datatypes.images.Tck attribute) (galaxy.datatypes.images.Tiff attribute) (galaxy.datatypes.images.Trk attribute) (galaxy.datatypes.images.Xbm attribute) (galaxy.datatypes.images.Xpm attribute) (galaxy.datatypes.interval.Bed attribute) (galaxy.datatypes.interval.Bed12 attribute) (galaxy.datatypes.interval.Bed6 attribute) (galaxy.datatypes.interval.BedGraph attribute) (galaxy.datatypes.interval.BedStrict attribute) (galaxy.datatypes.interval.ChromatinInteractions attribute) (galaxy.datatypes.interval.CustomTrack attribute) (galaxy.datatypes.interval.ENCODEPeak attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Gff3 attribute) (galaxy.datatypes.interval.Gtf attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.interval.ProBed attribute) (galaxy.datatypes.interval.ScIdx attribute) (galaxy.datatypes.interval.Wiggle attribute) (galaxy.datatypes.isa.IsaJson attribute) (galaxy.datatypes.isa.IsaTab attribute) (galaxy.datatypes.media.Flv attribute) (galaxy.datatypes.media.Mkv attribute) (galaxy.datatypes.media.Mp3 attribute) (galaxy.datatypes.media.Mp4 attribute) (galaxy.datatypes.media.Mpg attribute) (galaxy.datatypes.media.Wav attribute) (galaxy.datatypes.microarrays.Gal attribute) (galaxy.datatypes.microarrays.Gpr attribute) (galaxy.datatypes.molecules.CML attribute) (galaxy.datatypes.molecules.DRF attribute) (galaxy.datatypes.molecules.FPS attribute) (galaxy.datatypes.molecules.grd attribute) (galaxy.datatypes.molecules.grdtgz attribute) (galaxy.datatypes.molecules.InChI attribute) (galaxy.datatypes.molecules.MOL attribute) (galaxy.datatypes.molecules.MOL2 attribute) (galaxy.datatypes.molecules.OBFS attribute) (galaxy.datatypes.molecules.PDB attribute) (galaxy.datatypes.molecules.PDBQT attribute) (galaxy.datatypes.molecules.PHAR attribute) (galaxy.datatypes.molecules.PQR attribute) (galaxy.datatypes.molecules.SDF attribute) (galaxy.datatypes.molecules.SMILES attribute) (galaxy.datatypes.mothur.AccNos attribute) (galaxy.datatypes.mothur.AlignCheck attribute) (galaxy.datatypes.mothur.AlignReport attribute) (galaxy.datatypes.mothur.Axes attribute) (galaxy.datatypes.mothur.ConsensusTaxonomy attribute) (galaxy.datatypes.mothur.CountTable attribute) (galaxy.datatypes.mothur.DistanceMatrix attribute) (galaxy.datatypes.mothur.Frequency attribute) (galaxy.datatypes.mothur.Group attribute) (galaxy.datatypes.mothur.GroupAbund attribute) (galaxy.datatypes.mothur.LaneMask attribute) (galaxy.datatypes.mothur.LowerTriangleDistanceMatrix attribute) (galaxy.datatypes.mothur.Names attribute) (galaxy.datatypes.mothur.Oligos attribute) (galaxy.datatypes.mothur.Otu attribute) (galaxy.datatypes.mothur.PairwiseDistanceMatrix attribute) (galaxy.datatypes.mothur.Quantile attribute) (galaxy.datatypes.mothur.RefTaxonomy attribute) (galaxy.datatypes.mothur.Sabund attribute) (galaxy.datatypes.mothur.SecondaryStructureMap attribute) (galaxy.datatypes.mothur.SffFlow attribute) (galaxy.datatypes.mothur.SquareDistanceMatrix attribute) (galaxy.datatypes.mothur.Summary attribute) (galaxy.datatypes.mothur.TaxonomySummary attribute) (galaxy.datatypes.msa.Hmmer2 attribute) (galaxy.datatypes.msa.Hmmer3 attribute) (galaxy.datatypes.msa.HmmerPress attribute) (galaxy.datatypes.msa.InfernalCM attribute) (galaxy.datatypes.msa.MauveXmfa attribute) (galaxy.datatypes.msa.Msf attribute) (galaxy.datatypes.msa.Stockholm_1_0 attribute) (galaxy.datatypes.neo4j.Neo4jDB attribute) (galaxy.datatypes.neo4j.Neo4jDBzip attribute) (galaxy.datatypes.ngsindex.BowtieBaseIndex attribute) (galaxy.datatypes.ngsindex.BowtieColorIndex attribute) (galaxy.datatypes.phylip.Phylip attribute) (galaxy.datatypes.plant_tribes.PlantTribesKsComponents attribute) (galaxy.datatypes.plant_tribes.Smat attribute) (galaxy.datatypes.proteomics.ConsensusXML attribute) (galaxy.datatypes.proteomics.Dta attribute) (galaxy.datatypes.proteomics.Dta2d attribute) (galaxy.datatypes.proteomics.Edta attribute) (galaxy.datatypes.proteomics.FeatureXML attribute) (galaxy.datatypes.proteomics.IdXML attribute) (galaxy.datatypes.proteomics.ImzML attribute) (galaxy.datatypes.proteomics.Kroenik attribute) (galaxy.datatypes.proteomics.MascotDat attribute) (galaxy.datatypes.proteomics.MascotXML attribute) (galaxy.datatypes.proteomics.Mgf attribute) (galaxy.datatypes.proteomics.Ms2 attribute) (galaxy.datatypes.proteomics.Msp attribute) (galaxy.datatypes.proteomics.MzData attribute) (galaxy.datatypes.proteomics.MzIdentML attribute) (galaxy.datatypes.proteomics.MzML attribute) (galaxy.datatypes.proteomics.MzQuantML attribute) (galaxy.datatypes.proteomics.MzTab attribute) (galaxy.datatypes.proteomics.MzTab2 attribute) (galaxy.datatypes.proteomics.MzXML attribute) (galaxy.datatypes.proteomics.NmrML attribute) (galaxy.datatypes.proteomics.ParamXml attribute) (galaxy.datatypes.proteomics.PEFF attribute) (galaxy.datatypes.proteomics.PepList attribute) (galaxy.datatypes.proteomics.PepXml attribute) (galaxy.datatypes.proteomics.PepXmlReport attribute) (galaxy.datatypes.proteomics.ProtXML attribute) (galaxy.datatypes.proteomics.ProtXmlReport attribute) (galaxy.datatypes.proteomics.PSMS attribute) (galaxy.datatypes.proteomics.QCML attribute) (galaxy.datatypes.proteomics.Sf3 attribute) (galaxy.datatypes.proteomics.SPLib attribute) (galaxy.datatypes.proteomics.SPLibNoIndex attribute) (galaxy.datatypes.proteomics.TandemXML attribute) (galaxy.datatypes.proteomics.ThermoRAW attribute) (galaxy.datatypes.proteomics.TrafoXML attribute) (galaxy.datatypes.proteomics.TraML attribute) (galaxy.datatypes.proteomics.UniProtXML attribute) (galaxy.datatypes.proteomics.Wiff attribute) (galaxy.datatypes.proteomics.XHunterAslFormat attribute) (galaxy.datatypes.proteomics.XquestSpecXML attribute) (galaxy.datatypes.proteomics.XquestXML attribute) (galaxy.datatypes.qualityscore.QualityScore attribute) (galaxy.datatypes.qualityscore.QualityScore454 attribute) (galaxy.datatypes.qualityscore.QualityScoreIllumina attribute) (galaxy.datatypes.qualityscore.QualityScoreSolexa attribute) (galaxy.datatypes.qualityscore.QualityScoreSOLiD attribute) (galaxy.datatypes.sequence.Axt attribute) (galaxy.datatypes.sequence.BaseFastq attribute) (galaxy.datatypes.sequence.csFasta attribute) (galaxy.datatypes.sequence.DotBracket attribute) (galaxy.datatypes.sequence.Fasta attribute) (galaxy.datatypes.sequence.Fastg attribute) (galaxy.datatypes.sequence.Fastq attribute) (galaxy.datatypes.sequence.FastqCSSanger attribute) (galaxy.datatypes.sequence.FastqIllumina attribute) (galaxy.datatypes.sequence.FastqSanger attribute) (galaxy.datatypes.sequence.FastqSolexa attribute) (galaxy.datatypes.sequence.Genbank attribute) (galaxy.datatypes.sequence.Lav attribute) (galaxy.datatypes.sequence.Maf attribute) (galaxy.datatypes.sequence.MafCustomTrack attribute) (galaxy.datatypes.sequence.MemePsp attribute) (galaxy.datatypes.sequence.RNADotPlotMatrix attribute) (galaxy.datatypes.sequence.SequenceSplitLocations attribute) (galaxy.datatypes.spaln.SpalnNuclDb attribute) (galaxy.datatypes.spaln.SpalnProtDb attribute) (galaxy.datatypes.speech.BPF attribute) (galaxy.datatypes.speech.TextGrid attribute) (galaxy.datatypes.tabular.CMAP attribute) (galaxy.datatypes.tabular.ConnectivityTable attribute) (galaxy.datatypes.tabular.CSV attribute) (galaxy.datatypes.tabular.Eland attribute) (galaxy.datatypes.tabular.ElandMulti attribute) (galaxy.datatypes.tabular.FeatureLocationIndex attribute) (galaxy.datatypes.tabular.MatrixMarket attribute) (galaxy.datatypes.tabular.Pileup attribute) (galaxy.datatypes.tabular.Sam attribute) (galaxy.datatypes.tabular.TSV attribute) (galaxy.datatypes.tabular.Vcf attribute) (galaxy.datatypes.tabular.VcfGz attribute) (galaxy.datatypes.text.Arff attribute) (galaxy.datatypes.text.Biom1 attribute) (galaxy.datatypes.text.ExpressionJson attribute) (galaxy.datatypes.text.GeoJson attribute) (galaxy.datatypes.text.Gfa1 attribute) (galaxy.datatypes.text.Gfa2 attribute) (galaxy.datatypes.text.Html attribute) (galaxy.datatypes.text.ImgtJson attribute) (galaxy.datatypes.text.Ipynb attribute) (galaxy.datatypes.text.IQTree attribute) (galaxy.datatypes.text.Json attribute) (galaxy.datatypes.text.Obo attribute) (galaxy.datatypes.text.Paf attribute) (galaxy.datatypes.text.SnpEffDb attribute) (galaxy.datatypes.text.SnpSiftDbNSFP attribute) (galaxy.datatypes.tracks.GeneTrack attribute) (galaxy.datatypes.tracks.UCSCTrackHub attribute) (galaxy.datatypes.triples.HDT attribute) (galaxy.datatypes.triples.Jsonld attribute) (galaxy.datatypes.triples.N3 attribute) (galaxy.datatypes.triples.NTriples attribute) (galaxy.datatypes.triples.Rdf attribute) (galaxy.datatypes.triples.Triples attribute) (galaxy.datatypes.triples.Turtle attribute) (galaxy.datatypes.xml.CisML attribute) (galaxy.datatypes.xml.Dzi attribute) (galaxy.datatypes.xml.GenericXml attribute) (galaxy.datatypes.xml.MEMEXml attribute) (galaxy.datatypes.xml.Owl attribute) (galaxy.datatypes.xml.Phyloxml attribute) (galaxy.datatypes.xml.Sbml attribute)

file_iter() (in module galaxy.util.compression_utils) file_name() (galaxy.datatypes.metadata.MetadataTempFile property) (galaxy.model.Dataset property) (galaxy.model.DatasetInstance property) (galaxy.model.metadata.MetadataTempFile property) (galaxy.model.MetadataFile property) file_path (galaxy.model.Dataset attribute) file_reader() (in module galaxy.util) file_ready() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.cloud.Cloud method) (galaxy.objectstore.irods.IRODSObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.pulsar.PulsarObjectStore method) (galaxy.objectstore.s3.S3ObjectStore method) file_size (galaxy.model.Dataset attribute) file_size() (galaxy.datatypes.sniff.FilePrefix property) file_source() (galaxy.files.FileSourcePath property) file_states (tool_shed.webapp.model.Repository attribute) FileDataResolver (class in galaxy.tool_util.verify.test_data) FileDefaultsAction (class in galaxy.workflow.refactor.schema) FileLiteralTarget (class in galaxy.tool_util.cwl.util) FileLock (class in galaxy.util.filelock) FileLockException filename_in (galaxy.model.JobExternalOutputMetadata attribute) filename_kwds (galaxy.model.JobExternalOutputMetadata attribute) filename_out (galaxy.model.JobExternalOutputMetadata attribute) filename_override_metadata (galaxy.model.JobExternalOutputMetadata attribute) filename_results_code (galaxy.model.JobExternalOutputMetadata attribute) FileParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) FilePatternDatasetCollectionDescription (class in galaxy.tool_util.parser.output_collection_def) FilePrefix (class in galaxy.datatypes.sniff) files_contains() (in module galaxy.tool_util.verify) files_delta() (in module galaxy.tool_util.verify) files_diff() (in module galaxy.tool_util.verify) files_re_match() (in module galaxy.tool_util.verify) files_re_match_multiline() (in module galaxy.tool_util.verify) FileSourcePath (class in galaxy.files) FilesSource (class in galaxy.files.sources) FileToolParameter (class in galaxy.tools.parameters.basic) FileUploadTarget (class in galaxy.tool_util.cwl.util) fill() (galaxy.selenium.has_driver.HasDriver method) fill_defaults (galaxy.managers.workflows.WorkflowStateResolutionOptions attribute) fill_input_fields() (galaxy_test.selenium.test_change_password.ChangePasswordTestCase method) fill_region_alignment() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) fill_review_form() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) fill_template() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) (in module galaxy.util.template) fill_template_mako() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) fill_template_string() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) FillStepDefaultsAction (class in galaxy.workflow.refactor.schema) Filter (class in galaxy.tools.parameters.dynamic_options) filter() (galaxy.datatypes.dataproviders.base.FilteredDataProvider method) (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) (galaxy.datatypes.dataproviders.line.BlockDataProvider method) (galaxy.datatypes.dataproviders.line.FilteredLineDataProvider method) (galaxy.datatypes.dataproviders.line.RegexLineDataProvider method) (galaxy.model.search.ViewQueryBaseClass method) (galaxy.web.framework.helpers.grids.CommunityTagsColumn method) (galaxy.web.framework.helpers.grids.DeletedColumn method) (galaxy.web.framework.helpers.grids.GridColumn method) (galaxy.web.framework.helpers.grids.MulticolFilterColumn method) (galaxy.web.framework.helpers.grids.PurgedColumn method) (galaxy.web.framework.helpers.grids.SharingStatusColumn method) (galaxy.web.framework.helpers.grids.StateColumn method) (galaxy.web.framework.helpers.grids.TextColumn method) (galaxy.web.legacy_framework.grids.CommunityTagsColumn method) (galaxy.web.legacy_framework.grids.DeletedColumn method) (galaxy.web.legacy_framework.grids.GridColumn method) (galaxy.web.legacy_framework.grids.MulticolFilterColumn method) (galaxy.web.legacy_framework.grids.SharingStatusColumn method) (galaxy.web.legacy_framework.grids.StateColumn method) (galaxy.web.legacy_framework.grids.TextColumn method) (galaxy.web_stack.ApplicationStackLogFilter method) (galaxy.web_stack.UWSGILogFilter method) (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid.DbKeyColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.EmailColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.SpecifiedDateColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.StateColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.ToolColumn method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.EmailColumn method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.SpecifiedDateColumn method) (tool_shed.grids.admin_grids.UserGrid.EmailColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.EmailColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.RepositoryCategoryColumn method) (tool_shed.grids.repository_grids.ValidRepositoryGrid.RepositoryCategoryColumn method) filter_accessible() (galaxy.managers.secured.AccessibleManagerMixin method) filter_actions_after_binary_installation() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadBinary method) filter_and_persist_proprietary_tool_panel_configs() (galaxy.tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager method) filter_annotation_contains() (galaxy.managers.annotatable.AnnotatableFilterMixin method) filter_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method) filter_by_columns() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) filter_by_dataset() (galaxy.datatypes.display_applications.application.DisplayApplication method) (galaxy.datatypes.display_applications.application.DisplayApplicationLink method) filter_by_latest_downloadable_changeset_revision_that_has_missing_tool_test_components() (in module tool_shed.grids.util) filter_by_latest_metadata_changeset_revision_that_has_invalid_tools() (in module tool_shed.grids.util) filter_by_regex() (galaxy.datatypes.dataproviders.line.RegexLineDataProvider method) filter_file_fields() (galaxy.tools.data.TabularToolDataTable method) filter_only_if_compiling_contained_td() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) filter_options() (galaxy.tool_util.parser.output_actions.BooleanFilter method) (galaxy.tool_util.parser.output_actions.ColumnReplaceFilter method) (galaxy.tool_util.parser.output_actions.ColumnStripFilter method) (galaxy.tool_util.parser.output_actions.InsertColumnToolOutputActionOptionFilter method) (galaxy.tool_util.parser.output_actions.MetadataValueFilter method) (galaxy.tool_util.parser.output_actions.MultipleSplitterFilter method) (galaxy.tool_util.parser.output_actions.ParamValueToolOutputActionOptionFilter method) (galaxy.tool_util.parser.output_actions.StringFunctionFilter method) (galaxy.tool_util.parser.output_actions.ToolOutputActionOptionFilter method) (galaxy.tools.parameters.dynamic_options.AdditionalValueFilter method) (galaxy.tools.parameters.dynamic_options.AttributeValueSplitterFilter method) (galaxy.tools.parameters.dynamic_options.DataMetaFilter method) (galaxy.tools.parameters.dynamic_options.Filter method) (galaxy.tools.parameters.dynamic_options.MultipleSplitterFilter method) (galaxy.tools.parameters.dynamic_options.ParamValueFilter method) (galaxy.tools.parameters.dynamic_options.RegexpFilter method) (galaxy.tools.parameters.dynamic_options.RemoveValueFilter method) (galaxy.tools.parameters.dynamic_options.SortByColumnFilter method) (galaxy.tools.parameters.dynamic_options.StaticValueFilter method) (galaxy.tools.parameters.dynamic_options.UniqueValueFilter method) filter_output() (in module galaxy.tools.actions) filter_owned() (galaxy.managers.secured.OwnableManagerMixin method) filter_template() (galaxy.auth.util.Authenticator property) filter_type (in module galaxy.tool_util.parser.output_actions) FilterableMixin (class in galaxy.visualization.data_providers.genome) FilterDatasetsTool (class in galaxy.tools) FilteredDataProvider (class in galaxy.datatypes.dataproviders.base) FilteredLineDataProvider (class in galaxy.datatypes.dataproviders.line) FilterEmptyDatasetsTool (class in galaxy.tools) FilterFactory (class in galaxy.tools.toolbox.filters) FilterFailedDatasetsTool (class in galaxy.tools) FilterFromFileTool (class in galaxy.tools) filters (tool_shed.grids.repository_grid_filter_manager.RepositoryGridFilterManager attribute) final() (tool_shed.webapp.search.repo_search.RepoWeighting method) finalize() (galaxy.model.DatasetCollection method) (galaxy_test.base.instrument.StructuredTestDataPlugin method) finalize_config() (galaxy.web.framework.base.WebApplication method) find_anaconda_versions() (in module galaxy.tool_util.deps.mulled.get_tests) find_best_container_description() (galaxy.tool_util.deps.containers.ContainerFinder method) (galaxy.tool_util.deps.containers.ContainerRegistry method) find_class() (galaxy.util.aliaspickler.AliasUnpickler method) find_config() (in module galaxy.main) find_config_file() (in module galaxy.util.properties) find_container() (galaxy.tool_util.deps.containers.ContainerFinder method) (galaxy.tool_util.deps.containers.NullContainerFinder method) find_conversion_destination() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) find_conversion_destination_for_dataset_by_extensions() (galaxy.datatypes.registry.Registry method) find_dep() (galaxy.tool_util.deps.DependencyManager method) (galaxy.tool_util.deps.NullDependencyManager method) find_element_by_sizzle() (in module galaxy.selenium.sizzle) find_elements() (galaxy.selenium.has_driver.HasDriver method) find_elements_by_sizzle() (in module galaxy.selenium.sizzle) find_engine() (in module galaxy.tools.expressions) (in module galaxy.tools.expressions.util) find_fieldstorage() (galaxy.tools.Tool method) find_files() (galaxy.job_execution.output_collect.BaseJobContext method) find_implicit_input_collection() (galaxy.model.HistoryDatasetCollectionAssociation method) find_instance_nested() (in module galaxy.util) find_job_object_by_name() (in module galaxy.jobs.runners.util.pykube_util) find_output_def() (galaxy.tools.Tool method) find_pod_object_by_name() (in module galaxy.jobs.runners.util.pykube_util) find_possible_tools_from_path() (in module galaxy.tool_util.loader_directory) find_root() (in module galaxy.config) find_section_id() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) find_tools() (tool_shed.webapp.controllers.repository.RepositoryController method) finish() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.selenium.cli.DriverWrapper method) (galaxy.workflow.render.WorkflowCanvas method) finish_job() (galaxy.jobs.runners.AsynchronousJobRunner method) (galaxy.jobs.runners.chronos.ChronosJobRunner method) (galaxy.jobs.runners.kubernetes.KubernetesJobRunner method) finished() (galaxy.model.Job property) first_changeset_hash (in module tool_shed.test.functional.test_0420_citable_urls_for_repositories) first_dataset_element() (galaxy.model.DatasetCollection property) first_dataset_instance() (galaxy.model.DatasetCollectionElement method) FixedModuleCodeCompiler (class in galaxy.util.template) FLAGS_W_ARGS (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider attribute) FLAGS_WO_ARGS (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider attribute) flakey() (in module galaxy_test.base.populators) flat_map() (in module galaxy.util.rules_dsl) flatten() (galaxy.util.Params method) (in module galaxy.web.framework.base) FlattenTool (class in galaxy.tools) FLOAT (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute) float_nan() (in module galaxy.visualization.data_providers.genome) FloatToolParameter (class in galaxy.tools.parameters.basic) FluentTraceLogger (class in galaxy.util.custom_logging.fluent_log) flush() (galaxy.datatypes.util.maf_utilities.RegionAlignment method) (galaxy.datatypes.util.maf_utilities.TempFileHandler method) (galaxy.job_execution.output_collect.JobContext method) (galaxy.model.StorableObject method) (galaxy.model.store.discover.ModelPersistenceContext method) (galaxy.model.store.discover.SessionlessModelPersistenceContext method) (galaxy.model.store.SessionlessContext method) (galaxy.tools.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.TempFileHandler method) (galaxy.util.pastescript.serve.LazyWriter method) (in module tool_shed.test.base.test_db_util) Flv (class in galaxy.datatypes.media) fn_filter_parsers (galaxy.managers.base.ModelFilterParser attribute) Folder (class in tool_shed.utility_containers.utility_container_manager) folder (galaxy.model.LibraryDataset attribute) (galaxy.model.LibraryDatasetCollectionAssociation attribute) (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryFolderPermissions attribute) folder_id (galaxy.model.LibraryDataset attribute) (galaxy.model.LibraryDatasetCollectionAssociation attribute) folder_is_public() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) folder_is_unrestricted() (galaxy.model.security.GalaxyRBACAgent method) FolderContentsController (class in galaxy.webapps.galaxy.api.folder_contents) FolderManager (class in galaxy.managers.folders) folders (galaxy.model.LibraryFolder attribute) FoldersController (class in galaxy.webapps.galaxy.api.folders) for_collection_type() (galaxy.model.dataset_collections.type_description.CollectionTypeDescriptionFactory method) for_collections() (galaxy.model.dataset_collections.matching.MatchingCollections static method) for_dataset_collection() (galaxy.model.dataset_collections.structure.Tree static method) for_direct_import() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) for_state() (galaxy.tools.test.ParamContext method) (galaxy.tools.test.RootParamContext method) force_bed_field_count() (in module galaxy.datatypes.converters.interval_to_bedstrict_converter) force_symlink() (in module galaxy.util) foreign_key_name (galaxy.managers.base.ModelManager attribute) (galaxy.managers.cloudauthzs.CloudAuthzManager attribute) (galaxy.managers.datasets.DatasetManager attribute) (galaxy.managers.hdas.HDAManager attribute) (galaxy.managers.hdcas.HDCAManager attribute) (galaxy.managers.histories.HistoryManager attribute) (galaxy.managers.pages.PageManager attribute) (galaxy.managers.roles.RoleManager attribute) (galaxy.managers.tools.DynamicToolManager attribute) (galaxy.managers.users.UserManager attribute) (galaxy.managers.visualizations.VisualizationManager attribute) form_definition (galaxy.model.FormValues attribute) form_definition_current (galaxy.model.FormDefinition attribute) form_definition_current_id (galaxy.model.FormDefinition attribute) form_definition_id (galaxy.model.FormValues attribute) (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryInfoAssociation attribute) form_values_id (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryInfoAssociation attribute) (galaxy.model.User attribute) format (galaxy.web.framework.middleware.translogger.TransLogger attribute) format() (galaxy.job_metrics.formatting.JobMetricFormatter method) (galaxy.job_metrics.JobMetrics method) Format2ConverterGalaxyInterface (class in galaxy.managers.workflows) format_attrs() (in module galaxy.web.framework.helpers.tags) format_bool() (in module galaxy.webapps.galaxy.controllers.page) format_for_summary() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) format_param() (in module galaxy.workflow.modules) format_return_as_json() (in module galaxy.web) (in module galaxy.web.framework.decorators) format_traceback() (galaxy.tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) formats() (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter property) formatted() (galaxy.webapps.reports.controllers.tools.Tools method) formatter (galaxy.job_metrics.instrumenters.cgroup.CgroupPlugin attribute) (galaxy.job_metrics.instrumenters.collectl.CollectlPlugin attribute) (galaxy.job_metrics.instrumenters.core.CorePlugin attribute) (galaxy.job_metrics.instrumenters.cpuinfo.CpuInfoPlugin attribute) (galaxy.job_metrics.instrumenters.env.EnvPlugin attribute) (galaxy.job_metrics.instrumenters.hostname.HostnamePlugin attribute) (galaxy.job_metrics.instrumenters.InstrumentPlugin attribute) (galaxy.job_metrics.instrumenters.meminfo.MemInfoPlugin attribute) (galaxy.job_metrics.instrumenters.uname.UnamePlugin attribute) FormatToolOutputAction (class in galaxy.tool_util.parser.output_actions) FormDefinition (class in galaxy.model) FormDefinition.types (class in galaxy.model) FormDefinitionAddressFieldFactory (class in galaxy.forms.forms) FormDefinitionAPIController (class in galaxy.webapps.galaxy.api.forms) FormDefinitionCurrent (class in galaxy.model) FormDefinitionFactory (class in galaxy.forms.forms) FormDefinitionFieldFactory (class in galaxy.forms.forms) FormDefinitionHistoryFieldFactory (class in galaxy.forms.forms) FormDefinitionPasswordFieldFactory (class in galaxy.forms.forms) FormDefinitionSelectFieldFactory (class in galaxy.forms.forms) FormDefinitionTextFieldFactory (class in galaxy.forms.forms) FormDefinitionWorkflowFieldFactory (class in galaxy.forms.forms) FormDefinitionWorkflowMappingFieldFactory (class in galaxy.forms.forms) Forms (class in galaxy.webapps.galaxy.controllers.forms) forms (galaxy.model.FormDefinitionCurrent attribute) forms_grid (galaxy.webapps.galaxy.controllers.forms.Forms attribute) forms_list() (galaxy.webapps.galaxy.controllers.forms.Forms method) FormsGrid (class in galaxy.webapps.galaxy.controllers.forms) FormsGrid.DescriptionColumn (class in galaxy.webapps.galaxy.controllers.forms) FormsGrid.NameColumn (class in galaxy.webapps.galaxy.controllers.forms) FormsGrid.StatusColumn (class in galaxy.webapps.galaxy.controllers.forms) FormsGrid.TypeColumn (class in galaxy.webapps.galaxy.controllers.forms) FormValues (class in galaxy.model) Fped (class in galaxy.datatypes.genetics) Fphe (class in galaxy.datatypes.genetics) FPS (class in galaxy.datatypes.molecules) framework_tool_and_types (galaxy_test.selenium.framework.TestWithSeleniumMixin attribute) freebayes_repository_long_description (in module tool_shed.test.functional.test_0430_browse_utilities) Frequency (class in galaxy.datatypes.mothur) from_api() (galaxy.containers.docker_model.DockerTask class method) from_app() (galaxy.tools.repositories.ValidationContext static method) from_app_config() (galaxy.files.ConfiguredFileSources static method) (galaxy.files.ConfiguredFileSourcesConfig static method) from_args() (galaxy.tool_util.deps.brew_exts.RecipeContext static method) from_cli() (galaxy.containers.docker_model.DockerNode class method) (galaxy.containers.docker_model.DockerService class method) (galaxy.containers.docker_model.DockerTask class method) from_code() (galaxy.exceptions.MessageException static method) from_collection_type() (galaxy.tools.parameters.history_query.HistoryQuery static method) from_collection_types() (galaxy.tools.parameters.history_query.HistoryQuery static method) from_constraint_string_list() (galaxy.containers.docker_model.DockerServiceConstraints class method) from_dict() (galaxy.files.ConfiguredFileSources static method) (galaxy.files.ConfiguredFileSourcesConfig static method) (galaxy.selenium.components.Component static method) (galaxy.selenium.components.SelectorTemplate static method) (galaxy.tool_util.deps.dependencies.DependenciesDescription static method) (galaxy.tool_util.deps.requirements.ContainerDescription static method) (galaxy.tool_util.deps.requirements.RequirementSpecification static method) (galaxy.tool_util.deps.requirements.ToolRequirement static method) (galaxy.tool_util.deps.resolvers.RequirementMapping static method) (galaxy.tool_util.parser.interface.TestCollectionDef static method) (galaxy.tool_util.parser.interface.TestCollectionOutputDef static method) (galaxy.tool_util.parser.output_objects.ToolOutput static method) (galaxy.tool_util.parser.output_objects.ToolOutputCollection static method) (galaxy.tool_util.parser.output_objects.ToolOutputCollectionStructure static method) (galaxy.visualization.genomes.GenomeRegion static method) (galaxy.workflow.modules.SubWorkflowModule class method) (galaxy.workflow.modules.ToolModule class method) (galaxy.workflow.modules.WorkflowModule class method) (galaxy.workflow.modules.WorkflowModuleFactory method) from_elem() (galaxy.datatypes.display_applications.application.DisplayApplication class method) (galaxy.datatypes.display_applications.application.DisplayApplicationLink class method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter class method) (galaxy.forms.forms.FormDefinitionAddressFieldFactory method) (galaxy.forms.forms.FormDefinitionFactory method) (galaxy.forms.forms.FormDefinitionFieldFactory method) (galaxy.forms.forms.FormDefinitionHistoryFieldFactory method) (galaxy.forms.forms.FormDefinitionPasswordFieldFactory method) (galaxy.forms.forms.FormDefinitionSelectFieldFactory method) (galaxy.forms.forms.FormDefinitionTextFieldFactory method) (galaxy.forms.forms.FormDefinitionWorkflowFieldFactory method) (galaxy.forms.forms.FormDefinitionWorkflowMappingFieldFactory method) (galaxy.openid.providers.OpenIDProvider class method) (galaxy.openid.providers.OpenIDProviders class method) (galaxy.tool_util.parser.output_actions.ToolOutputAction class method) (galaxy.tool_util.parser.output_actions.ToolOutputActionConditionalWhen class method) (galaxy.tool_util.parser.output_actions.ToolOutputActionOption class method) (galaxy.tool_util.parser.output_actions.ToolOutputActionOptionFilter class method) (galaxy.tools.data.ToolDataTable class method) from_element() (galaxy.tools.parameters.dynamic_options.Filter class method) (galaxy.tools.parameters.input_translation.ToolInputTranslator class method) (galaxy.tools.parameters.sanitize.ToolParameterSanitizer class method) (galaxy.tools.parameters.validation.DatasetEmptyValidator class method) (galaxy.tools.parameters.validation.DatasetExtraFilesPathEmptyValidator class method) (galaxy.tools.parameters.validation.DatasetOkValidator class method) (galaxy.tools.parameters.validation.EmptyTextfieldValidator class method) (galaxy.tools.parameters.validation.ExpressionValidator class method) (galaxy.tools.parameters.validation.InRangeValidator class method) (galaxy.tools.parameters.validation.LengthValidator class method) (galaxy.tools.parameters.validation.MetadataInDataTableColumnValidator class method) (galaxy.tools.parameters.validation.MetadataInFileColumnValidator class method) (galaxy.tools.parameters.validation.MetadataInRangeValidator class method) (galaxy.tools.parameters.validation.MetadataValidator class method) (galaxy.tools.parameters.validation.NoOptionsValidator class method) (galaxy.tools.parameters.validation.RegexValidator class method) (galaxy.tools.parameters.validation.UnspecifiedBuildValidator class method) (galaxy.tools.parameters.validation.Validator class method) (galaxy.tools.parameters.validation.ValueInDataTableColumnValidator class method) from_external_value() (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.model.metadata.FileParameter method) (galaxy.model.metadata.MetadataParameter method) from_file() (galaxy.datatypes.display_applications.application.DisplayApplication class method) (galaxy.job_metrics.JobInstrumenter static method) (galaxy.openid.providers.OpenIDProvider class method) (galaxy.openid.providers.OpenIDProviders class method) (galaxy.tools.error_reports.ErrorPlugin static method) from_id() (galaxy.containers.Container method) (galaxy.containers.docker_model.DockerContainer class method) (galaxy.containers.docker_model.DockerNode class method) (galaxy.containers.docker_model.DockerService class method) from_JSON() (galaxy.datatypes.metadata.MetadataTempFile class method) (galaxy.model.metadata.MetadataTempFile class method) from_json() (galaxy.tools.parameters.basic.BaseURLToolParameter method) (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.FileToolParameter method) (galaxy.tools.parameters.basic.FloatToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.IntegerToolParameter method) (galaxy.tools.parameters.basic.LibraryDatasetToolParameter method) (galaxy.tools.parameters.basic.SelectTagParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.DataCollectionToolParameter method) (galaxy.tools.parameters.DataToolParameter method) (galaxy.tools.parameters.SelectToolParameter method) from_JSON_dict() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataCollection method) from_label_dictionary() (galaxy.containers.docker_model.DockerNodeLabels class method) from_list() (galaxy.tool_util.deps.requirements.ToolRequirements static method) from_order_index (galaxy.workflow.refactor.schema.RefactorActionExecutionMessage attribute) from_parameter() (galaxy.tools.parameters.history_query.HistoryQuery static method) from_path (galaxy.model.StoredWorkflow attribute) from_step_label (galaxy.workflow.refactor.schema.RefactorActionExecutionMessage attribute) from_str() (galaxy.containers.ContainerVolume method) (galaxy.containers.docker_model.DockerServiceConstraint class method) (galaxy.containers.docker_model.DockerVolume class method) (galaxy.visualization.genomes.GenomeRegion static method) from_tool() (galaxy.tools.toolbox.lineages.interface.ToolLineage static method) (galaxy.tools.toolbox.lineages.ToolLineage static method) from_tool_form (galaxy.managers.workflows.WorkflowStateResolutionOptions attribute) from_workflow_step() (galaxy.workflow.modules.SubWorkflowModule class method) (galaxy.workflow.modules.ToolModule class method) (galaxy.workflow.modules.WorkflowModule class method) (galaxy.workflow.modules.WorkflowModuleFactory method) from_xml() (galaxy.objectstore.BaseObjectStore class method) (galaxy.objectstore.DistributedObjectStore class method) (galaxy.tool_util.parser.interface.TestCollectionDef static method) FromDataTableOutputActionOption (class in galaxy.tool_util.parser.output_actions) FromFileToolOutputActionOption (class in galaxy.tool_util.parser.output_actions) FromParamToolOutputActionOption (class in galaxy.tool_util.parser.output_actions) ftp_dir() (galaxy.files.DictFileSourcesUserContext property) (galaxy.files.ProvidesUserFileSourcesUserContext property) FTPFileToolParameter (class in galaxy.tools.parameters.basic) full_delete() (galaxy.model.Dataset method) func_std_string() (in module galaxy.web.framework.middleware.profile) FunctionalTestCase (class in galaxy_test.base.testcase) futurize_preprocessor() (in module galaxy.util.template)

G

ga_refresh() (in module tool_shed.test.base.test_db_util) GAFASQLite (class in galaxy.datatypes.binary) Gal (class in galaxy.datatypes.microarrays) galactic_job_json() (in module galaxy.tool_util.cwl.util) galaxy module galaxy (galaxy.web.framework.middleware.batch.BatchMiddleware attribute) galaxy.actions module galaxy.actions.admin module galaxy.actions.library module galaxy.app module galaxy.auth module galaxy.auth.providers module galaxy.auth.providers.alwaysreject module galaxy.auth.providers.ldap_ad module galaxy.auth.providers.localdb module galaxy.auth.providers.pam_auth module galaxy.auth.util module galaxy.authnz module galaxy.authnz.custos_authnz module galaxy.authnz.managers module galaxy.authnz.psa_authnz module galaxy.config module galaxy.config.config_manage module galaxy.config.schema module galaxy.config.script module galaxy.config_watchers module galaxy.containers module galaxy.containers.docker module galaxy.containers.docker_decorators module galaxy.containers.docker_model module galaxy.containers.docker_swarm module galaxy.datatypes module galaxy.datatypes.annotation module galaxy.datatypes.anvio module galaxy.datatypes.assembly module galaxy.datatypes.binary module galaxy.datatypes.blast module galaxy.datatypes.checkers module galaxy.datatypes.chrominfo module galaxy.datatypes.constructive_solid_geometry module galaxy.datatypes.converters module galaxy.datatypes.converters.bed_to_gff_converter module galaxy.datatypes.converters.bgzip module galaxy.datatypes.converters.cram_to_bam module galaxy.datatypes.converters.fasta_to_len module galaxy.datatypes.converters.fasta_to_tabular_converter module galaxy.datatypes.converters.fastq_to_fqtoc module galaxy.datatypes.converters.fastqsolexa_to_fasta_converter module galaxy.datatypes.converters.fastqsolexa_to_qual_converter module galaxy.datatypes.converters.gff_to_bed_converter module galaxy.datatypes.converters.gff_to_interval_index_converter module galaxy.datatypes.converters.interval_to_bed_converter module galaxy.datatypes.converters.interval_to_bedstrict_converter module galaxy.datatypes.converters.interval_to_fli module galaxy.datatypes.converters.interval_to_interval_index_converter module galaxy.datatypes.converters.interval_to_tabix_converter module galaxy.datatypes.converters.lped_to_fped_converter module galaxy.datatypes.converters.lped_to_pbed_converter module galaxy.datatypes.converters.maf_to_fasta_converter module galaxy.datatypes.converters.maf_to_interval_converter module galaxy.datatypes.converters.pbed_ldreduced_converter module galaxy.datatypes.converters.pbed_to_lped_converter module galaxy.datatypes.converters.picard_interval_list_to_bed6_converter module galaxy.datatypes.converters.pileup_to_interval_index_converter module galaxy.datatypes.converters.ref_to_seq_taxonomy_converter module galaxy.datatypes.converters.tabular_csv module galaxy.datatypes.converters.tabular_to_dbnsfp module galaxy.datatypes.converters.vcf_to_interval_index_converter module galaxy.datatypes.converters.vcf_to_vcf_bgzip module galaxy.datatypes.converters.wiggle_to_simple_converter module galaxy.datatypes.coverage module galaxy.datatypes.data module galaxy.datatypes.dataproviders module galaxy.datatypes.dataproviders.base module galaxy.datatypes.dataproviders.chunk module galaxy.datatypes.dataproviders.column module galaxy.datatypes.dataproviders.dataset module galaxy.datatypes.dataproviders.decorators module galaxy.datatypes.dataproviders.exceptions module galaxy.datatypes.dataproviders.external module galaxy.datatypes.dataproviders.hierarchy module galaxy.datatypes.dataproviders.line module galaxy.datatypes.display_applications module galaxy.datatypes.display_applications.application module galaxy.datatypes.display_applications.parameters module galaxy.datatypes.display_applications.util module galaxy.datatypes.genetics module galaxy.datatypes.gis module galaxy.datatypes.graph module galaxy.datatypes.images module galaxy.datatypes.interval module galaxy.datatypes.isa module galaxy.datatypes.media module galaxy.datatypes.metadata module galaxy.datatypes.microarrays module galaxy.datatypes.molecules module galaxy.datatypes.mothur module galaxy.datatypes.msa module galaxy.datatypes.neo4j module galaxy.datatypes.ngsindex module galaxy.datatypes.phylip module galaxy.datatypes.plant_tribes module galaxy.datatypes.proteomics module galaxy.datatypes.qualityscore module galaxy.datatypes.registry module galaxy.datatypes.sequence module galaxy.datatypes.sniff module galaxy.datatypes.spaln module galaxy.datatypes.speech module galaxy.datatypes.tabular module galaxy.datatypes.text module galaxy.datatypes.tracks module galaxy.datatypes.triples module galaxy.datatypes.upload_util module galaxy.datatypes.util module galaxy.datatypes.util.generic_util module galaxy.datatypes.util.gff_util module galaxy.datatypes.util.maf_utilities module galaxy.datatypes.xml module galaxy.dependencies module galaxy.eggs module galaxy.exceptions module galaxy.exceptions.error_codes module galaxy.files module galaxy.files.sources module galaxy.files.sources.dropbox module galaxy.files.sources.galaxy module galaxy.files.sources.posix module galaxy.files.sources.s3 module galaxy.files.sources.webdav module galaxy.forms module galaxy.forms.forms module galaxy.job_execution module galaxy.job_execution.datasets module galaxy.job_execution.output_collect module galaxy.job_execution.ports module galaxy.job_execution.ports.view module galaxy.job_execution.setup module galaxy.job_metrics module galaxy.job_metrics.collectl module galaxy.job_metrics.collectl.cli module galaxy.job_metrics.collectl.processes module galaxy.job_metrics.collectl.stats module galaxy.job_metrics.collectl.subsystems module galaxy.job_metrics.formatting module galaxy.job_metrics.instrumenters module galaxy.job_metrics.instrumenters.cgroup module galaxy.job_metrics.instrumenters.collectl module galaxy.job_metrics.instrumenters.core module galaxy.job_metrics.instrumenters.cpuinfo module galaxy.job_metrics.instrumenters.env module galaxy.job_metrics.instrumenters.hostname module galaxy.job_metrics.instrumenters.meminfo module galaxy.job_metrics.instrumenters.uname module galaxy.jobs module galaxy.jobs.actions module galaxy.jobs.actions.post module galaxy.jobs.command_factory module galaxy.jobs.dynamic_tool_destination module galaxy.jobs.handler module galaxy.jobs.manager module galaxy.jobs.mapper module galaxy.jobs.rule_helper module galaxy.jobs.rules module galaxy.jobs.runners module galaxy.jobs.runners.chronos module galaxy.jobs.runners.cli module galaxy.jobs.runners.condor module galaxy.jobs.runners.drmaa module galaxy.jobs.runners.godocker module galaxy.jobs.runners.kubernetes module galaxy.jobs.runners.local module galaxy.jobs.runners.pbs module galaxy.jobs.runners.pulsar module galaxy.jobs.runners.slurm module galaxy.jobs.runners.state_handler_factory module galaxy.jobs.runners.state_handlers module galaxy.jobs.runners.state_handlers.resubmit module galaxy.jobs.runners.tasks module galaxy.jobs.runners.univa module galaxy.jobs.runners.util module galaxy.jobs.runners.util.cli module galaxy.jobs.runners.util.cli.factory module galaxy.jobs.runners.util.cli.job module galaxy.jobs.runners.util.cli.job.lsf module galaxy.jobs.runners.util.cli.job.slurm module galaxy.jobs.runners.util.cli.job.slurm_torque module galaxy.jobs.runners.util.cli.job.torque module galaxy.jobs.runners.util.cli.shell module galaxy.jobs.runners.util.cli.shell.local module galaxy.jobs.runners.util.cli.shell.rsh module galaxy.jobs.runners.util.condor module galaxy.jobs.runners.util.env module galaxy.jobs.runners.util.external module galaxy.jobs.runners.util.job_script module galaxy.jobs.runners.util.kill module galaxy.jobs.runners.util.process_groups module galaxy.jobs.runners.util.pykube_util module galaxy.jobs.runners.util.sudo module galaxy.jobs.splitters module galaxy.jobs.splitters.basic module galaxy.jobs.splitters.multi module galaxy.jobs.stock_rules module galaxy.jobs.transfer_manager module galaxy.main module galaxy.managers module galaxy.managers.annotatable module galaxy.managers.api_keys module galaxy.managers.base module galaxy.managers.citations module galaxy.managers.cloud module galaxy.managers.cloudauthzs module galaxy.managers.collections module galaxy.managers.collections_util module galaxy.managers.configuration module galaxy.managers.containers module galaxy.managers.context module galaxy.managers.datasets module galaxy.managers.deletable module galaxy.managers.executables module galaxy.managers.folders module galaxy.managers.hdas module galaxy.managers.hdcas module galaxy.managers.histories module galaxy.managers.history_contents module galaxy.managers.interactivetool module galaxy.managers.jobs module galaxy.managers.lddas module galaxy.managers.libraries module galaxy.managers.library_datasets module galaxy.managers.licenses module galaxy.managers.markdown_parse module galaxy.managers.markdown_util module galaxy.managers.pages module galaxy.managers.ratable module galaxy.managers.rbac_secured module galaxy.managers.roles module galaxy.managers.secured module galaxy.managers.session module galaxy.managers.sharable module galaxy.managers.taggable module galaxy.managers.tools module galaxy.managers.users module galaxy.managers.visualizations module galaxy.managers.workflows module galaxy.metadata module galaxy.metadata.set_metadata module galaxy.model module galaxy.model.base module galaxy.model.custom_types module galaxy.model.database_heartbeat module galaxy.model.dataset_collections module galaxy.model.dataset_collections.builder module galaxy.model.dataset_collections.matching module galaxy.model.dataset_collections.registry module galaxy.model.dataset_collections.structure module galaxy.model.dataset_collections.subcollections module galaxy.model.dataset_collections.type_description module galaxy.model.dataset_collections.types module galaxy.model.dataset_collections.types.list module galaxy.model.dataset_collections.types.paired module galaxy.model.item_attrs module galaxy.model.mapping module galaxy.model.metadata module galaxy.model.migrate module galaxy.model.migrate.check module galaxy.model.migrate.versions module galaxy.model.migrate.versions.0001_initial_tables module galaxy.model.migrate.versions.0002_metadata_file_table module galaxy.model.migrate.versions.0003_security_and_libraries module galaxy.model.migrate.versions.0004_indexes_and_defaults module galaxy.model.migrate.versions.0005_cleanup_datasets_fix module galaxy.model.migrate.versions.0006_change_qual_datatype module galaxy.model.migrate.versions.0007_sharing_histories module galaxy.model.migrate.versions.0008_galaxy_forms module galaxy.model.migrate.versions.0009_request_table module galaxy.model.migrate.versions.0010_hda_display_at_authz_table module galaxy.model.migrate.versions.0011_v0010_mysql_index_fix module galaxy.model.migrate.versions.0012_user_address module galaxy.model.migrate.versions.0013_change_lib_item_templates_to_forms module galaxy.model.migrate.versions.0014_pages module galaxy.model.migrate.versions.0015_tagging module galaxy.model.migrate.versions.0016_v0015_mysql_index_fix module galaxy.model.migrate.versions.0017_library_item_indexes module galaxy.model.migrate.versions.0018_ordered_tags_and_page_tags module galaxy.model.migrate.versions.0019_request_library_folder module galaxy.model.migrate.versions.0020_library_upload_job module galaxy.model.migrate.versions.0021_user_prefs module galaxy.model.migrate.versions.0022_visualization_tables module galaxy.model.migrate.versions.0023_page_published_and_deleted_columns module galaxy.model.migrate.versions.0024_page_slug_unique_constraint module galaxy.model.migrate.versions.0025_user_info module galaxy.model.migrate.versions.0026_cloud_tables module galaxy.model.migrate.versions.0027_request_events module galaxy.model.migrate.versions.0028_external_metadata_file_override module galaxy.model.migrate.versions.0029_user_actions module galaxy.model.migrate.versions.0030_history_slug_column module galaxy.model.migrate.versions.0031_community_and_workflow_tags module galaxy.model.migrate.versions.0032_stored_workflow_slug_column module galaxy.model.migrate.versions.0033_published_cols_for_histories_and_workflows module galaxy.model.migrate.versions.0034_page_user_share_association module galaxy.model.migrate.versions.0035_item_annotations_and_workflow_step_tags module galaxy.model.migrate.versions.0036_add_deleted_column_to_library_template_assoc_tables module galaxy.model.migrate.versions.0037_samples_library module galaxy.model.migrate.versions.0038_add_inheritable_column_to_library_template_assoc_tables module galaxy.model.migrate.versions.0039_add_synopsis_column_to_library_table module galaxy.model.migrate.versions.0040_page_annotations module galaxy.model.migrate.versions.0041_workflow_invocation module galaxy.model.migrate.versions.0042_workflow_invocation_fix module galaxy.model.migrate.versions.0043_visualization_sharing_tagging_annotating module galaxy.model.migrate.versions.0044_add_notify_column_to_request_table module galaxy.model.migrate.versions.0045_request_type_permissions_table module galaxy.model.migrate.versions.0046_post_job_actions module galaxy.model.migrate.versions.0047_job_table_user_id_column module galaxy.model.migrate.versions.0048_dataset_instance_state_column module galaxy.model.migrate.versions.0049_api_keys_table module galaxy.model.migrate.versions.0050_drop_cloud_tables module galaxy.model.migrate.versions.0051_imported_col_for_jobs_table module galaxy.model.migrate.versions.0052_sample_dataset_table module galaxy.model.migrate.versions.0053_item_ratings module galaxy.model.migrate.versions.0054_visualization_dbkey module galaxy.model.migrate.versions.0055_add_pja_assoc_for_jobs module galaxy.model.migrate.versions.0056_workflow_outputs module galaxy.model.migrate.versions.0057_request_notify module galaxy.model.migrate.versions.0058_history_import_export module galaxy.model.migrate.versions.0059_sample_dataset_file_path module galaxy.model.migrate.versions.0060_history_archive_import module galaxy.model.migrate.versions.0061_tasks module galaxy.model.migrate.versions.0062_user_openid_table module galaxy.model.migrate.versions.0063_sequencer_table module galaxy.model.migrate.versions.0064_add_run_and_sample_run_association_tables module galaxy.model.migrate.versions.0065_add_name_to_form_fields_and_values module galaxy.model.migrate.versions.0066_deferred_job_and_transfer_job_tables module galaxy.model.migrate.versions.0067_populate_sequencer_table module galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services module galaxy.model.migrate.versions.0069_rename_sequencer_form_type module galaxy.model.migrate.versions.0070_add_info_column_to_deferred_job_table module galaxy.model.migrate.versions.0071_add_history_and_workflow_to_sample module galaxy.model.migrate.versions.0072_add_pid_and_socket_columns_to_transfer_job_table module galaxy.model.migrate.versions.0073_add_ldda_to_implicit_conversion_table module galaxy.model.migrate.versions.0074_add_purged_column_to_library_dataset_table module galaxy.model.migrate.versions.0075_add_subindex_column_to_run_table module galaxy.model.migrate.versions.0076_fix_form_values_data_corruption module galaxy.model.migrate.versions.0077_create_tool_tag_association_table module galaxy.model.migrate.versions.0078_add_columns_for_disk_usage_accounting module galaxy.model.migrate.versions.0079_input_library_to_job_table module galaxy.model.migrate.versions.0080_quota_tables module galaxy.model.migrate.versions.0081_add_tool_version_to_hda_ldda module galaxy.model.migrate.versions.0082_add_tool_shed_repository_table module galaxy.model.migrate.versions.0083_add_prepare_files_to_task module galaxy.model.migrate.versions.0084_add_ldda_id_to_implicit_conversion_table module galaxy.model.migrate.versions.0085_add_task_info module galaxy.model.migrate.versions.0086_add_tool_shed_repository_table_columns module galaxy.model.migrate.versions.0087_tool_id_guid_map_table module galaxy.model.migrate.versions.0088_add_installed_changeset_revison_column module galaxy.model.migrate.versions.0089_add_object_store_id_columns module galaxy.model.migrate.versions.0090_add_tool_shed_repository_table_columns module galaxy.model.migrate.versions.0091_add_tool_version_tables module galaxy.model.migrate.versions.0092_add_migrate_tools_table module galaxy.model.migrate.versions.0093_add_job_params_col module galaxy.model.migrate.versions.0094_add_job_handler_col module galaxy.model.migrate.versions.0095_hda_subsets module galaxy.model.migrate.versions.0096_openid_provider module galaxy.model.migrate.versions.0097_add_ctx_rev_column module galaxy.model.migrate.versions.0098_genome_index_tool_data_table module galaxy.model.migrate.versions.0099_add_tool_dependency_table module galaxy.model.migrate.versions.0100_alter_tool_dependency_table_version_column module galaxy.model.migrate.versions.0101_drop_installed_changeset_revision_column module galaxy.model.migrate.versions.0102_add_tool_dependency_status_columns module galaxy.model.migrate.versions.0103_add_tool_shed_repository_status_columns module galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters module galaxy.model.migrate.versions.0105_add_cleanup_event_table module galaxy.model.migrate.versions.0106_add_missing_indexes module galaxy.model.migrate.versions.0107_add_exit_code_to_job_and_task module galaxy.model.migrate.versions.0108_add_extended_metadata module galaxy.model.migrate.versions.0109_add_repository_dependency_tables module galaxy.model.migrate.versions.0110_add_dataset_uuid module galaxy.model.migrate.versions.0111_add_job_destinations module galaxy.model.migrate.versions.0112_add_data_manager_history_association_and_data_manager_job_association_tables module galaxy.model.migrate.versions.0113_update_migrate_tools_table module galaxy.model.migrate.versions.0114_update_migrate_tools_table_again module galaxy.model.migrate.versions.0115_longer_user_password_field module galaxy.model.migrate.versions.0116_drop_update_available_col_add_tool_shed_status_col module galaxy.model.migrate.versions.0117_add_user_activation module galaxy.model.migrate.versions.0118_add_hda_extended_metadata module galaxy.model.migrate.versions.0119_job_metrics module galaxy.model.migrate.versions.0120_dataset_collections module galaxy.model.migrate.versions.0121_workflow_uuids module galaxy.model.migrate.versions.0122_grow_mysql_blobs module galaxy.model.migrate.versions.0123_add_workflow_request_tables module galaxy.model.migrate.versions.0124_job_state_history module galaxy.model.migrate.versions.0125_workflow_step_tracking module galaxy.model.migrate.versions.0126_password_reset module galaxy.model.migrate.versions.0127_output_collection_adjustments module galaxy.model.migrate.versions.0128_session_timeout module galaxy.model.migrate.versions.0129_job_external_output_metadata_validity module galaxy.model.migrate.versions.0130_change_pref_datatype module galaxy.model.migrate.versions.0131_subworkflow_and_input_parameter_modules module galaxy.model.migrate.versions.0132_add_lastpasswordchange_to_user module galaxy.model.migrate.versions.0133_add_dependency_column_to_job module galaxy.model.migrate.versions.0134_hda_set_deleted_if_purged module galaxy.model.migrate.versions.0135_add_library_tags module galaxy.model.migrate.versions.0136_collection_and_workflow_state module galaxy.model.migrate.versions.0137_add_copied_from_job_id_column module galaxy.model.migrate.versions.0138_add_hda_version module galaxy.model.migrate.versions.0139_add_history_dataset_association_history_table module galaxy.model.migrate.versions.0140_add_dataset_version_to_job_to_input_dataset_association_table module galaxy.model.migrate.versions.0141_add_oidc_tables module galaxy.model.migrate.versions.0142_change_numeric_metric_precision module galaxy.model.migrate.versions.0143_add_cloudauthz_tables module galaxy.model.migrate.versions.0144_add_cleanup_event_user_table module galaxy.model.migrate.versions.0145_add_workflow_step_input module galaxy.model.migrate.versions.0146_workflow_paths module galaxy.model.migrate.versions.0147_job_messages module galaxy.model.migrate.versions.0148_add_checksum_table module galaxy.model.migrate.versions.0149_dynamic_tools module galaxy.model.migrate.versions.0150_add_create_time_field_for_cloudauthz module galaxy.model.migrate.versions.0151_add_worker_process module galaxy.model.migrate.versions.0152_add_metadata_file_uuid module galaxy.model.migrate.versions.0153_add_custos_authnz_token_table module galaxy.model.migrate.versions.0154_created_from_basename module galaxy.model.migrate.versions.0155_job_galaxy_version module galaxy.model.migrate.versions.0156_add_interactivetools module galaxy.model.migrate.versions.0157_rework_dataset_validation module galaxy.model.migrate.versions.0158_workflow_reports module galaxy.model.migrate.versions.0159_add_job_external_id_index module galaxy.model.migrate.versions.0160_hda_set_deleted_if_purged_again module galaxy.model.migrate.versions.0161_add_workflow_invocation_output_table module galaxy.model.migrate.versions.0162_job_only_pjas module galaxy.model.migrate.versions.0163_worker_process_pid module galaxy.model.migrate.versions.0164_page_format module galaxy.model.migrate.versions.0165_add_content_update_time module galaxy.model.migrate.versions.0166_job_state_summary_view module galaxy.model.migrate.versions.0167_add_job_to_input_dataset_collection_element_association module galaxy.model.migrate.versions.0168_stored_workflow_hidden_col module galaxy.model.migrate.versions.0169_add_missing_indexes module galaxy.model.migrate.versions.0170_add_more_missing_indexes module galaxy.model.migrate.versions.0171_schemaorg_metadata module galaxy.model.migrate.versions.0172_it_entrypoint_requires_domain module galaxy.model.migrate.versions.util module galaxy.model.none_like module galaxy.model.orm module galaxy.model.orm.engine_factory module galaxy.model.orm.now module galaxy.model.orm.scripts module galaxy.model.search module galaxy.model.security module galaxy.model.store module galaxy.model.store.build_objects module galaxy.model.store.discover module galaxy.model.tags module galaxy.model.tool_shed_install module galaxy.model.tool_shed_install.mapping module galaxy.model.tool_shed_install.migrate module galaxy.model.tool_shed_install.migrate.check module galaxy.model.triggers module galaxy.model.view module galaxy.model.view.utils module galaxy.objectstore module galaxy.objectstore.azure_blob module galaxy.objectstore.cloud module galaxy.objectstore.irods module galaxy.objectstore.pithos module galaxy.objectstore.pulsar module galaxy.objectstore.s3 module galaxy.objectstore.s3_multipart_upload module galaxy.openid module galaxy.openid.openid_manager module galaxy.openid.providers module galaxy.queue_worker module galaxy.queues module galaxy.quota module galaxy.schema module galaxy.schema.fields module galaxy.schema.schema module galaxy.security module galaxy.security.idencoding module galaxy.security.passwords module galaxy.security.validate_user_input module galaxy.selenium module galaxy.selenium.cli module galaxy.selenium.components module galaxy.selenium.context module galaxy.selenium.data module galaxy.selenium.driver_factory module galaxy.selenium.has_driver module galaxy.selenium.navigates_galaxy module galaxy.selenium.scripts module galaxy.selenium.scripts.dump_tour module galaxy.selenium.sizzle module galaxy.selenium.smart_components module galaxy.selenium.toolbox module galaxy.selenium.toolbox.filters module galaxy.tool_shed module galaxy.tool_shed.galaxy_install module galaxy.tool_shed.galaxy_install.datatypes module galaxy.tool_shed.galaxy_install.datatypes.custom_datatype_manager module galaxy.tool_shed.galaxy_install.install_manager module galaxy.tool_shed.galaxy_install.installed_repository_manager module galaxy.tool_shed.galaxy_install.metadata module galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager module galaxy.tool_shed.galaxy_install.migrate module galaxy.tool_shed.galaxy_install.migrate.check module galaxy.tool_shed.galaxy_install.migrate.common module galaxy.tool_shed.galaxy_install.migrate.versions module galaxy.tool_shed.galaxy_install.migrate.versions.0001_tools module galaxy.tool_shed.galaxy_install.migrate.versions.0002_tools module galaxy.tool_shed.galaxy_install.migrate.versions.0003_tools module galaxy.tool_shed.galaxy_install.migrate.versions.0004_tools module galaxy.tool_shed.galaxy_install.migrate.versions.0005_tools module galaxy.tool_shed.galaxy_install.migrate.versions.0006_tools module galaxy.tool_shed.galaxy_install.migrate.versions.0007_tools module galaxy.tool_shed.galaxy_install.migrate.versions.0008_tools module galaxy.tool_shed.galaxy_install.migrate.versions.0009_tools module galaxy.tool_shed.galaxy_install.migrate.versions.0010_tools module galaxy.tool_shed.galaxy_install.migrate.versions.0011_tools module galaxy.tool_shed.galaxy_install.migrate.versions.0012_tools module galaxy.tool_shed.galaxy_install.repository_dependencies module galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager module galaxy.tool_shed.galaxy_install.tool_dependencies module galaxy.tool_shed.galaxy_install.tool_dependencies.env_manager module galaxy.tool_shed.galaxy_install.tool_dependencies.recipe module galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader module galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder module galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment module galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager module galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler module galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler module galaxy.tool_shed.galaxy_install.tool_migration_manager module galaxy.tool_shed.galaxy_install.tools module galaxy.tool_shed.galaxy_install.tools.data_manager module galaxy.tool_shed.galaxy_install.tools.tool_panel_manager module galaxy.tool_shed.galaxy_install.update_repository_manager module galaxy.tool_shed.metadata module galaxy.tool_shed.metadata.metadata_generator module galaxy.tool_shed.repository_type module galaxy.tool_shed.tool_shed_registry module galaxy.tool_shed.tools module galaxy.tool_shed.tools.data_table_manager module galaxy.tool_shed.tools.tool_validator module galaxy.tool_shed.util module galaxy.tool_shed.util.basic_util module galaxy.tool_shed.util.container_util module galaxy.tool_shed.util.hg_util module galaxy.tool_shed.util.metadata_util module galaxy.tool_shed.util.repository_util module galaxy.tool_shed.util.shed_util_common module galaxy.tool_shed.util.tool_dependency_util module galaxy.tool_shed.util.tool_util module galaxy.tool_util module galaxy.tool_util.client module galaxy.tool_util.client.staging module galaxy.tool_util.cwl module galaxy.tool_util.cwl.cwltool_deps module galaxy.tool_util.cwl.parser module galaxy.tool_util.cwl.representation module galaxy.tool_util.cwl.runnable module galaxy.tool_util.cwl.runtime_actions module galaxy.tool_util.cwl.schema module galaxy.tool_util.cwl.util module galaxy.tool_util.deps module galaxy.tool_util.deps.brew_exts module galaxy.tool_util.deps.brew_util module galaxy.tool_util.deps.commands module galaxy.tool_util.deps.conda_compat module galaxy.tool_util.deps.conda_util module galaxy.tool_util.deps.container_classes module galaxy.tool_util.deps.container_resolvers module galaxy.tool_util.deps.container_resolvers.explicit module galaxy.tool_util.deps.container_resolvers.mulled module galaxy.tool_util.deps.containers module galaxy.tool_util.deps.dependencies module galaxy.tool_util.deps.docker_util module galaxy.tool_util.deps.dockerfiles module galaxy.tool_util.deps.installable module galaxy.tool_util.deps.mulled module galaxy.tool_util.deps.mulled.get_tests module galaxy.tool_util.deps.mulled.mulled_build module galaxy.tool_util.deps.mulled.mulled_build_channel module galaxy.tool_util.deps.mulled.mulled_build_files module galaxy.tool_util.deps.mulled.mulled_build_tool module galaxy.tool_util.deps.mulled.mulled_list module galaxy.tool_util.deps.mulled.mulled_search module galaxy.tool_util.deps.mulled.mulled_update_singularity_containers module galaxy.tool_util.deps.mulled.util module galaxy.tool_util.deps.requirements module galaxy.tool_util.deps.resolvers module galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages module galaxy.tool_util.deps.resolvers.conda module galaxy.tool_util.deps.resolvers.galaxy_packages module galaxy.tool_util.deps.resolvers.homebrew module galaxy.tool_util.deps.resolvers.lmod module galaxy.tool_util.deps.resolvers.modules module galaxy.tool_util.deps.resolvers.resolver_mixins module galaxy.tool_util.deps.resolvers.tool_shed_packages module galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages module galaxy.tool_util.deps.singularity_util module galaxy.tool_util.deps.views module galaxy.tool_util.fetcher module galaxy.tool_util.lint module galaxy.tool_util.linters module galaxy.tool_util.linters.citations module galaxy.tool_util.linters.command module galaxy.tool_util.linters.cwl module galaxy.tool_util.linters.general module galaxy.tool_util.linters.help module galaxy.tool_util.linters.inputs module galaxy.tool_util.linters.outputs module galaxy.tool_util.linters.stdio module galaxy.tool_util.linters.tests module galaxy.tool_util.linters.xml_order module galaxy.tool_util.loader module galaxy.tool_util.loader_directory module galaxy.tool_util.locations module galaxy.tool_util.locations.dockstore module galaxy.tool_util.locations.file module galaxy.tool_util.locations.http module galaxy.tool_util.output_checker module galaxy.tool_util.parser module galaxy.tool_util.parser.cwl module galaxy.tool_util.parser.factory module galaxy.tool_util.parser.interface module galaxy.tool_util.parser.output_actions module galaxy.tool_util.parser.output_collection_def module galaxy.tool_util.parser.output_objects module galaxy.tool_util.parser.stdio module galaxy.tool_util.parser.util module galaxy.tool_util.parser.xml module galaxy.tool_util.parser.yaml module galaxy.tool_util.provided_metadata module galaxy.tool_util.verify module galaxy.tool_util.verify.asserts module galaxy.tool_util.verify.asserts.archive module galaxy.tool_util.verify.asserts.hdf5 module galaxy.tool_util.verify.asserts.size module galaxy.tool_util.verify.asserts.tabular module galaxy.tool_util.verify.asserts.text module galaxy.tool_util.verify.asserts.xml module galaxy.tool_util.verify.interactor module galaxy.tool_util.verify.script module galaxy.tool_util.verify.test_data module galaxy.tool_util.verify.wait module galaxy.tools module galaxy.tools.actions module galaxy.tools.actions.data_manager module galaxy.tools.actions.data_source module galaxy.tools.actions.history_imp_exp module galaxy.tools.actions.metadata module galaxy.tools.actions.model_operations module galaxy.tools.actions.upload module galaxy.tools.actions.upload_common module galaxy.tools.cache module galaxy.tools.data module galaxy.tools.data_fetch module galaxy.tools.data_manager module galaxy.tools.data_manager.manager module galaxy.tools.error_reports module galaxy.tools.error_reports.plugins module galaxy.tools.error_reports.plugins.base_git module galaxy.tools.error_reports.plugins.email module galaxy.tools.error_reports.plugins.github module galaxy.tools.error_reports.plugins.gitlab module galaxy.tools.error_reports.plugins.influxdb module galaxy.tools.error_reports.plugins.json module galaxy.tools.error_reports.plugins.sentry module galaxy.tools.errors module galaxy.tools.evaluation module galaxy.tools.exception_handling module galaxy.tools.execute module galaxy.tools.expressions module galaxy.tools.expressions.evaluation module galaxy.tools.expressions.script module galaxy.tools.expressions.util module galaxy.tools.filters module galaxy.tools.imp_exp module galaxy.tools.imp_exp.export_history module galaxy.tools.imp_exp.unpack_tar_gz_archive module galaxy.tools.parameters module galaxy.tools.parameters.basic module galaxy.tools.parameters.dataset_matcher module galaxy.tools.parameters.dynamic_options module galaxy.tools.parameters.grouping module galaxy.tools.parameters.history_query module galaxy.tools.parameters.input_translation module galaxy.tools.parameters.meta module galaxy.tools.parameters.sanitize module galaxy.tools.parameters.validation module galaxy.tools.parameters.wrapped module galaxy.tools.parameters.wrapped_json module galaxy.tools.recommendations module galaxy.tools.repositories module galaxy.tools.search module galaxy.tools.special_tools module galaxy.tools.test module galaxy.tools.toolbox module galaxy.tools.toolbox.base module galaxy.tools.toolbox.filters module galaxy.tools.toolbox.integrated_panel module galaxy.tools.toolbox.lineages module galaxy.tools.toolbox.lineages.factory module galaxy.tools.toolbox.lineages.interface module galaxy.tools.toolbox.panel module galaxy.tools.toolbox.parser module galaxy.tools.toolbox.tags module galaxy.tools.toolbox.watcher module galaxy.tools.util module galaxy.tools.util.galaxyops module galaxy.tools.util.maf_utilities module galaxy.tools.wrappers module galaxy.tours module galaxy.util module galaxy.util.aliaspickler module galaxy.util.bunch module galaxy.util.bytesize module galaxy.util.checkers module galaxy.util.commands module galaxy.util.compression_utils module galaxy.util.custom_logging module galaxy.util.custom_logging.fluent_log module galaxy.util.dbkeys module galaxy.util.dictifiable module galaxy.util.expressions module galaxy.util.facts module galaxy.util.filelock module galaxy.util.form_builder module galaxy.util.getargspec module galaxy.util.hash_util module galaxy.util.heartbeat module galaxy.util.image_util module galaxy.util.inflection module galaxy.util.json module galaxy.util.jstree module galaxy.util.lazy_process module galaxy.util.monitors module galaxy.util.object_wrapper module galaxy.util.odict module galaxy.util.oset module galaxy.util.pastescript module galaxy.util.pastescript.loadwsgi module galaxy.util.pastescript.serve module galaxy.util.path module galaxy.util.path.ntpath module galaxy.util.path.posixpath module galaxy.util.permutations module galaxy.util.plugin_config module galaxy.util.properties module galaxy.util.renamed_temporary_file module galaxy.util.rules_dsl module galaxy.util.sanitize_html module galaxy.util.script module galaxy.util.search module galaxy.util.simplegraph module galaxy.util.sleeper module galaxy.util.sockets module galaxy.util.specs module galaxy.util.sqlite module galaxy.util.submodules module galaxy.util.template module galaxy.util.tool_shed module galaxy.util.tool_shed.common_util module galaxy.util.tool_shed.encoding_util module galaxy.util.tool_shed.xml_util module galaxy.util.tool_version module galaxy.util.topsort module galaxy.util.ucsc module galaxy.util.validation module galaxy.util.watcher module galaxy.util.web_compat module galaxy.util.xml_macros module galaxy.util.yaml_util module galaxy.util.zipstream module galaxy.version module galaxy.visualization module galaxy.visualization.data_providers module galaxy.visualization.data_providers.basic module galaxy.visualization.data_providers.cigar module galaxy.visualization.data_providers.genome module galaxy.visualization.data_providers.phyloviz module galaxy.visualization.data_providers.phyloviz.baseparser module galaxy.visualization.data_providers.phyloviz.newickparser module galaxy.visualization.data_providers.phyloviz.nexusparser module galaxy.visualization.data_providers.phyloviz.phyloxmlparser module galaxy.visualization.data_providers.registry module galaxy.visualization.genome module galaxy.visualization.genomes module galaxy.visualization.plugins module galaxy.visualization.plugins.config_parser module galaxy.visualization.plugins.interactive_environments module galaxy.visualization.plugins.plugin module galaxy.visualization.plugins.registry module galaxy.visualization.plugins.resource_parser module galaxy.visualization.plugins.utils module galaxy.visualization.tracks module galaxy.web module galaxy.web.buildapp module galaxy.web.form_builder module galaxy.web.formatting module galaxy.web.framework module galaxy.web.framework.base module galaxy.web.framework.decorators module galaxy.web.framework.helpers module galaxy.web.framework.helpers.grids module galaxy.web.framework.helpers.tags module galaxy.web.framework.middleware module galaxy.web.framework.middleware.batch module galaxy.web.framework.middleware.error module galaxy.web.framework.middleware.profile module galaxy.web.framework.middleware.remoteuser module galaxy.web.framework.middleware.request_id module galaxy.web.framework.middleware.sentry module galaxy.web.framework.middleware.sqldebug module galaxy.web.framework.middleware.static module galaxy.web.framework.middleware.statsd module galaxy.web.framework.middleware.translogger module galaxy.web.framework.middleware.xforwardedhost module galaxy.web.legacy_framework module galaxy.web.legacy_framework.grids module galaxy.web.params module galaxy.web.proxy module galaxy.web.statsd_client module galaxy.web_stack module galaxy.web_stack.handlers module galaxy.web_stack.message module galaxy.web_stack.transport module galaxy.webapps module galaxy.webapps.base module galaxy.webapps.base.controller module galaxy.webapps.base.webapp module galaxy.webapps.galaxy module galaxy.webapps.galaxy.api module galaxy.webapps.galaxy.api.annotations module galaxy.webapps.galaxy.api.authenticate module galaxy.webapps.galaxy.api.cloud module galaxy.webapps.galaxy.api.cloudauthz module galaxy.webapps.galaxy.api.configuration module galaxy.webapps.galaxy.api.container_resolution module galaxy.webapps.galaxy.api.dataset_collections module galaxy.webapps.galaxy.api.datasets module galaxy.webapps.galaxy.api.datatypes module galaxy.webapps.galaxy.api.display_applications module galaxy.webapps.galaxy.api.dynamic_tools module galaxy.webapps.galaxy.api.extended_metadata module galaxy.webapps.galaxy.api.folder_contents module galaxy.webapps.galaxy.api.folders module galaxy.webapps.galaxy.api.forms module galaxy.webapps.galaxy.api.genomes module galaxy.webapps.galaxy.api.group_roles module galaxy.webapps.galaxy.api.group_users module galaxy.webapps.galaxy.api.groups module galaxy.webapps.galaxy.api.histories module galaxy.webapps.galaxy.api.history_contents module galaxy.webapps.galaxy.api.item_tags module galaxy.webapps.galaxy.api.job_files module galaxy.webapps.galaxy.api.job_lock module galaxy.webapps.galaxy.api.job_ports module galaxy.webapps.galaxy.api.jobs module galaxy.webapps.galaxy.api.libraries module galaxy.webapps.galaxy.api.library_contents module galaxy.webapps.galaxy.api.library_datasets module galaxy.webapps.galaxy.api.licenses module galaxy.webapps.galaxy.api.metrics module galaxy.webapps.galaxy.api.page_revisions module galaxy.webapps.galaxy.api.pages module galaxy.webapps.galaxy.api.plugins module galaxy.webapps.galaxy.api.provenance module galaxy.webapps.galaxy.api.quotas module galaxy.webapps.galaxy.api.remote_files module galaxy.webapps.galaxy.api.roles module galaxy.webapps.galaxy.api.search module galaxy.webapps.galaxy.api.tags module galaxy.webapps.galaxy.api.tool_data module galaxy.webapps.galaxy.api.tool_dependencies module galaxy.webapps.galaxy.api.tool_entry_points module galaxy.webapps.galaxy.api.tool_shed_repositories module galaxy.webapps.galaxy.api.tools module galaxy.webapps.galaxy.api.toolshed module galaxy.webapps.galaxy.api.tours module galaxy.webapps.galaxy.api.trs_consumer module galaxy.webapps.galaxy.api.trs_search module galaxy.webapps.galaxy.api.uploads module galaxy.webapps.galaxy.api.users module galaxy.webapps.galaxy.api.visualizations module galaxy.webapps.galaxy.api.webhooks module galaxy.webapps.galaxy.api.workflows module galaxy.webapps.galaxy.buildapp module galaxy.webapps.galaxy.controllers module galaxy.webapps.galaxy.controllers.admin module galaxy.webapps.galaxy.controllers.admin_toolshed module galaxy.webapps.galaxy.controllers.async module galaxy.webapps.galaxy.controllers.authnz module galaxy.webapps.galaxy.controllers.data_manager module galaxy.webapps.galaxy.controllers.dataset module galaxy.webapps.galaxy.controllers.error module galaxy.webapps.galaxy.controllers.forms module galaxy.webapps.galaxy.controllers.history module galaxy.webapps.galaxy.controllers.interactive_environments module galaxy.webapps.galaxy.controllers.library module galaxy.webapps.galaxy.controllers.openid module galaxy.webapps.galaxy.controllers.page module galaxy.webapps.galaxy.controllers.root module galaxy.webapps.galaxy.controllers.shed_tool_static module galaxy.webapps.galaxy.controllers.tag module galaxy.webapps.galaxy.controllers.tool_runner module galaxy.webapps.galaxy.controllers.user module galaxy.webapps.galaxy.controllers.userskeys module galaxy.webapps.galaxy.controllers.visualization module galaxy.webapps.galaxy.controllers.workflow module galaxy.webapps.galaxy.fast_app module galaxy.webapps.reports module galaxy.webapps.reports.app module galaxy.webapps.reports.buildapp module galaxy.webapps.reports.config module galaxy.webapps.reports.controllers module galaxy.webapps.reports.controllers.history module galaxy.webapps.reports.controllers.home module galaxy.webapps.reports.controllers.jobs module galaxy.webapps.reports.controllers.query module galaxy.webapps.reports.controllers.root module galaxy.webapps.reports.controllers.system module galaxy.webapps.reports.controllers.tools module galaxy.webapps.reports.controllers.users module galaxy.webapps.reports.controllers.workflows module galaxy.webapps.util module galaxy.webhooks module galaxy.work module galaxy.work.context module galaxy.workflow module galaxy.workflow.extract module galaxy.workflow.modules module galaxy.workflow.refactor module galaxy.workflow.refactor.execute module galaxy.workflow.refactor.schema module galaxy.workflow.render module galaxy.workflow.reports module galaxy.workflow.reports.generators module galaxy.workflow.reports.generators.markdown module galaxy.workflow.resources module galaxy.workflow.run module galaxy.workflow.run_request module galaxy.workflow.schedulers module galaxy.workflow.schedulers.core module galaxy.workflow.scheduling_manager module galaxy.workflow.steps module galaxy.workflow.trs_proxy module galaxy_directory() (in module galaxy.util) galaxy_driver_class (galaxy_test.base.testcase.FunctionalTestCase attribute) (galaxy_test.driver.testcase.DrivenFunctionalTestCase attribute) (galaxy_test.selenium.framework.SeleniumTestCase attribute) galaxy_ext module galaxy_ext.expressions module galaxy_ext.expressions.handle_job module galaxy_ext.metadata module galaxy_ext.metadata.set_metadata module galaxy_instance_id() (in module galaxy.jobs.runners.util.pykube_util) galaxy_lib_dir() (galaxy.jobs.JobWrapper property) galaxy_login() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) galaxy_logout() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) galaxy_param_type() (galaxy.tool_util.cwl.representation.TypeRepresentation property) galaxy_requests_post() (in module galaxy.tool_util.verify.interactor) galaxy_samples_directory() (in module galaxy.util) galaxy_session (galaxy.model.Event attribute) (galaxy.model.GalaxySessionToHistoryAssociation attribute) (galaxy.model.Job attribute) galaxy_sessions (galaxy.model.History attribute) (galaxy.model.User attribute) (tool_shed.webapp.model.User attribute) galaxy_system_pwent() (galaxy.jobs.JobWrapper property) galaxy_test module galaxy_test.api module galaxy_test.api.test_api_batch module galaxy_test.api.test_authenticate module galaxy_test.api.test_configuration module galaxy_test.api.test_dataset_collections module galaxy_test.api.test_datasets module galaxy_test.api.test_datatypes module galaxy_test.api.test_framework module galaxy_test.api.test_galaxy_interactor module galaxy_test.api.test_histories module galaxy_test.api.test_history_contents module galaxy_test.api.test_history_contents_provenance module galaxy_test.api.test_jobs module galaxy_test.api.test_libraries module galaxy_test.api.test_licenses module galaxy_test.api.test_page_revisions module galaxy_test.api.test_pages module galaxy_test.api.test_roles module galaxy_test.api.test_search module galaxy_test.api.test_tool_data module galaxy_test.api.test_tools module galaxy_test.api.test_tools_upload module galaxy_test.api.test_tours module galaxy_test.api.test_users module galaxy_test.api.test_visualizations module

galaxy_test.api.test_webhooks module galaxy_test.api.test_workflow_extraction module galaxy_test.api.test_workflows module galaxy_test.api.test_workflows_from_yaml module galaxy_test.base module galaxy_test.base.api module galaxy_test.base.api_asserts module galaxy_test.base.api_util module galaxy_test.base.constants module galaxy_test.base.env module galaxy_test.base.instrument module galaxy_test.base.interactor module galaxy_test.base.nose_util module galaxy_test.base.populators module galaxy_test.base.rules_test_data module galaxy_test.base.ssh_util module galaxy_test.base.testcase module galaxy_test.base.workflow_fixtures module galaxy_test.driver module galaxy_test.driver.driver_util module galaxy_test.driver.integration_util module galaxy_test.driver.test_logging module galaxy_test.driver.testcase module galaxy_test.selenium module galaxy_test.selenium.framework module galaxy_test.selenium.test_admin_app module galaxy_test.selenium.test_anon_history module galaxy_test.selenium.test_change_password module galaxy_test.selenium.test_collection_builders module galaxy_test.selenium.test_custom_builds module galaxy_test.selenium.test_histories_list module galaxy_test.selenium.test_history_copy_elements module galaxy_test.selenium.test_history_dataset_state module galaxy_test.selenium.test_history_multi_view module galaxy_test.selenium.test_history_options module galaxy_test.selenium.test_history_panel module galaxy_test.selenium.test_history_panel_collections module galaxy_test.selenium.test_history_panel_pagination module galaxy_test.selenium.test_history_sharing module galaxy_test.selenium.test_history_structure module galaxy_test.selenium.test_jupyter module galaxy_test.selenium.test_library_contents module galaxy_test.selenium.test_library_landing module galaxy_test.selenium.test_library_to_collections module galaxy_test.selenium.test_login module galaxy_test.selenium.test_navigates_galaxy module galaxy_test.selenium.test_pages module galaxy_test.selenium.test_personal_information module galaxy_test.selenium.test_published_histories_grid module galaxy_test.selenium.test_registration module galaxy_test.selenium.test_sign_out module galaxy_test.selenium.test_sizzle_loading module galaxy_test.selenium.test_stock_tours module galaxy_test.selenium.test_tool_describing_tours module galaxy_test.selenium.test_tool_form module galaxy_test.selenium.test_uploads module galaxy_test.selenium.test_workflow_editor module galaxy_test.selenium.test_workflow_management module galaxy_test.selenium.test_workflow_run module galaxy_token() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) galaxy_url() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) galaxy_version (galaxy.model.Job attribute) galaxy_virtual_env() (galaxy.jobs.JobWrapper property) GalaxyAppConfiguration (class in galaxy.config) GalaxyConfigBuilder (class in galaxy.main) GalaxyInteractorApi (class in galaxy.tool_util.verify.interactor) GalaxyInteractorBackwardCompatTestCase (class in galaxy_test.api.test_galaxy_interactor) GalaxyLargeBinary (class in galaxy.model.custom_types) GalaxyOutput (class in galaxy.tool_util.cwl.util) GalaxyPackageDependency (class in galaxy.tool_util.deps.resolvers.galaxy_packages) GalaxyPackageDependencyResolver (class in galaxy.tool_util.deps.resolvers.galaxy_packages) GalaxyParseError GalaxyQuery (class in galaxy.model.search) GalaxyQueryAnd (class in galaxy.model.search) GalaxyQueryComparison (class in galaxy.model.search) GalaxyQueueWorker (class in galaxy.queue_worker) GalaxyRBACAgent (class in galaxy.model.security) GalaxySearchEngine (class in galaxy.model.search) GalaxySeleniumContext (class in galaxy.selenium.context) GalaxySeleniumContextImpl (class in galaxy.selenium.context) GalaxySession (class in galaxy.model) (class in tool_shed.webapp.model) GalaxySessionManager (class in galaxy.managers.session) GalaxySessionToHistoryAssociation (class in galaxy.model) GalaxyStatsdClient (class in galaxy.web.statsd_client) GalaxyTagHandler (class in galaxy.model.tags) GalaxyTagHandlerSession (class in galaxy.model.tags) GalaxyUtilityContainerManager (class in tool_shed.galaxy_install.utility_containers) GalaxyWebApplication (class in galaxy.webapps.galaxy.buildapp) GalaxyWebTransaction (class in galaxy.webapps.base.webapp) gbrowse_links() (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Wiggle method) GeminiSQLite (class in galaxy.datatypes.binary) gen_edge_dicts() (galaxy.util.simplegraph.SimpleGraph method) gen_image() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) gen_node_dicts() (galaxy.util.simplegraph.SimpleGraph method) Genbank (class in galaxy.datatypes.sequence) generate_clone_url_for_installed_repository() (in module galaxy.util.tool_shed.common_util) generate_clone_url_for_repository_in_tool_shed() (in module galaxy.util.tool_shed.common_util) generate_clone_url_from_repo_info_tup() (in module galaxy.util.tool_shed.common_util) generate_complex_dependency_xml() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) generate_contents_url() (galaxy.managers.hdcas.HDCASerializer method) generate_data_manager_metadata() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) generate_datatypes_metadata() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) generate_deprecated_repository_img_str() (in module tool_shed.galaxy_install.grids.admin_toolshed_grids) generate_elements() (galaxy.model.dataset_collections.types.DatasetCollectionType method) (galaxy.model.dataset_collections.types.list.ListDatasetCollectionType method) (galaxy.model.dataset_collections.types.paired.PairedDatasetCollectionType method) generate_environment_dependency_metadata() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) generate_error() (galaxy.webapps.galaxy.controllers.root.RootController method) generate_guid_for_object() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) generate_hex() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) generate_includes_workflows_img_str() (in module tool_shed.galaxy_install.grids.admin_toolshed_grids) generate_json_error() (galaxy.webapps.galaxy.controllers.root.RootController method) generate_latest_revision_img_str() (in module tool_shed.galaxy_install.grids.admin_toolshed_grids) generate_message_for_invalid_repository_dependencies() (tool_shed.galaxy_install.dependency_display.DependencyDisplayer method) generate_message_for_invalid_tool_dependencies() (tool_shed.galaxy_install.dependency_display.DependencyDisplayer method) generate_message_for_invalid_tools() (in module galaxy.tool_shed.util.tool_util) generate_message_for_orphan_tool_dependencies() (tool_shed.galaxy_install.dependency_display.DependencyDisplayer method) generate_message_for_repository_type_change() (in module tool_shed.repository_types.util) generate_metadata_for_changeset_revision() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) generate_package_dependency_metadata() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) generate_password() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) generate_primary_file() (galaxy.datatypes.anvio.AnvioComposite method) (galaxy.datatypes.assembly.Velvet method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.genetics.IdeasPre method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.genetics.Rgenetics method) (galaxy.datatypes.gis.Shapefile method) (galaxy.datatypes.images.Analyze75 method) (galaxy.datatypes.neo4j.Neo4j method) (galaxy.datatypes.ngsindex.BowtieIndex method) (galaxy.datatypes.proteomics.ImzML method) (galaxy.datatypes.proteomics.SPLib method) (galaxy.datatypes.proteomics.Wiff method) (galaxy.datatypes.text.SnpSiftDbNSFP method) (galaxy.datatypes.tracks.UCSCTrackHub method) generate_process_statistics() (in module galaxy.job_metrics.collectl.processes) generate_report() (in module galaxy.workflow.reports) generate_report_json() (galaxy.workflow.reports.generators.WorkflowMarkdownGeneratorPlugin method) (galaxy.workflow.reports.generators.WorkflowReportGeneratorPlugin method) generate_report_pdf() (galaxy.workflow.reports.generators.WorkflowMarkdownGeneratorPlugin method) (galaxy.workflow.reports.generators.WorkflowReportGeneratorPlugin method) generate_repository_dependencies_folder_label_from_key() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) generate_repository_dependencies_key_for_repository() (in module galaxy.tool_shed.util.container_util) (in module tool_shed.util.container_util) generate_repository_dependency_metadata() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) generate_repository_info_elem() (galaxy.tool_shed.tools.data_table_manager.ShedToolDataTableManager method) generate_repository_info_elem_from_repository() (galaxy.tool_shed.tools.data_table_manager.ShedToolDataTableManager method) generate_revision_updates_img_str() (in module tool_shed.galaxy_install.grids.admin_toolshed_grids) generate_revision_upgrades_img_str() (in module tool_shed.galaxy_install.grids.admin_toolshed_grids) generate_sharable_link_for_repository_in_tool_shed() (in module tool_shed.util.repository_util) generate_simple_dependency_xml() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) generate_ssh_keys() (in module galaxy_test.base.ssh_util) generate_statistics() (tool_shed.webapp.util.shed_statistics.ShedCounter method) generate_temp_path() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) generate_tool_dependencies_key() (tool_shed.utility_containers.ToolShedUtilityContainerManager method) generate_tool_dependency_metadata() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) generate_tool_elem() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_guid() (in module galaxy.tool_shed.util.shed_util_common) (in module tool_shed.util.shed_util_common) generate_tool_metadata() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) generate_tool_panel_dict_for_new_install() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_panel_dict_for_tool_config() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_panel_dict_from_shed_tool_conf_entries() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_panel_elem_list() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_section_dicts() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_section_element_from_dict() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_shed_repository_install_dir() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) generate_unknown_img_str() (in module tool_shed.galaxy_install.grids.admin_toolshed_grids) generate_workflow_metadata() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) generateJsonableDict() (galaxy.visualization.data_providers.phyloviz.baseparser.PhyloTree method) GenericAsn1 (class in galaxy.datatypes.data) GenericAsn1Binary (class in galaxy.datatypes.binary) GenericMicroarrayFile (class in galaxy.datatypes.microarrays) GenericMolFile (class in galaxy.datatypes.molecules) GenericXml (class in galaxy.datatypes.xml) GeneTrack (class in galaxy.datatypes.tracks) Genome (class in galaxy.visualization.genomes) genome_build (galaxy.model.History attribute) (galaxy.model.LibraryFolder attribute) genome_build() (galaxy.managers.base.ModelValidator method) genome_index_tool_data (galaxy.model.Dataset attribute) GenomeBuildParameter (class in galaxy.tools.parameters.basic) GenomeBuilds (class in galaxy.util.dbkeys) GenomeDataProvider (class in galaxy.visualization.data_providers.genome) GenomeGraphs (class in galaxy.datatypes.genetics) GenomeIndexToolData (class in galaxy.model) GenomeRegion (class in galaxy.visualization.genomes) Genomes (class in galaxy.visualization.genomes) GenomesController (class in galaxy.webapps.galaxy.api.genomes) genomic_region_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.tabular.BaseVcf method) (galaxy.datatypes.tabular.Pileup method) (galaxy.datatypes.tabular.Sam method) genomic_region_dict_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.tabular.BaseVcf method) (galaxy.datatypes.tabular.Pileup method) (galaxy.datatypes.tabular.Sam method) GenomicRegionAlignment (class in galaxy.datatypes.util.maf_utilities) (class in galaxy.tools.util.maf_utilities) GenomicRegionDataProvider (class in galaxy.datatypes.dataproviders.dataset) GenotypeMatrix (class in galaxy.datatypes.genetics) GeoJson (class in galaxy.datatypes.text) get() (galaxy.config.CommonConfigurationMixin method) (galaxy.containers.ContainerInterfaceConfig method) (galaxy.containers.docker_model.DockerAttributeContainer method) (galaxy.datatypes.metadata.MetadataElementSpec method) (galaxy.managers.cloud.CloudManager method) (galaxy.managers.datasets.DatasetRBACPermissions method) (galaxy.managers.folders.FolderManager method) (galaxy.managers.interactivetool.InteractiveToolSqlite method) (galaxy.managers.lddas.LDDAManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.managers.library_datasets.LibraryDatasetsManager method) (galaxy.managers.licenses.LicensesManager method) (galaxy.managers.roles.RoleManager method) (galaxy.model.dataset_collections.registry.DatasetCollectionTypesRegistry method) (galaxy.model.metadata.MetadataElementSpec method) (galaxy.model.PSAAssociation class method) (galaxy.openid.providers.OpenIDProviders method) (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) (galaxy.tool_util.parser.yaml.YamlInputSource method) (galaxy.tools.cache.ToolDocumentCache method) (galaxy.tools.data.ToolDataTableManager method) (galaxy.tools.toolbox.lineages.factory.LineageMap method) (galaxy.tools.toolbox.lineages.LineageMap method) (galaxy.tools.wrappers.DatasetFilenameWrapper.MetadataWrapper method) (galaxy.util.bunch.Bunch method) (galaxy.util.Params method) (galaxy.webapps.galaxy.api.cloud.CloudController method) (galaxy.webapps.galaxy.api.licenses.FastAPILicenses method) (galaxy.webapps.galaxy.api.licenses.LicensesController method) (galaxy.webapps.reports.config.Configuration method) (galaxy_test.base.api.ApiTestInteractor method) (tool_shed.managers.groups.GroupManager method) (tool_shed.managers.repositories.RepoManager method) get_absolute_path_to_file_in_repository() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_accepted_filters() (galaxy.web.framework.helpers.grids.DeletedColumn method) (galaxy.web.framework.helpers.grids.GridColumn method) (galaxy.web.framework.helpers.grids.PurgedColumn method) (galaxy.web.framework.helpers.grids.SharingStatusColumn method) (galaxy.web.framework.helpers.grids.StateColumn method) (galaxy.web.legacy_framework.grids.DeletedColumn method) (galaxy.web.legacy_framework.grids.GridColumn method) (galaxy.web.legacy_framework.grids.SharingStatusColumn method) (galaxy.web.legacy_framework.grids.StateColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.DeletedColumn method) get_access_roles() (galaxy.managers.libraries.LibraryManager method) (galaxy.model.Dataset method) (galaxy.model.HistoryDatasetAssociation method) (galaxy.model.Library method) (galaxy.model.LibraryDatasetDatasetAssociation method) get_accessible() (galaxy.managers.secured.AccessibleManagerMixin method) get_accessible_job() (galaxy.managers.jobs.JobManager method) get_accessible_libraries() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) get_action() (galaxy.security.RBACAgent method) (tool_shed.webapp.security.RBACAgent method) get_actions() (galaxy.security.RBACAgent method) (tool_shed.webapp.security.RBACAgent method) get_actions_for_items() (galaxy.model.security.GalaxyRBACAgent method) get_active_folders() (galaxy.model.Library method) get_active_processes() (galaxy.model.database_heartbeat.DatabaseHeartbeat method) get_add_roles() (galaxy.managers.libraries.LibraryManager method) get_additional_repository_information() (galaxy.tool_util.deps.mulled.mulled_search.QuaySearch method) get_address_input_field() (galaxy_test.selenium.test_personal_information.ManageInformationTestCase method) get_admin_user() (in module galaxy.webapps.galaxy.api) get_all_dependencies() (in module tool_shed.util.metadata_util) get_all_forms() (galaxy.webapps.base.controller.UsesFormDefinitionsMixin method) get_all_inputs() (galaxy.workflow.modules.InputModule method) (galaxy.workflow.modules.PauseModule method) (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_all_installed_repositories() (in module tool_shed.test.base.test_db_util) get_all_outputs() (galaxy.workflow.modules.InputDataCollectionModule method) (galaxy.workflow.modules.InputDataModule method) (galaxy.workflow.modules.InputParameterModule method) (galaxy.workflow.modules.PauseModule method) (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_all_repositories() (in module tool_shed.test.base.test_db_util) get_all_roles() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) get_all_users() (galaxy.webapps.galaxy.controllers.userskeys.User method) get_allowed_idps() (galaxy.authnz.managers.AuthnzManager method) get_alternative_versions() (in module galaxy.tool_util.deps.mulled.get_tests) get_amount() (galaxy.model.Quota method) get_anaconda_url() (in module galaxy.tool_util.deps.mulled.get_tests) get_annotation_async() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) get_api_key() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) (galaxy.webapps.galaxy.api.authenticate.AuthenticationController method) (galaxy.webapps.galaxy.api.users.UserAPIController method) get_api_user() (in module galaxy.webapps.galaxy.api) get_app() (in module galaxy.webapps.galaxy.api) get_app_kwds() (galaxy.web_stack.ApplicationStack class method) (galaxy.web_stack.UWSGIApplicationStack class method) (in module galaxy.web_stack) get_app_option() (galaxy.config.schema.Schema method) (galaxy.tool_util.deps.DependencyManager method) get_attributes_from_fasta_header() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_authenticators() (in module galaxy.auth.util) get_available_tracks() (galaxy.datatypes.registry.Registry method) get_ave_item_rating_data() (galaxy.model.item_attrs.UsesItemRatings method) get_base_dir() (galaxy.tools.data.TabularToolDataField method) get_base_path() (galaxy.tools.data.TabularToolDataField method) get_bibtex() (galaxy.managers.citations.DoiCache method) get_biocompute_object() (galaxy_test.base.populators.BaseWorkflowPopulator method) get_blurb() (galaxy.datatypes.constructive_solid_geometry.Vtk method) get_bool() (galaxy.config.CommonConfigurationMixin method) (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) (galaxy.tool_util.parser.yaml.YamlInputSource method) get_bounds() (in module galaxy.visualization.data_providers.genome) get_build() (galaxy.visualization.genomes.Genomes method) get_cache_region() (galaxy.tools.ToolBox method) get_categories() (in module tool_shed.util.shed_util_common) get_category() (in module tool_shed.util.shed_util_common) get_category_by_name() (in module tool_shed.test.base.test_db_util) (in module tool_shed.util.shed_util_common) get_certified_level_one_clause_list() (tool_shed.repository_registry.Registry method) get_certified_level_one_tuple() (tool_shed.repository_registry.Registry method) get_change_lines_in_file_for_tag() (in module tool_shed.util.commit_util) get_changectx_for_changeset() (in module galaxy.tool_shed.util.hg_util) (in module tool_shed.util.hg_util) get_changeset_revision_and_ctx_rev() (tool_shed.webapp.controllers.repository.RepositoryController method) get_changesets_for_setting_metadata() (tool_shed.repository_types.metadata.Metadata method) (tool_shed.repository_types.metadata.TipOnly method) (tool_shed.webapp.model.Repository method) get_charset_from_http_headers() (in module galaxy.util) get_check_interval() (galaxy.model.DeferredJob method) get_children() (galaxy.datatypes.dataproviders.hierarchy.XMLDataProvider method) get_chopped_blocks_for_region() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_chopped_blocks_with_index_offset_for_region() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_chrom_info() (galaxy.tools.actions.ToolExecutionCache method) (galaxy.util.dbkeys.GenomeBuilds method) get_chunk() (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.tabular.ConnectivityTable method) (galaxy.datatypes.tabular.TabularData method) get_cilogon_idps() (galaxy.webapps.galaxy.controllers.authnz.OIDC method) get_class() (galaxy.webapps.base.controller.BaseController method) (in module galaxy.managers.base) get_class_by_label() (tool_shed.repository_types.registry.Registry method) get_cli_plugins() (galaxy.jobs.runners.cli.ShellJobRunner method) get_cloud_access_credentials() (galaxy.authnz.managers.AuthnzManager method) get_cloud_access_credentials_in_file() (galaxy.authnz.managers.AuthnzManager method) get_code() (galaxy.model.PSACode class method) get_collection_contents_qry() (galaxy.managers.collections.DatasetCollectionManager method) get_column_list() (galaxy.tools.parameters.basic.ColumnListParameter method) get_column_metadata_from_dataset() (galaxy.datatypes.dataproviders.dataset.DatasetDataProvider class method) get_column_name_list() (galaxy.tools.data.TabularToolDataTable method) get_column_names() (galaxy.datatypes.tabular.SraManifest method) (galaxy.datatypes.tabular.Tabular method) get_column_type() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) get_command() (in module galaxy.tool_util.linters.command) get_command_line() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.model.Job method) (galaxy.model.Task method) get_commands_from_yaml() (in module galaxy.tool_util.deps.mulled.get_tests) get_community_tags() (galaxy.model.tags.TagHandler method) get_component() (in module tool_shed.util.review_util) get_component_associations() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) get_component_by_name() (in module tool_shed.util.review_util) get_component_review() (in module tool_shed.util.review_util) get_component_review_by_repository_review_id_component_id() (in module tool_shed.util.review_util) get_components() (in module tool_shed.util.review_util) get_components_by_src() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_components_by_src_start() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_components_from_key() (in module galaxy.tool_shed.util.container_util) (in module tool_shed.util.container_util) get_components_from_repository_dependency_for_installed_repository() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) get_composite_dataset_name() (galaxy.tools.parameters.grouping.UploadDataset method) get_composite_extensions() (galaxy.datatypes.registry.Registry method) get_composite_files() (galaxy.datatypes.data.Data method) get_compressed_formats() (in module galaxy.tool_util.verify) get_concrete_store_description_markdown() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) get_concrete_store_name() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) get_conda_envs() (in module galaxy.tool_util.deps.mulled.mulled_list) get_conditional_requirements() (galaxy.dependencies.ConditionalDependencies method) get_conf_dict() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) get_config() (in module galaxy.model.orm.scripts) get_config_dict() (galaxy.webapps.galaxy.api.configuration.ConfigurationController method) get_config_form() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_config_from_disk() (in module galaxy.tool_shed.util.hg_util) (in module tool_shed.util.hg_util) get_configured_driver() (in module galaxy_test.selenium.framework) get_configured_job_handler() (galaxy.tools.Tool method) get_consumer() (galaxy.openid.openid_manager.OpenIDManager method) get_consumers() (galaxy.queue_worker.GalaxyQueueWorker method) get_container() (galaxy.containers.ContainerInterface method) get_container_host() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) get_container_port_mapping() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) get_containing_library_from_library_dataset() (in module galaxy.managers.libraries) get_containing_repository_for_tool_dependency() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_containing_tool_sections() (galaxy.tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager method) get_content_as_text() (galaxy.webapps.galaxy.api.datasets.DatasetsController method) get_content_id() (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_content_type() (galaxy.web.framework.base.Response method) get_converted_dataset() (galaxy.model.DatasetInstance method) get_converted_dataset_deps() (galaxy.model.DatasetInstance method) get_converted_files_by_type() (galaxy.model.DatasetInstance method) get_converter_and_display_paths() (galaxy.tool_shed.galaxy_install.datatypes.custom_datatype_manager.CustomDatatypeLoader method) get_converter_by_target_type() (galaxy.datatypes.registry.Registry method) get_converter_types() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) get_converters_by_datatype() (galaxy.datatypes.registry.Registry method) get_cookie() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) get_copied_from_job_id() (galaxy.model.Job method) get_cram_version() (galaxy.datatypes.binary.CRAM method) get_created_from_basename() (galaxy.model.DatasetInstance method) get_ctx_file_path_from_manifest() (in module galaxy.tool_shed.util.hg_util) (in module tool_shed.util.hg_util) get_ctx_rev() (in module galaxy.tool_shed.util.shed_util_common) (in module tool_shed.util.shed_util_common) (tool_shed.webapp.controllers.repository.RepositoryController method) get_current() (galaxy.managers.histories.HistoryManager method) get_current_case() (galaxy.tools.parameters.grouping.Conditional method) get_current_form() (galaxy.webapps.galaxy.controllers.forms.Forms method) get_current_item() (galaxy.web.framework.helpers.grids.Grid method) (galaxy.web.legacy_framework.grids.Grid method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid method) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid method) (tool_shed.grids.admin_grids.UserGrid method) get_current_repository_metadata_for_changeset_revision() (in module tool_shed.util.metadata_util) get_current_roles() (galaxy.managers.folders.FolderManager method) (galaxy.managers.libraries.LibraryManager method) get_current_thread_object_dict() (in module galaxy.util.heartbeat) get_current_user_roles() (galaxy.managers.context.ProvidesUserContext method) (galaxy.work.context.WorkRequestContext method) get_custom_builds() (galaxy.webapps.galaxy.api.users.UserAPIController method) (galaxy_test.selenium.test_custom_builds.CustomBuildsTestcase method) get_custom_builds_metadata() (galaxy.webapps.galaxy.api.histories.HistoriesController method) get_data() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.visualization.data_providers.basic.BaseDataProvider method) (galaxy.visualization.data_providers.basic.ColumnDataProvider method) (galaxy.visualization.data_providers.genome.BBIDataProvider method) (galaxy.visualization.data_providers.genome.FeatureLocationIndexDataProvider method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) (galaxy.visualization.data_providers.phyloviz.PhylovizDataProvider method) get_data_dir() (in module galaxy.util.properties) get_data_inputs() (galaxy.workflow.modules.WorkflowModule method) get_data_outputs() (galaxy.workflow.modules.WorkflowModule method) get_data_provider() (galaxy.visualization.data_providers.registry.DataProviderRegistry method) get_database_engine_options() (in module galaxy.config) (in module galaxy.webapps.reports.config) get_database_url() (in module galaxy.config) get_dataset_collection() (galaxy.managers.collections.DatasetCollectionManager method) get_dataset_collection_instance() (galaxy.managers.collections.DatasetCollectionManager method) get_dataset_finish_context() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) get_dataset_matcher_factory() (in module galaxy.tools.parameters.dataset_matcher) get_dataset_meta() (galaxy.tool_util.provided_metadata.BaseToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.LegacyToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.ToolProvidedMetadata method) get_dataset_state() (galaxy.model.DatasetInstance method) get_datasets_for_group() (galaxy.tools.wrappers.DatasetCollectionWrapper method) (galaxy.tools.wrappers.DatasetListWrapper method) get_datasources() (galaxy.model.DatasetInstance method) get_datatype() (galaxy.tools.parameters.grouping.UploadDataset method) get_datatype_by_extension() (galaxy.datatypes.registry.Registry method) get_datatype_class_by_name() (galaxy.datatypes.registry.Registry method) get_datatype_ext() (galaxy.tools.parameters.grouping.UploadDataset method) get_datatypes_count() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_db() (in module galaxy.webapps.galaxy.api) get_dbkey() (galaxy.model.DatasetInstance method) (galaxy.tools.parameters.grouping.UploadDataset method) get_dbkeys() (galaxy.visualization.genomes.Genomes method) get_default_history_by_trans() (galaxy.tools.DataManagerTool method) (galaxy.tools.Tool method) get_default_max_vals() (galaxy.visualization.data_providers.genome.ChromatinInteractionsDataProvider method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) get_default_parsers() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) get_default_user_permissions_by_role() (in module tool_shed.test.base.test_db_util) get_default_user_permissions_by_user() (in module tool_shed.test.base.test_db_util) get_dependencies() (galaxy.model.Job method) (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.SelectTagParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.DataToolParameter method) (galaxy.tools.parameters.SelectToolParameter method) get_dependencies_for_metadata_revision() (in module tool_shed.util.metadata_util) get_dependencies_for_repository() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_dependency_name() (galaxy.tools.parameters.dynamic_options.DataMetaFilter method) (galaxy.tools.parameters.dynamic_options.Filter method) (galaxy.tools.parameters.dynamic_options.ParamValueFilter method) (galaxy.tools.parameters.dynamic_options.UniqueValueFilter method) get_dependency_names() (galaxy.tools.parameters.dynamic_options.DynamicOptions method) get_destination() (galaxy.jobs.JobConfiguration method) get_destination_configuration() (galaxy.jobs.JobWrapper method) (galaxy.model.Job method) get_destination_info_for_container_type() (galaxy.tool_util.deps.DependencyManager method) get_destination_list_from_job_config() (in module galaxy.jobs.dynamic_tool_destination) get_destinations() (galaxy.jobs.JobConfiguration method) get_dict_checksums() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.Download method) get_directory() (galaxy.tool_util.verify.test_data.TestDataResolver method) get_disk_usage() (galaxy.model.GalaxySession method) (galaxy.model.User method) (galaxy.webapps.reports.controllers.system.System method) (tool_shed.webapp.model.User method) get_display_application() (galaxy.datatypes.data.Data method) get_display_applications() (galaxy.model.DatasetInstance method) get_display_applications_by_dataset() (galaxy.datatypes.data.Data method) get_display_label() (galaxy.datatypes.data.Data method) get_display_links() (galaxy.datatypes.data.Data method) get_display_name() (galaxy.model.HasName method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationListGrid method) get_display_sites() (galaxy.datatypes.registry.Registry method) get_display_text() (galaxy.tools.wrappers.ToolParameterValueWrapper method) get_display_types() (galaxy.datatypes.data.Data method) get_display_url() (galaxy.datatypes.display_applications.application.DisplayApplicationLink method) get_download_path() (galaxy_test.selenium.framework.TestWithSeleniumMixin method) get_download_url_for_platform() (in module galaxy.tool_shed.util.tool_dependency_util) get_edit() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) get_edit_distance() (in module galaxy.jobs.dynamic_tool_destination) get_editor_iframe() (galaxy.webapps.galaxy.controllers.page.PageController method) get_elem_checksums() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.Download method) get_elements() (galaxy.util.topsort.CycleError method) get_embed_html_async() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) get_empty_field_by_name() (galaxy.tools.data.ToolDataTable method) get_entries() (galaxy.tools.data.TabularToolDataTable method) get_entry() (galaxy.tools.data.TabularToolDataTable method) (tool_shed.util.hgweb_config.HgWebConfigManager method) get_env_setup_clause() (galaxy.jobs.JobWrapper method) get_env_sh_path() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_env_shell_file_path() (galaxy.model.tool_shed_install.ToolDependency method) (galaxy.tool_shed.galaxy_install.tool_dependencies.env_manager.EnvManager method) get_env_shell_file_paths() (galaxy.tool_shed.galaxy_install.tool_dependencies.env_manager.EnvManager method) get_env_shell_file_paths_from_setup_environment_elem() (galaxy.tool_shed.galaxy_install.tool_dependencies.env_manager.EnvManager method) get_env_var_values() (in module galaxy.tool_shed.util.basic_util) get_envs() (galaxy.jobs.JobConfiguration static method) get_errors() (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_estimated_display_viewport() (galaxy.datatypes.interval.BedGraph method) (galaxy.datatypes.interval.CustomTrack method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.Wiggle method) get_executable() (in module galaxy.util) get_exit_code() (galaxy.jobs.TaskWrapper method) get_expanded_tool_source() (galaxy.tools.ToolBox method) get_export_dataset_filename() (in module galaxy.model.store) get_export_state() (galaxy.workflow.modules.InputModule method) (galaxy.workflow.modules.InputParameterModule method) (galaxy.workflow.modules.WorkflowModule method) get_export_url() (galaxy_test.base.populators.BaseDatasetPopulator method) get_exports() (galaxy.managers.histories.HistoryExportView method) get_ext() (in module galaxy.util.path) get_ext_or_implicit_ext() (in module galaxy.tools.actions) get_extension() (galaxy.datatypes.registry.Registry method) get_external_output_metadata() (galaxy.model.Job method) (galaxy.model.Task method) get_externally_referenced_paths() (galaxy.tools.Tool class method) get_extra_files_path() (galaxy.model.Dataset method) get_facts() (in module galaxy.util.facts) get_failure_reason() (galaxy.jobs.runners.util.cli.job.BaseJobExec method) (galaxy.jobs.runners.util.cli.job.lsf.LSF method) get_fasta_header() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_field() (galaxy.datatypes.metadata.ColumnParameter method) (galaxy.datatypes.metadata.DBKeyParameter method) (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.datatypes.metadata.PythonObjectParameter method) (galaxy.datatypes.metadata.RangeParameter method) (galaxy.datatypes.metadata.SelectParameter method) (galaxy.model.metadata.ColumnParameter method) (galaxy.model.metadata.DBKeyParameter method) (galaxy.model.metadata.FileParameter method) (galaxy.model.metadata.MetadataParameter method) (galaxy.model.metadata.PythonObjectParameter method) (galaxy.model.metadata.RangeParameter method) (galaxy.model.metadata.SelectParameter method) (galaxy.tools.data.TabularToolDataTable method) get_field_by_name_for_value() (galaxy.tools.parameters.dynamic_options.DynamicOptions method) get_fields() (galaxy.tools.data.TabularToolDataTable method) (galaxy.tools.parameters.dynamic_options.DynamicOptions method) get_fields_by_value() (galaxy.tools.parameters.dynamic_options.DynamicOptions method) get_file_base_name() (galaxy.tools.parameters.grouping.UploadDataset method) get_file_contents() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (tool_shed.webapp.controllers.repository.RepositoryController method) get_file_context_from_ctx() (in module galaxy.tool_shed.util.hg_util) (in module tool_shed.util.hg_util) get_file_count() (galaxy.tools.parameters.grouping.UploadDataset method) get_file_name() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) get_file_peek() (galaxy.datatypes.genetics.RexpBase method) (in module galaxy.datatypes.data) get_file_size() (in module galaxy.util) get_file_source() (galaxy.files.ConfiguredFileSources method) get_file_source_path() (galaxy.files.ConfiguredFileSources method) get_file_sources() (in module galaxy.tools.data_fetch) (in module galaxy.tools.imp_exp.export_history) (in module galaxy.tools.imp_exp.unpack_tar_gz_archive) get_file_type() (galaxy.tools.parameters.grouping.UploadDataset method) get_file_type_str() (in module galaxy.tool_shed.util.basic_util) get_filecontent() (galaxy.tool_util.verify.test_data.TestDataResolver method) get_filename() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.tool_util.verify.test_data.TestDataResolver method) (galaxy_test.base.testcase.FunctionalTestCase method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_filename_for_source() (galaxy.tools.data.TabularToolDataTable method) get_fileobj() (in module galaxy.util.compression_utils) get_fileobj_raw() (in module galaxy.util.compression_utils) get_files() (galaxy.tools.data.TabularToolDataField method) get_filesize_map() (galaxy.tools.data.TabularToolDataField method) get_filter() (galaxy.web.framework.helpers.grids.CommunityTagsColumn method) (galaxy.web.framework.helpers.grids.IndividualTagsColumn method) (galaxy.web.framework.helpers.grids.TextColumn method) (galaxy.web.legacy_framework.grids.CommunityTagsColumn method) (galaxy.web.legacy_framework.grids.IndividualTagsColumn method) (galaxy.web.legacy_framework.grids.TextColumn method) (tool_shed.grids.repository_grid_filter_manager.RepositoryGridFilterManager method) get_filter_set() (galaxy.workflow.modules.InputDataModule method) get_filters() (galaxy.visualization.data_providers.genome.BamDataProvider method) (galaxy.visualization.data_providers.genome.ENCODEPeakTabixDataProvider method) (galaxy.visualization.data_providers.genome.FilterableMixin method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) get_fingerprint() (galaxy.tools.data.TabularToolDataField method) get_first_line() (in module galaxy.tool_util.verify.asserts.tabular) get_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) get_folder_dict() (galaxy.managers.folders.FolderManager method) get_foreign_key() (in module galaxy.model.item_attrs) get_form() (in module galaxy.webapps.galaxy.controllers.forms) get_form_values() (galaxy.webapps.base.controller.UsesFormDefinitionsMixin method) get_func_list() (in module galaxy.web.framework.middleware.profile) get_galaxy_private_role() (in module tool_shed.test.base.test_db_util) get_galaxy_repository_by_name_owner_changeset_revision() (in module tool_shed.test.base.test_db_util) get_galaxy_session() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) (galaxy.webapps.base.webapp.GalaxyWebTransaction method) (galaxy.work.context.SessionRequestContext method) get_galaxy_user() (in module tool_shed.test.base.test_db_util) get_genome_build_names() (galaxy.util.dbkeys.GenomeBuilds method) get_genome_data() (galaxy.visualization.data_providers.genome.GenomeDataProvider method) get_genomic_region_indeces() (galaxy.datatypes.dataproviders.dataset.DatasetDataProvider method) get_grabbable_handler_assignment_method() (galaxy.jobs.handler.ItemGrabber static method) get_grid_title() (tool_shed.grids.repository_grid_filter_manager.RepositoryGridFilterManager method) get_group() (galaxy.webapps.base.controller.BaseController method) (in module galaxy.webapps.galaxy.controllers.admin) (in module tool_shed.util.admin_util) get_guid() (galaxy.tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager method) get_handler() (galaxy.model.Job method) get_hashed_dependencies_path() (galaxy.tool_util.deps.CachedDependencyManager method) get_hda() (galaxy.webapps.base.controller.UsesVisualizationMixin method) get_hda_manager() (in module galaxy.webapps.galaxy.api.jobs) get_hda_or_ldda() (galaxy.webapps.base.controller.UsesVisualizationMixin method) get_hdca() (galaxy.job_execution.output_collect.JobContext method) (galaxy.job_execution.output_collect.SessionlessJobContext method) (galaxy.model.store.discover.SessionlessModelPersistenceContext method) get_headers() (galaxy.util.zipstream.ZipstreamWrapper method) (in module galaxy.datatypes.sniff) get_hg_repo() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_histories() (galaxy_test.base.populators.BaseDatasetPopulator method) (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase method) get_history() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) (galaxy.work.context.WorkRequestContext method) get_history_collection_details() (galaxy_test.base.populators.BaseDatasetPopulator method) get_history_dataset_content() (galaxy_test.base.populators.BaseDatasetPopulator method) get_history_dataset_details() (galaxy_test.base.populators.BaseDatasetPopulator method) get_history_dataset_details_raw() (galaxy_test.base.populators.BaseDatasetPopulator method) get_history_dataset_extra_files() (galaxy_test.base.populators.BaseDatasetPopulator method) get_history_tags_cell() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) get_hook() (galaxy.tools.Tool method) get_id() (galaxy.tool_util.cwl.runnable.CwlWorkflowOutput method) (galaxy.tool_util.cwl.runnable.ToolOutput method) (in module galaxy.webapps.galaxy.api.genomes) get_id_col_in_item_tag_assoc_table() (galaxy.model.tags.TagHandler method) get_id_tag() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.model.Job method) (galaxy.model.Task method) get_id_token() (galaxy.model.UserAuthnzToken method) get_identifier() (galaxy.model.SerializationOptions method) get_identifier_for_id() (galaxy.model.SerializationOptions method) get_ids() (galaxy.web.framework.helpers.grids.Grid method) (galaxy.web.legacy_framework.grids.Grid method) get_ids_of_tool_shed_repositories_being_installed() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_import_model_store_for_directory() (in module galaxy.model.store) get_imported() (galaxy.model.Job method) get_indeces_by_column_names() (galaxy.datatypes.dataproviders.dataset.DatasetDataProvider method) get_index() (galaxy.tools.test.RootParamContext method) get_index_flag() (galaxy.datatypes.binary.Bam method) get_info() (galaxy.model.Job method) (galaxy.model.LibraryDataset method) (galaxy.model.Task method) get_information() (galaxy.webapps.galaxy.api.users.UserAPIController method) get_inital_values() (galaxy.datatypes.display_applications.application.DisplayApplicationLink method) get_initial_value() (galaxy.tools.parameters.basic.BaseDataToolParameter method) (galaxy.tools.parameters.basic.BaseURLToolParameter method) (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.ColorToolParameter method) (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.FloatToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.HiddenToolParameter method) (galaxy.tools.parameters.basic.IntegerToolParameter method) (galaxy.tools.parameters.basic.SelectTagParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.SimpleTextToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.grouping.Conditional method) (galaxy.tools.parameters.grouping.Group method) (galaxy.tools.parameters.grouping.Repeat method) (galaxy.tools.parameters.grouping.Section method) (galaxy.tools.parameters.grouping.UploadDataset method) (galaxy.tools.parameters.SelectToolParameter method) get_input() (galaxy.model.WorkflowStep method) get_input_dataset_fnames() (galaxy.jobs.JobWrapper method) get_input_datasets() (galaxy.model.Job method) get_input_fnames() (galaxy.jobs.JobWrapper method) get_input_library_datasets() (galaxy.model.Job method) get_input_object() (galaxy.model.WorkflowInvocation method) get_input_path() (galaxy.jobs.JobWrapper method) get_input_paths() (galaxy.jobs.JobWrapper method) get_input_source() (in module galaxy.tool_util.parser) (in module galaxy.tool_util.parser.factory) get_inputs() (galaxy.workflow.modules.InputDataCollectionModule method) (galaxy.workflow.modules.InputDataModule method) (galaxy.workflow.modules.InputParameterModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_installable_revisions() (tool_shed.webapp.api.repositories.RepositoriesController method) get_installed_and_missing_repository_dependencies() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_installed_and_missing_repository_dependencies_for_new_or_updated_install() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_installed_and_missing_tool_dependencies_for_installed_repository() (tool_shed.galaxy_install.dependency_display.DependencyDisplayer method) get_installed_and_missing_tool_dependencies_for_repository() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_installed_repository() (galaxy.tools.cache.ToolShedRepositoryCache method) (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_installed_repository_by_id() (in module tool_shed.test.base.test_db_util) get_installed_repository_by_name_owner() (in module tool_shed.test.base.test_db_util) get_installed_tool_shed_repository() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_integrated_section_for_tool() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) get_interesting_stack_frame() (galaxy.util.heartbeat.Heartbeat method) get_internal_version() (galaxy.model.StoredWorkflow method) get_invalid_file_tups() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) get_invocation() (galaxy.managers.workflows.WorkflowsManager method) (galaxy_test.base.populators.BaseWorkflowPopulator method) get_invocation_report() (galaxy.managers.workflows.WorkflowsManager method) get_invocation_step() (galaxy.managers.workflows.WorkflowsManager method) get_ip() (in module galaxy.util.sockets) get_ip_address() (in module galaxy_test.base.env) get_item() (galaxy.webapps.base.controller.SharableMixin method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) get_item_actions() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) (tool_shed.webapp.security.RBACAgent method) get_item_annotation_obj() (galaxy.model.item_attrs.UsesAnnotations method) get_item_annotation_str() (galaxy.model.item_attrs.UsesAnnotations method) get_item_content_async() (galaxy.webapps.base.controller.SharableMixin method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) get_item_extended_metadata_obj() (galaxy.webapps.base.controller.UsesExtendedMetadataMixin method) get_iterator() (galaxy.visualization.data_providers.basic.BaseDataProvider method) (galaxy.visualization.data_providers.genome.BamDataProvider method) (galaxy.visualization.data_providers.genome.BedDataProvider method) (galaxy.visualization.data_providers.genome.ChromatinInteractionsTabixDataProvider method) (galaxy.visualization.data_providers.genome.ENCODEPeakDataProvider method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) (galaxy.visualization.data_providers.genome.IntervalDataProvider method) (galaxy.visualization.data_providers.genome.IntervalIndexDataProvider method) (galaxy.visualization.data_providers.genome.RawBedDataProvider method) (galaxy.visualization.data_providers.genome.RawGFFDataProvider method) (galaxy.visualization.data_providers.genome.RawVcfDataProvider method) (galaxy.visualization.data_providers.genome.TabixDataProvider method) get_job() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.model.Job method) (galaxy.model.Task method) (in module galaxy.webapps.reports.controllers.jobs) get_job_destination() (galaxy.jobs.mapper.JobRunnerMapper method) (galaxy.tools.Tool method) get_job_details() (galaxy_test.base.populators.BaseDatasetPopulator method) get_job_file() (galaxy.jobs.runners.BaseJobRunner method) get_job_interface() (galaxy.jobs.runners.util.cli.CliInterface method) get_job_manager() (in module galaxy.webapps.galaxy.api) get_job_runner() (galaxy.jobs.JobWrapper method) get_job_runner_external_id() (galaxy.model.Job method) (galaxy.model.Task method) get_job_runner_name() (galaxy.model.Job method) (galaxy.model.Task method) get_job_runner_plugins() (galaxy.jobs.JobConfiguration method) get_job_runner_url() (galaxy.jobs.JobWrapper method) get_job_search() (in module galaxy.webapps.galaxy.api.jobs) get_job_stdio() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) get_job_tool_configurations() (galaxy.jobs.JobConfiguration method) get_json() (galaxy.tool_util.deps.mulled.mulled_search.CondaSearch method) (galaxy.tool_util.deps.mulled.mulled_search.GitHubSearch method) get_key_for_repository_changeset_revision() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) get_keys_from_dict() (in module galaxy.jobs.dynamic_tool_destination) get_label() (galaxy.tools.error_reports.plugins.github.GithubPlugin method) (galaxy.tools.parameters.basic.HiddenToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.toolbox.panel.ToolPanelElements method) get_last_check() (galaxy.model.DeferredJob method) get_last_reviewed_revision_by_user() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_latest_changeset_revision() (in module tool_shed.util.metadata_util) get_latest_downloadable_changeset_revision() (in module tool_shed.util.metadata_util) (tool_shed.webapp.controllers.repository.RepositoryController method) get_latest_downloadable_repository_metadata() (in module tool_shed.grids.util) get_latest_downloadable_repository_metadata_if_it_includes_tools() (in module tool_shed.grids.util) get_latest_id() (in module galaxy.model.migrate.versions.0067_populate_sequencer_table) get_latest_repository_metadata() (in module tool_shed.grids.util) (in module tool_shed.util.metadata_util) get_latest_repository_metadata_if_it_includes_invalid_tools() (in module tool_shed.grids.util) get_latest_tool_config_revision_from_repository_manifest() (tool_shed.tools.tool_validator.ToolValidator method) get_legacy_sites_by_build() (galaxy.datatypes.registry.Registry method) get_legal_names() (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.SelectToolParameter method) get_legal_values() (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.GenomeBuildParameter method) (galaxy.tools.parameters.basic.SelectTagParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.SelectToolParameter method) get_legitimate_roles() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) get_level() (galaxy.model.dataset_collections.builder.CollectionBuilder method) get_libraries() (galaxy_test.base.populators.LibraryPopulator method) get_library() (galaxy.webapps.base.controller.UsesLibraryMixin method) get_library_contents_with_path() (galaxy_test.base.populators.LibraryPopulator method) get_library_dataset() (galaxy.webapps.base.controller.UsesLibraryMixinItems method) get_library_dataset_dataset_association() (galaxy.webapps.base.controller.UsesLibraryMixinItems method) get_library_dict() (galaxy.managers.libraries.LibraryManager method) get_library_folder() (galaxy.job_execution.output_collect.JobContext method) (galaxy.model.store.discover.SessionlessModelPersistenceContext method) (galaxy.webapps.base.controller.UsesLibraryMixinItems method) get_license_by_id() (galaxy.managers.licenses.LicensesManager method) get_licenses() (galaxy.managers.licenses.LicensesManager method) get_licenses_manager() (in module galaxy.webapps.galaxy.api.licenses) get_link() (galaxy.datatypes.display_applications.application.DisplayApplication method) (galaxy.web.framework.helpers.grids.GridColumn method) (galaxy.web.framework.helpers.grids.PublicURLColumn method) (galaxy.web.legacy_framework.grids.GridColumn method) (galaxy.web.legacy_framework.grids.PublicURLColumn method) (galaxy.web.legacy_framework.grids.SharingStatusColumn method) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid.HistoryListNameColumn method) get_list_from_file() (in module galaxy.tool_util.deps.mulled.mulled_update_singularity_containers) get_list_of_copied_sample_files() (tool_shed.tools.tool_validator.ToolValidator method) get_loaded_tools_by_lineage() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) get_local_driver() (in module galaxy.selenium.driver_factory) get_logged_in_user() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) get_logger() (in module galaxy.util.custom_logging) get_logout_url() (galaxy.webapps.galaxy.controllers.authnz.OIDC method) get_manage_permissions_roles() (galaxy.model.Dataset method) (galaxy.model.LibraryDatasetDatasetAssociation method) get_manage_roles() (galaxy.managers.libraries.LibraryManager method) get_manager() (galaxy.tools.data_manager.manager.DataManagers method) get_mapping_by_name() (galaxy.tools.parameters.sanitize.ToolParameterSanitizer class method) get_master_api_key() (in module galaxy_test.base.api_util) get_matcher() (galaxy.datatypes.molecules.PQR method) get_max_optional_metadata_filesize() (galaxy.datatypes.data.Data method) get_mercurial_default_options_dict() (in module tool_shed.webapp.controllers.repository) get_message() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) get_message_for_no_shed_tool_config() (in module galaxy.webapps.galaxy.api.tool_shed_repositories) get_metadata() (galaxy.model.DatasetInstance method) get_metadata_column_index_by_name() (galaxy.datatypes.dataproviders.dataset.DatasetDataProvider method) get_metadata_column_names() (galaxy.datatypes.dataproviders.dataset.DatasetDataProvider method) get_metadata_column_types() (galaxy.datatypes.dataproviders.dataset.DatasetDataProvider method) get_metadata_compute_strategy() (in module galaxy.metadata) get_metadata_dataset() (galaxy.model.DatasetInstance method) get_metadata_dict() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) get_metadata_file() (galaxy.webapps.galaxy.api.datasets.DatasetsController method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) get_metadata_parameter() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataCollection method) get_metadata_revisions() (in module tool_shed.util.metadata_util) get_metadata_source() (galaxy.job_execution.output_collect.MetadataSourceProvider method) (galaxy.model.store.discover.MetadataSourceProvider method) (galaxy.model.store.discover.UnusedMetadataSourceProvider method) get_mime() (galaxy.datatypes.anvio.AnvioComposite method) (galaxy.datatypes.binary.Binary method) (galaxy.datatypes.binary.ExcelXls method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.data.Text method) (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.genetics.Rgenetics method) (galaxy.datatypes.genetics.rgTabList method) (galaxy.datatypes.images.Gmaj method) (galaxy.datatypes.media.Wav method) (galaxy.datatypes.microarrays.GenericMicroarrayFile method) (galaxy.datatypes.molecules.GenericMolFile method) (galaxy.datatypes.molecules.OBFS method) (galaxy.datatypes.neo4j.Neo4j method) (galaxy.datatypes.text.Html method) (galaxy.datatypes.text.Json method) (galaxy.model.DatasetInstance method) get_mimetype_by_extension() (galaxy.datatypes.registry.Registry method) get_missing_containers() (in module galaxy.tool_util.deps.mulled.mulled_list) get_missing_envs() (in module galaxy.tool_util.deps.mulled.mulled_list) get_modify_roles() (galaxy.managers.libraries.LibraryManager method) get_modules() (galaxy.workflow.modules.SubWorkflowModule method) get_monitor_id() (in module galaxy.webapps.reports.controllers.jobs) get_most_recent_history() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) get_mutable_output_fnames() (galaxy.jobs.JobWrapper method) get_name() (galaxy.model.LibraryDataset method) (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_name_and_link_async() (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) get_named_fields_list() (galaxy.tools.data.TabularToolDataTable method) get_named_tmpfile_from_ctx() (in module tool_shed.util.hg_util) get_native_spec() (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) get_new_dataset_meta_by_basename() (galaxy.tool_util.provided_metadata.BaseToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.LegacyToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.ToolProvidedMetadata method) get_new_datasets() (galaxy.tool_util.provided_metadata.BaseToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.LegacyToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.ToolProvidedMetadata method) get_new_datasets_for_metadata_collection() (galaxy.tool_util.provided_metadata.BaseToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.LegacyToolProvidedMetadata method) get_new_guid() (galaxy.security.idencoding.IdEncodingHelper method) get_new_tables() (in module galaxy.model.migrate.versions.0136_collection_and_workflow_state) get_new_track_config() (galaxy.webapps.base.controller.UsesVisualizationMixin method) get_next_downloadable_changeset_revision() (in module tool_shed.util.metadata_util) get_next_line() (in module galaxy.datatypes.constructive_solid_geometry) get_next_prior_import_or_install_required_dict_entry() (in module galaxy.tool_shed.util.shed_util_common) (in module tool_shed.util.shed_util_common) get_non_shed_tool_panel_configs() (in module galaxy.util.tool_shed.common_util) get_nonterminal_for_user_by_trans() (galaxy.managers.interactivetool.InteractiveToolManager method) get_object() (galaxy.webapps.base.controller.BaseAPIController method) (galaxy.webapps.base.controller.BaseController method) (galaxy.webapps.base.controller.BaseUIController method) (in module galaxy.managers.base) get_object_url() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) get_observer_class() (in module galaxy.util.watcher) get_open_tempfile() (galaxy.datatypes.util.maf_utilities.TempFileHandler method) (galaxy.tools.util.maf_utilities.TempFileHandler method) get_option() (galaxy.tools.data_fetch.UploadConfig method) get_options() (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.GenomeBuildParameter method) (galaxy.tools.parameters.basic.SelectTagParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.dynamic_options.DynamicOptions method) (galaxy.tools.parameters.SelectToolParameter method) get_options_filter_attribute() (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.DataToolParameter method) get_or_add_input() (galaxy.model.WorkflowStep method) (tool_shed.webapp.model.WorkflowStep method) get_or_create_api_key() (galaxy.managers.api_keys.ApiKeyManager method) (galaxy.webapps.galaxy.api.users.UserAPIController method) get_or_create_default_history() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) get_or_create_index() (in module galaxy.tools.search) get_or_create_remote_user() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) get_or_create_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_or_create_tool_section() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) get_or_create_tool_shed_repository() (galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) get_or_create_valid_api_key() (galaxy.managers.users.UserManager method) get_ordered_installable_revisions() (tool_shed.webapp.api.repositories.RepositoriesController method) get_oriented_chopped_blocks_for_region() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_oriented_chopped_blocks_with_index_offset_for_region() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_output_basenames() (galaxy.jobs.JobWrapper method) get_output_datasets() (galaxy.model.Job method) get_output_destination() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) get_output_file_id() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) get_output_fnames() (galaxy.jobs.JobWrapper method) get_output_hdas_and_fnames() (galaxy.jobs.JobWrapper method) get_output_library_datasets() (galaxy.model.Job method) get_output_name() (galaxy.tools.actions.DefaultToolAction method) get_output_object() (galaxy.model.WorkflowInvocation method) get_output_path() (galaxy.jobs.JobWrapper method) get_output_sizes() (galaxy.jobs.JobWrapper method) get_outputs() (in module galaxy.tool_util.cwl.runnable) get_owned() (galaxy.managers.secured.OwnableManagerMixin method) get_owned_ids() (galaxy.managers.hdas.HDAManager method) get_owned_workflow() (galaxy.managers.workflows.WorkflowsManager method) get_package_hash() (in module galaxy.tool_util.deps.mulled.mulled_search) get_page() (galaxy.webapps.galaxy.controllers.page.PageController method) get_page_identifiers() (in module galaxy.managers.pages) get_pairlist() (galaxy.util.topsort.CycleError method) get_panel_section() (galaxy.tools.Tool method) get_parallelism() (galaxy.jobs.JobWrapper method) get_param() (galaxy.tools.Tool method) get_param_dict() (galaxy.jobs.JobWrapper method) get_param_filename() (galaxy.model.Job method) get_param_name_by_url() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) get_param_value() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) get_param_values() (galaxy.model.Job method) (galaxy.model.Task method) get_parameters() (galaxy.model.Job method) (galaxy.model.Task method) get_params() (galaxy.jobs.JobConfiguration static method) (galaxy.model.Job method) (galaxy.web.params.BaseParamParser method) get_parent() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataCollection method) get_parent_id() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) get_partial() (galaxy.util.topsort.CycleError method) get_password() (galaxy.webapps.galaxy.api.users.UserAPIController method) get_path_key() (in module galaxy.managers.jobs) get_peek() (galaxy.datatypes.genetics.RexpBase method) get_percent() (galaxy.quota.NoQuotaAgent method) get_permissions() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) (galaxy.webapps.galaxy.api.folders.FoldersController method) (galaxy.webapps.galaxy.api.libraries.LibrariesController method) (galaxy.webapps.galaxy.api.users.UserAPIController method) get_permitted_actions() (in module galaxy.security) (in module tool_shed.webapp.security) get_permitted_libraries() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) get_phecols() (galaxy.datatypes.genetics.RexpBase method) get_pheno() (galaxy.datatypes.genetics.RexpBase method) get_platform_info_dict() (in module galaxy.tool_shed.util.tool_dependency_util) get_plugin() (galaxy.visualization.plugins.registry.VisualizationsRegistry method) get_plugins() (galaxy.jobs.runners.util.cli.CliInterface method) (galaxy.visualization.plugins.registry.VisualizationsRegistry method) get_post_job_actions() (galaxy.model.Job method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_pred_counts() (galaxy.util.topsort.CycleError method) get_predictions() (galaxy.tools.recommendations.ToolRecommendations method) get_preds() (galaxy.util.topsort.CycleError method) get_prefix() (galaxy.files.sources.BaseFilesSource method) (galaxy.files.sources.galaxy.LibraryImportFilesSource method) (galaxy.files.sources.galaxy.UserFtpFilesSource method) (galaxy.files.sources.galaxy.UserLibraryImportFilesSource method) get_prepare_input_files_cmd() (galaxy.model.Task method) get_prepare_steps() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) get_previous_metadata_changeset_revision() (in module tool_shed.util.metadata_util) get_previous_repository_reviews() (in module tool_shed.util.review_util) get_prior_import_or_install_required_dict() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_prior_install_required_dict() (galaxy.tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager method) get_prior_installation_required_and_only_if_compiling_contained_td() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) get_private_role() (in module tool_shed.test.base.test_db_util) get_private_user_role() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) (tool_shed.webapp.security.RBACAgent method) get_proprietary_tool_panel_elems() (galaxy.tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager method) get_protocol_from_tool_shed_url() (in module galaxy.util.tool_shed.common_util) get_published_visualizations() (galaxy.webapps.base.controller.UsesVisualizationMixin method) get_quay_containers() (in module galaxy.tool_util.deps.mulled.mulled_list) get_query_for_setting_metadata_on_repositories() (galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) get_quota() (galaxy.quota.NoQuotaAgent method) (galaxy.webapps.base.controller.UsesQuotaMixin method) (in module galaxy.webapps.galaxy.controllers.admin) get_quota_agent() (in module galaxy.quota) get_quota_params() (galaxy.web.params.QuotaParamParser method) get_quotas() (galaxy_test.base.populators.BaseDatasetPopulator method) get_random_name() (galaxy_test.base.populators.BaseDatasetPopulator method) get_raw_data() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) get_readable_ctx_date() (in module tool_shed.util.hg_util) get_readme_files() (tool_shed.webapp.controllers.repository.RepositoryController method) get_readme_files_dict_for_display() (in module tool_shed.util.readme_util) get_ready_jeha() (galaxy.managers.histories.HistoryExportView method) get_ref() (galaxy.tool_util.parser.output_actions.ToolOutputActionConditionalWhen method) get_ref_based_read_seq_and_cigar() (in module galaxy.visualization.data_providers.cigar) get_region_alignment() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_relative_path_to_repository_file() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) get_remote_driver() (in module galaxy.selenium.driver_factory) get_remote_files() (galaxy_test.base.populators.BaseDatasetPopulator method) get_removed_tool() (galaxy.tools.cache.ToolCache method) get_replacement_parameters() (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_repo_info_dict() (in module tool_shed.util.repository_util) get_repo_info_tuple_contents() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repo_path() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_repos() (in module tool_shed.util.shed_index) get_repositories() (tool_shed.webapp.api.categories.CategoriesController method) get_repositories_by_category() (in module tool_shed.util.repository_util) get_repositories_category_api() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_repository_admin_role_name() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repository_and_repository_dependencies_from_repo_info_dict() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repository_by_id() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.test.base.test_db_util) (in module tool_shed.util.repository_util) get_repository_by_name() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repository_by_name_and_owner() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.test.base.test_db_util) (in module tool_shed.util.repository_util) get_repository_categories() (in module tool_shed.util.shed_util_common) get_repository_changelog_tuples() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_repository_components_for_installation() (galaxy.tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) get_repository_datatypes_count() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_repository_dependencies() (in module galaxy.util.tool_shed.common_util) (tool_shed.webapp.controllers.repository.RepositoryController method) (tool_shed.webapp.model.Repository method) get_repository_dependencies_for_changeset_revision() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) get_repository_dependencies_for_installed_tool_shed_repository() (galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) get_repository_dependency_as_key() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) get_repository_dependency_by_repository_id() (galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) get_repository_dependency_tups_for_installed_repository() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_repository_dependency_tups_from_repository_metadata() (in module tool_shed.util.metadata_util) get_repository_dependency_types() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repository_downloadable_revisions() (in module tool_shed.test.base.test_db_util) get_repository_file_contents() (in module tool_shed.util.shed_util_common) get_repository_file_list() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_repository_for_dependency_relationship() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repository_heads() (in module tool_shed.util.hg_util) get_repository_id() (tool_shed.webapp.controllers.repository.RepositoryController method) get_repository_ids_requiring_prior_import_or_install() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repository_in_tool_shed() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repository_information() (tool_shed.webapp.controllers.repository.RepositoryController method) get_repository_install_dir() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_repository_metadata() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_repository_metadata_by_changeset_revision() (in module tool_shed.util.metadata_util) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_repository_metadata_by_id() (in module tool_shed.util.metadata_util) get_repository_metadata_by_repository_id_changeset_revision() (in module tool_shed.test.base.test_db_util) (in module tool_shed.util.metadata_util) get_repository_metadata_for_changeset_revision() (in module tool_shed.test.base.test_db_util) get_repository_metadata_revisions() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_repository_metadata_revisions_for_review() (in module tool_shed.util.metadata_util) get_repository_owner() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repository_owner_from_clone_url() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repository_query() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_repository_review_by_user_id_changeset_revision() (in module tool_shed.test.base.test_db_util) get_repository_reviewer_role() (tool_shed.webapp.security.CommunityRBACAgent method) get_repository_reviews() (in module tool_shed.test.base.test_db_util) get_repository_revision_install_info() (tool_shed.webapp.api.repositories.RepositoriesController method) get_repository_role_association() (in module tool_shed.test.base.test_db_util) get_repository_tip() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_repository_tools_tups() (galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) get_repository_tuple_for_installed_repository_manager() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_repository_type() (tool_shed.webapp.controllers.repository.RepositoryController method) get_repository_type_from_tool_shed() (in module tool_shed.util.shed_util_common) get_required_enctype() (galaxy.tools.parameters.basic.FileToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) get_required_item() (in module galaxy.model.store.discover) get_required_repo_info_dict() (tool_shed.webapp.controllers.repository.RepositoryController method) get_required_repo_info_dicts() (galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) get_required_repository_package_env_sh_path() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Repository method) get_requirements_from_repository() (in module tool_shed.util.shed_util_common) get_requirements_from_tools() (in module tool_shed.util.shed_util_common) get_requirements_status() (galaxy.tool_util.deps.views.DependencyResolversView method) get_reset_token() (galaxy.managers.users.UserManager method) get_resolution_cache() (galaxy.tool_util.deps.containers.ContainerRegistry method) get_resolver_option() (galaxy.tool_util.deps.DependencyManager method) get_resource_group() (galaxy.jobs.JobToolConfiguration method) get_resource_mapper_function() (in module galaxy.workflow.resources) get_resource_parameters() (galaxy.jobs.HasResourceParameters method) get_resubmits() (galaxy.jobs.JobConfiguration static method) get_results() (galaxy.model.search.ViewQueryBaseClass method) get_rev_label_changeset_revision_from_repository_metadata() (in module tool_shed.util.hg_util) get_rev_label_from_changeset_revision() (in module tool_shed.util.hg_util) get_reversed_changelog_changesets() (in module tool_shed.util.hg_util) get_review() (in module tool_shed.util.review_util) get_review_by_repository_id_changeset_revision_user_id() (in module tool_shed.util.review_util) get_reviews_by_repository_id_changeset_revision() (in module tool_shed.util.review_util) get_reviews_ordered_by_changeset_revision() (in module tool_shed.test.base.test_db_util) get_revision_label() (in module tool_shed.util.hg_util) get_revision_label_from_ctx() (in module tool_shed.util.hg_util) get_role() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.webapps.base.controller.BaseController method) (in module galaxy.webapps.galaxy.controllers.admin) (in module tool_shed.test.base.test_db_util) (in module tool_shed.util.admin_util) get_role_by_id() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_role_by_name() (in module tool_shed.test.base.test_db_util) get_role_manager() (in module galaxy.webapps.galaxy.api.roles) get_roles() (galaxy_test.base.populators.BaseDatasetPopulator method) get_roles_for_action() (galaxy.model.security.GalaxyRBACAgent method) get_rules_specification() (in module galaxy.util.rules_dsl) get_run_test() (in module galaxy.tool_util.deps.mulled.get_tests) get_runtime_dependent_tool_dependency_tuples() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_runtime_inputs() (galaxy.workflow.modules.InputDataCollectionModule method) (galaxy.workflow.modules.InputDataModule method) (galaxy.workflow.modules.InputParameterModule method) (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_runtime_state() (galaxy.workflow.modules.InputModule method) (galaxy.workflow.modules.InputParameterModule method) (galaxy.workflow.modules.PauseModule method) (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_sample_files_from_disk() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) get_scheme() (galaxy.files.sources.BaseFilesSource method) (galaxy.files.sources.FilesSource method) (galaxy.files.sources.galaxy.LibraryImportFilesSource method) (galaxy.files.sources.galaxy.UserFtpFilesSource method) (galaxy.files.sources.galaxy.UserLibraryImportFilesSource method) get_schemes() (galaxy.files.ConfiguredFileSources method) get_section() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) get_sections() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) get_sequence() (galaxy.datatypes.util.maf_utilities.RegionAlignment method) (galaxy.datatypes.util.maf_utilities.SplicedAlignment method) (galaxy.tools.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.SplicedAlignment method) get_sequence_reverse_complement() (galaxy.datatypes.util.maf_utilities.RegionAlignment method) (galaxy.datatypes.util.maf_utilities.SplicedAlignment method) (galaxy.tools.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.SplicedAlignment method) get_sequencer_id() (in module galaxy.model.migrate.versions.0067_populate_sequencer_table) get_sequences_per_file() (galaxy.datatypes.sequence.Sequence static method) get_servers() (galaxy.webapps.galaxy.api.trs_consumer.TrsConsumeAPIController method) (galaxy.workflow.trs_proxy.TrsProxy method) get_session() (galaxy.openid.openid_manager.OpenIDManager method) (in module galaxy.webapps.galaxy.api) get_session_from_session_key() (galaxy.managers.session.GalaxySessionManager method) get_session_id() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.model.Job method) (galaxy.model.Task method) get_session_manager() (in module galaxy.webapps.galaxy.api) get_setting() (galaxy.authnz.psa_authnz.Strategy method) get_sharable_url() (galaxy.model.tool_shed_install.ToolShedRepository method) get_share_assocs() (galaxy.managers.sharable.SharableModelManager method) get_sharing_roles() (galaxy.model.security.GalaxyRBACAgent method) get_shed_config_dict() (galaxy.model.tool_shed_install.ToolShedRepository method) get_shed_config_dict_by_filename() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) get_shed_tool_conf_dict() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) get_shell() (in module galaxy.jobs.runners.util.cli.factory) get_shell_plugin() (galaxy.jobs.runners.util.cli.CliInterface method) get_short_str() (galaxy.jobs.actions.post.ActionBox class method) (galaxy.jobs.actions.post.ChangeDatatypeAction class method) (galaxy.jobs.actions.post.ColumnSetAction class method) (galaxy.jobs.actions.post.DefaultJobAction class method) (galaxy.jobs.actions.post.DeleteDatasetAction class method) (galaxy.jobs.actions.post.DeleteIntermediatesAction class method) (galaxy.jobs.actions.post.EmailAction class method) (galaxy.jobs.actions.post.HideDatasetAction class method) (galaxy.jobs.actions.post.RenameDatasetAction class method) (galaxy.jobs.actions.post.TagDatasetAction class method) (galaxy.jobs.actions.post.ValidateOutputsAction class method) get_showable_folders() (galaxy.model.security.GalaxyRBACAgent method) get_signature_file() (galaxy.datatypes.binary.BafTar method) (galaxy.datatypes.binary.MassHunterTar method) (galaxy.datatypes.binary.MassLynxTar method) (galaxy.datatypes.binary.TdfTar method) (galaxy.datatypes.binary.YepTar method) get_single_filter() (galaxy.web.framework.helpers.grids.BooleanColumn method) (galaxy.web.framework.helpers.grids.IntegerColumn method) (galaxy.web.framework.helpers.grids.OwnerAnnotationColumn method) (galaxy.web.framework.helpers.grids.TextColumn method) (galaxy.web.legacy_framework.grids.BooleanColumn method) (galaxy.web.legacy_framework.grids.IntegerColumn method) (galaxy.web.legacy_framework.grids.OwnerAnnotationColumn method) (galaxy.web.legacy_framework.grids.TextColumn method) get_single_status() (galaxy.jobs.runners.util.cli.job.BaseJobExec method) (galaxy.jobs.runners.util.cli.job.lsf.LSF method) (galaxy.jobs.runners.util.cli.job.slurm.Slurm method) (galaxy.jobs.runners.util.cli.job.torque.Torque method) get_singularity_containers() (in module galaxy.tool_util.deps.mulled.mulled_list) get_singularity_target_kwds() (galaxy.tool_util.deps.container_classes.SingularityContainer method) get_size() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) get_sniffers_count() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_social_auth() (galaxy.model.UserAuthnzToken class method) get_social_auth_for_user() (galaxy.model.UserAuthnzToken class method) get_spark_time() (in module galaxy.webapps.reports.controllers.jobs) get_species_in_block() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_species_in_maf() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_species_names() (galaxy.datatypes.util.maf_utilities.RegionAlignment method) (galaxy.datatypes.util.maf_utilities.SplicedAlignment method) (galaxy.tools.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.SplicedAlignment method) get_spliced_region_alignment() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_split_commands_sequential() (galaxy.datatypes.sequence.Sequence static method) get_split_commands_with_toc() (galaxy.datatypes.sequence.Sequence static method) get_sreg() (galaxy.openid.openid_manager.OpenIDManager method) get_stack_facts() (in module galaxy.web_stack) get_stage_in_out() (galaxy.jobs.runners.pbs.PBSJobRunner method) get_starts_ends_fields_from_gene_bed() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) get_state() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.jobs.transfer_manager.TransferManager method) (galaxy.model.Job method) (galaxy.model.Task method) (galaxy.workflow.modules.WorkflowModule method) get_static_param_values() (galaxy.tools.Tool method) get_status() (galaxy.jobs.runners.util.cli.job.BaseJobExec method) (galaxy.jobs.runners.util.cli.job.lsf.LSF method) (galaxy.jobs.runners.util.cli.job.slurm.Slurm method) (galaxy.jobs.runners.util.cli.job.slurm_torque.SlurmTorque method) (galaxy.jobs.runners.util.cli.job.torque.Torque method) get_step_handler_by_type() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager.StepManager method) get_step_map_over() (galaxy.managers.workflows.WorkflowContentsManager static method) get_store_by() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) get_store_usage_percent() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) get_stored_accessible_workflow() (galaxy.managers.workflows.WorkflowsManager method) get_stored_workflow() (galaxy.managers.workflows.WorkflowsManager method) (galaxy.webapps.base.controller.UsesStoredWorkflowMixin method) get_stored_workflow_steps() (galaxy.webapps.base.controller.UsesStoredWorkflowMixin method) get_structure() (in module galaxy.model.dataset_collections.structure) get_subsystem() (in module galaxy.job_metrics.collectl.subsystems) get_subworkflow_invocation_association_for_step() (galaxy.model.WorkflowInvocation method) get_subworkflow_invocation_for_step() (galaxy.model.WorkflowInvocation method) get_succs() (galaxy.util.topsort.CycleError method) get_suite() (in module galaxy.tools.parameters.validation) (in module galaxy.util.form_builder) get_table_names_by_path() (galaxy.tools.data.ToolDataTableManager method) get_tables() (galaxy.tools.data.ToolDataTableManager method) get_tag_assoc_class() (galaxy.model.tags.TagHandler method) get_tag_by_id() (galaxy.model.tags.TagHandler method) get_tag_by_name() (galaxy.model.tags.TagHandler method) get_tag_handler() (galaxy.webapps.base.controller.UsesTagsMixin method) get_tag_handler_by_tag() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager.TagManager method) get_tag_list() (galaxy.tools.parameters.basic.SelectTagParameter method) get_tagging_elt_async() (galaxy.webapps.galaxy.controllers.tag.TagsController method) get_tags() (galaxy.managers.taggable.TaggableManagerMixin method) get_tags_str() (galaxy.model.tags.TagHandler method) get_target_install_dir() (galaxy.tool_shed.tools.data_table_manager.ShedToolDataTableManager method) get_task() (galaxy.jobs.runners.godocker.GodockerJobRunner method) (galaxy.jobs.TaskWrapper method) get_task_runner_external_id() (galaxy.model.Task method) get_task_runner_name() (galaxy.model.Task method) get_task_status() (galaxy.jobs.runners.godocker.GodockerJobRunner method) get_tasks() (galaxy.model.Job method) get_test_config() (galaxy.tool_util.verify.interactor.DictClientTestConfig method) (galaxy.tool_util.verify.interactor.NullClientTestConfig method) get_test_fname() (in module galaxy.datatypes.data) (in module galaxy.datatypes.sniff) get_test_from_anaconda() (in module galaxy.tool_util.deps.mulled.get_tests) get_tests_summary() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) get_timer() (galaxy.app.ExecutionTimerFactory method) get_timestamp_drop_sql() (in module galaxy.model.triggers) get_timestamp_install_sql() (in module galaxy.model.triggers) get_tool() (galaxy.tools.cache.ToolCache method) (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) (galaxy.webapps.galaxy.api.trs_consumer.TrsConsumeAPIController method) (galaxy.workflow.trs_proxy.TrsProxy method) get_tool_by_id() (galaxy.managers.tools.DynamicToolManager method) (galaxy.tools.cache.ToolCache method) get_tool_by_tool_id() (galaxy.managers.tools.DynamicToolManager method) get_tool_by_uuid() (galaxy.managers.tools.DynamicToolManager method) get_tool_components() (galaxy.tools.ToolBox method) get_tool_conf_watcher() (in module galaxy.tools.toolbox.watcher) get_tool_def() (galaxy.webapps.base.controller.UsesVisualizationMixin method) get_tool_dependencies() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (in module galaxy.util.tool_shed.common_util) (tool_shed.webapp.controllers.repository.RepositoryController method) (tool_shed.webapp.model.Repository method) get_tool_dependencies_config_contents() (tool_shed.webapp.controllers.repository.RepositoryController method) get_tool_dependency() (in module galaxy.tool_shed.util.tool_dependency_util) get_tool_dependency_by_name_type_repository() (in module galaxy.tool_shed.util.tool_dependency_util) get_tool_dependency_by_name_version_type() (in module galaxy.tool_shed.util.tool_dependency_util) get_tool_dependency_by_name_version_type_repository() (in module galaxy.tool_shed.util.tool_dependency_util) get_tool_dependency_definition_metadata() (tool_shed.webapp.controllers.repository.RepositoryController method) get_tool_dependency_definition_metadata_from_tool_shed() (in module tool_shed.util.shed_util_common) get_tool_dependency_ids() (in module galaxy.tool_shed.util.tool_dependency_util) get_tool_dependency_install_dir() (in module galaxy.tool_shed.util.tool_dependency_util) get_tool_dependency_path() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_tool_dependency_tuple_for_installed_repository_manager() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_tool_id() (galaxy.model.Job method) (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) get_tool_index_sample_files() (galaxy.tool_shed.tools.data_table_manager.ShedToolDataTableManager method) get_tool_panel_config_tool_path_install_dir() (in module galaxy.tool_shed.util.shed_util_common) (in module tool_shed.util.shed_util_common) get_tool_panel_section_from_api() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_tool_panel_section_from_repository_metadata() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_tool_path_by_shed_tool_conf_filename() (in module tool_shed.util.shed_util_common) get_tool_path_install_dir() (in module galaxy.tool_shed.util.tool_util) get_tool_predictions() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) get_tool_provided_job_metadata() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) get_tool_relative_path() (galaxy.model.tool_shed_install.ToolShedRepository method) (galaxy.tools.toolbox.base.ToolConfRepository method) get_tool_repository_from_xml_item() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) get_tool_resource_xml() (galaxy.jobs.JobConfiguration method) get_tool_shed_api_key() (tool_shed.webapp.api.authenticate.ToolShedAuthenticationController method) get_tool_shed_from_clone_url() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_tool_shed_repo_requirements() (in module tool_shed.util.shed_util_common) get_tool_shed_repository_by_id() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_tool_shed_repository_ids() (in module galaxy.util.tool_shed.common_util) get_tool_shed_repository_info_dict() (galaxy.tools.data_manager.manager.DataManager method) get_tool_shed_repository_install_dir() (galaxy.tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) get_tool_shed_repository_status_label() (in module tool_shed.util.repository_util) get_tool_shed_repository_url() (in module galaxy.util.tool_shed.common_util) get_tool_shed_status_for_installed_repository() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) get_tool_shed_url_from_tool_shed_registry() (in module galaxy.util.tool_shed.common_util) get_tool_source() (in module galaxy.tool_util.parser) (in module galaxy.tool_util.parser.factory) get_tool_source_from_representation() (in module galaxy.tool_util.parser) get_tool_source_path() (galaxy.tool_util.locations.dockstore.DockStoreResolver method) (galaxy.tool_util.locations.file.HttpToolResolver method) (galaxy.tool_util.locations.http.HttpToolResolver method) (galaxy.tool_util.locations.ToolLocationResolver method) get_tool_state() (galaxy.workflow.modules.WorkflowModule method) get_tool_tags() (galaxy.model.tags.TagHandler method) get_tool_tests() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) get_tool_to_dict() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) get_tool_version() (galaxy.model.Job method) (tool_shed.tools.tool_version_manager.ToolVersionManager method) get_tool_version_association() (tool_shed.tools.tool_version_manager.ToolVersionManager method) get_tool_versions() (tool_shed.webapp.controllers.repository.RepositoryController method) get_tool_watcher() (in module galaxy.tools.toolbox.watcher) get_tool_with_id() (galaxy.tools.toolbox.panel.ToolPanelElements method) get_toolbox() (galaxy.managers.context.ProvidesAppContext method) (galaxy.webapps.base.controller.BaseController method) get_toolbox_filters() (galaxy.webapps.galaxy.api.users.UserAPIController method) get_toolbox_parser() (in module galaxy.tools.toolbox.parser) get_tools() (galaxy.workflow.trs_proxy.TrsProxy method) get_tools_from_repository_metadata() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) get_tooltip() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_tooltip_text() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) get_total_job_count_per_destination() (galaxy.jobs.handler.JobHandlerQueue method) get_total_size() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) get_tours() (galaxy.tours.ToursRegistry method) get_tours_registry() (in module galaxy.webapps.galaxy.api.tours) get_track_resolution() (galaxy.datatypes.coverage.LastzCoverage method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.Wiggle method) get_trans() (in module galaxy.webapps.galaxy.api) get_trigger_name() (in module galaxy.model.triggers) get_type() (galaxy.datatypes.binary.BafTar method) (galaxy.datatypes.binary.MassHunterTar method) (galaxy.datatypes.binary.MassLynxTar method) (galaxy.datatypes.binary.TdfTar method) (galaxy.datatypes.binary.WiffTar method) (galaxy.datatypes.binary.YepTar method) (galaxy.workflow.modules.WorkflowModule method) get_type_class() (tool_shed.webapp.model.Repository method) get_typo_correction() (in module galaxy.jobs.dynamic_tool_destination) get_unique_slug() (galaxy.managers.sharable.SharableModelManager method) get_unnamed_outputs() (galaxy.tool_util.provided_metadata.BaseToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.LegacyToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.ToolProvidedMetadata method) get_update_to_changeset_revision_and_ctx_rev() (galaxy.tool_shed.galaxy_install.update_repository_manager.UpdateRepositoryManager method) get_updated_changeset_revisions() (in module tool_shed.util.metadata_util) get_updated_changeset_revisions_for_repository_dependencies() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) get_updated_changeset_revisions_from_tool_shed() (in module galaxy.tool_shed.util.metadata_util) get_updated_repository_information() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (tool_shed.webapp.controllers.repository.RepositoryController method) get_upload_metadata_params() (galaxy.datatypes.registry.Registry method) get_upload_point() (in module tool_shed.util.commit_util) get_uploaded_datasets() (galaxy.tools.parameters.grouping.UploadDataset method) (in module galaxy.tools.actions.upload_common) get_uri_root() (galaxy.files.sources.BaseFilesSource method) (galaxy.files.sources.FilesSource method) get_url_args() (galaxy.web.framework.helpers.grids.DisplayByUsernameAndSlugGridOperation method) (galaxy.web.framework.helpers.grids.GridColumnFilter method) (galaxy.web.framework.helpers.grids.GridOperation method) (galaxy.web.legacy_framework.grids.DisplayByUsernameAndSlugGridOperation method) (galaxy.web.legacy_framework.grids.GridColumnFilter method) (galaxy.web.legacy_framework.grids.GridOperation method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationListGrid method) get_user() (galaxy.model.Job method) (galaxy.model.UserAuthnzToken class method) (galaxy.webapps.base.controller.BaseController method) (galaxy.webapps.base.webapp.GalaxyWebTransaction method) (galaxy.work.context.WorkRequestContext method) (in module galaxy.tool_shed.util.shed_util_common) (in module galaxy.webapps.galaxy.api) (in module galaxy.webapps.galaxy.controllers.admin) (in module tool_shed.test.base.test_db_util) (in module tool_shed.util.admin_util) (in module tool_shed.util.shed_util_common) get_user_api_key() (in module galaxy_test.base.api_util) get_user_by_identity() (galaxy.managers.users.UserManager method) get_user_by_name() (in module tool_shed.test.base.test_db_util) get_user_by_username() (in module galaxy.util.tool_shed.common_util) get_user_id() (galaxy.model.Job method) (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) get_user_item_rating() (galaxy.model.item_attrs.UsesItemRatings method) get_user_job_count() (galaxy.jobs.handler.JobHandlerQueue method) get_user_job_count_per_destination() (galaxy.jobs.handler.JobHandlerQueue method) get_user_manager() (in module galaxy.webapps.galaxy.api) get_user_tags_used() (galaxy.webapps.base.controller.UsesTagsMixin method) get_username() (galaxy.model.UserAuthnzToken class method) get_users_by_email() (galaxy.model.UserAuthnzToken class method) get_valid_by_name() (galaxy.tools.parameters.sanitize.ToolParameterSanitizer class method) get_valid_roles() (galaxy.model.security.GalaxyRBACAgent method) get_value() (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationTemplateParameter method) (galaxy.tool_util.parser.output_actions.FromDataTableOutputActionOption method) (galaxy.tool_util.parser.output_actions.FromFileToolOutputActionOption method) (galaxy.tool_util.parser.output_actions.FromParamToolOutputActionOption method) (galaxy.tool_util.parser.output_actions.NullToolOutputActionOption method) (galaxy.tool_util.parser.output_actions.ToolOutputActionOption method) (galaxy.web.framework.helpers.grids.CommunityRatingColumn method) (galaxy.web.framework.helpers.grids.CommunityTagsColumn method) (galaxy.web.framework.helpers.grids.GridColumn method) (galaxy.web.framework.helpers.grids.IndividualTagsColumn method) (galaxy.web.framework.helpers.grids.OwnerAnnotationColumn method) (galaxy.web.framework.helpers.grids.OwnerColumn method) (galaxy.web.framework.helpers.grids.SharingStatusColumn method) (galaxy.web.framework.helpers.grids.StateColumn method) (galaxy.web.legacy_framework.grids.CommunityRatingColumn method) (galaxy.web.legacy_framework.grids.CommunityTagsColumn method) (galaxy.web.legacy_framework.grids.GridColumn method) (galaxy.web.legacy_framework.grids.IndividualTagsColumn method) (galaxy.web.legacy_framework.grids.OwnerAnnotationColumn method) (galaxy.web.legacy_framework.grids.OwnerColumn method) (galaxy.web.legacy_framework.grids.SharingStatusColumn method) (galaxy.web.legacy_framework.grids.StateColumn method) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid.NameColumn method) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid.RolesColumn method) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid.StatusColumn method) (galaxy.webapps.galaxy.controllers.admin.GroupListGrid.UsersColumn method) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.AmountColumn method) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.DescriptionColumn method) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.GroupsColumn method) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.NameColumn method) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.StatusColumn method) (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.UsersColumn method) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid.DescriptionColumn method) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid.GroupsColumn method) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid.NameColumn method) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid.StatusColumn method) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid.TypeColumn method) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid.UsersColumn method) (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid.ToolIdColumn method) (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid.ToolVersionsColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.ActivatedColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.DiskUsageColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.EmailColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.ExternalColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.GroupsColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.LastLoginColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.RolesColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.StatusColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.TimeCreatedColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.UserNameColumn method) (galaxy.webapps.galaxy.controllers.forms.FormsGrid.DescriptionColumn method) (galaxy.webapps.galaxy.controllers.forms.FormsGrid.NameColumn method) (galaxy.webapps.galaxy.controllers.forms.FormsGrid.StatusColumn method) (galaxy.webapps.galaxy.controllers.forms.FormsGrid.TypeColumn method) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid.DeletedColumn method) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid.ItemCountColumn method) (galaxy.webapps.galaxy.controllers.history.NameColumn method) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid.DatasetsByStateColumn method) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid.SharedByColumn method) (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid.NameColumn method) (galaxy.webapps.galaxy.controllers.page.PageListGrid.URLColumn method) (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid.HistoryColumn method) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid.StepsColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.CreateTimeColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.JobIdColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.StateColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.ToolColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.UserColumn method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.CreateTimeColumn method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.UserColumn method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.WorkflowNameColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.DescriptionColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.NameColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.OwnerColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.RevisionColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.StatusColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.ToolShedColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.ToolShedStatusColumn method) (tool_shed.grids.admin_grids.AdminRepositoryGrid.DeletedColumn method) (tool_shed.grids.admin_grids.GroupGrid.NameColumn method) (tool_shed.grids.admin_grids.GroupGrid.RolesColumn method) (tool_shed.grids.admin_grids.GroupGrid.StatusColumn method) (tool_shed.grids.admin_grids.GroupGrid.UsersColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.DatatypesColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.DeletedColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.DeprecatedColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.IdColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.MaliciousColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.NameColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.OwnerColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.RevisionColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.ToolsColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.WorkflowsColumn method) (tool_shed.grids.admin_grids.RoleGrid.DescriptionColumn method) (tool_shed.grids.admin_grids.RoleGrid.GroupsColumn method) (tool_shed.grids.admin_grids.RoleGrid.NameColumn method) (tool_shed.grids.admin_grids.RoleGrid.RepositoriesColumn method) (tool_shed.grids.admin_grids.RoleGrid.StatusColumn method) (tool_shed.grids.admin_grids.RoleGrid.TypeColumn method) (tool_shed.grids.admin_grids.RoleGrid.UsersColumn method) (tool_shed.grids.admin_grids.UserGrid.ExternalColumn method) (tool_shed.grids.admin_grids.UserGrid.GroupsColumn method) (tool_shed.grids.admin_grids.UserGrid.LastLoginColumn method) (tool_shed.grids.admin_grids.UserGrid.RolesColumn method) (tool_shed.grids.admin_grids.UserGrid.StatusColumn method) (tool_shed.grids.admin_grids.UserGrid.UserLoginColumn method) (tool_shed.grids.admin_grids.UserGrid.UserNameColumn method) (tool_shed.grids.repository_grids.CategoryGrid.DescriptionColumn method) (tool_shed.grids.repository_grids.CategoryGrid.NameColumn method) (tool_shed.grids.repository_grids.CategoryGrid.RepositoriesColumn method) (tool_shed.grids.repository_grids.DatatypesGrid.DatatypesColumn method) (tool_shed.grids.repository_grids.MatchedRepositoryGrid.DescriptionColumn method) (tool_shed.grids.repository_grids.MatchedRepositoryGrid.NameColumn method) (tool_shed.grids.repository_grids.MatchedRepositoryGrid.RevisionColumn method) (tool_shed.grids.repository_grids.MatchedRepositoryGrid.UserColumn method) (tool_shed.grids.repository_grids.RepositoriesWithInvalidToolsGrid.InvalidToolConfigColumn method) (tool_shed.grids.repository_grids.RepositoryDependenciesGrid.RequiredRepositoryColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.CategoryColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.DeprecatedColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.DescriptionColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.EmailAlertsColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.HeadsColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.LatestInstallableRevisionColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.MetadataRevisionColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.NameColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.TipRevisionColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.TypeColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.UserColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.ChangesetRevisionColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.DownloadableColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.HasRepositoryDependenciesColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.IncludesDatatypesColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.IncludesToolDependenciesColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.IncludesToolsColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.IncludesWorkflowsColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.MaliciousColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.RepositoryNameColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.RepositoryOwnerColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.RepositoryTypeColumn method) (tool_shed.grids.repository_grids.ToolDependenciesGrid.ToolDependencyColumn method) (tool_shed.grids.repository_grids.ToolsGrid.ToolsColumn method) (tool_shed.grids.repository_grids.ValidCategoryGrid.RepositoriesColumn method) (tool_shed.grids.repository_grids.ValidRepositoryGrid.CategoryColumn method) (tool_shed.grids.repository_grids.ValidRepositoryGrid.InstallableRevisionColumn method) (tool_shed.grids.repository_review_grids.ComponentGrid.DescriptionColumn method) (tool_shed.grids.repository_review_grids.ComponentGrid.NameColumn method) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid.ApprovedColumn method) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid.RatingColumn method) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid.ReviewersColumn method) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn method) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid.WithReviewsRevisionColumn method) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid.RatingColumn method) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid.RepositoryDescriptionColumn method) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid.RepositoryNameColumn method) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid.RevisionColumn method) get_version() (galaxy.webapps.galaxy.api.trs_consumer.TrsConsumeAPIController method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) (galaxy.workflow.trs_proxy.TrsProxy method) get_version_descriptor() (galaxy.workflow.trs_proxy.TrsProxy method) get_version_fields() (galaxy.tools.data.TabularToolDataTable method) get_version_ids() (galaxy.tools.toolbox.lineages.interface.ToolLineage method) (galaxy.tools.toolbox.lineages.ToolLineage method) get_version_lineage_for_tool() (tool_shed.tools.tool_version_manager.ToolVersionManager method) get_version_string_path() (galaxy.jobs.JobWrapper method) get_version_string_path_legacy() (galaxy.jobs.JobWrapper method) get_versions() (galaxy.tools.toolbox.lineages.interface.ToolLineage method) (galaxy.tools.toolbox.lineages.ToolLineage method) (galaxy.webapps.galaxy.api.trs_consumer.TrsConsumeAPIController method) (galaxy.workflow.trs_proxy.TrsProxy method) get_visualization() (galaxy.visualization.plugins.registry.VisualizationsRegistry method) (galaxy.webapps.base.controller.UsesVisualizationMixin method) get_visualization_config() (galaxy.webapps.base.controller.UsesVisualizationMixin method) get_visualization_dict() (galaxy.webapps.base.controller.UsesVisualizationMixin method) get_visualization_revision_dict() (galaxy.webapps.base.controller.UsesVisualizationMixin method) get_visualization_summary_dict() (galaxy.webapps.base.controller.UsesVisualizationMixin method) get_visualizations() (galaxy.datatypes.data.Data method) (galaxy.datatypes.data.Newick method) (galaxy.datatypes.data.Nexus method) (galaxy.datatypes.xml.Dzi method) (galaxy.datatypes.xml.Phyloxml method) (galaxy.model.DatasetInstance method) (galaxy.visualization.plugins.registry.VisualizationsRegistry method) get_visualizations_by_user() (galaxy.webapps.base.controller.UsesVisualizationMixin method) get_visualizations_shared_with_user() (galaxy.webapps.base.controller.UsesVisualizationMixin method) get_watcher() (in module galaxy.util.watcher) get_webapp_global_conf() (in module galaxy_test.driver.driver_util) get_work_dir_outputs() (galaxy.jobs.runners.BaseJobRunner method) get_workflow() (in module galaxy.webapps.reports.controllers.workflows) get_workflow_menu() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) get_workflow_parameter_list() (in module galaxy.workflow.resources) get_workflows_list() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) get_working_directory() (galaxy.model.Task method) get_writable() (galaxy.files.sources.BaseFilesSource method) (galaxy.files.sources.FilesSource method) get_xml_default() (galaxy.web_stack.handlers.ConfiguresHandlers static method) getattr_recursive() (in module galaxy.visualization.plugins.utils) getdefault() (in module galaxy.tool_util.cwl.cwltool_deps) getfullargspec() (in module galaxy.util.getargspec) getmember() (galaxy.util.compression_utils.CompressedFile method) getmembers() (galaxy.util.compression_utils.CompressedFile method) getmembers_tar() (galaxy.util.compression_utils.CompressedFile method) getmembers_zip() (galaxy.util.compression_utils.CompressedFile method) getMissval() (in module galaxy.datatypes.converters.lped_to_pbed_converter) getModuleCode() (galaxy.util.template.FixedModuleCodeCompiler method) getname() (galaxy.util.compression_utils.CompressedFile method) getname_tar() (galaxy.util.compression_utils.CompressedFile method) getname_zip() (galaxy.util.compression_utils.CompressedFile method) getSnpeffVersionFromFile() (galaxy.datatypes.text.SnpEffDb method) Gfa1 (class in galaxy.datatypes.text) Gfa2 (class in galaxy.datatypes.text) Gff (class in galaxy.datatypes.interval) Gff3 (class in galaxy.datatypes.interval) gff_attributes_to_str() (in module galaxy.datatypes.util.gff_util) GFFFeature (class in galaxy.datatypes.util.gff_util) GFFInterval (class in galaxy.datatypes.util.gff_util) GFFIntervalToBEDReaderWrapper (class in galaxy.datatypes.util.gff_util) GFFReaderWrapper (class in galaxy.datatypes.util.gff_util) GiDatasetCollectionPopulator (class in galaxy_test.base.populators) GiDatasetPopulator (class in galaxy_test.base.populators) gie_list() (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) GIE_SPAWN (galaxy.selenium.navigates_galaxy.WAIT_TYPES attribute) Gif (class in galaxy.datatypes.images) Gifti (class in galaxy.datatypes.images) GiPostGetMixin (class in galaxy_test.base.populators) git_default_repo_name (galaxy.tools.error_reports.plugins.base_git.BaseGitPlugin attribute) git_default_repo_only (galaxy.tools.error_reports.plugins.base_git.BaseGitPlugin attribute) git_default_repo_owner (galaxy.tools.error_reports.plugins.base_git.BaseGitPlugin attribute) git_execute() (in module galaxy.tool_util.deps.brew_exts) git_project_cache (galaxy.tools.error_reports.plugins.base_git.BaseGitPlugin attribute) git_username_id_cache (galaxy.tools.error_reports.plugins.base_git.BaseGitPlugin attribute) GitDataResolver (class in galaxy.tool_util.verify.test_data) GithubPlugin (class in galaxy.tools.error_reports.plugins.github) GitHubSearch (class in galaxy.tool_util.deps.mulled.mulled_search) gitlab_connect() (galaxy.tools.error_reports.plugins.gitlab.GitLabPlugin method) GitLabPlugin (class in galaxy.tools.error_reports.plugins.gitlab) GiWorkflowPopulator (class in galaxy_test.base.populators) glob() (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method) global_actions (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.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageListGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.ManageCategoryGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.EmailAlertsRepositoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) global_conf() (galaxy.main.GalaxyConfigBuilder method) GlobusSecureShell (class in galaxy.jobs.runners.util.cli.shell.rsh) Gmaj (class in galaxy.datatypes.images) GmxBinary (class in galaxy.datatypes.binary) GodockerJobRunner (class in galaxy.jobs.runners.godocker) GolangProxyLauncher (class in galaxy.web.proxy) Gpr (class in galaxy.datatypes.microarrays) grab_unhandled_items() (galaxy.jobs.handler.ItemGrabber method) grant() (galaxy.managers.rbac_secured.AccessDatasetRBACPermission method) (galaxy.managers.rbac_secured.ManageDatasetRBACPermission method) (galaxy.managers.rbac_secured.RBACPermission method) grant_role_to_user() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) grant_write_access() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) grd (class in galaxy.datatypes.molecules) grdtgz (class in galaxy.datatypes.molecules) Grid (class in galaxy.web.framework.helpers.grids) (class in galaxy.web.legacy_framework.grids) grid_fields() (galaxy.model.FormDefinition method) GridAction (class in galaxy.web.framework.helpers.grids) (class in galaxy.web.legacy_framework.grids) GridColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.web.legacy_framework.grids) GridColumnFilter (class in galaxy.web.framework.helpers.grids) (class in galaxy.web.legacy_framework.grids) GridOperation (class in galaxy.web.framework.helpers.grids) (class in galaxy.web.legacy_framework.grids) groom_dataset_content() (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.data.Data method) Group (class in galaxy.datatypes.mothur) (class in galaxy.model) (class in galaxy.tools.parameters.grouping) (class in tool_shed.webapp.controllers.groups) (class in tool_shed.webapp.model) group (galaxy.model.GroupQuotaAssociation attribute) (galaxy.model.GroupRoleAssociation attribute) (galaxy.model.UserGroupAssociation attribute) (tool_shed.webapp.model.GroupRoleAssociation attribute) (tool_shed.webapp.model.UserGroupAssociation attribute) group_assoc (galaxy.managers.roles.RoleManager attribute) group_by_day() (galaxy.webapps.reports.controllers.query.ReportQueryBuilder method) group_by_month() (galaxy.webapps.reports.controllers.query.ReportQueryBuilder method) group_id (galaxy.model.GroupQuotaAssociation attribute) (galaxy.model.GroupRoleAssociation attribute) (galaxy.model.UserGroupAssociation attribute) (tool_shed.webapp.model.GroupRoleAssociation attribute) (tool_shed.webapp.model.UserGroupAssociation attribute) group_ids (galaxy.managers.roles.RoleDefinitionModel attribute) group_list_grid (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) (tool_shed.util.admin_util.Admin attribute) (tool_shed.webapp.controllers.admin.AdminController attribute) group_name (galaxy.util.pastescript.serve.Command attribute) group_title() (galaxy.tools.parameters.grouping.UploadDataset method) GroupAbund (class in galaxy.datatypes.mothur) GroupAPIController (class in galaxy.webapps.galaxy.api.groups) GroupGrid (class in tool_shed.grids.admin_grids) GroupGrid.NameColumn (class in tool_shed.grids.admin_grids) GroupGrid.RolesColumn (class in tool_shed.grids.admin_grids) GroupGrid.StatusColumn (class in tool_shed.grids.admin_grids) GroupGrid.UsersColumn (class in tool_shed.grids.admin_grids) GroupListGrid (class in galaxy.webapps.galaxy.controllers.admin) GroupListGrid.NameColumn (class in galaxy.webapps.galaxy.controllers.admin) GroupListGrid.RolesColumn (class in galaxy.webapps.galaxy.controllers.admin) GroupListGrid.StatusColumn (class in galaxy.webapps.galaxy.controllers.admin) GroupListGrid.UsersColumn (class in galaxy.webapps.galaxy.controllers.admin) GroupManager (class in tool_shed.managers.groups) GroupQuotaAssociation (class in galaxy.model) GroupRoleAssociation (class in galaxy.model) (class in tool_shed.webapp.model) GroupRolesAPIController (class in galaxy.webapps.galaxy.api.group_roles) groups (galaxy.model.Quota attribute) (galaxy.model.Role attribute) (galaxy.model.User attribute) (tool_shed.webapp.model.Role attribute) groups() (tool_shed.util.admin_util.Admin method) groups_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) GroupsController (class in tool_shed.webapp.api.groups) GroupUsersAPIController (class in galaxy.webapps.galaxy.api.group_users) Gtf (class in galaxy.datatypes.interval) GtfTabixDataProvider (class in galaxy.visualization.data_providers.genome) guess_artifact_type() (in module galaxy.tool_util.cwl.util) guess_derived_permissions() (galaxy.model.security.GalaxyRBACAgent method) guess_derived_permissions_for_datasets() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) guess_ext() (in module galaxy.datatypes.sniff) guess_shed_config() (galaxy.model.tool_shed_install.ToolShedRepository method) guess_type() (galaxy.datatypes.tabular.BaseCSV method) guest_ports() (galaxy.jobs.JobWrapper property) GUID_TYPE (galaxy.tools.data_manager.manager.DataManager attribute) GzDynamicCompressedArchive (class in galaxy.datatypes.binary) GzipDataProvider (class in galaxy.datatypes.dataproviders.external) GzipFilter (class in galaxy.config.config_manage)

H

H5 (class in galaxy.datatypes.binary) Hamamatsu (class in galaxy.datatypes.images) handle (galaxy.model.PSAAssociation attribute) handle_action_shell_file_paths() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder.EnvFileBuilder method) handle_bz2() (in module tool_shed.util.commit_util) handle_charref() (galaxy.managers.pages.PageContentProcessor method) handle_circular_repository_dependency() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) handle_command() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method) handle_comment() (galaxy.managers.pages.PageContentProcessor method) handle_complex_command() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method) handle_complex_dependency_elem() (tool_shed.dependencies.attribute_handlers.RepositoryDependencyAttributeHandler method) handle_complex_repository_dependency_for_package() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Repository method) handle_composite_file() (in module galaxy.datatypes.sniff) handle_compressed_file() (in module galaxy.datatypes.sniff) handle_controller_exception() (galaxy.web.framework.base.WebApplication method) (galaxy.webapps.base.webapp.WebApplication method) handle_current_repository_dependency() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) handle_data() (galaxy.managers.pages.PageContentProcessor method) (galaxy.webapps.galaxy.controllers.workflow.SingleTagContentsParser method) handle_dataset_as_image() (galaxy.datatypes.images.Image method) handle_decl() (galaxy.managers.pages.PageContentProcessor method) handle_directory_changes() (in module tool_shed.util.commit_util) handle_elem() (tool_shed.dependencies.attribute_handlers.RepositoryDependencyAttributeHandler method) handle_email_alerts() (in module tool_shed.util.shed_util_common) handle_endtag() (galaxy.managers.pages.PageContentProcessor method) handle_entityref() (galaxy.managers.pages.PageContentProcessor method) handle_environment_variables() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetEnvironment method) handle_exception() (galaxy.web.framework.middleware.batch.BatchMiddleware method) (galaxy.web.framework.middleware.sentry.Sentry method) (in module galaxy.web.framework.middleware.error) handle_existing_tool_dependencies_that_changed_in_update() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) handle_found_index_file() (galaxy.tools.data.TabularToolDataTable method) handle_galaxy_config_kwds() (galaxy_test.driver.integration_util.IntegrationInstance class method) handle_galaxy_url() (in module galaxy.util.tool_shed.common_util) handle_gzip() (in module tool_shed.util.commit_util) handle_incoming() (galaxy.jobs.actions.post.ActionBox class method) handle_input() (galaxy.tools.Tool method) handle_key_rd_dicts_for_repository() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) handle_last_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method) handle_library_params() (in module galaxy.tools.actions.upload_common) handle_metadata_externally() (galaxy.jobs.runners.cli.ShellJobRunner method) handle_missing_data_table_entry() (galaxy.tool_shed.tools.data_table_manager.ShedToolDataTableManager method) handle_missing_index_file() (in module galaxy.tool_shed.util.tool_util) handle_next_repository_dependency() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) handle_operation() (galaxy.web.framework.helpers.grids.Grid method) (galaxy.web.legacy_framework.grids.Grid method) handle_outputs() (in module galaxy.tool_util.cwl) (in module galaxy.tool_util.cwl.runtime_actions) handle_pi() (galaxy.managers.pages.PageContentProcessor method) handle_population_failed() (galaxy.model.DatasetCollection method) handle_repository_contents() (galaxy.tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager method) handle_repository_dependencies_container_entry() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) handle_repository_elem() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) handle_request() (galaxy.web.framework.base.WebApplication method) (tool_shed.webapp.controllers.hg.HgController method) handle_requests() (galaxy.web.proxy.JsonFileProxyIpc method) (galaxy.web.proxy.ProxyIpc method) (galaxy.web.proxy.RestGolangProxyIpc method) (galaxy.web.proxy.SqliteProxyIpc method) handle_role_associations() (in module tool_shed.util.repository_util) handle_sample_files_and_load_tool_from_disk() (tool_shed.tools.tool_validator.ToolValidator method) handle_sample_files_and_load_tool_from_tmp_config() (tool_shed.tools.tool_validator.ToolValidator method) handle_sample_tool_data_table_conf_file() (galaxy.tool_shed.tools.data_table_manager.ShedToolDataTableManager method) handle_signal() (in module galaxy.main) handle_single_execution() (galaxy.tools.Tool method) handle_slow_request() (galaxy.web.framework.middleware.sentry.Sentry method) handle_starttag() (galaxy.managers.pages.PageContentProcessor method) (galaxy.webapps.galaxy.controllers.workflow.SingleTagContentsParser method) handle_step() (galaxy.selenium.navigates_galaxy.NullTourCallback method) (galaxy.selenium.scripts.dump_tour.DumpTourCallback method) handle_stop() (galaxy.jobs.runners.AsynchronousJobRunner method) handle_sub_elem() (tool_shed.dependencies.attribute_handlers.RepositoryDependencyAttributeHandler method) handle_tag_attributes() (tool_shed.dependencies.attribute_handlers.RepositoryDependencyAttributeHandler method) (tool_shed.dependencies.attribute_handlers.ToolDependencyAttributeHandler method) handle_tags() (galaxy.tools.toolbox.tags.AbstractToolTagManager method) (galaxy.tools.toolbox.tags.NullToolTagManager method) (galaxy.tools.toolbox.tags.PersistentToolTagManager method) handle_tool_panel_section() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) handle_tool_panel_selection() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) handle_tool_shed_repositories() (galaxy.tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) handle_tool_shed_url_protocol() (in module galaxy.util.tool_shed.common_util) handle_upload() (in module galaxy.datatypes.upload_util) handle_uploaded_dataset_file() (in module galaxy.datatypes.sniff) handle_uploaded_dataset_file_internal() (in module galaxy.datatypes.sniff) handle_user_login() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) handle_user_logout() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) handle_uwsgi_cli_command() (galaxy_test.driver.integration_util.IntegrationInstance class method) handler (galaxy.model.Job attribute) (galaxy.model.WorkflowInvocation attribute) HANDLER_ASSIGNMENT_METHODS (class in galaxy.web_stack.handlers) handler_count() (galaxy.web_stack.message.ApplicationStackMessageDispatcher property) handler_tags() (galaxy.web_stack.handlers.ConfiguresHandlers property) HandlerAssignmentError HandlerAssignmentSkip hapmapmart() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) has_access_permission() (galaxy.managers.datasets.DatasetManager method) has_accessible_folders() (galaxy.model.security.GalaxyRBACAgent method) has_accessible_library_datasets() (galaxy.model.security.GalaxyRBACAgent method) has_base_pool() (galaxy.web_stack.ApplicationStack method) has_been_resubmitted() (galaxy.managers.hdas.HDAManager method) has_class() (galaxy.selenium.smart_components.SmartTarget method) has_collections() (galaxy.model.dataset_collections.matching.CollectionsToMatch method) has_cycles (galaxy.model.Workflow attribute) has_data() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) (galaxy.visualization.data_providers.basic.BaseDataProvider method) (galaxy.visualization.data_providers.genome.BBIDataProvider method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) has_dataprovider() (galaxy.datatypes.data.Data method) has_dataproviders() (in module galaxy.datatypes.dataproviders.decorators) has_doi() (galaxy.managers.citations.BaseCitation method) (galaxy.managers.citations.DoiCitation method) has_env() (galaxy.tool_util.deps.conda_util.CondaContext method) has_errors (galaxy.model.Workflow attribute) has_errors() (galaxy.util.rules_dsl.RuleSet property) has_ext() (in module galaxy.util.path) has_failed_outputs() (galaxy.tool_util.provided_metadata.BaseToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.LegacyToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.ToolProvidedMetadata method) has_input_for_step() (galaxy.model.WorkflowInvocation method) has_limits() (galaxy.jobs.JobWrapper method) has_manage_permissions_roles() (galaxy.model.Dataset method) (galaxy.model.LibraryDatasetDatasetAssociation method) has_outputs_defined() (galaxy.model.Workflow method) has_pool() (galaxy.web_stack.ApplicationStack method) has_possible_members() (galaxy.model.History property) has_post_authentication_actions() (galaxy.openid.providers.OpenIDProvider method) has_previous_repository_reviews() (in module tool_shed.util.review_util) has_readme_files() (galaxy.model.tool_shed_install.ToolShedRepository property) has_reference_data() (galaxy.visualization.genomes.Genomes method) has_reloaded() (galaxy.tools.ToolBox method) has_repository_dependencies (tool_shed.webapp.model.RepositoryMetadata attribute) has_repository_dependencies() (galaxy.model.tool_shed_install.ToolShedRepository property) has_repository_dependencies_only_if_compiling_contained_td() (galaxy.model.tool_shed_install.ToolShedRepository property) has_resolution() (galaxy.datatypes.data.Data property) has_subcollections() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) (galaxy.model.DatasetCollection property) has_subcollections_of_type() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) has_tool() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) has_tool_with_id() (galaxy.tools.toolbox.panel.ToolPanelElements method) has_value() (galaxy.web_stack.handlers.HANDLER_ASSIGNMENT_METHODS class method) HasAModelManager (class in galaxy.managers.base) hasattr_recursive() (in module galaxy.visualization.plugins.utils) HasDatasets (class in galaxy.tools.wrappers) HasDockerLikeVolumes (class in galaxy.tool_util.deps.container_classes) HasDriver (class in galaxy.selenium.has_driver) HasDriver.TimeoutException hash() (galaxy.containers.docker_model.DockerAttributeContainer method) (galaxy.tools.cache.ToolHash property) hash_dependencies() (galaxy.tool_util.deps.CachedDependencyManager method) hash_function (galaxy.model.DatasetHash attribute) (galaxy.model.DatasetSourceHash attribute) hash_password() (in module galaxy.security.passwords) hash_password_PBKDF2() (in module galaxy.security.passwords) hash_value (galaxy.model.DatasetHash attribute) (galaxy.model.DatasetSourceHash attribute) hashed_test_search() (in module galaxy.tool_util.deps.mulled.get_tests) hashes (galaxy.model.Dataset attribute) (galaxy.model.DatasetSource attribute) hashes() (galaxy.model.store.discover.JsonCollectedDatasetMatch property) HasName (class in galaxy.model) HasPanelItems (class in galaxy.tools.toolbox.panel) HasResourceParameters (class in galaxy.jobs) HasSettings (class in galaxy.datatypes.dataproviders.base) HasTags (class in galaxy.model) have_shed_tool_conf_for_install() (in module galaxy.tool_shed.util.shed_util_common) (in module tool_shed.util.shed_util_common) hda (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.HistoryDatasetAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociationRatingAssociation attribute) (galaxy.model.HistoryDatasetAssociationSubset attribute) hda_click_primary_action_button() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) hda_id (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) (galaxy.model.MetadataFile attribute) hda_manager (galaxy.webapps.galaxy.api.jobs.FastAPIJobs attribute) hda_parent_id (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) HDADeserializer (class in galaxy.managers.hdas) HDAFilterParser (class in galaxy.managers.hdas) HDAManager (class in galaxy.managers.hdas) HDAProvenanceController (class in galaxy.webapps.galaxy.api.provenance) hdas (galaxy.model.HistoryDatasetAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociationRatingAssociation attribute) HDASerializer (class in galaxy.managers.hdas) hdca_id (galaxy.model.view.HistoryDatasetCollectionJobStateSummary attribute) HDCAManager (class in galaxy.managers.hdcas) HDCASerializer (class in galaxy.managers.hdcas) HDT (class in galaxy.datatypes.triples) header (galaxy.datatypes.speech.TextGrid attribute) header_check() (galaxy.datatypes.genetics.AllegroLOD method) (galaxy.datatypes.genetics.GenotypeMatrix method) (galaxy.datatypes.genetics.MarkerMap method) header_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.tabular.Sam method) header_regexp (galaxy.datatypes.tabular.ConnectivityTable attribute) headless_selenium() (in module galaxy_test.selenium.framework) Heartbeat (class in galaxy.util.heartbeat) help() (galaxy.tools.Tool property) (tool_shed.webapp.controllers.repository.RepositoryController method) help_by_page() (galaxy.tools.Tool property) hg_repo() (tool_shed.webapp.model.Repository property) HgController (class in tool_shed.webapp.controllers.hg) hgweb_config() (tool_shed.util.hgweb_config.HgWebConfigManager property) HgWebConfigManager (class in tool_shed.util.hgweb_config) hid (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy_test.selenium.test_history_dataset_state.HistoryDatasetStateTestCase attribute) hid_counter (galaxy.model.History attribute) hid_to_history_item() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) hidden (galaxy.model.DynamicTool attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.util.pastescript.serve.Command attribute) hidden_beneath_collection_instance (galaxy.model.HistoryDatasetAssociation attribute) hidden_beneath_collection_instance_id (galaxy.model.HistoryDatasetAssociation attribute) hidden_dataset_instances (galaxy.model.HistoryDatasetCollectionAssociation attribute) HiddenDataToolParameter (class in galaxy.tools.parameters.basic) HiddenToolParameter (class in galaxy.tools.parameters.basic) HideDatasetAction (class in galaxy.jobs.actions.post)

HierarchalDataProvider (class in galaxy.datatypes.dataproviders.hierarchy) HierarchicalObjectStore (class in galaxy.objectstore) histories (galaxy.model.GalaxySession attribute) (galaxy.model.HistoryAnnotationAssociation attribute) (galaxy.model.HistoryRatingAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.User attribute) histories_click_advanced_search() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) histories_get_history_names() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) histories_shared_by_others (galaxy.model.User attribute) HistoriesApiTestCase (class in galaxy_test.api.test_histories) HistoriesController (class in galaxy.webapps.galaxy.api.histories) History (class in galaxy.model) (class in galaxy.webapps.reports.controllers.history) history (galaxy.model.DataManagerHistoryAssociation attribute) (galaxy.model.DefaultHistoryPermissions attribute) (galaxy.model.Event attribute) (galaxy.model.GalaxySessionToHistoryAssociation attribute) (galaxy.model.HistoryAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.HistoryRatingAssociation attribute) (galaxy.model.HistoryUserShareAssociation attribute) (galaxy.model.Job attribute) (galaxy.model.JobExportHistoryArchive attribute) (galaxy.model.JobImportHistoryArchive attribute) (galaxy.model.WorkflowInvocation attribute) history() (galaxy.webapps.base.webapp.GalaxyWebTransaction property) (galaxy.work.context.WorkRequestContext property) history_add_to() (galaxy.webapps.galaxy.controllers.root.RootController method) history_and_dataset_per_user() (galaxy.webapps.reports.controllers.history.History method) history_and_dataset_type() (galaxy.webapps.reports.controllers.history.History method) history_associations (galaxy.model.Dataset attribute) history_attrs_filename (galaxy.model.JobExportHistoryArchive attribute) history_click_create_new() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_content_id() (galaxy.tool_util.cwl.util.GalaxyOutput property) history_content_type (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) history_content_type() (galaxy.model.HistoryDatasetAssociation property) (galaxy.model.HistoryDatasetCollectionAssociation property) (galaxy.tool_util.cwl.util.GalaxyOutput property) history_contents() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_data() (galaxy.webapps.galaxy.controllers.history.HistoryController method) history_dataset (galaxy.model.MetadataFile attribute) history_dataset_association (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization attribute) (galaxy.model.JobExternalOutputMetadata attribute) history_dataset_association_id (galaxy.model.HistoryDatasetAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization attribute) (galaxy.model.HistoryDatasetAssociationHistory attribute) (galaxy.model.HistoryDatasetAssociationRatingAssociation attribute) (galaxy.model.HistoryDatasetAssociationSubset attribute) (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.JobExternalOutputMetadata attribute) history_dataset_association_subset_id (galaxy.model.HistoryDatasetAssociationSubset attribute) history_dataset_collection (galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetCollectionRatingAssociation attribute) history_dataset_collection_associations (galaxy.model.ImplicitCollectionJobs attribute) (galaxy.model.Job attribute) history_dataset_collection_id (galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetCollectionRatingAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) history_dataset_collections() (galaxy.managers.collections.DatasetCollectionManager method) history_dataset_extended_metadata_filter() (in module galaxy.model.search) history_dataset_handle_tag() (in module galaxy.model.search) history_delete() (galaxy.webapps.galaxy.controllers.root.RootController method) history_get_default_permissions() (galaxy.model.security.GalaxyRBACAgent method) history_handle_annotation() (in module galaxy.model.search) history_handle_tag() (in module galaxy.model.search) history_id (galaxy.model.DataManagerHistoryAssociation attribute) (galaxy.model.DefaultHistoryPermissions attribute) (galaxy.model.Event attribute) (galaxy.model.GalaxySessionToHistoryAssociation attribute) (galaxy.model.HistoryAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.HistoryRatingAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.HistoryUserShareAssociation attribute) (galaxy.model.Job attribute) (galaxy.model.JobExportHistoryArchive attribute) (galaxy.model.JobImportHistoryArchive attribute) (galaxy.model.WorkflowInvocation attribute) history_id() (galaxy.tool_util.cwl.util.GalaxyOutput property) (galaxy_test.api.test_workflow_extraction.RunJobsSummary property) (galaxy_test.base.populators.RunJobsSummary property) history_import() (galaxy.webapps.galaxy.controllers.root.RootController method) history_invocations() (galaxy_test.base.populators.BaseWorkflowPopulator method) history_item_wait_for() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_jobs() (galaxy_test.base.populators.BaseDatasetPopulator method) history_length() (galaxy_test.base.populators.BaseDatasetPopulator method) history_manager() (galaxy.tools.Tool property) history_multi_view_display_collection_contents() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_new() (galaxy.webapps.galaxy.controllers.root.RootController method) history_panel_add_tags() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_click_copy_elements() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_click_item_title() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_click_to_rename() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_create_new() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_create_new_with_name() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_ensure_showing_item_details() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_item_available_visualizations() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_item_available_visualizations_elements() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_item_body_component() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_item_click_visualization() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_item_click_visualization_menu() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_item_component() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_item_get_nametags() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_item_selector() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_item_showing_details() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_muli_operation_select_hid() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_multi_operation_action_click() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_multi_operations_show() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_name() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_name_element() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_refresh_click() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_rename() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_wait_for_hid_hidden() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_wait_for_hid_ok() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_wait_for_hid_state() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_wait_for_hid_visible() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_panel_wait_for_history_loaded() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_per_user() (galaxy.webapps.reports.controllers.users.Users method) history_set_default_permissions() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) history_tag_associations (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) HistoryAllPublishedGrid (class in galaxy.webapps.galaxy.controllers.history) HistoryAllPublishedGrid.NameURLColumn (class in galaxy.webapps.galaxy.controllers.history) HistoryAnnotationAssociation (class in galaxy.model) HistoryAnnotationsController (class in galaxy.webapps.galaxy.api.annotations) HistoryContentAnnotationsController (class in galaxy.webapps.galaxy.api.annotations) HistoryContentsApiTestCase (class in galaxy_test.api.test_history_contents) HistoryContentsController (class in galaxy.webapps.galaxy.api.history_contents) HistoryContentsFilters (class in galaxy.managers.history_contents) HistoryContentsManager (class in galaxy.managers.history_contents) HistoryContentsSerializer (class in galaxy.managers.history_contents) HistoryContentTagsController (class in galaxy.webapps.galaxy.api.item_tags) HistoryController (class in galaxy.webapps.galaxy.controllers.history) HistoryCopyElementsTestCase (class in galaxy_test.selenium.test_history_copy_elements) HistoryDatasetAssociation (class in galaxy.model) HistoryDatasetAssociationAnnotationAssociation (class in galaxy.model) HistoryDatasetAssociationDisplayAtAuthorization (class in galaxy.model) HistoryDatasetAssociationHistory (class in galaxy.model) HistoryDatasetAssociationNoHistoryException HistoryDatasetAssociationRatingAssociation (class in galaxy.model) HistoryDatasetAssociationSelectionGrid (class in galaxy.webapps.galaxy.controllers.page) HistoryDatasetAssociationSubset (class in galaxy.model) HistoryDatasetAssociationTagAssociation (class in galaxy.model) HistoryDatasetCollectionAssociation (class in galaxy.model) HistoryDatasetCollectionAssociationAnnotationAssociation (class in galaxy.model) HistoryDatasetCollectionJobStateSummary (class in galaxy.model.view) HistoryDatasetCollectionRatingAssociation (class in galaxy.model) HistoryDatasetCollectionTagAssociation (class in galaxy.model) HistoryDatasetExtendMetadataController (class in galaxy.webapps.galaxy.api.extended_metadata) HistoryDatasetsSelectionGrid (class in galaxy.webapps.galaxy.controllers.visualization) HistoryDatasetsSelectionGrid.DbKeyColumn (class in galaxy.webapps.galaxy.controllers.visualization) HistoryDatasetsSelectionGrid.HistoryColumn (class in galaxy.webapps.galaxy.controllers.visualization) HistoryDatasetStateTestCase (class in galaxy_test.selenium.test_history_dataset_state) HistoryDatasetView (class in galaxy.model.search) HistoryDeserializer (class in galaxy.managers.histories) HistoryExportView (class in galaxy.managers.histories) HistoryField (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) HistoryFilters (class in galaxy.managers.histories) HistoryGridTestCase (class in galaxy_test.selenium.test_published_histories_grid) HistoryListGrid (class in galaxy.webapps.galaxy.controllers.history) HistoryListGrid.DeletedColumn (class in galaxy.webapps.galaxy.controllers.history) HistoryListGrid.HistoryListNameColumn (class in galaxy.webapps.galaxy.controllers.history) HistoryListGrid.ItemCountColumn (class in galaxy.webapps.galaxy.controllers.history) HistoryManager (class in galaxy.managers.histories) HistoryMultiViewTestCase (class in galaxy_test.selenium.test_history_multi_view) HistoryOptionsTestCase (class in galaxy_test.selenium.test_history_options) HistoryPanelCollectionsTestCase (class in galaxy_test.selenium.test_history_panel_collections) HistoryPanelPaginationTestCase (class in galaxy_test.selenium.test_history_panel_pagination) HistoryPanelTestCase (class in galaxy_test.selenium.test_history_panel) HistoryQuery (class in galaxy.tools.parameters.history_query) HistoryRatingAssociation (class in galaxy.model) HistorySelectionGrid (class in galaxy.webapps.galaxy.controllers.page) HistorySerializer (class in galaxy.managers.histories) HistorySharingTestCase (class in galaxy_test.selenium.test_history_sharing) HistoryStructureTestCase (class in galaxy_test.selenium.test_history_structure) HistoryTagAssociation (class in galaxy.model) HistoryTagsController (class in galaxy.webapps.galaxy.api.item_tags) HistoryUserShareAssociation (class in galaxy.model) HistoryView (class in galaxy.model.search) hmac_new() (in module galaxy.util.hash_util) Hmmer (class in galaxy.datatypes.msa) Hmmer2 (class in galaxy.datatypes.msa) Hmmer3 (class in galaxy.datatypes.msa) HmmerPress (class in galaxy.datatypes.msa) home() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) home_directory() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.JobWrapper method) (galaxy.jobs.SharedComputeEnvironment method) home_target() (galaxy.jobs.JobWrapper property) HomebrewDependency (class in galaxy.tool_util.deps.resolvers.resolver_mixins) HomebrewDependencyResolver (class in galaxy.tool_util.deps.resolvers.homebrew) HomebrewRecipe (class in galaxy.tool_util.deps.brew_util) HomebrewToolShedDependencyResolver (class in galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages) HomePage (class in galaxy.webapps.reports.controllers.home) homepage_url (tool_shed.webapp.model.Repository attribute) host (galaxy.model.InteractiveToolEntryPoint attribute) host() (galaxy.containers.docker.DockerInterface property) (galaxy.web.proxy.ProxyMapping property) host_config_option_map (galaxy.containers.docker.DockerAPIInterface attribute) host_iter() (galaxy.containers.docker.DockerInterface property) hostaddr() (galaxy.containers.ContainerPort property) HostAgent (class in galaxy.model.security) hostname (galaxy.model.WorkerProcess attribute) HostnamePlugin (class in galaxy.job_metrics.instrumenters.hostname) hostport() (galaxy.containers.ContainerPort property) Html (class in galaxy.datatypes.images) (class in galaxy.datatypes.text) html() (galaxy.authnz.psa_authnz.Strategy method) html_table (galaxy.datatypes.genetics.RexpBase attribute) HttpsToolResolver (class in galaxy.tool_util.locations.http) HttpToolResolver (class in galaxy.tool_util.locations.file) (class in galaxy.tool_util.locations.http)

I

ICM (class in galaxy.datatypes.binary) id (galaxy.managers.roles.RoleModel attribute) (galaxy.model.APIKeys attribute) (galaxy.model.CloudAuthz attribute) (galaxy.model.CustosAuthnzToken attribute) (galaxy.model.DataManagerHistoryAssociation attribute) (galaxy.model.DataManagerJobAssociation attribute) (galaxy.model.Dataset attribute) (galaxy.model.DatasetCollection attribute) (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.DatasetHash attribute) (galaxy.model.DatasetPermissions attribute) (galaxy.model.DatasetSource attribute) (galaxy.model.DatasetSourceHash attribute) (galaxy.model.DefaultHistoryPermissions attribute) (galaxy.model.DefaultQuotaAssociation attribute) (galaxy.model.DefaultUserPermissions attribute) (galaxy.model.DeferredJob attribute) (galaxy.model.DynamicTool attribute) (galaxy.model.Event attribute) (galaxy.model.ExtendedMetadata attribute) (galaxy.model.ExtendedMetadataIndex attribute) (galaxy.model.FormDefinition attribute) (galaxy.model.FormDefinitionCurrent attribute) (galaxy.model.FormValues attribute) (galaxy.model.GalaxySession attribute) (galaxy.model.GalaxySessionToHistoryAssociation attribute) (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.Group attribute) (galaxy.model.GroupQuotaAssociation attribute) (galaxy.model.GroupRoleAssociation attribute) (galaxy.model.History attribute) (galaxy.model.HistoryAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization attribute) (galaxy.model.HistoryDatasetAssociationHistory attribute) (galaxy.model.HistoryDatasetAssociationRatingAssociation attribute) (galaxy.model.HistoryDatasetAssociationSubset attribute) (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetCollectionRatingAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryRatingAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.HistoryUserShareAssociation attribute) (galaxy.model.ImplicitCollectionJobs attribute) (galaxy.model.ImplicitCollectionJobsJobAssociation attribute) (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) (galaxy.model.ImplicitlyCreatedDatasetCollectionInput attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.Job attribute) (galaxy.model.JobContainerAssociation attribute) (galaxy.model.JobExportHistoryArchive attribute) (galaxy.model.JobExternalOutputMetadata attribute) (galaxy.model.JobImportHistoryArchive attribute) (galaxy.model.JobMetricNumeric attribute) (galaxy.model.JobMetricText attribute) (galaxy.model.JobParameter attribute) (galaxy.model.JobStateHistory attribute) (galaxy.model.JobToImplicitOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetAssociation attribute) (galaxy.model.JobToInputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetCollectionElementAssociation attribute) (galaxy.model.JobToInputLibraryDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToOutputLibraryDatasetAssociation attribute) (galaxy.model.Library attribute) (galaxy.model.LibraryDataset attribute) (galaxy.model.LibraryDatasetCollectionAnnotationAssociation attribute) (galaxy.model.LibraryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetCollectionRatingAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationPermissions attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) (galaxy.model.LibraryDatasetPermissions attribute) (galaxy.model.LibraryFolder attribute) (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryFolderPermissions attribute) (galaxy.model.LibraryInfoAssociation attribute) (galaxy.model.LibraryPermissions attribute) (galaxy.model.MetadataFile attribute) (galaxy.model.Page attribute) (galaxy.model.PageAnnotationAssociation attribute) (galaxy.model.PageRatingAssociation attribute) (galaxy.model.PageRevision attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.PageUserShareAssociation attribute) (galaxy.model.PostJobAction attribute) (galaxy.model.PostJobActionAssociation attribute) (galaxy.model.PSAAssociation attribute) (galaxy.model.PSACode attribute) (galaxy.model.PSANonce attribute) (galaxy.model.PSAPartial attribute) (galaxy.model.Quota attribute) (galaxy.model.Role attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.StoredWorkflowAnnotationAssociation attribute) (galaxy.model.StoredWorkflowMenuEntry attribute) (galaxy.model.StoredWorkflowRatingAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.StoredWorkflowUserShareAssociation attribute) (galaxy.model.Tag attribute) (galaxy.model.Task attribute) (galaxy.model.TaskMetricNumeric attribute) (galaxy.model.TaskMetricText attribute) (galaxy.model.tool_shed_install.RepositoryDependency attribute) (galaxy.model.tool_shed_install.RepositoryRepositoryDependencyAssociation attribute) (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.model.tool_shed_install.ToolVersion attribute) (galaxy.model.tool_shed_install.ToolVersionAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.TransferJob attribute) (galaxy.model.User attribute) (galaxy.model.UserAction attribute) (galaxy.model.UserAddress attribute) (galaxy.model.UserAuthnzToken attribute) (galaxy.model.UserGroupAssociation attribute) (galaxy.model.UserPreference attribute) (galaxy.model.UserQuotaAssociation attribute) (galaxy.model.UserRoleAssociation attribute) (galaxy.model.Visualization attribute) (galaxy.model.VisualizationAnnotationAssociation attribute) (galaxy.model.VisualizationRatingAssociation attribute) (galaxy.model.VisualizationRevision attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.VisualizationUserShareAssociation attribute) (galaxy.model.WorkerProcess attribute) (galaxy.model.Workflow attribute) (galaxy.model.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.WorkflowOutput attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.model.WorkflowRequestInputStepParameter attribute) (galaxy.model.WorkflowRequestStepState attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowStep attribute) (galaxy.model.WorkflowStepAnnotationAssociation attribute) (galaxy.model.WorkflowStepConnection attribute) (galaxy.model.WorkflowStepInput attribute) (galaxy.model.WorkflowStepTagAssociation attribute) (galaxy.tours.Tour attribute) (tool_shed.webapp.model.APIKeys attribute) (tool_shed.webapp.model.Category attribute) (tool_shed.webapp.model.Component 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.RepositoryCategoryAssociation 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.Tag attribute) (tool_shed.webapp.model.User attribute) (tool_shed.webapp.model.UserGroupAssociation attribute) (tool_shed.webapp.model.UserRoleAssociation attribute) id() (galaxy.containers.Container property) (galaxy.containers.docker_model.DockerNode property) (galaxy.containers.docker_model.DockerTask property) (galaxy.tools.data_manager.manager.DataManager property) (galaxy.util.jstree.Path property) id_based() (galaxy.tools.toolbox.lineages.interface.ToolLineageVersion property) id_seq_qual_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.tabular.Sam method) id_token (galaxy.model.CustosAuthnzToken attribute) Idat (class in galaxy.datatypes.binary) IdeasPre (class in galaxy.datatypes.genetics) IdEncodingHelper (class in galaxy.security.idencoding) identifier() (galaxy.tools.wrappers.ElementIdentifierMapper method) identifier_columns() (galaxy.util.rules_dsl.RuleSet property) IdentityProvider (class in galaxy.authnz) IdpDB (class in galaxy.datatypes.binary) IdXML (class in galaxy.datatypes.proteomics) iff() (in module galaxy.web.framework.helpers) Im (class in galaxy.datatypes.images) Image (class in galaxy.datatypes.images) image() (galaxy.containers.docker_model.DockerService property) image_inspect() (galaxy.containers.docker.DockerAPIInterface method) (galaxy.containers.docker.DockerCLIInterface method) image_name() (in module galaxy.tool_util.deps.mulled.util) image_repodigest() (galaxy.containers.docker.DockerInterface method) image_type() (in module galaxy.util.image_util) ImgtJson (class in galaxy.datatypes.text) immediate_actions (galaxy.jobs.actions.post.ActionBox attribute) imp() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) impersonate() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) impersonate_operation (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) impl (galaxy.model.custom_types.JSONType attribute) (galaxy.model.custom_types.TrimmedString attribute) (galaxy.model.custom_types.UUIDType attribute) implicit_collection_jobs (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.ImplicitCollectionJobsJobAssociation attribute) (galaxy.model.WorkflowInvocationStep attribute) implicit_collection_jobs_association (galaxy.model.Job attribute) implicit_collection_jobs_id (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.ImplicitCollectionJobsJobAssociation attribute) (galaxy.model.WorkflowInvocationStep attribute) implicit_collection_jobs_properties() (galaxy.model.store.BaseDirectoryImportModelStore method) implicit_input_collections (galaxy.model.HistoryDatasetCollectionAssociation attribute) implicit_output_name (galaxy.model.HistoryDatasetCollectionAssociation attribute) ImplicitCollectionJobs (class in galaxy.model) ImplicitCollectionJobs.populated_states (class in galaxy.model) ImplicitCollectionJobsJobAssociation (class in galaxy.model) ImplicitConversionRequired implicitly_converted_datasets (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) implicitly_converted_parent_datasets (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) ImplicitlyConvertedDatasetAssociation (class in galaxy.model) ImplicitlyCreatedDatasetCollectionInput (class in galaxy.model) import_history() (galaxy_test.base.populators.BaseDatasetPopulator method) import_history_and_wait_for_name() (galaxy_test.base.populators.BaseDatasetPopulator method) import_new_workflow_deprecated() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) import_shared_workflow_deprecated() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) import_submodules() (in module galaxy.util.submodules) import_tool() (galaxy_test.base.populators.WorkflowPopulator method) import_tools (galaxy.managers.workflows.WorkflowCreateOptions attribute) import_visualization() (galaxy.webapps.base.controller.UsesVisualizationMixin method) import_workflow() (galaxy.managers.workflows.Format2ConverterGalaxyInterface method) (galaxy_test.api.test_workflows.BaseWorkflowsApiTestCase method) (galaxy_test.base.populators.WorkflowPopulator method) (galaxy_test.selenium.framework.SeleniumSessionWorkflowPopulator method) import_workflow_from_path() (galaxy_test.base.populators.BaseWorkflowPopulator method) importable (galaxy.managers.workflows.WorkflowCreateOptions attribute) (galaxy.model.History attribute) (galaxy.model.Page attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.Visualization attribute) imported (galaxy.model.Job attribute) imported_macro_paths() (in module galaxy.tool_util.loader) (in module galaxy.util.xml_macros) imported_store_for_metadata() (in module galaxy.model.store) importer() (in module galaxy.jobs.dynamic_tool_destination) ImportExportHistoryTestCase (class in galaxy_test.api.test_histories) ImportHistoryTool (class in galaxy.tools) ImportHistoryToolAction (class in galaxy.tools.actions.history_imp_exp) importing (galaxy.model.History attribute) ImportOptions (class in galaxy.model.store) ImportsHistoryMixin (class in galaxy.webapps.base.controller) ImzML (class in galaxy.datatypes.proteomics) in_all_repository_dependencies() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) in_circular_repository_dependencies() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) in_directory() (in module galaxy.util) in_error_state() (galaxy.model.tool_shed_install.ToolDependency property) (galaxy.model.tool_shed_install.ToolShedRepository property) in_key_rd_dicts() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) in_pool() (galaxy.web_stack.ApplicationStack method) (galaxy.web_stack.UWSGIApplicationStack method) (galaxy.web_stack.WeblessApplicationStack method) in_ready_state() (galaxy.model.Dataset method) in_state() (galaxy.containers.docker_model.DockerNode method) (galaxy.containers.docker_model.DockerService method) (galaxy.containers.docker_model.DockerTask method) in_tool_dict() (in module tool_shed.util.search_util) in_workflow_dict() (in module tool_shed.util.search_util) InappropriateDatasetContentError InChI (class in galaxy.datatypes.molecules) include() (galaxy.util.yaml_util.OrderedLoader method) includes_data_managers() (galaxy.model.tool_shed_install.ToolShedRepository property) includes_datatypes (galaxy.model.tool_shed_install.ToolShedRepository attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) includes_tool_dependencies (tool_shed.webapp.model.RepositoryMetadata attribute) includes_tool_dependencies() (galaxy.model.tool_shed_install.ToolShedRepository property) includes_tools (tool_shed.webapp.model.RepositoryMetadata attribute) includes_tools() (galaxy.model.tool_shed_install.ToolShedRepository property) includes_tools_for_display_in_tool_panel() (galaxy.model.tool_shed_install.ToolShedRepository property) (tool_shed.webapp.model.RepositoryMetadata property) includes_workflows (tool_shed.webapp.model.RepositoryMetadata attribute) includes_workflows() (galaxy.model.tool_shed_install.ToolShedRepository property) InconsistentDatabase incr() (galaxy.web.statsd_client.GalaxyStatsdClient method) increase_running_job_count() (galaxy.jobs.handler.JobHandlerQueue method) index() (galaxy.managers.licenses.LicensesManager method) (galaxy.tool_util.deps.views.ContainerResolutionView method) (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController method) (galaxy.webapps.galaxy.api.cloud.CloudController method) (galaxy.webapps.galaxy.api.cloudauthz.CloudAuthzController method) (galaxy.webapps.galaxy.api.configuration.ConfigurationController method) (galaxy.webapps.galaxy.api.container_resolution.ContainerResolutionAPIController method) (galaxy.webapps.galaxy.api.dataset_collections.DatasetCollectionsController method) (galaxy.webapps.galaxy.api.datasets.DatasetsController method) (galaxy.webapps.galaxy.api.datatypes.DatatypesController method) (galaxy.webapps.galaxy.api.display_applications.DisplayApplicationsController 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.FoldersController method) (galaxy.webapps.galaxy.api.forms.FormDefinitionAPIController method) (galaxy.webapps.galaxy.api.genomes.GenomesController method) (galaxy.webapps.galaxy.api.group_roles.GroupRolesAPIController method) (galaxy.webapps.galaxy.api.group_users.GroupUsersAPIController method) (galaxy.webapps.galaxy.api.groups.GroupAPIController method) (galaxy.webapps.galaxy.api.histories.HistoriesController method) (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method) (galaxy.webapps.galaxy.api.item_tags.BaseItemTagsController method) (galaxy.webapps.galaxy.api.job_files.JobFilesAPIController method) (galaxy.webapps.galaxy.api.jobs.JobController method) (galaxy.webapps.galaxy.api.libraries.LibrariesController method) (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method) (galaxy.webapps.galaxy.api.licenses.FastAPILicenses method) (galaxy.webapps.galaxy.api.licenses.LicensesController method) (galaxy.webapps.galaxy.api.page_revisions.PageRevisionsController method) (galaxy.webapps.galaxy.api.pages.PagesController method) (galaxy.webapps.galaxy.api.plugins.PluginsController method) (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method) (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method) (galaxy.webapps.galaxy.api.remote_files.RemoteFilesAPIController method) (galaxy.webapps.galaxy.api.roles.FastAPIRoles method) (galaxy.webapps.galaxy.api.roles.RoleAPIController method) (galaxy.webapps.galaxy.api.tool_data.ToolData method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) (galaxy.webapps.galaxy.api.tool_entry_points.ToolEntryPointsAPIController method) (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) (galaxy.webapps.galaxy.api.tools.ToolsController method) (galaxy.webapps.galaxy.api.toolshed.ToolShedController method) (galaxy.webapps.galaxy.api.tours.FastAPITours method) (galaxy.webapps.galaxy.api.tours.ToursController method) (galaxy.webapps.galaxy.api.trs_search.TrsSearchAPIController 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.admin.AdminGalaxy method) (galaxy.webapps.galaxy.controllers.async.ASync method) (galaxy.webapps.galaxy.controllers.authnz.OIDC method) (galaxy.webapps.galaxy.controllers.error.Error method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.root.RootController method) (galaxy.webapps.galaxy.controllers.shed_tool_static.ShedToolStatic method) (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) (galaxy.webapps.galaxy.controllers.userskeys.User method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) (galaxy.webapps.reports.controllers.root.Report method) (galaxy.webapps.reports.controllers.system.System method) (tool_shed.util.admin_util.Admin method) (tool_shed.webapp.api.categories.CategoriesController method) (tool_shed.webapp.api.groups.GroupsController method) (tool_shed.webapp.api.repositories.RepositoriesController method) (tool_shed.webapp.api.repository_revisions.RepositoryRevisionsController method) (tool_shed.webapp.api.tools.ToolsController method) (tool_shed.webapp.api.users.UsersController method) (tool_shed.webapp.controllers.groups.Group method) (tool_shed.webapp.controllers.repository.RepositoryController method) (tool_shed.webapp.controllers.user.User method) index_exports() (galaxy.webapps.galaxy.api.histories.HistoriesController method) index_invocations() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) index_jobs_summary() (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method) index_of_tool_id() (galaxy.tools.toolbox.panel.ToolPanelElements method) indexer (galaxy.model.GenomeIndexToolData attribute) indexes() (galaxy.webapps.galaxy.api.genomes.GenomesController method) IndividualTagsColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.web.legacy_framework.grids) InfernalCM (class in galaxy.datatypes.msa) Inflector (class in galaxy.util.inflection) InfluxDBPlugin (class in galaxy.tools.error_reports.plugins.influxdb) info (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.Job attribute) (galaxy.model.JobStateHistory attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryInfoAssociation attribute) (galaxy.model.Task attribute) (galaxy.model.TransferJob attribute) info() (galaxy.model.LibraryDataset property) (galaxy.tool_util.lint.LintContext method) info_association (galaxy.model.Library attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryFolder attribute) info_message() (galaxy.tool_util.verify.script.Results method) info_text (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.web.legacy_framework.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) inheritable (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryInfoAssociation attribute) inheritable() (galaxy.model.LibraryDatasetDatasetInfoAssociation property) init() (in module galaxy.model.mapping) (in module galaxy.model.tool_shed_install.mapping) (in module tool_shed.webapp.model.mapping) init_job_handling() (galaxy.web_stack.ApplicationStack method) init_late_prefork() (galaxy.web_stack.ApplicationStack method) (galaxy.web_stack.MessageApplicationStack method) (galaxy.web_stack.transport.ApplicationStackTransport method) (galaxy.web_stack.transport.UWSGIFarmMessageTransport method) init_meta() (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.binary.SQlite method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.mothur.DistanceMatrix method) (galaxy.datatypes.mothur.GroupAbund method) (galaxy.datatypes.mothur.LowerTriangleDistanceMatrix method) (galaxy.datatypes.mothur.Sabund method) (galaxy.datatypes.mothur.SquareDistanceMatrix method) (galaxy.datatypes.sequence.Maf method) (galaxy.datatypes.tabular.Pileup method) (galaxy.model.DatasetInstance method)

init_models_from_config() (in module galaxy.config) init_new_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method) init_on_load() (galaxy.model.History method) init_repository() (in module tool_shed.util.hg_util) initialize() (galaxy.tools.DefaultToolState method) initialize_all_repository_dependencies() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) initialize_fast_app() (in module galaxy.webapps.galaxy.fast_app) initiate_installation_process() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) initiate_repository_installation() (galaxy.tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) initiate_tool_dependency_installation() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) inject() (galaxy.workflow.modules.WorkflowModuleInjector method) input (galaxy.workflow.refactor.schema.ConnectAction attribute) (galaxy.workflow.refactor.schema.DisconnectAction attribute) (galaxy.workflow.refactor.schema.ExtractInputAction attribute) input_associations() (galaxy.model.WorkflowInvocation property) input_combinations() (galaxy.tools.parameters.meta.WorkflowParameterExpansion property) input_connections() (galaxy.model.WorkflowStep property) (tool_shed.webapp.model.WorkflowStep property) input_connections_by_name() (galaxy.model.WorkflowStep property) input_dataset_collection (galaxy.model.ImplicitlyCreatedDatasetCollectionInput attribute) input_dataset_collection_elements (galaxy.model.Job attribute) input_dataset_collection_id (galaxy.model.ImplicitlyCreatedDatasetCollectionInput attribute) input_dataset_collections (galaxy.model.Job attribute) (galaxy.model.WorkflowInvocation attribute) input_datasets (galaxy.model.Job attribute) (galaxy.model.WorkflowInvocation attribute) input_default_value() (galaxy.model.WorkflowStep property) input_extra_files_rewrite() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) input_library_datasets (galaxy.model.Job attribute) input_metadata_rewrite() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) input_name (galaxy.workflow.refactor.schema.InputReferenceByLabel attribute) (galaxy.workflow.refactor.schema.InputReferenceByOrderIndex attribute) (galaxy.workflow.refactor.schema.RefactorActionExecutionMessage attribute) input_name() (galaxy.model.WorkflowStepConnection property) input_parameters (galaxy.model.WorkflowInvocation attribute) input_path_rewrite() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) input_step() (galaxy.model.WorkflowStepConnection property) input_step_id() (galaxy.model.WorkflowStepConnection property) input_step_input (galaxy.model.WorkflowStepConnection attribute) input_step_input_id (galaxy.model.WorkflowStepConnection attribute) input_step_parameters (galaxy.model.WorkflowInvocation attribute) input_step_types (galaxy.model.Workflow attribute) input_steps() (galaxy.model.Workflow property) input_subworkflow_step (galaxy.model.WorkflowStepConnection attribute) input_subworkflow_step_id (galaxy.model.WorkflowStepConnection attribute) INPUT_TYPE (class in galaxy.tool_util.cwl.representation) input_type() (galaxy.model.WorkflowStep property) InputDataCollectionModule (class in galaxy.workflow.modules) InputDataModule (class in galaxy.workflow.modules) InputKey (class in galaxy.tools.parameters.meta) InputMatchedException InputModule (class in galaxy.workflow.modules) InputParameterModule (class in galaxy.workflow.modules) InputProxy (class in galaxy.workflow.modules) InputReferenceByLabel (class in galaxy.workflow.refactor.schema) InputReferenceByOrderIndex (class in galaxy.workflow.refactor.schema) inputs (galaxy.model.WorkflowStep attribute) inputs() (galaxy.webapps.galaxy.api.jobs.JobController method) (galaxy_test.api.test_workflow_extraction.RunJobsSummary property) (galaxy_test.base.populators.RunJobsSummary property) inputs_defined() (galaxy.tool_util.parser.interface.PagesSource property) (galaxy.tool_util.parser.xml.XmlPagesSource property) InputSource (class in galaxy.tool_util.parser.interface) InputValueWrapper (class in galaxy.tools.wrappers) InRangeValidator (class in galaxy.tools.parameters.validation) insert() (galaxy.model.custom_types.MutationList method) (galaxy.util.odict.odict method) insert_tool() (galaxy.tools.toolbox.panel.ToolPanelElements method) InsertColumnToolOutputActionOptionFilter (class in galaxy.tool_util.parser.output_actions) inspect() (galaxy.containers.docker.DockerAPIInterface method) (galaxy.containers.docker.DockerCLIInterface method) (galaxy.containers.docker_model.DockerContainer property) (galaxy.containers.docker_model.DockerNode property) (galaxy.containers.docker_model.DockerService property) (galaxy.containers.docker_model.DockerTask property) inspect_container() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) Install (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler) install() (galaxy.tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) install_all() (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method) install_and_build_package() (galaxy.tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) install_and_build_package_via_fabric() (galaxy.tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) install_conda() (in module galaxy.tool_util.deps.conda_util) install_conda_target() (in module galaxy.tool_util.deps.conda_util) install_data_managers() (galaxy.tool_shed.galaxy_install.tools.data_manager.DataManagerHandler method) install_dependencies() (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tools.ToolsController method) install_dependency() (galaxy.tool_util.deps.resolvers.DependencyResolver method) (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) install_environment() (galaxy.tool_util.deps.conda_util.CondaTarget property) install_latest_repository_revision() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) install_matched_repository_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) install_model() (galaxy.managers.context.ProvidesAppContext property) install_options() (galaxy.managers.workflows.WorkflowCreateOptions property) install_package() (galaxy.tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) install_repositories() (galaxy.tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) install_repositories_by_revision() (tool_shed.webapp.controllers.repository.RepositoryController method) install_repository() (galaxy.tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) install_repository_dependencies (galaxy.managers.workflows.WorkflowCreateOptions attribute) install_repository_revision() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) install_repository_revisions() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) install_resolver_dependencies (galaxy.managers.workflows.WorkflowCreateOptions attribute) install_specified_tool_dependencies() (galaxy.tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) install_timestamp_triggers() (in module galaxy.model.triggers) install_tool_data_tables() (galaxy.tool_shed.tools.data_table_manager.ShedToolDataTableManager method) install_tool_dependencies (galaxy.managers.workflows.WorkflowCreateOptions attribute) install_tool_dependencies_with_update() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) install_tool_shed_repository() (galaxy.tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) install_via_fabric() (galaxy.tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) install_views() (in module galaxy.model.view.utils) install_virtualenv() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupVirtualEnv method) installable_description (galaxy.tool_util.deps.conda_util.CondaContext attribute) installable_description() (galaxy.tool_util.deps.installable.InstallableContext property) installable_resolvers() (galaxy.tool_util.deps.views.DependencyResolversView property) installable_revisions() (tool_shed.webapp.model.Repository method) InstallableContext (class in galaxy.tool_util.deps.installable) installation_complete() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader.AsynchronousReader method) installation_directory() (galaxy.model.tool_shed_install.ToolDependency method) installation_status (galaxy.model.tool_shed_install.ToolDependency attribute) INSTALLED (galaxy.model.tool_shed_install.ToolShedRepository.installation_status attribute) installed_changeset_revision (galaxy.model.tool_shed_install.ToolShedRepository attribute) installed_len_files (galaxy.webapps.galaxy.controllers.user.User attribute) installed_repository_dependencies() (galaxy.model.tool_shed_install.ToolShedRepository property) installed_repository_grid (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed attribute) installed_tool_dependencies() (galaxy.model.tool_shed_install.ToolShedRepository property) (galaxy.tools.Tool property) InstalledRepositoryGrid (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) InstalledRepositoryGrid.DeletedColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) InstalledRepositoryGrid.DescriptionColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) InstalledRepositoryGrid.NameColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) InstalledRepositoryGrid.OwnerColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) InstalledRepositoryGrid.RevisionColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) InstalledRepositoryGrid.StatusColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) InstalledRepositoryGrid.ToolShedColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) InstalledRepositoryGrid.ToolShedStatusColumn (class in tool_shed.galaxy_install.grids.admin_toolshed_grids) InstalledRepositoryManager (class in galaxy.tool_shed.galaxy_install.installed_repository_manager) InstalledRepositoryMetadataManager (class in galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager) InstallEnvironment (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment) INSTALLING (galaxy.model.tool_shed_install.ToolDependency.states attribute) (galaxy.model.tool_shed_install.ToolShedRepository.states attribute) INSTALLING_REPOSITORY_DEPENDENCIES (galaxy.model.tool_shed_install.ToolShedRepository.installation_status attribute) INSTALLING_TOOL_DEPENDENCIES (galaxy.model.tool_shed_install.ToolShedRepository.installation_status attribute) InstallMatchedRepositoryGrid (class in tool_shed.grids.repository_grids) InstallRepositoryManager (class in galaxy.tool_shed.galaxy_install.install_manager) InstallToolDependencyManager (class in galaxy.tool_shed.galaxy_install.install_manager) instance_id() (galaxy.web_stack.UWSGIApplicationStack property) institution (galaxy.model.UserAddress attribute) InstrumentPlugin (class in galaxy.job_metrics.instrumenters) InsufficientPermissionsException int() (galaxy.managers.base.ModelValidator method) int_range() (galaxy.managers.base.ModelValidator method) int_to_octet() (in module galaxy.webapps.reports.controllers.history) (in module galaxy.webapps.reports.controllers.tools) INTEGER (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute) IntegerColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.web.legacy_framework.grids) IntegerToolParameter (class in galaxy.tools.parameters.basic) integration_module_instance() (in module galaxy_test.driver.integration_util) integration_tool_runner() (in module galaxy_test.driver.integration_util) IntegrationInstance (class in galaxy_test.driver.integration_util) IntegrationTestCase (class in galaxy_test.driver.integration_util) INTENV_REQUEST_FACTORY (galaxy.visualization.plugins.plugin.InteractiveEnvironmentPlugin attribute) InteractiveEnvironmentPlugin (class in galaxy.visualization.plugins.plugin) InteractiveEnvironmentRequest (class in galaxy.visualization.plugins.interactive_environments) InteractiveEnvironmentsController (class in galaxy.webapps.galaxy.controllers.interactive_environments) InteractiveTool (class in galaxy.tools) interactivetool_entry_points (galaxy.model.Job attribute) InteractiveToolEntryPoint (class in galaxy.model) InteractiveToolManager (class in galaxy.managers.interactivetool) InteractiveToolSqlite (class in galaxy.managers.interactivetool) InteractorStaging (class in galaxy.tool_util.client.staging) internal_galaxy_markdown_to_pdf() (in module galaxy.managers.markdown_util) InternalServerError InterruptedUpload Interval (class in galaxy.datatypes.interval) interval_dataprovider() (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) interval_dict_dataprovider() (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) IntervalDataProvider (class in galaxy.datatypes.dataproviders.dataset) (class in galaxy.visualization.data_providers.genome) IntervalIndexDataProvider (class in galaxy.visualization.data_providers.genome) IntervalTabixDataProvider (class in galaxy.visualization.data_providers.genome) INVALID (galaxy.model.DatasetInstance.validated_states attribute) invalid() (galaxy.datatypes.data.DatatypeValidation static method) invalidate_external_metadata() (galaxy.jobs.JobWrapper method) (galaxy.metadata.MetadataCollectionStrategy method) InvalidDataManager (class in tool_shed.utility_containers.utility_container_manager) InvalidDataProviderSource InvalidFileFormatError InvalidRepositoryDependency (class in tool_shed.utility_containers) InvalidTool (class in tool_shed.utility_containers.utility_container_manager) InvalidToolDependency (class in tool_shed.utility_containers) invocation() (galaxy_test.base.populators.RunJobsSummary property) invocation_id() (galaxy_test.base.populators.RunJobsSummary property) invocation_job_source_iter() (in module galaxy.managers.jobs) invocation_jobs_summary() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) invocation_step() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) invocation_step_jobs_summary() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) invocation_to_output() (in module galaxy.tool_util.cwl.util) invoke() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) (in module galaxy.util.pastescript.serve) (in module galaxy.workflow.run) invoke_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method) invoke_workflow_raw() (galaxy_test.base.populators.BaseWorkflowPopulator method) io_dicts() (galaxy.model.Job method) Ipynb (class in galaxy.datatypes.text) IQTree (class in galaxy.datatypes.text) IRODSObjectStore (class in galaxy.objectstore.irods) IRREGULAR_WORDS (galaxy.util.inflection.Inflector attribute) is_a_yaml_with_class() (in module galaxy.tool_util.loader_directory) is_accessible() (galaxy.managers.datasets.DatasetAssociationManager method) (galaxy.managers.datasets.DatasetManager method) (galaxy.managers.hdas.HDAManager method) (galaxy.managers.secured.AccessibleManagerMixin method) (galaxy.managers.sharable.SharableModelManager method) is_active() (galaxy.model.User method) is_admin() (galaxy.managers.users.UserManager method) is_admin_user() (galaxy.config.CommonConfigurationMixin method) is_anonymous() (galaxy.managers.users.UserManager method) is_authenticated() (galaxy.model.User method) is_bam() (galaxy.datatypes.binary.BamNative class method) is_binary (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.data.Text attribute) (galaxy.datatypes.media.Wav attribute) is_binary() (in module galaxy.util) is_bz2() (in module galaxy.datatypes.checkers) (in module galaxy.util.checkers) is_case() (galaxy.tool_util.parser.output_actions.DatatypeIsInstanceToolOutputActionConditionalWhen method) (galaxy.tool_util.parser.output_actions.ToolOutputActionConditionalWhen method) (galaxy.tool_util.parser.output_actions.ValueToolOutputActionConditionalWhen method) is_check_time() (galaxy.model.DeferredJob property) is_checked() (galaxy.util.form_builder.CheckboxField static method) (galaxy.web.form_builder.CheckboxField static method) is_circular_repository_dependency() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) is_collection() (galaxy.model.DatasetCollectionElement property) (galaxy.tools.wrappers.DatasetCollectionWrapper property) (galaxy.tools.wrappers.DatasetFilenameWrapper property) is_column_based() (in module galaxy.datatypes.sniff) is_composite() (galaxy.managers.datasets.DatasetAssociationManager method) is_conda_installed() (galaxy.tool_util.deps.conda_util.CondaContext method) is_config_watcher() (galaxy.model.database_heartbeat.DatabaseHeartbeat property) is_current_version() (galaxy.tools.data.ToolDataTable method) is_data_index_sample_file() (in module galaxy.tool_shed.util.tool_util) is_datatype_change_allowed() (galaxy.datatypes.data.Data class method) is_datatype_converter() (galaxy.tools.Tool property) is_deactivated_or_installed() (galaxy.model.tool_shed_install.ToolShedRepository property) is_deprecated_in_tool_shed() (galaxy.model.tool_shed_install.ToolShedRepository property) is_dict() (in module galaxy.tool_util.parser.util) is_displayed() (galaxy.selenium.has_driver.HasDriver method) (galaxy.selenium.smart_components.SmartTarget property) is_downloadable() (in module tool_shed.util.metadata_util) is_extension_unsniffable_binary() (galaxy.datatypes.registry.Registry method) is_file_empty() (galaxy.tools.parameters.basic.ColumnListParameter method) is_float() (galaxy.datatypes.tabular.BaseCSV method) is_gzip() (in module galaxy.datatypes.checkers) (in module galaxy.util.checkers) is_handler() (galaxy.web_stack.handlers.ConfiguresHandlers property) is_hashable() (in module galaxy.util.hash_util) is_hda() (in module galaxy.model) is_id() (galaxy.jobs.JobConfiguration method) is_importable() (galaxy.managers.workflows.WorkflowCreateOptions property) is_in() (in module galaxy.util.specs) is_in_repo_info_dicts() (galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) is_input_supplied() (galaxy.tools.wrappers.DatasetCollectionWrapper property) is_installed() (galaxy.model.tool_shed_install.ToolDependency property) (galaxy.model.tool_shed_install.ToolShedRepository property) (galaxy.tool_util.deps.conda_util.CondaContext method) (galaxy.tool_util.deps.installable.InstallableContext method) is_int() (galaxy.datatypes.tabular.BaseCSV method) is_integrity_error() (galaxy.authnz.psa_authnz.Storage class method) is_job_handler() (galaxy.app.UniverseApplication property) is_JSONified_value() (galaxy.datatypes.metadata.MetadataTempFile class method) (galaxy.model.metadata.MetadataTempFile class method) is_latest_installable_revision() (galaxy.model.tool_shed_install.ToolShedRepository property) is_latest_version() (galaxy.tools.Tool property) is_leaf() (galaxy.model.dataset_collections.structure.Leaf property) (galaxy.model.dataset_collections.structure.Tree property) (galaxy.model.dataset_collections.structure.UninitializedTree property) is_level_one_certified() (tool_shed.repository_registry.Registry method) is_logged_in() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) is_malicious() (in module tool_shed.util.metadata_util) is_managed() (galaxy.containers.docker_model.DockerNode method) is_mapped_over() (galaxy.model.dataset_collections.matching.MatchingCollections method) is_missing_shed_tool() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) is_named_collection_part_name() (galaxy.tool_util.parser.output_objects.ToolOutputCollectionPart static method) (galaxy.tool_util.parser.ToolOutputCollectionPart static method) is_new() (galaxy.model.Dataset property) (galaxy.model.tool_shed_install.ToolShedRepository property) (galaxy.model.WorkflowInvocationStep property) (tool_shed.webapp.model.Repository method) is_new_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method) is_object_applicable() (galaxy.visualization.plugins.registry.VisualizationsRegistry method) is_of_type() (galaxy.tools.wrappers.DatasetFilenameWrapper method) is_ok() (galaxy.containers.docker_model.DockerNode method) (galaxy.model.DatasetInstance property) is_outside_grace_period() (galaxy.webapps.galaxy.controllers.user.User method) is_over_quota() (galaxy.quota.NoQuotaAgent method) is_owner() (galaxy.managers.hdas.HDAManager method) (galaxy.managers.histories.HistoryManager method) (galaxy.managers.secured.OwnableManagerMixin method) (galaxy.managers.sharable.SharableModelManager method) is_path_browsable() (in module tool_shed.util.shed_util_common) is_path_within_dependency_dir() (in module tool_shed.util.shed_util_common) is_path_within_repo() (in module tool_shed.util.shed_util_common) is_pending() (galaxy.model.DatasetInstance property) is_permitted() (galaxy.managers.rbac_secured.AccessDatasetRBACPermission method) (galaxy.managers.rbac_secured.ManageDatasetRBACPermission method) (galaxy.managers.rbac_secured.RBACPermission method) is_preparing() (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter method) is_public() (galaxy.managers.libraries.LibraryManager method) (galaxy.managers.rbac_secured.AccessDatasetRBACPermission method) is_read_only_query() (in module galaxy.util.sqlite) is_ready() (galaxy.containers.Container method) (galaxy.containers.docker_model.DockerContainer method) (galaxy.containers.docker_model.DockerService method) is_ready_for_resubmission() (galaxy.jobs.JobWrapper method) is_repository_admin_role() (tool_shed.webapp.model.Role property) is_runtime_context() (in module galaxy.tools.parameters.basic) is_runtime_value() (in module galaxy.tools.parameters.basic) is_set() (galaxy.config.BaseAppConfiguration method) is_site_up() (in module galaxy_test.base.populators) is_subcollection_of_type() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) is_subfolder_of() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) is_tag() (galaxy.jobs.JobConfiguration method) is_tool_load_error() (in module galaxy.tool_util.loader_directory) is_tool_module_type() (in module galaxy.workflow.modules) is_tool_shed_client() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) is_true() (in module galaxy.web.framework.helpers) is_uuid() (in module galaxy.util) is_valid (galaxy.model.GalaxySession attribute) (galaxy.model.JobExternalOutputMetadata attribute) (tool_shed.webapp.model.GalaxySession attribute) is_valid() (tool_shed.repository_registry.Registry method) is_valid_filter() (tool_shed.grids.repository_grid_filter_manager.RepositoryGridFilterManager method) is_valid_for_type() (tool_shed.repository_types.metadata.Metadata method) (tool_shed.repository_types.repository_suite_definition.RepositorySuiteDefinition method) (tool_shed.repository_types.tool_dependency_definition.ToolDependencyDefinition method) (tool_shed.repository_types.unrestricted.Unrestricted method) is_valid_slug() (galaxy.managers.sharable.SharableModelManager method) (in module galaxy.managers.base) is_view (galaxy.model.view.utils.View attribute) is_view_model() (in module galaxy.model.view.utils) is_virtual_display_available() (in module galaxy.selenium.driver_factory) is_workflow_compatible() (galaxy.tools.Tool property) is_zip() (in module galaxy.util.checkers) IsaJson (class in galaxy.datatypes.isa) IsaTab (class in galaxy.datatypes.isa) isDeprecatedLicenseId (galaxy.managers.licenses.LicenseMetadataModel attribute) isdir() (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method) (galaxy.util.compression_utils.CompressedFile method) isdir_tar() (galaxy.util.compression_utils.CompressedFile method) isdir_zip() (galaxy.util.compression_utils.CompressedFile method) isfile() (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method) (galaxy.util.compression_utils.CompressedFile method) isinstance_datatype() (galaxy.managers.datasets.DatasetAssociationFilterParser method) isolate_galaxy_config (galaxy_test.driver.integration_util.IntegrationInstance attribute) isOsiApproved (galaxy.managers.licenses.LicenseMetadataModel attribute) issue_cache (galaxy.tools.error_reports.plugins.base_git.BaseGitPlugin attribute) issued (galaxy.model.PSAAssociation attribute) item_count (galaxy.model.LibraryFolder attribute) item_has_tag() (galaxy.model.tags.TagHandler method) item_permission_map_for_add() (galaxy.model.security.GalaxyRBACAgent method) item_permission_map_for_manage() (galaxy.model.security.GalaxyRBACAgent method) item_permission_map_for_modify() (galaxy.model.security.GalaxyRBACAgent method) item_to_api_value() (galaxy.model.search.SearchQuery method) ItemAccessibilityException ItemDeletionException ItemGrabber (class in galaxy.jobs.handler) ItemOwnershipException ItemRatingAssociation (class in galaxy.model) (class in tool_shed.webapp.model) ItemRatings (class in tool_shed.webapp.util.ratings_util) items() (galaxy.model.dataset_collections.matching.CollectionsToMatch method) (galaxy.tools.wrappers.DatasetFilenameWrapper.MetadataWrapper method) (galaxy.util.bunch.Bunch method) (galaxy.util.odict.odict method) ItemSelectionGrid (class in galaxy.webapps.galaxy.controllers.page) ItemSelectionGrid.NameColumn (class in galaxy.webapps.galaxy.controllers.page) ItemTagAssociation (class in galaxy.model) (class in tool_shed.webapp.model) ItemTagAssocInfo (class in galaxy.model.tags) iter_blocks_split_by_species() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) iter_blocks_split_by_src() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) iter_components_by_src() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) iter_components_by_src_start() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) iter_fasta_alignment() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) iter_headers() (in module galaxy.datatypes.sniff) iter_start_of_line() (in module galaxy.util) iterable_has_all() (in module galaxy.managers.rbac_secured) iterate_file() (in module galaxy.web.framework.base) iteritems() (galaxy.util.odict.odict method) iterkeys() (galaxy.util.odict.odict method) ITERPARSE_ALL_EVENTS (galaxy.datatypes.dataproviders.hierarchy.XMLDataProvider attribute) itervalues() (galaxy.util.odict.odict method)

J

javascript_boolean() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) javascript_link() (in module galaxy.web.framework.helpers.tags) Job (class in galaxy.model) job (galaxy.model.DataManagerJobAssociation attribute) (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.ImplicitCollectionJobsJobAssociation attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.Job attribute) (galaxy.model.JobContainerAssociation attribute) (galaxy.model.JobExportHistoryArchive attribute) (galaxy.model.JobExternalOutputMetadata attribute) (galaxy.model.JobImportHistoryArchive attribute) (galaxy.model.JobMetricNumeric attribute) (galaxy.model.JobMetricText attribute) (galaxy.model.JobStateHistory attribute) (galaxy.model.JobToImplicitOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetAssociation attribute) (galaxy.model.JobToInputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetCollectionElementAssociation attribute) (galaxy.model.JobToInputLibraryDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToOutputLibraryDatasetAssociation attribute) (galaxy.model.PostJobActionAssociation attribute) (galaxy.model.Task attribute) (galaxy.model.WorkflowInvocationStep attribute) Job.states (class in galaxy.model) JOB_COMPLETION (galaxy.selenium.navigates_galaxy.WAIT_TYPES attribute) job_config_xml_to_dict() (in module galaxy.jobs) job_count() (galaxy.jobs.rule_helper.RuleHelper method) job_destination() (galaxy.jobs.JobWrapper property) job_export_history_archive (galaxy.model.Dataset attribute) job_failed() (galaxy.tools.InteractiveTool method) (galaxy.tools.SetMetadataTool method) (galaxy.tools.Tool method) job_hash() (galaxy.jobs.rule_helper.RuleHelper method) job_id (galaxy.model.DataManagerJobAssociation attribute) (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.ImplicitCollectionJobsJobAssociation attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.JobContainerAssociation attribute) (galaxy.model.JobExportHistoryArchive attribute) (galaxy.model.JobExternalOutputMetadata attribute) (galaxy.model.JobImportHistoryArchive attribute) (galaxy.model.JobMetricNumeric attribute) (galaxy.model.JobMetricText attribute) (galaxy.model.JobParameter attribute) (galaxy.model.JobStateHistory attribute) (galaxy.model.JobToImplicitOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetAssociation attribute) (galaxy.model.JobToInputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetCollectionElementAssociation attribute) (galaxy.model.JobToInputLibraryDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToOutputLibraryDatasetAssociation attribute) (galaxy.model.PostJobActionAssociation attribute) (galaxy.model.Task attribute) (galaxy.model.WorkflowInvocationStep attribute) job_id() (galaxy.job_execution.output_collect.JobContext method) (galaxy.job_execution.output_collect.SessionlessJobContext method) (galaxy.model.store.discover.ModelPersistenceContext method) job_info() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) (galaxy.webapps.reports.controllers.jobs.Jobs method) job_input_hda_filter() (in module galaxy.model.search) job_input_ldda_filter() (in module galaxy.model.search) job_list() (galaxy.model.ImplicitCollectionJobs property) job_lock() (galaxy.managers.jobs.JobManager method) job_lock_status() (in module galaxy.webapps.galaxy.api.job_lock) job_manager (galaxy.webapps.galaxy.api.jobs.FastAPIJobs attribute) job_messages (galaxy.model.Job attribute) (galaxy.model.Task attribute) JOB_NAME_PREFIX (galaxy.jobs.runners.chronos.ChronosJobRunner attribute) job_object_dict() (in module galaxy.jobs.runners.util.pykube_util) job_output_hda_filter() (in module galaxy.model.search) job_pair_for_id() (galaxy.jobs.handler.JobHandlerQueue method) job_param_filter() (in module galaxy.model.search) job_properties() (galaxy.job_metrics.instrumenters.cgroup.CgroupPlugin method) (galaxy.job_metrics.instrumenters.collectl.CollectlPlugin method) (galaxy.job_metrics.instrumenters.core.CorePlugin method) (galaxy.job_metrics.instrumenters.cpuinfo.CpuInfoPlugin method) (galaxy.job_metrics.instrumenters.env.EnvPlugin method) (galaxy.job_metrics.instrumenters.hostname.HostnamePlugin method) (galaxy.job_metrics.instrumenters.InstrumentPlugin method) (galaxy.job_metrics.instrumenters.meminfo.MemInfoPlugin method) (galaxy.job_metrics.instrumenters.uname.UnamePlugin method) JOB_RESOURCE_CONDITIONAL_XML (galaxy.jobs.JobConfiguration attribute) job_rule_modules() (in module galaxy.queue_worker) job_rules_paths() (galaxy.config_watchers.ConfigWatchers property) job_runner_external_id (galaxy.model.Job attribute) job_runner_external_pid (galaxy.model.JobExternalOutputMetadata attribute) job_runner_name (galaxy.model.Job attribute) job_script() (in module galaxy.jobs.runners.util.job_script) job_script_kwargs() (galaxy.jobs.runners.util.cli.job.BaseJobExec method) (galaxy.jobs.runners.util.cli.job.lsf.LSF method) (galaxy.jobs.runners.util.cli.job.slurm.Slurm method) (galaxy.jobs.runners.util.cli.job.torque.Torque method)

job_search (galaxy.webapps.galaxy.api.jobs.FastAPIJobs attribute) job_source_id() (galaxy.model.HistoryDatasetCollectionAssociation property) job_source_type() (galaxy.model.HistoryDatasetCollectionAssociation property) job_state_summary (galaxy.model.HistoryDatasetCollectionAssociation attribute) job_states (in module galaxy.jobs.runners.util.cli.job) job_stderr (galaxy.model.Job attribute) (galaxy.model.Task attribute) job_stdout (galaxy.model.Job attribute) (galaxy.model.Task attribute) job_wrapper() (galaxy.jobs.handler.JobHandlerQueue method) JobConfiguration (class in galaxy.jobs) JobContainerAssociation (class in galaxy.model) JobContext (class in galaxy.job_execution.output_collect) JobController (class in galaxy.webapps.galaxy.api.jobs) JobDestination (class in galaxy.jobs) JobExportHistoryArchive (class in galaxy.model) JobExportHistoryArchiveWrapper (class in galaxy.tools.imp_exp) JobExternalOutputMetadata (class in galaxy.model) JobFilesAPIController (class in galaxy.webapps.galaxy.api.job_files) JobHandler (class in galaxy.jobs.handler) JobHandlerMessage (class in galaxy.web_stack.message) JobHandlerQueue (class in galaxy.jobs.handler) JobHandlerStopQueue (class in galaxy.jobs.handler) JobImportHistoryArchive (class in galaxy.model) JobImportHistoryArchiveWrapper (class in galaxy.tools.imp_exp) JobInfo (class in galaxy.tool_util.deps.dependencies) JobInstrumenter (class in galaxy.job_metrics) JobLike (class in galaxy.model) JobLock (class in galaxy.managers.jobs) JobManager (class in galaxy.jobs.manager) (class in galaxy.managers.jobs) JobMappingConfigurationException JobMappingException JobMetricFormatter (class in galaxy.job_metrics.formatting) JobMetricNumeric (class in galaxy.model) JobMetrics (class in galaxy.job_metrics) JobMetricText (class in galaxy.model) JobNotReadyException JobOutputsError JobParameter (class in galaxy.model) JobPortsAPIController (class in galaxy.webapps.galaxy.api.job_ports) JobPortsView (class in galaxy.job_execution.ports) (class in galaxy.job_execution.ports.view) JobRunnerMapper (class in galaxy.jobs.mapper) Jobs (class in galaxy.webapps.reports.controllers.jobs) jobs (galaxy.model.History attribute) (galaxy.model.ImplicitCollectionJobs attribute) jobs() (galaxy.model.WorkflowInvocationStep property) (galaxy_test.api.test_workflow_extraction.RunJobsSummary property) (galaxy_test.base.populators.RunJobsSummary property) jobs_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) jobs_properties() (galaxy.model.store.BaseDirectoryImportModelStore method) (galaxy.model.store.ModelImportStore method) JobsApiTestCase (class in galaxy_test.api.test_jobs) JobSearch (class in galaxy.managers.jobs) JobState (class in galaxy.jobs.runners) JobStateHistory (class in galaxy.model) JobToImplicitOutputDatasetCollectionAssociation (class in galaxy.model) JobToInputDatasetAssociation (class in galaxy.model) JobToInputDatasetCollectionAssociation (class in galaxy.model) JobToInputDatasetCollectionElementAssociation (class in galaxy.model) JobToInputLibraryDatasetAssociation (class in galaxy.model) JobToolConfiguration (class in galaxy.jobs) JobToOutputDatasetAssociation (class in galaxy.model) JobToOutputDatasetCollectionAssociation (class in galaxy.model) JobToOutputLibraryDatasetAssociation (class in galaxy.model) JobView (class in galaxy.model.search) JobWrapper (class in galaxy.jobs) join() (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method) joinext() (in module galaxy.util.path) Jpg (class in galaxy.datatypes.images) JS_APP_MAKO_FILEPATH (galaxy.webapps.base.controller.JSAppLauncher attribute) js_helper() (in module galaxy.web.framework.helpers) js_nullable() (in module galaxy.web.framework.helpers) JSAppLauncher (class in galaxy.webapps.base.controller) Json (class in galaxy.datatypes.text) json() (in module galaxy.web) (in module galaxy.web.framework.decorators) (tool_shed.webapp.api.tools.ToolsController method) json_dumps() (galaxy.managers.workflows.RefactorResponse.Config method) json_pretty() (in module galaxy.web) (in module galaxy.web.framework.decorators) json_wrap() (in module galaxy.tools.parameters.wrapped_json) JsonCollectedDatasetMatch (class in galaxy.model.store.discover) jsonData() (galaxy.util.jstree.JSTree method) (galaxy.util.jstree.Node method) JsonFileProxyIpc (class in galaxy.web.proxy) Jsonld (class in galaxy.datatypes.triples) JsonPlugin (class in galaxy.tools.error_reports.plugins.json) jsonrpc_request() (in module galaxy.util.json) jsonrpc_response() (in module galaxy.util.json) JSONType (class in galaxy.model.custom_types) JSTree (class in galaxy.util.jstree) JupyterTestCase (class in galaxy_test.selenium.test_jupyter)

K

k8s_config_path() (in module galaxy_test.driver.integration_util) key (galaxy.model.APIKeys attribute) (tool_shed.webapp.model.APIKeys attribute) key() (galaxy.containers.ContainerInterface property) key_is_current_repositorys_key() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) keys() (galaxy.tools.wrappers.DatasetCollectionWrapper method) (galaxy.util.bunch.Bunch method) (galaxy.util.odict.odict method)

kill_command() (in module galaxy.tool_util.deps.docker_util) kill_pg() (in module galaxy.jobs.runners.util.process_groups) kill_pid() (in module galaxy.jobs.runners.util) (in module galaxy.jobs.runners.util.kill) known_outputs() (galaxy.tool_util.parser.output_objects.ToolOutputCollection method) Kroenik (class in galaxy.datatypes.proteomics) KubernetesJobRunner (class in galaxy.jobs.runners.kubernetes)

L

Label (class in galaxy.selenium.components) label (galaxy.model.WorkflowOutput attribute) (galaxy.model.WorkflowStep attribute) (galaxy.workflow.refactor.schema.AddInputAction attribute) (galaxy.workflow.refactor.schema.AddStepAction attribute) (galaxy.workflow.refactor.schema.ExtractInputAction attribute) (galaxy.workflow.refactor.schema.ExtractUntypedParameter attribute) (galaxy.workflow.refactor.schema.StepReferenceByLabel attribute) (galaxy.workflow.refactor.schema.UpdateStepLabelAction attribute) label() (galaxy.containers.docker_model.DockerServiceConstraint property) (galaxy.tool_util.cwl.representation.TypeRepresentation property) (galaxy.tools.parameters.grouping.Conditional property) (galaxy.tools.parameters.grouping.Repeat method) (galaxy.tools.parameters.grouping.Section method) (galaxy.workflow.modules.InputProxy property) label_add() (galaxy.containers.docker_model.DockerNode method) label_cache (galaxy.tools.error_reports.plugins.base_git.BaseGitPlugin attribute) LABEL_END (galaxy.jobs.runners.kubernetes.KubernetesJobRunner attribute) LABEL_REGEX (galaxy.jobs.runners.kubernetes.KubernetesJobRunner attribute) LABEL_START (galaxy.jobs.runners.kubernetes.KubernetesJobRunner attribute) labels() (galaxy.containers.docker_model.DockerNode property) (galaxy.containers.docker_model.DockerServiceConstraints property) labels_as_constraints() (galaxy.containers.docker_model.DockerNode property) Laj (class in galaxy.datatypes.images) LaneMask (class in galaxy.datatypes.mothur) last_access_date() (galaxy.webapps.reports.controllers.users.Users method) last_action (galaxy.model.GalaxySession attribute) (tool_shed.webapp.model.GalaxySession attribute) last_activity (galaxy.model.CloudAuthz attribute) last_check() (galaxy.model.DeferredJob property) last_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) last_password_change (galaxy.model.User attribute) last_update (galaxy.model.CloudAuthz attribute) last_url() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) LastDb (class in galaxy.datatypes.blast) LastzCoverage (class in galaxy.datatypes.coverage) latest_export() (galaxy.model.History property) latest_form (galaxy.model.FormDefinitionCurrent attribute) latest_form_id (galaxy.model.FormDefinitionCurrent attribute) latest_history_item() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) latest_revision (galaxy.model.Page attribute) (galaxy.model.Visualization attribute) latest_revision_id (galaxy.model.Page attribute) (galaxy.model.Visualization attribute) latest_version() (galaxy.tools.Tool property) latest_workflow (galaxy.model.StoredWorkflow attribute) latest_workflow_id (galaxy.model.StoredWorkflow attribute) launch() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) launch_proxy_command() (galaxy.web.proxy.GolangProxyLauncher method) (galaxy.web.proxy.NodeProxyLauncher method) (galaxy.web.proxy.ProxyLauncher method) Lav (class in galaxy.datatypes.sequence) layout (galaxy.model.FormDefinition attribute) lazy_property (in module galaxy.web.framework.base) LazyProcess (class in galaxy.util.lazy_process) LazyProperty (class in galaxy.web.framework.base) LazyWriter (class in galaxy.util.pastescript.serve) lda_id (galaxy.model.MetadataFile attribute) LDAP (class in galaxy.auth.providers.ldap_ad) ldap_search() (galaxy.auth.providers.ldap_ad.LDAP method) ldda (galaxy.model.DatasetCollectionElement attribute) ldda_id (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) (galaxy.model.JobToInputLibraryDatasetAssociation attribute) (galaxy.model.JobToOutputLibraryDatasetAssociation attribute) ldda_parent_id (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) ldda_parent_library_filter() (in module galaxy.model.search) LDDAManager (class in galaxy.managers.lddas) LDDAProvenanceController (class in galaxy.webapps.galaxy.api.provenance) ldIndep (class in galaxy.datatypes.genetics) Leaf (class in galaxy.model.dataset_collections.structure) left (galaxy.workflow.refactor.schema.Position attribute) legacy_expose_api() (in module galaxy.web) (in module galaxy.web.framework.decorators) legacy_expose_api_anonymous() (in module galaxy.web) (in module galaxy.web.framework.decorators) legacy_expose_api_raw() (in module galaxy.web) (in module galaxy.web.framework.decorators) legacy_expose_api_raw_anonymous() (in module galaxy.web) (in module galaxy.web.framework.decorators) legacy_tool_shed_endpoint() (in module galaxy.webapps.galaxy.controllers.admin_toolshed) LegacyToolProvidedMetadata (class in galaxy.tool_util.provided_metadata) legal_values() (galaxy.tools.parameters.basic.BooleanToolParameter property) legend (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.web.legacy_framework.grids.Grid attribute) legend() (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid property) LengthValidator (class in galaxy.tools.parameters.validation) libary_dataset_collection (galaxy.model.LibraryDatasetCollectionRatingAssociation attribute) libraries_click_dataset_import() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_dataset_import_from_history() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_dataset_import_from_history_click_ok() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_dataset_import_from_history_select() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_dataset_import_from_path() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_folder_create() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_index_click_create_new() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_index_click_search() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_index_create() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_index_search_for() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_index_sort_click() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_index_sort_selector() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_index_table_elements() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_open() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_open_with_name() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) libraries_table_elements() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) LibrariesApiTestCase (class in galaxy_test.api.test_libraries) LibrariesController (class in galaxy.webapps.galaxy.api.libraries) Library (class in galaxy.model) (class in galaxy.webapps.galaxy.controllers.library) library (galaxy.model.LibraryInfoAssociation attribute) (galaxy.model.LibraryPermissions attribute) library_actions (galaxy.model.Role attribute) library_associations (galaxy.model.Dataset attribute) library_dataset (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryDatasetPermissions attribute) (galaxy.model.MetadataFile attribute) library_dataset_actions (galaxy.model.Role attribute) library_dataset_collection (galaxy.model.LibraryDatasetCollectionAnnotationAssociation attribute) library_dataset_collection_id (galaxy.model.LibraryDatasetCollectionAnnotationAssociation attribute) (galaxy.model.LibraryDatasetCollectionRatingAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) library_dataset_dataset_actions (galaxy.model.Role attribute) library_dataset_dataset_association (galaxy.model.JobExternalOutputMetadata attribute) (galaxy.model.LibraryDataset attribute) (galaxy.model.LibraryDatasetDatasetAssociationPermissions attribute) (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) library_dataset_dataset_association_id (galaxy.model.JobExternalOutputMetadata attribute) (galaxy.model.LibraryDataset attribute) (galaxy.model.LibraryDatasetDatasetAssociationPermissions attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) library_dataset_id (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryDatasetPermissions attribute) library_dataset_name_filter() (in module galaxy.model.search) library_extended_metadata_filter() (in module galaxy.model.search) library_folder (galaxy.model.Job attribute) library_folder_actions (galaxy.model.Role attribute) library_folder_id (galaxy.model.Job attribute) (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryFolderPermissions attribute) library_folder_parent_library_id_filter() (in module galaxy.model.search) library_id (galaxy.model.LibraryInfoAssociation attribute) (galaxy.model.LibraryPermissions attribute) library_is_public() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) library_is_unrestricted() (galaxy.model.security.GalaxyRBACAgent method) library_path() (galaxy.model.LibraryFolder property) library_path_filter() (in module galaxy.model.search) library_properties() (galaxy.model.store.BaseDirectoryImportModelStore method) (galaxy.model.store.ModelImportStore method) library_root (galaxy.model.LibraryFolder attribute) LibraryActions (class in galaxy.actions.library) LibraryContentsController (class in galaxy.webapps.galaxy.api.library_contents) LibraryContentsTestCase (class in galaxy_test.selenium.test_library_contents) LibraryDataset (class in galaxy.model) LibraryDatasetCollectionAnnotationAssociation (class in galaxy.model) LibraryDatasetCollectionAssociation (class in galaxy.model) LibraryDatasetCollectionRatingAssociation (class in galaxy.model) LibraryDatasetCollectionTagAssociation (class in galaxy.model) LibraryDatasetDatasetAssociation (class in galaxy.model) LibraryDatasetDatasetAssociationPermissions (class in galaxy.model) LibraryDatasetDatasetAssociationTagAssociation (class in galaxy.model) LibraryDatasetDatasetInfoAssociation (class in galaxy.model) LibraryDatasetDatasetView (class in galaxy.model.search) LibraryDatasetExtendMetadataController (class in galaxy.webapps.galaxy.api.extended_metadata) LibraryDatasetPermissions (class in galaxy.model) LibraryDatasetsController (class in galaxy.webapps.galaxy.api.library_datasets) LibraryDatasetsManager (class in galaxy.managers.library_datasets) LibraryDatasetsSelectionGrid (class in galaxy.webapps.galaxy.controllers.visualization) LibraryDatasetToolParameter (class in galaxy.tools.parameters.basic) LibraryDatasetView (class in galaxy.model.search) LibraryFolder (class in galaxy.model) LibraryFolderAsContainerManagerMixin (class in galaxy.managers.containers) LibraryFolderInfoAssociation (class in galaxy.model) LibraryFolderPermissions (class in galaxy.model) LibraryFolderView (class in galaxy.model.search) LibraryImportFilesSource (class in galaxy.files.sources.galaxy) LibraryInfoAssociation (class in galaxy.model) LibraryLandingTestCase (class in galaxy_test.selenium.test_library_landing) LibraryManager (class in galaxy.managers.libraries) LibraryPermissions (class in galaxy.model) LibraryPopulator (class in galaxy_test.base.populators) LibraryToCollectionsTestCase (class in galaxy_test.selenium.test_library_to_collections) LibraryView (class in galaxy.model.search) license (galaxy.model.Workflow attribute) (galaxy.workflow.refactor.schema.UpdateLicenseAction attribute) licenseId (galaxy.managers.licenses.LicenseMetadataModel attribute) LicenseMetadataModel (class in galaxy.managers.licenses) licenses_manager (galaxy.webapps.galaxy.api.licenses.FastAPILicenses attribute) LicensesApiTestCase (class in galaxy_test.api.test_licenses) LicensesController (class in galaxy.webapps.galaxy.api.licenses) LicensesManager (class in galaxy.managers.licenses) lifetime (galaxy.model.PSAAssociation attribute) (galaxy.model.UserAuthnzToken attribute) LimitedOffsetDataProvider (class in galaxy.datatypes.dataproviders.base) line_class (galaxy.datatypes.data.Text attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.tabular.Pileup attribute) line_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.data.Text method) (galaxy.datatypes.tabular.Sam method) line_enumerator() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) line_iterator() (galaxy.datatypes.sniff.FilePrefix method) lineage() (galaxy.tools.Tool property) LineageMap (class in galaxy.tools.toolbox.lineages) (class in galaxy.tools.toolbox.lineages.factory) lineages_by_id (galaxy.tools.toolbox.lineages.interface.ToolLineage attribute) (galaxy.tools.toolbox.lineages.ToolLineage attribute) LineCount (class in galaxy.datatypes.data) lines() (galaxy.datatypes.util.gff_util.GFFFeature method) link_data() (galaxy.model.store.discover.JsonCollectedDatasetMatch property) link_to() (galaxy.model.DatasetInstance method) LinkageStudies (class in galaxy.datatypes.genetics) lint() (galaxy.tool_util.lint.LintContext method) lint_citations() (in module galaxy.tool_util.linters.citations) lint_command() (in module galaxy.tool_util.linters.command)

lint_cwl_validation() (in module galaxy.tool_util.linters.cwl) lint_description() (in module galaxy.tool_util.linters.cwl) lint_docker_image() (in module galaxy.tool_util.linters.cwl) lint_general() (in module galaxy.tool_util.linters.general) lint_help() (in module galaxy.tool_util.linters.help) lint_inputs() (in module galaxy.tool_util.linters.inputs) lint_new_draft() (in module galaxy.tool_util.linters.cwl) lint_output() (in module galaxy.tool_util.linters.outputs) lint_repeats() (in module galaxy.tool_util.linters.inputs) lint_stdio() (in module galaxy.tool_util.linters.stdio) lint_tool_source() (in module galaxy.tool_util.lint) lint_tool_source_with() (in module galaxy.tool_util.lint) lint_tsts() (in module galaxy.tool_util.linters.tests) lint_xml() (in module galaxy.tool_util.lint) lint_xml_order() (in module galaxy.tool_util.linters.xml_order) lint_xml_with() (in module galaxy.tool_util.lint) LintContext (class in galaxy.tool_util.lint) list() (galaxy.files.sources.FilesSource method) (galaxy.files.sources.posix.PosixFilesSource method) (galaxy.managers.base.ModelManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.library.Library method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) (tool_shed.managers.groups.GroupManager method) list_accessible() (galaxy.managers.secured.AccessibleManagerMixin method) list_as_xml() (galaxy.webapps.galaxy.controllers.history.HistoryController method) list_by_owner() (tool_shed.managers.repositories.RepoManager method) list_datasets_for_selection() (galaxy.webapps.galaxy.controllers.page.PageController method) list_dependencies() (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method) (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependencyResolver method) (galaxy.tool_util.deps.resolvers.ListableDependencyResolver method) list_displayable_roles() (galaxy.managers.roles.RoleManager method) list_dynamic_tools() (galaxy_test.base.populators.BaseDatasetPopulator method) list_grid() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) list_histories_for_selection() (galaxy.webapps.galaxy.controllers.page.PageController method) list_history_datasets() (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) list_identifiers() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method) list_libraries() (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) list_library_datasets() (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) list_owned() (galaxy.managers.secured.OwnableManagerMixin method) list_pages_for_selection() (galaxy.webapps.galaxy.controllers.page.PageController method) list_published() (galaxy.managers.sharable.SharableModelManager 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) list_shared() (galaxy.webapps.galaxy.controllers.history.HistoryController method) list_shared_with() (galaxy.managers.sharable.SharableModelManager method) list_tools() (galaxy.managers.tools.DynamicToolManager method) list_tracks() (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) list_visualizations_for_selection() (galaxy.webapps.galaxy.controllers.page.PageController method) list_workflows_for_selection() (galaxy.webapps.galaxy.controllers.page.PageController method) ListableDependencyResolver (class in galaxy.tool_util.deps.resolvers) ListDatasetCollectionType (class in galaxy.model.dataset_collections.types.list) listdir() (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method) listify() (in module galaxy.util) (tool_shed.utility_containers.utility_container_manager.RepositoryDependency property) (tool_shed.utility_containers.utility_container_manager.ToolDependency property) listify_options (galaxy.config.BaseAppConfiguration attribute) (galaxy.config.GalaxyAppConfiguration attribute) ListParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) ListParser (class in galaxy.visualization.plugins.config_parser) live_pidfile() (in module galaxy.util.pastescript.serve) LmodDependencyResolver (class in galaxy.tool_util.deps.resolvers.lmod) load() (galaxy.model.PSAPartial class method) (galaxy.util.aliaspickler.AliasPickleModule method) (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method) (in module galaxy.util.xml_macros) load_allowed_images() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) load_app_properties() (in module galaxy.util.properties) load_certified_level_one_repository_and_suite_tuple() (tool_shed.repository_registry.Registry method) load_changeset_in_tool_shed() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) load_checkable_revisions() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) load_citable_url() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) load_container_interface() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) load_data_dict() (in module galaxy_test.base.populators) load_datatype_converters() (galaxy.datatypes.registry.Registry method) load_datatype_sniffers() (galaxy.datatypes.registry.Registry method) load_datatypes() (galaxy.datatypes.registry.Registry method) load_deploy_config() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) load_dialect_impl() (galaxy.model.custom_types.JSONType method) (galaxy.model.custom_types.UUIDType method) load_display_applications() (galaxy.datatypes.registry.Registry method) load_display_tool_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) load_dynamic_tool() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) load_external_metadata_tool() (galaxy.datatypes.registry.Registry method) load_from_config_file() (galaxy.tools.data.ToolDataTableManager method) load_from_element() (galaxy.tools.data_manager.manager.DataManager method) load_from_xml() (galaxy.tools.data_manager.manager.DataManagers method) load_galaxy_app() (in module galaxy.main) load_galaxy_tool_migrations_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) load_hidden_lib_tool() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) load_hidden_tool() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) load_installed_datatype_converters() (galaxy.tool_shed.galaxy_install.datatypes.custom_datatype_manager.CustomDatatypeLoader method) load_installed_datatypes() (galaxy.tool_shed.galaxy_install.datatypes.custom_datatype_manager.CustomDatatypeLoader method) load_installed_display_applications() (galaxy.tool_shed.galaxy_install.datatypes.custom_datatype_manager.CustomDatatypeLoader method) load_invalid_tool() (tool_shed.webapp.controllers.repository.RepositoryController method) load_invalid_tool_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) load_item() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) load_job_metadata() (in module galaxy.metadata.set_metadata) load_job_proxy() (in module galaxy.tool_util.cwl.parser) load_lib_tools() (in module galaxy.tools.special_tools) load_manager_from_elem() (galaxy.tools.data_manager.manager.DataManagers method) load_metadata() (galaxy.metadata.ExtendedDirectoryMetadataGenerator method) (galaxy.metadata.MetadataCollectionStrategy method) (galaxy.metadata.PortableDirectoryMetadataGenerator method) load_module_sections() (in module galaxy.workflow.modules) load_one_dir() (in module tool_shed.util.shed_index) load_page_for_installed_tool() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) load_plugins() (in module galaxy.util.plugin_config) load_proprietary_converters_and_display_applications() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) load_proprietary_datatypes() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) load_random_x2_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method) load_repository_and_suite_tuple() (tool_shed.repository_registry.Registry method) load_repository_and_suite_tuples() (tool_shed.repository_registry.Registry method) load_step_handlers() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager.StepManager method) load_tag_handlers() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager.TagManager method) load_tool() (galaxy.tools.data_manager.manager.DataManager method) (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) (in module galaxy.tool_util.loader) load_tool_elements_from_path() (in module galaxy.tool_util.loader_directory) load_tool_from_cache() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) load_tool_from_changeset_revision() (tool_shed.tools.tool_validator.ToolValidator method) load_tool_from_config() (galaxy.tool_shed.tools.tool_validator.ToolValidator method) load_tool_from_tmp_config() (tool_shed.tools.tool_validator.ToolValidator method) load_tool_sources_from_path() (in module galaxy.tool_util.loader_directory) load_tool_with_refereces() (in module galaxy.tool_util.loader) load_tour() (galaxy.tours.ToursRegistry method) load_versioned_deps() (in module galaxy.tool_util.deps.brew_exts) load_viewable_repositories_and_suites_by_category() (tool_shed.repository_registry.Registry method) load_webhook_from_config() (galaxy.webhooks.WebhooksRegistry method) load_webhooks() (galaxy.webhooks.WebhooksRegistry method) load_with_references() (in module galaxy.util.xml_macros) load_workflow() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) (galaxy_test.base.populators.BaseWorkflowPopulator method) load_workflow_from_resource() (galaxy_test.base.populators.BaseWorkflowPopulator method) loadapp() (in module galaxy.util.pastescript.loadwsgi) loadfilter() (in module galaxy.util.pastescript.loadwsgi) loading_context() (galaxy.tool_util.cwl.schema.RawProcessReference property) (galaxy.tool_util.cwl.schema.ResolvedProcessDefinition property) (galaxy.tool_util.cwl.schema.SchemaLoader method) LOADING_PROPRIETARY_DATATYPES (galaxy.model.tool_shed_install.ToolShedRepository.installation_status attribute) LoadingContext (class in galaxy.tool_util.cwl.cwltool_deps) loads() (galaxy.util.aliaspickler.AliasPickleModule method) loadserver() (in module galaxy.util.pastescript.loadwsgi) local_extra_dirs() (in module galaxy.objectstore) local_storage() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) LocalDB (class in galaxy.auth.providers.localdb) localhost_addrs (galaxy.web_stack.UWSGIApplicationStack attribute) LocalJobRunner (class in galaxy.jobs.runners.local) LocalShell (class in galaxy.jobs.runners.util.cli.shell.local) localtimestamp() (in module galaxy.model.migrate.versions.util) (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) location (galaxy.model.HistoryDatasetAssociationSubset attribute) lock (galaxy.tools.toolbox.lineages.interface.ToolLineage attribute) (galaxy.tools.toolbox.lineages.ToolLineage attribute) LOG (galaxy.tool_util.parser.stdio.StdioErrorLevel attribute) log() (galaxy.util.custom_logging.fluent_log.FluentTraceLogger method) (galaxy.util.custom_logging.TraceLogger method) log_action() (galaxy.managers.context.ProvidesAppContext method) log_event() (galaxy.managers.context.ProvidesAppContext method) log_filter() (galaxy.web_stack.ApplicationStack class method) log_filter_class (galaxy.web_stack.ApplicationStack attribute) (galaxy.web_stack.UWSGIApplicationStack attribute) log_format (galaxy.web_stack.ApplicationStack attribute) (galaxy.web_stack.UWSGIApplicationStack attribute) log_request_query_counts() (in module galaxy.model.orm.engine_factory) log_results() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method) log_startup() (galaxy.web_stack.ApplicationStack method) (galaxy.web_stack.UWSGIApplicationStack method) log_str() (galaxy.model.JobLike method) (galaxy.model.Workflow method) (galaxy.model.WorkflowInvocation method) (galaxy.model.WorkflowStep method) LoggedInToolFormTestCase (class in galaxy_test.selenium.test_tool_form) LOGGING_CONFIG_DEFAULT (in module galaxy.config) logging_file_config() (galaxy.util.pastescript.serve.Command method) login() (galaxy.jobs.runners.godocker.GodockerJobRunner method) (galaxy.webapps.galaxy.controllers.authnz.OIDC method) (galaxy.webapps.galaxy.controllers.root.RootController method) (galaxy.webapps.galaxy.controllers.user.User method) (galaxy_test.selenium.framework.TestWithSeleniumMixin method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) (tool_shed.webapp.controllers.user.User method) LoginTestCase (class in galaxy_test.selenium.test_login) logout() (galaxy.authnz.custos_authnz.CustosAuthnz method) (galaxy.authnz.IdentityProvider method) (galaxy.authnz.managers.AuthnzManager method) (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) (galaxy.webapps.galaxy.controllers.authnz.OIDC method) (galaxy.webapps.galaxy.controllers.user.User method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) (tool_shed.webapp.controllers.user.User method) logout_if_needed() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) logs_command() (in module galaxy.tool_util.deps.docker_util) long_description (tool_shed.webapp.model.Repository attribute) looks_like_a_cwl_artifact() (in module galaxy.tool_util.loader_directory) looks_like_a_tool_cwl() (in module galaxy.tool_util.loader_directory) looks_like_a_tool_xml() (in module galaxy.tool_util.loader_directory) looks_like_a_tool_yaml() (in module galaxy.tool_util.loader_directory) looks_like_uri() (galaxy.files.ConfiguredFileSources method) Loom (class in galaxy.datatypes.binary) LowerTriangleDistanceMatrix (class in galaxy.datatypes.mothur) Lped (class in galaxy.datatypes.genetics) LSF (class in galaxy.jobs.runners.util.cli.job.lsf)

M

macro_paths() (galaxy.tool_util.parser.interface.ToolSource property) (galaxy.tool_util.parser.ToolSource property) (galaxy.tool_util.parser.xml.XmlToolSource property) Maf (class in galaxy.datatypes.sequence) maf_index_by_uid() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) MafCustomTrack (class in galaxy.datatypes.sequence) magic_header() (galaxy.datatypes.sniff.FilePrefix method) magic_number (galaxy.datatypes.binary.Cpt attribute) (galaxy.datatypes.binary.Edr attribute) (galaxy.datatypes.binary.GmxBinary attribute) (galaxy.datatypes.binary.Trr attribute) (galaxy.datatypes.binary.Xtc attribute) main() (in module galaxy.config.config_manage) (in module galaxy.config.script) (in module galaxy.datatypes.converters.bgzip) (in module galaxy.datatypes.converters.cram_to_bam) (in module galaxy.datatypes.converters.fastq_to_fqtoc) (in module galaxy.datatypes.converters.gff_to_interval_index_converter) (in module galaxy.datatypes.converters.interval_to_fli) (in module galaxy.datatypes.converters.interval_to_interval_index_converter) (in module galaxy.datatypes.converters.interval_to_tabix_converter) (in module galaxy.datatypes.converters.lped_to_fped_converter) (in module galaxy.datatypes.converters.lped_to_pbed_converter) (in module galaxy.datatypes.converters.pbed_ldreduced_converter) (in module galaxy.datatypes.converters.pbed_to_lped_converter) (in module galaxy.datatypes.converters.pileup_to_interval_index_converter) (in module galaxy.datatypes.converters.tabular_csv) (in module galaxy.datatypes.converters.tabular_to_dbnsfp) (in module galaxy.datatypes.converters.vcf_to_interval_index_converter) (in module galaxy.datatypes.converters.vcf_to_vcf_bgzip) (in module galaxy.datatypes.converters.wiggle_to_simple_converter) (in module galaxy.main) (in module galaxy.model.store.build_objects) (in module galaxy.selenium.scripts.dump_tour) (in module galaxy.tool_util.deps.brew_exts) (in module galaxy.tool_util.deps.mulled.mulled_build) (in module galaxy.tool_util.deps.mulled.mulled_build_channel) (in module galaxy.tool_util.deps.mulled.mulled_build_files) (in module galaxy.tool_util.deps.mulled.mulled_build_tool) (in module galaxy.tool_util.deps.mulled.mulled_list) (in module galaxy.tool_util.deps.mulled.mulled_search) (in module galaxy.tool_util.deps.mulled.mulled_update_singularity_containers) (in module galaxy.tool_util.verify.script) (in module galaxy.tools.data_fetch) (in module galaxy.tools.imp_exp.export_history) (in module galaxy.tools.imp_exp.unpack_tar_gz_archive) (in module galaxy.util.script) main_factory() (in module galaxy.util.script) main_panel() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) main_test_search() (in module galaxy.tool_util.deps.mulled.get_tests) make_accessible_and_publishable() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) make_backup() (tool_shed.util.hgweb_config.HgWebConfigManager method) make_body_iterable() (galaxy.web.framework.base.WebApplication method) (galaxy.webapps.base.webapp.WebApplication method) make_catching_iter() (galaxy.web.framework.middleware.error.ErrorMiddleware method) make_copy() (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.model.metadata.FileParameter method) (galaxy.model.metadata.MetadataParameter method) make_dataset_public() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) make_dict_copy() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataCollection method) (in module galaxy.tools.parameters.wrapped) make_directory() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MakeDirectory method) make_filter() (in module galaxy.web.framework.middleware.translogger) make_folder_public() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) make_html_peek_header() (galaxy.datatypes.tabular.TabularData method) make_html_peek_rows() (galaxy.datatypes.tabular.TabularData method) make_html_table() (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.mothur.SffFlow method) (galaxy.datatypes.sequence.Maf method) (galaxy.datatypes.tabular.Eland method) (galaxy.datatypes.tabular.TabularData method) make_importable() (galaxy.managers.sharable.SharableModelManager method) make_library_public() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) make_non_importable() (galaxy.managers.sharable.SharableModelManager method) make_private() (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy_test.base.populators.BaseDatasetPopulator method) make_public() (galaxy.managers.libraries.LibraryManager method) make_same_length() (in module tool_shed.util.search_util) make_static() (in module galaxy.web.framework.middleware.static) make_tag_string_list() (galaxy.model.HasTags method) make_temp_fname() (in module galaxy.tool_util.verify) MakeDirectory (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) MakeInstall (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) makeLDreduced() (in module galaxy.datatypes.converters.pbed_ldreduced_converter) makeNode() (galaxy.visualization.data_providers.phyloviz.baseparser.PhyloTree method) maketrans() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) MAKO_TEMPLATE (galaxy.visualization.plugins.plugin.ChartVisualizationPlugin attribute) (galaxy.visualization.plugins.plugin.ScriptVisualizationPlugin attribute) MalformedContents MalformedId MalformedYMLException malicious (tool_shed.webapp.model.RepositoryMetadata attribute) MAlist (class in galaxy.datatypes.genetics) manage_categories() (tool_shed.webapp.controllers.admin.AdminController method) manage_category_grid (tool_shed.webapp.controllers.admin.AdminController attribute) manage_components() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method) manage_db() (in module galaxy.model.orm.scripts) manage_email_alerts() (tool_shed.webapp.controllers.repository.RepositoryController method) manage_repositories_ready_for_review() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method) manage_repositories_reviewed_by_me() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method) manage_repositories_with_invalid_tests() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method) manage_repositories_with_reviews() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method) manage_repositories_without_reviews() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method) manage_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (tool_shed.webapp.controllers.repository.RepositoryController method) manage_repository_admins() (tool_shed.webapp.controllers.repository.RepositoryController method) manage_repository_reviews() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method) manage_repository_reviews_of_revision() (tool_shed.webapp.controllers.repository.RepositoryController method) (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method) manage_review_components() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) manage_role_associations() (tool_shed.webapp.controllers.admin.AdminController method) manage_roles_and_groups_for_user() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (tool_shed.util.admin_util.Admin method) manage_tool_dependencies() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) manage_user_info() (tool_shed.webapp.controllers.user.User method) manage_users_and_groups_for_quota() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) manage_users_and_groups_for_role() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (tool_shed.util.admin_util.Admin method) manage_users_and_roles_for_group() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (tool_shed.util.admin_util.Admin method) ManageCategoryGrid (class in tool_shed.grids.admin_grids) managed_history() (in module galaxy_test.selenium.framework) ManageDatasetRBACPermission (class in galaxy.managers.rbac_secured) ManageInformationTestCase (class in galaxy_test.selenium.test_personal_information) manager (galaxy.webapps.base.controller.SharableMixin attribute) manager() (galaxy.managers.base.HasAModelManager property) manager_dependency() (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) manager_requirements() (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) ManagesIntegratedToolPanelMixin (class in galaxy.tools.toolbox.integrated_panel) mandatory_headers (galaxy.datatypes.speech.BPF attribute) map_datasets() (galaxy.managers.hdcas.HDCAManager method) (galaxy.managers.history_contents.HistoryContentsManager method) map_over_action_tuples() (galaxy.model.dataset_collections.matching.MatchingCollections method) map_over_collection_type() (in module galaxy.model.dataset_collections.type_description) map_port() (galaxy.containers.Container method) map_tool_to_destination() (in module galaxy.jobs.dynamic_tool_destination) MappableDependencyResolver (class in galaxy.tool_util.deps.resolvers) mapped_over_output_actions (galaxy.jobs.actions.post.ActionBox attribute) mapping() (galaxy.webapps.galaxy.api.datatypes.DatatypesController method) mapping_as_dict() (galaxy.util.rules_dsl.RuleSet property) MAPPING_PRESET (galaxy.tools.parameters.sanitize.ToolParameterSanitizer attribute) MappingContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit) mark_as_failed() (galaxy.jobs.runners.AsynchronousJobRunner method) mark_as_finished() (galaxy.jobs.runners.AsynchronousJobRunner method) mark_as_populated() (galaxy.model.DatasetCollection method) mark_as_queued() (galaxy.jobs.runners.BaseJobRunner method) mark_as_resubmitted() (galaxy.jobs.JobWrapper method) (galaxy.jobs.runners.BaseJobRunner method) mark_category_deleted() (tool_shed.webapp.controllers.admin.AdminController method) mark_deleted() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) (galaxy.model.Job method) mark_failed() (galaxy.model.Job method) mark_group_deleted() (tool_shed.util.admin_util.Admin method) mark_obj_deleted() (in module tool_shed.test.base.test_db_util) mark_role_deleted() (tool_shed.util.admin_util.Admin method) mark_stopped() (galaxy.model.Job method) mark_tool_dependency_installed() (galaxy.tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) mark_undeleted() (galaxy.model.DatasetInstance method) mark_unhidden() (galaxy.model.DatasetInstance method) mark_user_deleted() (tool_shed.util.admin_util.Admin method) markdown (galaxy.workflow.refactor.schema.Report attribute) MarkdownWorkflowMarkdownReportGeneratorPlugin (class in galaxy.workflow.reports.generators.markdown) MarkerMap (class in galaxy.datatypes.genetics) marshal() (galaxy.datatypes.metadata.FileParameter class method) (galaxy.datatypes.metadata.MetadataParameter class method) (galaxy.datatypes.metadata.PythonObjectParameter class method) (galaxy.datatypes.metadata.RangeParameter class method) (galaxy.datatypes.metadata.SelectParameter class method) (galaxy.model.metadata.FileParameter class method) (galaxy.model.metadata.MetadataParameter class method) (galaxy.model.metadata.PythonObjectParameter class method) (galaxy.model.metadata.RangeParameter class method) (galaxy.model.metadata.SelectParameter class method) MascotDat (class in galaxy.datatypes.proteomics) MascotXML (class in galaxy.datatypes.proteomics) MashSketch (class in galaxy.datatypes.binary) mask_password_from_url() (in module galaxy.util) MassHunterTar (class in galaxy.datatypes.binary) MassLynxTar (class in galaxy.datatypes.binary) match() (galaxy.job_execution.output_collect.DatasetCollector method) (galaxy.model.store.discover.DiscoveredFile property) (galaxy.model.store.discover.DiscoveredFileError property) match_collections() (galaxy.managers.collections.DatasetCollectionManager method) (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.DataCollectionToolParameter method) match_multirun_collections() (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.DataCollectionToolParameter method) matched_repository_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) MatchedRepositoryGrid (class in tool_shed.grids.repository_grids) MatchedRepositoryGrid.DescriptionColumn (class in tool_shed.grids.repository_grids) MatchedRepositoryGrid.NameColumn (class in tool_shed.grids.repository_grids) MatchedRepositoryGrid.RevisionColumn (class in tool_shed.grids.repository_grids) MatchedRepositoryGrid.UserColumn (class in tool_shed.grids.repository_grids) matches_any() (galaxy.datatypes.binary.DynamicCompressedArchive method) (galaxy.datatypes.data.Data method) matches_requirement() (galaxy.tool_util.deps.resolvers.RequirementMapping method) matches_selector() (galaxy.datatypes.dataproviders.hierarchy.XMLDataProvider method) MatchingCollections (class in galaxy.model.dataset_collections.matching) MatrixMarket (class in galaxy.datatypes.tabular) MauveXmfa (class in galaxy.datatypes.msa) MAX (galaxy.tool_util.parser.stdio.StdioErrorLevel attribute) max_args (galaxy.util.pastescript.serve.Command attribute) max_args_error (galaxy.util.pastescript.serve.Command attribute) MAX_CHUNK_SIZE (galaxy.datatypes.dataproviders.chunk.ChunkDataProvider attribute) max_edit_dist (in module galaxy.jobs.dynamic_tool_destination) MAX_LINES_RETURNED (galaxy.visualization.data_providers.basic.ColumnDataProvider attribute) MAX_NUMERIC (galaxy.model.JobLike attribute) max_optional_metadata_filesize() (galaxy.datatypes.data.Data property) MAX_SEQUENCE_SIZE (galaxy.datatypes.util.maf_utilities.RegionAlignment attribute) (galaxy.tools.util.maf_utilities.RegionAlignment attribute) MCool (class in galaxy.datatypes.binary) md5() (in module galaxy.util.hash_util) (in module galaxy.web.framework.helpers) MEM_SELF (galaxy.web_stack.handlers.HANDLER_ASSIGNMENT_METHODS attribute) member_class (galaxy.containers.docker_model.DockerNodeLabels attribute) (galaxy.containers.docker_model.DockerServiceConstraints attribute) members (galaxy.model.Group attribute) members() (galaxy.containers.docker_model.DockerAttributeContainer property) MemePsp (class in galaxy.datatypes.sequence) MEMEXml (class in galaxy.datatypes.xml) MemInfoPlugin (class in galaxy.job_metrics.instrumenters.meminfo) merge() (galaxy.datatypes.binary.BamNative static method) (galaxy.datatypes.blast.BlastXml static method) (galaxy.datatypes.data.Data static method) (galaxy.datatypes.graph.Sif static method) (galaxy.datatypes.graph.Xgmml static method) (galaxy.datatypes.molecules.CML static method) (galaxy.datatypes.molecules.FPS static method) (galaxy.datatypes.molecules.OBFS method) (galaxy.datatypes.tabular.BaseVcf static method) (galaxy.datatypes.tabular.Sam static method) (galaxy.datatypes.xml.GenericXml static method) merge_containers_dicts_for_new_install() (tool_shed.galaxy_install.dependency_display.DependencyDisplayer method) merge_missing_repository_dependencies_to_installed_container() (tool_shed.galaxy_install.dependency_display.DependencyDisplayer method) merge_missing_tool_dependencies_to_installed_container() (tool_shed.galaxy_install.dependency_display.DependencyDisplayer method) merge_sorted_iterables() (in module galaxy.util) merge_tool_data_table() (galaxy.tools.data.TabularToolDataTable method) (galaxy.tools.data.ToolDataTable method) merge_type (galaxy.model.WorkflowStepInput attribute) MergeCollectionTool (class in galaxy.tools) merged_environment_name() (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method) Meryldb (class in galaxy.datatypes.binary) message (galaxy.model.Event attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.workflow.refactor.schema.RefactorActionExecutionMessage attribute) message() (galaxy.util.pastescript.serve.BadCommand property) (galaxy.util.pastescript.serve.Command.BadCommand property) message_exception() (galaxy.webapps.base.controller.BaseUIController method) message_type (galaxy.workflow.refactor.schema.RefactorActionExecutionMessage attribute) MessageApplicationStack (class in galaxy.web_stack) MessageException messages (galaxy.workflow.refactor.schema.RefactorActionExecution attribute) META_PARAMETERS (galaxy.model.WorkflowRequestInputParameter.types attribute) Metadata (class in tool_shed.repository_types.metadata) metadata (galaxy.model.tool_shed_install.ToolShedRepository attribute) (in module galaxy.model.migrate.versions.0121_workflow_uuids) MetaData (in module galaxy.tool_util.deps.conda_compat) metadata (tool_shed.webapp.model.RepositoryMetadata attribute) metadata() (galaxy.model.DatasetInstance property) (galaxy.tool_util.cwl.util.GalaxyOutput property) (tool_shed.webapp.api.repositories.RepositoriesController method) metadata_file_types() (galaxy.model.DatasetInstance property) metadata_revisions (tool_shed.webapp.model.Repository attribute) metadata_safe (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) metadata_spec (galaxy.datatypes.annotation.Augustus attribute) (galaxy.datatypes.annotation.SnapHmm attribute) (galaxy.datatypes.anvio.AnvioComposite attribute) (galaxy.datatypes.anvio.AnvioContigsDB attribute) (galaxy.datatypes.anvio.AnvioDB attribute) (galaxy.datatypes.anvio.AnvioGenomesDB attribute) (galaxy.datatypes.anvio.AnvioPanDB attribute) (galaxy.datatypes.anvio.AnvioProfileDB attribute) (galaxy.datatypes.anvio.AnvioSamplesDB attribute) (galaxy.datatypes.anvio.AnvioStructureDB attribute) (galaxy.datatypes.assembly.Amos attribute) (galaxy.datatypes.assembly.Roadmaps attribute) (galaxy.datatypes.assembly.Sequences attribute) (galaxy.datatypes.assembly.Velvet attribute) (galaxy.datatypes.binary.Ab1 attribute) (galaxy.datatypes.binary.Anndata attribute) (galaxy.datatypes.binary.BafTar attribute) (galaxy.datatypes.binary.Bam attribute) (galaxy.datatypes.binary.BamInputSorted attribute) (galaxy.datatypes.binary.BamNative attribute) (galaxy.datatypes.binary.BamQuerynameSorted attribute) (galaxy.datatypes.binary.BaseBcf attribute) (galaxy.datatypes.binary.Bcf attribute) (galaxy.datatypes.binary.BcfUncompressed attribute) (galaxy.datatypes.binary.BigBed attribute) (galaxy.datatypes.binary.BigWig attribute) (galaxy.datatypes.binary.Binary attribute) (galaxy.datatypes.binary.Biom2 attribute) (galaxy.datatypes.binary.BlibSQlite attribute) (galaxy.datatypes.binary.Bz2DynamicCompressedArchive attribute) (galaxy.datatypes.binary.Cel attribute) (galaxy.datatypes.binary.ChiraSQLite attribute) (galaxy.datatypes.binary.CompressedArchive attribute) (galaxy.datatypes.binary.CompressedZipArchive attribute) (galaxy.datatypes.binary.Cool attribute) (galaxy.datatypes.binary.Cpt attribute) (galaxy.datatypes.binary.CRAM attribute) (galaxy.datatypes.binary.CuffDiffSQlite attribute) (galaxy.datatypes.binary.DAA attribute) (galaxy.datatypes.binary.Dcd attribute) (galaxy.datatypes.binary.DlibSQlite attribute) (galaxy.datatypes.binary.DMND attribute) (galaxy.datatypes.binary.DynamicCompressedArchive attribute) (galaxy.datatypes.binary.Edr attribute) (galaxy.datatypes.binary.ElibSQlite attribute) (galaxy.datatypes.binary.ExcelXls attribute) (galaxy.datatypes.binary.Fast5Archive attribute) (galaxy.datatypes.binary.Fast5ArchiveBz2 attribute) (galaxy.datatypes.binary.Fast5ArchiveGz attribute) (galaxy.datatypes.binary.GAFASQLite attribute) (galaxy.datatypes.binary.GeminiSQLite attribute) (galaxy.datatypes.binary.GenericAsn1Binary attribute) (galaxy.datatypes.binary.GmxBinary attribute) (galaxy.datatypes.binary.GzDynamicCompressedArchive attribute) (galaxy.datatypes.binary.H5 attribute) (galaxy.datatypes.binary.ICM attribute) (galaxy.datatypes.binary.Idat attribute) (galaxy.datatypes.binary.IdpDB attribute) (galaxy.datatypes.binary.Loom attribute) (galaxy.datatypes.binary.MashSketch attribute) (galaxy.datatypes.binary.MassHunterTar attribute) (galaxy.datatypes.binary.MassLynxTar attribute) (galaxy.datatypes.binary.MCool attribute) (galaxy.datatypes.binary.Meryldb attribute) (galaxy.datatypes.binary.MzSQlite attribute) (galaxy.datatypes.binary.NcbiTaxonomySQlite attribute) (galaxy.datatypes.binary.NetCDF attribute) (galaxy.datatypes.binary.OSW attribute) (galaxy.datatypes.binary.OxliBinary attribute) (galaxy.datatypes.binary.OxliCountGraph attribute) (galaxy.datatypes.binary.OxliGraphLabels attribute) (galaxy.datatypes.binary.OxliNodeGraph attribute) (galaxy.datatypes.binary.OxliStopTags attribute) (galaxy.datatypes.binary.OxliSubset attribute) (galaxy.datatypes.binary.OxliTagSet attribute) (galaxy.datatypes.binary.Parquet attribute) (galaxy.datatypes.binary.PostgresqlArchive attribute) (galaxy.datatypes.binary.PQP attribute) (galaxy.datatypes.binary.ProBam attribute) (galaxy.datatypes.binary.RData attribute) (galaxy.datatypes.binary.RMA6 attribute) (galaxy.datatypes.binary.Scf attribute) (galaxy.datatypes.binary.SearchGuiArchive attribute) (galaxy.datatypes.binary.Sff attribute) (galaxy.datatypes.binary.SQlite attribute) (galaxy.datatypes.binary.SQmass attribute) (galaxy.datatypes.binary.Sra attribute) (galaxy.datatypes.binary.TdfTar attribute) (galaxy.datatypes.binary.Trr attribute) (galaxy.datatypes.binary.TwoBit attribute) (galaxy.datatypes.binary.Vel attribute) (galaxy.datatypes.binary.WiffTar attribute) (galaxy.datatypes.binary.Xlsx attribute) (galaxy.datatypes.binary.Xtc attribute) (galaxy.datatypes.binary.YepTar attribute) (galaxy.datatypes.blast.BlastDomainDb attribute) (galaxy.datatypes.blast.BlastDomainDb5 attribute) (galaxy.datatypes.blast.BlastNucDb attribute) (galaxy.datatypes.blast.BlastNucDb5 attribute) (galaxy.datatypes.blast.BlastProtDb attribute) (galaxy.datatypes.blast.BlastProtDb5 attribute) (galaxy.datatypes.blast.BlastXml attribute) (galaxy.datatypes.blast.LastDb attribute) (galaxy.datatypes.chrominfo.ChromInfo attribute) (galaxy.datatypes.constructive_solid_geometry.PlyAscii attribute) (galaxy.datatypes.constructive_solid_geometry.PlyBinary attribute) (galaxy.datatypes.constructive_solid_geometry.STL attribute) (galaxy.datatypes.constructive_solid_geometry.VtkAscii attribute) (galaxy.datatypes.constructive_solid_geometry.VtkBinary attribute) (galaxy.datatypes.coverage.LastzCoverage attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.data.Directory attribute) (galaxy.datatypes.data.GenericAsn1 attribute) (galaxy.datatypes.data.LineCount attribute) (galaxy.datatypes.data.Newick attribute) (galaxy.datatypes.data.Nexus attribute) (galaxy.datatypes.data.Text attribute) (galaxy.datatypes.genetics.Affybatch attribute) (galaxy.datatypes.genetics.AllegroLOD attribute) (galaxy.datatypes.genetics.DataIn attribute) (galaxy.datatypes.genetics.Eigenstratgeno attribute) (galaxy.datatypes.genetics.Eigenstratpca attribute) (galaxy.datatypes.genetics.Eset attribute) (galaxy.datatypes.genetics.Fped attribute) (galaxy.datatypes.genetics.Fphe attribute) (galaxy.datatypes.genetics.GenomeGraphs attribute) (galaxy.datatypes.genetics.GenotypeMatrix attribute) (galaxy.datatypes.genetics.IdeasPre attribute) (galaxy.datatypes.genetics.ldIndep attribute) (galaxy.datatypes.genetics.LinkageStudies attribute) (galaxy.datatypes.genetics.Lped attribute) (galaxy.datatypes.genetics.MAlist attribute) (galaxy.datatypes.genetics.MarkerMap attribute) (galaxy.datatypes.genetics.Pbed attribute) (galaxy.datatypes.genetics.Phe attribute) (galaxy.datatypes.genetics.Pheno attribute) (galaxy.datatypes.genetics.Pphe attribute) (galaxy.datatypes.genetics.RexpBase attribute) (galaxy.datatypes.genetics.Rgenetics attribute) (galaxy.datatypes.genetics.rgFeatureList attribute) (galaxy.datatypes.genetics.rgSampleList attribute) (galaxy.datatypes.genetics.rgTabList attribute) (galaxy.datatypes.genetics.SNPMatrix attribute) (galaxy.datatypes.genetics.Snptest attribute) (galaxy.datatypes.gis.Shapefile attribute) (galaxy.datatypes.graph.Sif attribute) (galaxy.datatypes.graph.Xgmml attribute) (galaxy.datatypes.images.Analyze75 attribute) (galaxy.datatypes.images.Bmp attribute) (galaxy.datatypes.images.Eps attribute) (galaxy.datatypes.images.Gif attribute) (galaxy.datatypes.images.Gifti attribute) (galaxy.datatypes.images.Gmaj attribute) (galaxy.datatypes.images.Hamamatsu attribute) (galaxy.datatypes.images.Html attribute) (galaxy.datatypes.images.Im attribute) (galaxy.datatypes.images.Image attribute) (galaxy.datatypes.images.Jpg attribute) (galaxy.datatypes.images.Laj attribute) (galaxy.datatypes.images.Mirax attribute) (galaxy.datatypes.images.Nifti1 attribute) (galaxy.datatypes.images.Nifti2 attribute) (galaxy.datatypes.images.Nrrd attribute) (galaxy.datatypes.images.Pbm attribute) (galaxy.datatypes.images.Pcd attribute) (galaxy.datatypes.images.Pcx attribute) (galaxy.datatypes.images.Pdf attribute) (galaxy.datatypes.images.Pgm attribute) (galaxy.datatypes.images.Png attribute) (galaxy.datatypes.images.Ppm attribute) (galaxy.datatypes.images.Psd attribute) (galaxy.datatypes.images.Rast attribute) (galaxy.datatypes.images.Rgb attribute) (galaxy.datatypes.images.Sakura attribute) (galaxy.datatypes.images.Tck attribute) (galaxy.datatypes.images.Tiff attribute) (galaxy.datatypes.images.Trk attribute) (galaxy.datatypes.images.Xbm attribute) (galaxy.datatypes.images.Xpm attribute) (galaxy.datatypes.interval.Bed attribute) (galaxy.datatypes.interval.Bed12 attribute) (galaxy.datatypes.interval.Bed6 attribute) (galaxy.datatypes.interval.BedGraph attribute) (galaxy.datatypes.interval.BedStrict attribute) (galaxy.datatypes.interval.ChromatinInteractions attribute) (galaxy.datatypes.interval.CustomTrack attribute) (galaxy.datatypes.interval.ENCODEPeak attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Gff3 attribute) (galaxy.datatypes.interval.Gtf attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.interval.ProBed attribute) (galaxy.datatypes.interval.ScIdx attribute) (galaxy.datatypes.interval.Wiggle attribute) (galaxy.datatypes.isa.IsaJson attribute) (galaxy.datatypes.isa.IsaTab attribute) (galaxy.datatypes.media.Audio attribute) (galaxy.datatypes.media.Flv attribute) (galaxy.datatypes.media.Mkv attribute) (galaxy.datatypes.media.Mp3 attribute) (galaxy.datatypes.media.Mp4 attribute) (galaxy.datatypes.media.Mpg attribute) (galaxy.datatypes.media.Video attribute) (galaxy.datatypes.media.Wav attribute) (galaxy.datatypes.microarrays.Gal attribute) (galaxy.datatypes.microarrays.GenericMicroarrayFile attribute) (galaxy.datatypes.microarrays.Gpr attribute) (galaxy.datatypes.molecules.CML attribute) (galaxy.datatypes.molecules.DRF attribute) (galaxy.datatypes.molecules.FPS attribute) (galaxy.datatypes.molecules.GenericMolFile attribute) (galaxy.datatypes.molecules.grd attribute) (galaxy.datatypes.molecules.grdtgz attribute) (galaxy.datatypes.molecules.InChI attribute) (galaxy.datatypes.molecules.MOL attribute) (galaxy.datatypes.molecules.MOL2 attribute) (galaxy.datatypes.molecules.OBFS attribute) (galaxy.datatypes.molecules.PDB attribute) (galaxy.datatypes.molecules.PDBQT attribute) (galaxy.datatypes.molecules.PHAR attribute) (galaxy.datatypes.molecules.PQR attribute) (galaxy.datatypes.molecules.SDF attribute) (galaxy.datatypes.molecules.SMILES attribute) (galaxy.datatypes.mothur.AccNos attribute) (galaxy.datatypes.mothur.AlignCheck attribute) (galaxy.datatypes.mothur.AlignReport attribute) (galaxy.datatypes.mothur.Axes attribute) (galaxy.datatypes.mothur.ConsensusTaxonomy attribute) (galaxy.datatypes.mothur.CountTable attribute) (galaxy.datatypes.mothur.DistanceMatrix attribute) (galaxy.datatypes.mothur.Frequency attribute) (galaxy.datatypes.mothur.Group attribute) (galaxy.datatypes.mothur.GroupAbund attribute) (galaxy.datatypes.mothur.LaneMask attribute) (galaxy.datatypes.mothur.LowerTriangleDistanceMatrix attribute) (galaxy.datatypes.mothur.Names attribute) (galaxy.datatypes.mothur.Oligos attribute) (galaxy.datatypes.mothur.Otu attribute) (galaxy.datatypes.mothur.PairwiseDistanceMatrix attribute) (galaxy.datatypes.mothur.Quantile attribute) (galaxy.datatypes.mothur.RefTaxonomy attribute) (galaxy.datatypes.mothur.Sabund attribute) (galaxy.datatypes.mothur.SecondaryStructureMap attribute) (galaxy.datatypes.mothur.SffFlow attribute) (galaxy.datatypes.mothur.SquareDistanceMatrix attribute) (galaxy.datatypes.mothur.Summary attribute) (galaxy.datatypes.mothur.TaxonomySummary attribute) (galaxy.datatypes.msa.Hmmer attribute) (galaxy.datatypes.msa.Hmmer2 attribute) (galaxy.datatypes.msa.Hmmer3 attribute) (galaxy.datatypes.msa.HmmerPress attribute) (galaxy.datatypes.msa.InfernalCM attribute) (galaxy.datatypes.msa.MauveXmfa attribute) (galaxy.datatypes.msa.Msf attribute) (galaxy.datatypes.msa.Stockholm_1_0 attribute) (galaxy.datatypes.neo4j.Neo4j attribute) (galaxy.datatypes.neo4j.Neo4jDB attribute) (galaxy.datatypes.neo4j.Neo4jDBzip attribute) (galaxy.datatypes.ngsindex.BowtieBaseIndex attribute) (galaxy.datatypes.ngsindex.BowtieColorIndex attribute) (galaxy.datatypes.ngsindex.BowtieIndex attribute) (galaxy.datatypes.phylip.Phylip attribute) (galaxy.datatypes.plant_tribes.PlantTribesKsComponents attribute) (galaxy.datatypes.plant_tribes.Smat attribute) (galaxy.datatypes.proteomics.ConsensusXML attribute) (galaxy.datatypes.proteomics.Dta attribute) (galaxy.datatypes.proteomics.Dta2d attribute) (galaxy.datatypes.proteomics.Edta attribute) (galaxy.datatypes.proteomics.FeatureXML attribute) (galaxy.datatypes.proteomics.IdXML attribute) (galaxy.datatypes.proteomics.ImzML attribute) (galaxy.datatypes.proteomics.Kroenik attribute) (galaxy.datatypes.proteomics.MascotDat attribute) (galaxy.datatypes.proteomics.MascotXML attribute) (galaxy.datatypes.proteomics.Mgf attribute) (galaxy.datatypes.proteomics.Ms2 attribute) (galaxy.datatypes.proteomics.Msp attribute) (galaxy.datatypes.proteomics.MzData attribute) (galaxy.datatypes.proteomics.MzIdentML attribute) (galaxy.datatypes.proteomics.MzML attribute) (galaxy.datatypes.proteomics.MzQuantML attribute) (galaxy.datatypes.proteomics.MzTab attribute) (galaxy.datatypes.proteomics.MzTab2 attribute) (galaxy.datatypes.proteomics.MzXML attribute) (galaxy.datatypes.proteomics.NmrML attribute) (galaxy.datatypes.proteomics.ParamXml attribute) (galaxy.datatypes.proteomics.PEFF attribute) (galaxy.datatypes.proteomics.PepList attribute) (galaxy.datatypes.proteomics.PepXml attribute) (galaxy.datatypes.proteomics.PepXmlReport attribute) (galaxy.datatypes.proteomics.ProteomicsXml attribute) (galaxy.datatypes.proteomics.ProtXML attribute) (galaxy.datatypes.proteomics.ProtXmlReport attribute) (galaxy.datatypes.proteomics.PSMS attribute) (galaxy.datatypes.proteomics.QCML attribute) (galaxy.datatypes.proteomics.Sf3 attribute) (galaxy.datatypes.proteomics.SPLib attribute) (galaxy.datatypes.proteomics.SPLibNoIndex attribute) (galaxy.datatypes.proteomics.TandemXML attribute) (galaxy.datatypes.proteomics.ThermoRAW attribute) (galaxy.datatypes.proteomics.TrafoXML attribute) (galaxy.datatypes.proteomics.TraML attribute) (galaxy.datatypes.proteomics.UniProtXML attribute) (galaxy.datatypes.proteomics.Wiff attribute) (galaxy.datatypes.proteomics.XHunterAslFormat attribute) (galaxy.datatypes.proteomics.XquestSpecXML attribute) (galaxy.datatypes.proteomics.XquestXML attribute) (galaxy.datatypes.qualityscore.QualityScore attribute) (galaxy.datatypes.qualityscore.QualityScore454 attribute) (galaxy.datatypes.qualityscore.QualityScoreIllumina attribute) (galaxy.datatypes.qualityscore.QualityScoreSolexa attribute) (galaxy.datatypes.qualityscore.QualityScoreSOLiD attribute) (galaxy.datatypes.sequence.Alignment attribute) (galaxy.datatypes.sequence.Axt attribute) (galaxy.datatypes.sequence.BaseFastq attribute) (galaxy.datatypes.sequence.csFasta attribute) (galaxy.datatypes.sequence.DotBracket attribute) (galaxy.datatypes.sequence.Fasta attribute) (galaxy.datatypes.sequence.Fastg attribute) (galaxy.datatypes.sequence.Fastq attribute) (galaxy.datatypes.sequence.FastqCSSanger attribute) (galaxy.datatypes.sequence.FastqIllumina attribute) (galaxy.datatypes.sequence.FastqSanger attribute) (galaxy.datatypes.sequence.FastqSolexa attribute) (galaxy.datatypes.sequence.Genbank attribute) (galaxy.datatypes.sequence.Lav attribute) (galaxy.datatypes.sequence.Maf attribute) (galaxy.datatypes.sequence.MafCustomTrack attribute) (galaxy.datatypes.sequence.MemePsp attribute) (galaxy.datatypes.sequence.RNADotPlotMatrix attribute) (galaxy.datatypes.sequence.Sequence attribute) (galaxy.datatypes.sequence.SequenceSplitLocations attribute) (galaxy.datatypes.spaln.SpalnNuclDb attribute) (galaxy.datatypes.spaln.SpalnProtDb attribute) (galaxy.datatypes.speech.BPF attribute) (galaxy.datatypes.speech.TextGrid attribute) (galaxy.datatypes.tabular.BaseCSV attribute) (galaxy.datatypes.tabular.BaseVcf attribute) (galaxy.datatypes.tabular.CMAP attribute) (galaxy.datatypes.tabular.ConnectivityTable attribute) (galaxy.datatypes.tabular.CSV attribute) (galaxy.datatypes.tabular.Eland attribute) (galaxy.datatypes.tabular.ElandMulti attribute) (galaxy.datatypes.tabular.FeatureLocationIndex attribute) (galaxy.datatypes.tabular.MatrixMarket attribute) (galaxy.datatypes.tabular.Pileup attribute) (galaxy.datatypes.tabular.Sam attribute) (galaxy.datatypes.tabular.SraManifest attribute) (galaxy.datatypes.tabular.Tabular attribute) (galaxy.datatypes.tabular.TabularData attribute) (galaxy.datatypes.tabular.Taxonomy attribute) (galaxy.datatypes.tabular.TSV attribute) (galaxy.datatypes.tabular.Vcf attribute) (galaxy.datatypes.tabular.VcfGz attribute) (galaxy.datatypes.text.Arff attribute) (galaxy.datatypes.text.Biom1 attribute) (galaxy.datatypes.text.ExpressionJson attribute) (galaxy.datatypes.text.GeoJson attribute) (galaxy.datatypes.text.Gfa1 attribute) (galaxy.datatypes.text.Gfa2 attribute) (galaxy.datatypes.text.Html attribute) (galaxy.datatypes.text.ImgtJson attribute) (galaxy.datatypes.text.Ipynb attribute) (galaxy.datatypes.text.IQTree attribute) (galaxy.datatypes.text.Json attribute) (galaxy.datatypes.text.Obo attribute) (galaxy.datatypes.text.Paf attribute) (galaxy.datatypes.text.SnpEffDb attribute) (galaxy.datatypes.text.SnpSiftDbNSFP attribute) (galaxy.datatypes.tracks.GeneTrack attribute) (galaxy.datatypes.tracks.UCSCTrackHub attribute) (galaxy.datatypes.triples.HDT attribute) (galaxy.datatypes.triples.Jsonld attribute) (galaxy.datatypes.triples.N3 attribute) (galaxy.datatypes.triples.NTriples attribute) (galaxy.datatypes.triples.Rdf attribute) (galaxy.datatypes.triples.Triples attribute) (galaxy.datatypes.triples.Turtle attribute) (galaxy.datatypes.xml.CisML attribute) (galaxy.datatypes.xml.Dzi attribute) (galaxy.datatypes.xml.GenericXml attribute) (galaxy.datatypes.xml.MEMEXml attribute) (galaxy.datatypes.xml.Owl attribute) (galaxy.datatypes.xml.Phyloxml attribute) (galaxy.datatypes.xml.Sbml attribute) MetadataCollection (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) MetadataCollectionStrategy (class in galaxy.metadata) MetadataElement (in module galaxy.model.metadata) MetadataElementSpec (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) MetadataFile (class in galaxy.model) MetadataGenerator (class in galaxy.tool_shed.metadata.metadata_generator) (class in tool_shed.metadata.metadata_generator) MetadataInDataTableColumnValidator (class in galaxy.tools.parameters.validation) MetadataInFileColumnValidator (class in galaxy.tools.parameters.validation) MetadataInRangeValidator (class in galaxy.tools.parameters.validation) MetadataNotInDataTableColumnValidator (class in galaxy.tools.parameters.validation) MetadataParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) MetadataSourceProvider (class in galaxy.job_execution.output_collect) (class in galaxy.model.store.discover) MetadataSpecCollection (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) MetadataTempFile (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) MetadataToolOutputAction (class in galaxy.tool_util.parser.output_actions) MetadataType (class in galaxy.model.custom_types) MetadataValidator (class in galaxy.tools.parameters.validation) MetadataValueFilter (class in galaxy.tool_util.parser.output_actions) metric_name (galaxy.model.JobMetricNumeric attribute) (galaxy.model.JobMetricText attribute) (galaxy.model.TaskMetricNumeric attribute) (galaxy.model.TaskMetricText attribute) metric_query() (galaxy.jobs.rule_helper.RuleHelper method) metric_value (galaxy.model.JobMetricNumeric attribute) (galaxy.model.JobMetricText attribute) (galaxy.model.TaskMetricNumeric attribute) (galaxy.model.TaskMetricText attribute) metrics() (galaxy.model.JobLike property) (galaxy.webapps.galaxy.api.jobs.JobController method) MetricsController (class in galaxy.webapps.galaxy.api.metrics) Mgf (class in galaxy.datatypes.proteomics) MiddlewareWrapUnsupported migrate_to_current_version() (in module galaxy.model.migrate.check) (in module galaxy.model.tool_shed_install.migrate.check) (in module galaxy.tool_shed.galaxy_install.migrate.check) (in module tool_shed.webapp.model.migrate.check) MigrateTools (class in galaxy.model.tool_shed_install) MigrateToolsApplication (class in galaxy.tool_shed.galaxy_install.migrate.common) mime_type() (galaxy.datatypes.display_applications.parameters.DisplayDataValueWrapper method) (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper method) min_args (galaxy.util.pastescript.serve.Command attribute) (galaxy.util.pastescript.serve.ServeCommand attribute) min_args_error (galaxy.util.pastescript.serve.Command attribute) Mirax (class in galaxy.datatypes.images) missing_meta() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) (galaxy.model.none_like.NoneDataset method) missing_repository_dependencies() (galaxy.model.tool_shed_install.ToolShedRepository property) missing_test_components (tool_shed.webapp.model.RepositoryMetadata attribute) missing_tool_data_table_name() (galaxy.tools.parameters.dynamic_options.DynamicOptions property) missing_tool_dependencies() (galaxy.model.tool_shed_install.ToolShedRepository property) missing_tools() (galaxy.managers.workflows.CreatedWorkflow property) MissingTestComponent (class in tool_shed.utility_containers) MissingToolsException mkdtemp() (galaxy_test.driver.driver_util.TestDriver method) mkstemp_ln() (in module galaxy.util) Mkv (class in galaxy.datatypes.media) modal_body_selector() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) mode_is_valid() (galaxy.containers.ContainerVolume property) model() (galaxy.managers.context.ProvidesAppContext property) model_class (galaxy.managers.base.ModelFilterParser attribute) (galaxy.managers.base.ModelManager attribute) (galaxy.managers.cloud.CloudManager attribute) (galaxy.managers.cloudauthzs.CloudAuthzManager attribute) (galaxy.managers.datasets.DatasetAssociationFilterParser attribute) (galaxy.managers.datasets.DatasetAssociationManager attribute) (galaxy.managers.datasets.DatasetManager attribute) (galaxy.managers.hdas.HDAFilterParser attribute) (galaxy.managers.hdas.HDAManager attribute) (galaxy.managers.hdcas.HDCAManager attribute) (galaxy.managers.histories.HistoryFilters attribute) (galaxy.managers.histories.HistoryManager attribute) (galaxy.managers.history_contents.HistoryContentsFilters attribute) (galaxy.managers.lddas.LDDAManager attribute) (galaxy.managers.library_datasets.LibraryDatasetsManager attribute) (galaxy.managers.pages.PageManager attribute) (galaxy.managers.roles.RoleManager attribute) (galaxy.managers.roles.RoleModel attribute) (galaxy.managers.sharable.SharableModelFilters attribute) (galaxy.managers.tools.DynamicToolManager attribute) (galaxy.managers.users.AdminUserFilterParser attribute) (galaxy.managers.visualizations.VisualizationManager attribute) (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.GroupGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) model_manager_class (galaxy.managers.base.HasAModelManager attribute) (galaxy.managers.base.ModelDeserializer attribute) (galaxy.managers.base.ModelSerializer attribute) (galaxy.managers.base.ModelValidator attribute) (galaxy.managers.cloudauthzs.CloudAuthzsDeserializer attribute) (galaxy.managers.cloudauthzs.CloudAuthzsSerializer attribute) (galaxy.managers.configuration.AdminConfigSerializer attribute) (galaxy.managers.configuration.ConfigSerializer attribute) (galaxy.managers.datasets.DatasetAssociationDeserializer attribute) (galaxy.managers.datasets.DatasetAssociationSerializer attribute) (galaxy.managers.datasets.DatasetSerializer attribute) (galaxy.managers.hdas.HDADeserializer attribute) (galaxy.managers.hdas.HDAFilterParser attribute) (galaxy.managers.hdas.HDASerializer attribute) (galaxy.managers.hdcas.DCASerializer attribute) (galaxy.managers.hdcas.DCESerializer attribute) (galaxy.managers.hdcas.DCSerializer attribute) (galaxy.managers.hdcas.HDCASerializer attribute) (galaxy.managers.histories.HistoryDeserializer attribute) (galaxy.managers.histories.HistoryFilters attribute) (galaxy.managers.histories.HistorySerializer attribute) (galaxy.managers.history_contents.HistoryContentsSerializer attribute) (galaxy.managers.pages.PageDeserializer attribute) (galaxy.managers.pages.PageSerializer attribute) (galaxy.managers.sharable.SharableModelDeserializer attribute) (galaxy.managers.users.AdminUserFilterParser attribute) (galaxy.managers.users.CurrentUserSerializer attribute) (galaxy.managers.users.UserDeserializer attribute) (galaxy.managers.users.UserSerializer attribute) (galaxy.managers.visualizations.VisualizationDeserializer attribute) (galaxy.managers.visualizations.VisualizationSerializer attribute) ModelDeserializer (class in galaxy.managers.base) ModelDeserializingError ModelExportStore (class in galaxy.model.store) ModelFilterParser (class in galaxy.managers.base) ModelImportStore (class in galaxy.model.store) ModelManager (class in galaxy.managers.base) ModelMapping (class in galaxy.model.base) ModelOperationToolAction (class in galaxy.tools.actions.model_operations) ModelPersistenceContext (class in galaxy.model.store.discover) ModelSerializer (class in galaxy.managers.base) ModelSerializingError ModelValidator (class in galaxy.managers.base) modified_time (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.JobContainerAssociation attribute) modify_environ() (galaxy.tool_util.deps.brew_exts.EnvAction method) module galaxy galaxy.actions galaxy.actions.admin galaxy.actions.library galaxy.app galaxy.auth galaxy.auth.providers galaxy.auth.providers.alwaysreject galaxy.auth.providers.ldap_ad galaxy.auth.providers.localdb galaxy.auth.providers.pam_auth galaxy.auth.util galaxy.authnz galaxy.authnz.custos_authnz galaxy.authnz.managers galaxy.authnz.psa_authnz galaxy.config galaxy.config.config_manage galaxy.config.schema galaxy.config.script galaxy.config_watchers galaxy.containers galaxy.containers.docker galaxy.containers.docker_decorators galaxy.containers.docker_model galaxy.containers.docker_swarm galaxy.datatypes galaxy.datatypes.annotation galaxy.datatypes.anvio galaxy.datatypes.assembly galaxy.datatypes.binary galaxy.datatypes.blast galaxy.datatypes.checkers galaxy.datatypes.chrominfo galaxy.datatypes.constructive_solid_geometry galaxy.datatypes.converters galaxy.datatypes.converters.bed_to_gff_converter galaxy.datatypes.converters.bgzip galaxy.datatypes.converters.cram_to_bam galaxy.datatypes.converters.fasta_to_len galaxy.datatypes.converters.fasta_to_tabular_converter galaxy.datatypes.converters.fastq_to_fqtoc galaxy.datatypes.converters.fastqsolexa_to_fasta_converter galaxy.datatypes.converters.fastqsolexa_to_qual_converter galaxy.datatypes.converters.gff_to_bed_converter galaxy.datatypes.converters.gff_to_interval_index_converter galaxy.datatypes.converters.interval_to_bed_converter galaxy.datatypes.converters.interval_to_bedstrict_converter galaxy.datatypes.converters.interval_to_fli galaxy.datatypes.converters.interval_to_interval_index_converter galaxy.datatypes.converters.interval_to_tabix_converter galaxy.datatypes.converters.lped_to_fped_converter galaxy.datatypes.converters.lped_to_pbed_converter galaxy.datatypes.converters.maf_to_fasta_converter galaxy.datatypes.converters.maf_to_interval_converter galaxy.datatypes.converters.pbed_ldreduced_converter galaxy.datatypes.converters.pbed_to_lped_converter galaxy.datatypes.converters.picard_interval_list_to_bed6_converter galaxy.datatypes.converters.pileup_to_interval_index_converter galaxy.datatypes.converters.ref_to_seq_taxonomy_converter galaxy.datatypes.converters.tabular_csv galaxy.datatypes.converters.tabular_to_dbnsfp galaxy.datatypes.converters.vcf_to_interval_index_converter galaxy.datatypes.converters.vcf_to_vcf_bgzip galaxy.datatypes.converters.wiggle_to_simple_converter galaxy.datatypes.coverage galaxy.datatypes.data galaxy.datatypes.dataproviders galaxy.datatypes.dataproviders.base galaxy.datatypes.dataproviders.chunk galaxy.datatypes.dataproviders.column galaxy.datatypes.dataproviders.dataset galaxy.datatypes.dataproviders.decorators galaxy.datatypes.dataproviders.exceptions galaxy.datatypes.dataproviders.external galaxy.datatypes.dataproviders.hierarchy galaxy.datatypes.dataproviders.line galaxy.datatypes.display_applications galaxy.datatypes.display_applications.application galaxy.datatypes.display_applications.parameters galaxy.datatypes.display_applications.util galaxy.datatypes.genetics galaxy.datatypes.gis galaxy.datatypes.graph galaxy.datatypes.images galaxy.datatypes.interval galaxy.datatypes.isa galaxy.datatypes.media galaxy.datatypes.metadata galaxy.datatypes.microarrays galaxy.datatypes.molecules galaxy.datatypes.mothur galaxy.datatypes.msa galaxy.datatypes.neo4j galaxy.datatypes.ngsindex galaxy.datatypes.phylip galaxy.datatypes.plant_tribes galaxy.datatypes.proteomics galaxy.datatypes.qualityscore galaxy.datatypes.registry galaxy.datatypes.sequence galaxy.datatypes.sniff galaxy.datatypes.spaln galaxy.datatypes.speech galaxy.datatypes.tabular galaxy.datatypes.text galaxy.datatypes.tracks galaxy.datatypes.triples galaxy.datatypes.upload_util galaxy.datatypes.util galaxy.datatypes.util.generic_util galaxy.datatypes.util.gff_util galaxy.datatypes.util.maf_utilities galaxy.datatypes.xml galaxy.dependencies galaxy.eggs galaxy.exceptions galaxy.exceptions.error_codes galaxy.files galaxy.files.sources galaxy.files.sources.dropbox galaxy.files.sources.galaxy galaxy.files.sources.posix galaxy.files.sources.s3 galaxy.files.sources.webdav galaxy.forms galaxy.forms.forms galaxy.job_execution galaxy.job_execution.datasets galaxy.job_execution.output_collect galaxy.job_execution.ports galaxy.job_execution.ports.view galaxy.job_execution.setup galaxy.job_metrics galaxy.job_metrics.collectl galaxy.job_metrics.collectl.cli galaxy.job_metrics.collectl.processes galaxy.job_metrics.collectl.stats galaxy.job_metrics.collectl.subsystems galaxy.job_metrics.formatting galaxy.job_metrics.instrumenters galaxy.job_metrics.instrumenters.cgroup galaxy.job_metrics.instrumenters.collectl galaxy.job_metrics.instrumenters.core galaxy.job_metrics.instrumenters.cpuinfo galaxy.job_metrics.instrumenters.env galaxy.job_metrics.instrumenters.hostname galaxy.job_metrics.instrumenters.meminfo galaxy.job_metrics.instrumenters.uname galaxy.jobs galaxy.jobs.actions galaxy.jobs.actions.post galaxy.jobs.command_factory galaxy.jobs.dynamic_tool_destination galaxy.jobs.handler galaxy.jobs.manager galaxy.jobs.mapper galaxy.jobs.rule_helper galaxy.jobs.rules galaxy.jobs.runners galaxy.jobs.runners.chronos galaxy.jobs.runners.cli galaxy.jobs.runners.condor galaxy.jobs.runners.drmaa galaxy.jobs.runners.godocker galaxy.jobs.runners.kubernetes galaxy.jobs.runners.local galaxy.jobs.runners.pbs galaxy.jobs.runners.pulsar galaxy.jobs.runners.slurm galaxy.jobs.runners.state_handler_factory galaxy.jobs.runners.state_handlers galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners.tasks galaxy.jobs.runners.univa galaxy.jobs.runners.util galaxy.jobs.runners.util.cli galaxy.jobs.runners.util.cli.factory galaxy.jobs.runners.util.cli.job galaxy.jobs.runners.util.cli.job.lsf galaxy.jobs.runners.util.cli.job.slurm galaxy.jobs.runners.util.cli.job.slurm_torque galaxy.jobs.runners.util.cli.job.torque galaxy.jobs.runners.util.cli.shell galaxy.jobs.runners.util.cli.shell.local galaxy.jobs.runners.util.cli.shell.rsh galaxy.jobs.runners.util.condor galaxy.jobs.runners.util.env galaxy.jobs.runners.util.external galaxy.jobs.runners.util.job_script galaxy.jobs.runners.util.kill galaxy.jobs.runners.util.process_groups galaxy.jobs.runners.util.pykube_util galaxy.jobs.runners.util.sudo galaxy.jobs.splitters galaxy.jobs.splitters.basic galaxy.jobs.splitters.multi galaxy.jobs.stock_rules galaxy.jobs.transfer_manager galaxy.main galaxy.managers galaxy.managers.annotatable galaxy.managers.api_keys galaxy.managers.base galaxy.managers.citations galaxy.managers.cloud galaxy.managers.cloudauthzs galaxy.managers.collections galaxy.managers.collections_util galaxy.managers.configuration galaxy.managers.containers galaxy.managers.context galaxy.managers.datasets galaxy.managers.deletable galaxy.managers.executables galaxy.managers.folders galaxy.managers.hdas galaxy.managers.hdcas galaxy.managers.histories galaxy.managers.history_contents galaxy.managers.interactivetool galaxy.managers.jobs galaxy.managers.lddas galaxy.managers.libraries galaxy.managers.library_datasets galaxy.managers.licenses galaxy.managers.markdown_parse galaxy.managers.markdown_util galaxy.managers.pages galaxy.managers.ratable galaxy.managers.rbac_secured galaxy.managers.roles galaxy.managers.secured galaxy.managers.session galaxy.managers.sharable galaxy.managers.taggable galaxy.managers.tools galaxy.managers.users galaxy.managers.visualizations galaxy.managers.workflows galaxy.metadata galaxy.metadata.set_metadata galaxy.model galaxy.model.base galaxy.model.custom_types 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galaxy.model.migrate.versions.0008_galaxy_forms galaxy.model.migrate.versions.0009_request_table galaxy.model.migrate.versions.0010_hda_display_at_authz_table galaxy.model.migrate.versions.0011_v0010_mysql_index_fix galaxy.model.migrate.versions.0012_user_address galaxy.model.migrate.versions.0013_change_lib_item_templates_to_forms galaxy.model.migrate.versions.0014_pages galaxy.model.migrate.versions.0015_tagging galaxy.model.migrate.versions.0016_v0015_mysql_index_fix galaxy.model.migrate.versions.0017_library_item_indexes galaxy.model.migrate.versions.0018_ordered_tags_and_page_tags galaxy.model.migrate.versions.0019_request_library_folder galaxy.model.migrate.versions.0020_library_upload_job galaxy.model.migrate.versions.0021_user_prefs galaxy.model.migrate.versions.0022_visualization_tables galaxy.model.migrate.versions.0023_page_published_and_deleted_columns galaxy.model.migrate.versions.0024_page_slug_unique_constraint galaxy.model.migrate.versions.0025_user_info galaxy.model.migrate.versions.0026_cloud_tables galaxy.model.migrate.versions.0027_request_events galaxy.model.migrate.versions.0028_external_metadata_file_override galaxy.model.migrate.versions.0029_user_actions galaxy.model.migrate.versions.0030_history_slug_column galaxy.model.migrate.versions.0031_community_and_workflow_tags galaxy.model.migrate.versions.0032_stored_workflow_slug_column galaxy.model.migrate.versions.0033_published_cols_for_histories_and_workflows galaxy.model.migrate.versions.0034_page_user_share_association galaxy.model.migrate.versions.0035_item_annotations_and_workflow_step_tags galaxy.model.migrate.versions.0036_add_deleted_column_to_library_template_assoc_tables galaxy.model.migrate.versions.0037_samples_library galaxy.model.migrate.versions.0038_add_inheritable_column_to_library_template_assoc_tables galaxy.model.migrate.versions.0039_add_synopsis_column_to_library_table galaxy.model.migrate.versions.0040_page_annotations galaxy.model.migrate.versions.0041_workflow_invocation galaxy.model.migrate.versions.0042_workflow_invocation_fix galaxy.model.migrate.versions.0043_visualization_sharing_tagging_annotating galaxy.model.migrate.versions.0044_add_notify_column_to_request_table galaxy.model.migrate.versions.0045_request_type_permissions_table galaxy.model.migrate.versions.0046_post_job_actions galaxy.model.migrate.versions.0047_job_table_user_id_column galaxy.model.migrate.versions.0048_dataset_instance_state_column galaxy.model.migrate.versions.0049_api_keys_table galaxy.model.migrate.versions.0050_drop_cloud_tables galaxy.model.migrate.versions.0051_imported_col_for_jobs_table galaxy.model.migrate.versions.0052_sample_dataset_table galaxy.model.migrate.versions.0053_item_ratings galaxy.model.migrate.versions.0054_visualization_dbkey galaxy.model.migrate.versions.0055_add_pja_assoc_for_jobs galaxy.model.migrate.versions.0056_workflow_outputs galaxy.model.migrate.versions.0057_request_notify galaxy.model.migrate.versions.0058_history_import_export galaxy.model.migrate.versions.0059_sample_dataset_file_path galaxy.model.migrate.versions.0060_history_archive_import galaxy.model.migrate.versions.0061_tasks galaxy.model.migrate.versions.0062_user_openid_table galaxy.model.migrate.versions.0063_sequencer_table galaxy.model.migrate.versions.0064_add_run_and_sample_run_association_tables galaxy.model.migrate.versions.0065_add_name_to_form_fields_and_values galaxy.model.migrate.versions.0066_deferred_job_and_transfer_job_tables galaxy.model.migrate.versions.0067_populate_sequencer_table galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services galaxy.model.migrate.versions.0069_rename_sequencer_form_type galaxy.model.migrate.versions.0070_add_info_column_to_deferred_job_table galaxy.model.migrate.versions.0071_add_history_and_workflow_to_sample galaxy.model.migrate.versions.0072_add_pid_and_socket_columns_to_transfer_job_table galaxy.model.migrate.versions.0073_add_ldda_to_implicit_conversion_table galaxy.model.migrate.versions.0074_add_purged_column_to_library_dataset_table galaxy.model.migrate.versions.0075_add_subindex_column_to_run_table galaxy.model.migrate.versions.0076_fix_form_values_data_corruption galaxy.model.migrate.versions.0077_create_tool_tag_association_table galaxy.model.migrate.versions.0078_add_columns_for_disk_usage_accounting galaxy.model.migrate.versions.0079_input_library_to_job_table galaxy.model.migrate.versions.0080_quota_tables galaxy.model.migrate.versions.0081_add_tool_version_to_hda_ldda galaxy.model.migrate.versions.0082_add_tool_shed_repository_table galaxy.model.migrate.versions.0083_add_prepare_files_to_task galaxy.model.migrate.versions.0084_add_ldda_id_to_implicit_conversion_table galaxy.model.migrate.versions.0085_add_task_info galaxy.model.migrate.versions.0086_add_tool_shed_repository_table_columns galaxy.model.migrate.versions.0087_tool_id_guid_map_table 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tool_shed.dependencies.repository.relation_builder tool_shed.dependencies.tool tool_shed.dependencies.tool.tag_attribute_handler tool_shed.galaxy_install tool_shed.galaxy_install.dependency_display tool_shed.galaxy_install.grids tool_shed.galaxy_install.grids.admin_toolshed_grids tool_shed.galaxy_install.utility_containers tool_shed.grids tool_shed.grids.admin_grids tool_shed.grids.repository_grid_filter_manager tool_shed.grids.repository_grids tool_shed.grids.repository_review_grids tool_shed.grids.util tool_shed.managers tool_shed.managers.groups tool_shed.managers.repositories tool_shed.metadata tool_shed.metadata.metadata_generator tool_shed.metadata.repository_metadata_manager tool_shed.repository_registry tool_shed.repository_types tool_shed.repository_types.metadata tool_shed.repository_types.registry tool_shed.repository_types.repository_suite_definition tool_shed.repository_types.tool_dependency_definition tool_shed.repository_types.unrestricted tool_shed.repository_types.util tool_shed.test tool_shed.test.base tool_shed.test.base.common tool_shed.test.base.test_db_util tool_shed.test.base.twilltestcase tool_shed.test.functional tool_shed.test.functional.test_0000_basic_repository_features tool_shed.test.functional.test_0010_repository_with_tool_dependencies tool_shed.test.functional.test_0020_basic_repository_dependencies tool_shed.test.functional.test_0030_repository_dependency_revisions tool_shed.test.functional.test_0040_repository_circular_dependencies tool_shed.test.functional.test_0050_circular_dependencies_4_levels tool_shed.test.functional.test_0070_invalid_tool tool_shed.test.functional.test_0080_advanced_circular_dependencies tool_shed.test.functional.test_0090_tool_search tool_shed.test.functional.test_0100_complex_repository_dependencies tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners tool_shed.test.functional.test_0130_datatype_converters tool_shed.test.functional.test_0140_tool_help_images tool_shed.test.functional.test_0150_prior_installation_required tool_shed.test.functional.test_0160_circular_prior_installation_required tool_shed.test.functional.test_0170_complex_prior_installation_required tool_shed.test.functional.test_0300_reset_all_metadata tool_shed.test.functional.test_0310_hg_api_features tool_shed.test.functional.test_0400_repository_component_reviews tool_shed.test.functional.test_0410_repository_component_review_access_control tool_shed.test.functional.test_0420_citable_urls_for_repositories tool_shed.test.functional.test_0430_browse_utilities tool_shed.test.functional.test_0440_deleting_dependency_definitions tool_shed.test.functional.test_0460_upload_to_repository tool_shed.test.functional.test_0470_tool_dependency_repository_type tool_shed.test.functional.test_0480_tool_dependency_xml_verification tool_shed.test.functional.test_0530_repository_admin_feature tool_shed.test.functional.test_0540_get_all_metadata_from_api tool_shed.test.functional.test_0550_metadata_updated_dependencies tool_shed.test.functional.test_1000_install_basic_repository tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies tool_shed.test.functional.test_1050_circular_dependencies_4_levels tool_shed.test.functional.test_1070_invalid_tool tool_shed.test.functional.test_1080_advanced_circular_dependency_installation tool_shed.test.functional.test_1090_repository_dependency_handling tool_shed.test.functional.test_1100_install_updated_repository_dependencies tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners tool_shed.test.functional.test_1150_datatype_converters tool_shed.test.functional.test_1160_tool_help_images tool_shed.test.functional.test_1170_prior_installation_required tool_shed.test.functional.test_1180_circular_prior_installation_required tool_shed.test.functional.test_1190_complex_prior_installation_required tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies tool_shed.test.functional.test_1220_uninstall_reinstall_repository_with_repository_dependencies tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions tool_shed.test.functional.test_1300_reset_all_metadata tool_shed.test.functional.test_1410_update_manager tool_shed.test.functional.test_1420_tool_dependency_environment_inheritance tool_shed.test.functional.test_1430_repair_installed_repository tool_shed.test.functional.test_1440_missing_env_sh_files tool_shed.test.functional.test_1450_installing_datatypes_sniffers tool_shed.test.functional.test_1460_data_managers tool_shed.test.functional.test_1470_updating_installed_repositories tool_shed.test.functional_tests tool_shed.tools tool_shed.tools.data_table_manager tool_shed.tools.tool_validator tool_shed.tools.tool_version_manager tool_shed.util tool_shed.util.admin_util tool_shed.util.basic_util tool_shed.util.commit_util tool_shed.util.common_util tool_shed.util.container_util tool_shed.util.encoding_util tool_shed.util.hg_util tool_shed.util.hgweb_config tool_shed.util.metadata_util tool_shed.util.readme_util tool_shed.util.repository_content_util tool_shed.util.repository_util tool_shed.util.review_util tool_shed.util.search_util tool_shed.util.shed_index tool_shed.util.shed_util_common tool_shed.util.tool_dependency_util tool_shed.util.tool_util tool_shed.util.web_util tool_shed.util.xml_util tool_shed.utility_containers tool_shed.utility_containers.utility_container_manager tool_shed.webapp tool_shed.webapp.api tool_shed.webapp.api.authenticate tool_shed.webapp.api.categories tool_shed.webapp.api.configuration tool_shed.webapp.api.groups tool_shed.webapp.api.repositories tool_shed.webapp.api.repository_revisions tool_shed.webapp.api.tools tool_shed.webapp.api.users tool_shed.webapp.app tool_shed.webapp.buildapp tool_shed.webapp.config tool_shed.webapp.controllers tool_shed.webapp.controllers.admin tool_shed.webapp.controllers.groups tool_shed.webapp.controllers.hg tool_shed.webapp.controllers.repository tool_shed.webapp.controllers.repository_review tool_shed.webapp.controllers.upload tool_shed.webapp.controllers.user tool_shed.webapp.framework tool_shed.webapp.framework.middleware tool_shed.webapp.framework.middleware.remoteuser tool_shed.webapp.model tool_shed.webapp.model.mapping tool_shed.webapp.model.migrate tool_shed.webapp.model.migrate.check tool_shed.webapp.model.migrate.versions tool_shed.webapp.model.migrate.versions.0001_initial_tables tool_shed.webapp.model.migrate.versions.0002_add_tool_suite_column tool_shed.webapp.model.migrate.versions.0003_review_and_review_association_tables tool_shed.webapp.model.migrate.versions.0004_repository_tables tool_shed.webapp.model.migrate.versions.0005_drop_tool_related_tables tool_shed.webapp.model.migrate.versions.0006_add_email_alerts_column tool_shed.webapp.model.migrate.versions.0007_add_long_description_times_downloaded_columns tool_shed.webapp.model.migrate.versions.0008_add_repository_metadata_table tool_shed.webapp.model.migrate.versions.0009_add_malicious_column tool_shed.webapp.model.migrate.versions.0010_add_new_repo_alert_column tool_shed.webapp.model.migrate.versions.0011_add_tool_versions_column tool_shed.webapp.model.migrate.versions.0012_add_downloadable_column tool_shed.webapp.model.migrate.versions.0013_add_review_tables tool_shed.webapp.model.migrate.versions.0014_add_deprecated_column tool_shed.webapp.model.migrate.versions.0015_add_api_keys_table tool_shed.webapp.model.migrate.versions.0016_add_do_not_test_tools_functionally_correct_errors_columns tool_shed.webapp.model.migrate.versions.0017_add_galaxy_utility_columns_to_repository_metadata_table tool_shed.webapp.model.migrate.versions.0018_add_repository_metadata_flag_columns tool_shed.webapp.model.migrate.versions.0019_add_skip_tool_test_table_and_test_install_error_column tool_shed.webapp.model.migrate.versions.0020_add_repository_type_column tool_shed.webapp.model.migrate.versions.0021_change_repository_type_value tool_shed.webapp.model.migrate.versions.0022_add_repository_admin_roles tool_shed.webapp.model.migrate.versions.0023_add_repository_url_and_hompeage_url tool_shed.webapp.model.migrate.versions.0024_password_reset tool_shed.webapp.model.migrate.versions.0025_session_timeout tool_shed.webapp.model.migrate.versions.0026_add_numeric_revision_column tool_shed.webapp.search tool_shed.webapp.search.repo_search tool_shed.webapp.search.tool_search tool_shed.webapp.security tool_shed.webapp.util tool_shed.webapp.util.ratings_util tool_shed.webapp.util.shed_statistics

module_code (galaxy.util.template.FixedModuleCodeCompiler attribute) ModuleDependencyResolver (class in galaxy.tool_util.deps.resolvers.modules) MOL (class in galaxy.datatypes.molecules) MOL2 (class in galaxy.datatypes.molecules) monitor() (galaxy.jobs.handler.JobHandlerStopQueue method) (galaxy.jobs.runners.AsynchronousJobRunner method) (galaxy.tools.toolbox.watcher.ToolConfWatcher method) (galaxy.util.watcher.BaseWatcher method) monitor_job() (galaxy.jobs.runners.AsynchronousJobRunner method) monitor_repository_installation() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) monitor_step() (galaxy.jobs.handler.JobHandlerStopQueue method) Monitors (class in galaxy.util.monitors) most_recent() (galaxy.managers.histories.HistoryManager method) move_directory_files() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MoveDirectoryFiles method) move_file() (in module galaxy.tool_shed.util.basic_util) move_merge() (in module galaxy.util) MoveDirectoryFiles (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) MoveFile (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) Mp3 (class in galaxy.datatypes.media) Mp4 (class in galaxy.datatypes.media) mp_from_ids() (in module galaxy.objectstore.s3_multipart_upload) Mpg (class in galaxy.datatypes.media) Ms2 (class in galaxy.datatypes.proteomics) Msf (class in galaxy.datatypes.msa) Msp (class in galaxy.datatypes.proteomics) mulled_tags_for() (in module galaxy.tool_util.deps.mulled.util) MulledDockerContainerResolver (class in galaxy.tool_util.deps.container_resolvers.mulled) MulledSingularityContainerResolver (class in galaxy.tool_util.deps.container_resolvers.mulled) multi_select_email_alerts() (tool_shed.webapp.controllers.repository.RepositoryController method) MulticolFilterColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.web.legacy_framework.grids) multipart_upload() (in module galaxy.objectstore.s3_multipart_upload) MultipleDependencyResolver (class in galaxy.tool_util.deps.resolvers) MultipleSplitterFilter (class in galaxy.tool_util.parser.output_actions) (class in galaxy.tools.parameters.dynamic_options) multiply() (galaxy.model.dataset_collections.structure.Leaf method) (galaxy.model.dataset_collections.structure.Tree method) (galaxy.model.dataset_collections.structure.UninitializedTree method) (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) MultiSourceDataProvider (class in galaxy.datatypes.dataproviders.base) munge_lists() (in module galaxy.managers.base) MutationDict (class in galaxy.model.custom_types) MutationList (class in galaxy.model.custom_types) MutationObj (class in galaxy.model.custom_types) my_writable_repositories_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) my_writable_repositories_missing_tool_test_components_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) my_writable_repositories_with_invalid_tools_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) MyWritableRepositoriesGrid (class in tool_shed.grids.repository_grids) MyWritableRepositoriesMissingToolTestComponentsGrid (class in tool_shed.grids.repository_grids) MyWritableRepositoriesWithInvalidToolsGrid (class in tool_shed.grids.repository_grids) MzData (class in galaxy.datatypes.proteomics) MzIdentML (class in galaxy.datatypes.proteomics) MzML (class in galaxy.datatypes.proteomics) MzQuantML (class in galaxy.datatypes.proteomics) MzSQlite (class in galaxy.datatypes.binary) MzTab (class in galaxy.datatypes.proteomics) MzTab2 (class in galaxy.datatypes.proteomics) MzXML (class in galaxy.datatypes.proteomics)

N

N3 (class in galaxy.datatypes.triples) name (galaxy.jobs.actions.post.ChangeDatatypeAction attribute) (galaxy.jobs.actions.post.ColumnSetAction attribute) (galaxy.jobs.actions.post.DefaultJobAction attribute) (galaxy.jobs.actions.post.DeleteDatasetAction attribute) (galaxy.jobs.actions.post.DeleteIntermediatesAction attribute) (galaxy.jobs.actions.post.EmailAction attribute) (galaxy.jobs.actions.post.HideDatasetAction attribute) (galaxy.jobs.actions.post.RemoveTagDatasetAction attribute) (galaxy.jobs.actions.post.RenameDatasetAction attribute) (galaxy.jobs.actions.post.SetMetadataAction attribute) (galaxy.jobs.actions.post.TagDatasetAction attribute) (galaxy.jobs.actions.post.ValidateOutputsAction attribute) (galaxy.managers.licenses.LicenseMetadataModel attribute) (galaxy.managers.roles.RoleDefinitionModel attribute) (galaxy.managers.roles.RoleModel attribute) (galaxy.model.FormDefinition attribute) (galaxy.model.Group attribute) (galaxy.model.History attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetAssociationHistory attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.ImplicitlyCreatedDatasetCollectionInput attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.JobParameter attribute) (galaxy.model.JobToImplicitOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetAssociation attribute) (galaxy.model.JobToInputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetCollectionElementAssociation attribute) (galaxy.model.JobToInputLibraryDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToOutputLibraryDatasetAssociation attribute) (galaxy.model.Library attribute) (galaxy.model.LibraryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryFolder attribute) (galaxy.model.MetadataFile attribute) (galaxy.model.Quota attribute) (galaxy.model.Role attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.Tag attribute) (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.model.UserAddress attribute) (galaxy.model.UserPreference attribute) (galaxy.model.Workflow attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowStepInput attribute) (galaxy.tours.TourCore attribute) (galaxy.web_stack.ApplicationStack attribute) (galaxy.web_stack.PasteApplicationStack attribute) (galaxy.web_stack.UWSGIApplicationStack attribute) (galaxy.web_stack.WeblessApplicationStack attribute) (galaxy.workflow.modules.InputDataCollectionModule attribute) (galaxy.workflow.modules.InputDataModule attribute) (galaxy.workflow.modules.InputParameterModule attribute) (galaxy.workflow.modules.PauseModule attribute) (galaxy.workflow.modules.SubWorkflowModule attribute) (galaxy.workflow.modules.ToolModule attribute) (galaxy.workflow.refactor.schema.ExtractUntypedParameter attribute) (galaxy.workflow.refactor.schema.UpdateNameAction attribute) (galaxy_test.base.instrument.StructuredTestDataPlugin attribute) (tool_shed.webapp.model.Category attribute) (tool_shed.webapp.model.Component attribute) (tool_shed.webapp.model.Group attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.Role attribute) (tool_shed.webapp.model.Tag attribute) name() (galaxy.config.config_manage.OptionValue property) (galaxy.containers.Container property) (galaxy.containers.docker_model.DockerNode property) (galaxy.containers.docker_model.DockerNodeLabel property) (galaxy.containers.docker_model.DockerServiceConstraint property) (galaxy.containers.docker_model.DockerTask property) (galaxy.datatypes.util.gff_util.GFFFeature method) (galaxy.model.LibraryDataset property) (galaxy.model.store.discover.JsonCollectedDatasetMatch property) (galaxy.selenium.navigates_galaxy.WaitType property) (galaxy.tool_util.cwl.representation.TypeRepresentation property) (galaxy.tool_util.deps.resolvers.ContainerDependency property) (galaxy.workflow.modules.InputProxy property) name_autocomplete_data() (tool_shed.util.admin_util.Admin method) NameColumn (class in galaxy.webapps.galaxy.controllers.history) Names (class in galaxy.datatypes.mothur) navigate_to_custom_builds_page() (galaxy_test.selenium.test_custom_builds.CustomBuildsTestcase method) navigate_to_histories_page() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) navigate_to_history_share_page() (galaxy_test.selenium.test_history_sharing.HistorySharingTestCase method) navigate_to_history_user_share_page() (galaxy_test.selenium.test_history_sharing.HistorySharingTestCase method) navigate_to_manage_information() (galaxy_test.selenium.test_personal_information.ManageInformationTestCase method) navigate_to_pages() (galaxy_test.selenium.test_pages.PagesTestCase method) navigate_to_published_histories_page() (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase method) navigate_to_user_preferences() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) NavigatesGalaxy (class in galaxy.selenium.navigates_galaxy) NavigatesGalaxySeleniumTestCase (class in galaxy_test.selenium.test_navigates_galaxy) navigation() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy property) NcbiTaxonomySQlite (class in galaxy.datatypes.binary) needs_shell_quoting() (in module galaxy.tool_util.cwl) (in module galaxy.tool_util.cwl.cwltool_deps) Neo4j (class in galaxy.datatypes.neo4j) Neo4jDB (class in galaxy.datatypes.neo4j) Neo4jDBzip (class in galaxy.datatypes.neo4j) nested_collection_identifiers() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method) NestedObjectStore (class in galaxy.objectstore) NetCDF (class in galaxy.datatypes.binary) NEVER_SANITIZE (galaxy.util.Params attribute) NEW (galaxy.model.Dataset.states attribute) (galaxy.model.DatasetCollection.populated_states attribute) (galaxy.model.DatasetInstance.states attribute) (galaxy.model.DeferredJob.states attribute) (galaxy.model.ImplicitCollectionJobs.populated_states attribute) (galaxy.model.Job.states attribute) (galaxy.model.Task.states attribute) (galaxy.model.tool_shed_install.ToolShedRepository.installation_status attribute) (galaxy.model.TransferJob.states attribute) new (galaxy.model.view.HistoryDatasetCollectionJobStateSummary attribute) NEW (galaxy.model.WorkflowInvocation.states attribute) (galaxy.model.WorkflowInvocationStep.states attribute) new() (galaxy.forms.forms.FormDefinitionAddressFieldFactory method) (galaxy.forms.forms.FormDefinitionFactory method) (galaxy.forms.forms.FormDefinitionFieldFactory method) (galaxy.forms.forms.FormDefinitionHistoryFieldFactory method) (galaxy.forms.forms.FormDefinitionPasswordFieldFactory method) (galaxy.forms.forms.FormDefinitionSelectFieldFactory method) (galaxy.forms.forms.FormDefinitionTextFieldFactory method) (galaxy.forms.forms.FormDefinitionWorkflowFieldFactory method) (galaxy.forms.forms.FormDefinitionWorkflowMappingFieldFactory method) (galaxy.jobs.transfer_manager.TransferManager method) new_dataset() (galaxy_test.base.populators.BaseDatasetPopulator method) new_dataset_request() (galaxy_test.base.populators.BaseDatasetPopulator method) new_datatypes_metadata_required() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) new_file() (galaxy.datatypes.metadata.FileParameter method) (galaxy.model.metadata.FileParameter method) new_file_path() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) new_history() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) (galaxy.webapps.base.webapp.GalaxyWebTransaction method) (galaxy_test.base.populators.BaseDatasetPopulator method) new_history_properties() (galaxy.model.store.BaseDirectoryImportModelStore method) (galaxy.model.store.ModelImportStore method) new_library() (galaxy_test.base.populators.LibraryPopulator method) new_library_dataset() (galaxy_test.base.populators.LibraryPopulator method) new_library_dataset_in_private_library() (galaxy_test.base.populators.LibraryPopulator method) new_metadata_required_for_utilities() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) new_private_library() (galaxy_test.base.populators.LibraryPopulator method) new_provider_from_identifier() (galaxy.openid.providers.OpenIDProviders method) new_readme_files_metadata_required() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) new_repo_alert (tool_shed.webapp.model.User attribute) new_repository_dependency_metadata_required() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) new_secure_hash() (in module galaxy.util.hash_util) new_state() (galaxy.tools.Tool method) (in module galaxy.tool_shed.util.tool_util) new_tool_dependency_metadata_required() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) new_tool_metadata_required() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) new_tool_panel_section_label (galaxy.managers.workflows.WorkflowCreateOptions attribute) new_upload() (in module galaxy.tools.actions.upload_common) new_workflow_metadata_required() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) Newick (class in galaxy.datatypes.data) Newick_Parser (class in galaxy.visualization.data_providers.phyloviz.newickparser) next() (galaxy.tools.exception_handling.UCSCOutWrapper method) (galaxy.util.ucsc.UCSCOutWrapper method) next_installable_changeset_revision() (tool_shed.webapp.controllers.repository.RepositoryController method) next_line_starts_with() (galaxy.datatypes.proteomics.Msp static method) next_step (galaxy.model.PSAPartial attribute) nextval() (in module galaxy.model.migrate.versions.util) (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) Nexus (class in galaxy.datatypes.data) Nexus_Parser (class in galaxy.visualization.data_providers.phyloviz.nexusparser) nice_size() (in module galaxy.util) (in module galaxy.webapps.reports.controllers.system) nice_total_disk_usage() (galaxy.model.User property) (tool_shed.webapp.model.User property) NicerConfigParser (class in galaxy.util.properties) NicerConfigParser.InterpolateWrapper (class in galaxy.util.properties) Nifti1 (class in galaxy.datatypes.images)

Nifti2 (class in galaxy.datatypes.images) NmrML (class in galaxy.datatypes.proteomics) NO_CHROMOSOME (galaxy.model.Dataset.conversion_messages attribute) (galaxy.model.DatasetInstance.conversion_messages attribute) NO_CONVERTER (galaxy.model.Dataset.conversion_messages attribute) (galaxy.model.DatasetInstance.conversion_messages attribute) NO_DATA (galaxy.model.Dataset.conversion_messages attribute) (galaxy.model.DatasetInstance.conversion_messages attribute) NO_ERROR (galaxy.tool_util.parser.stdio.StdioErrorLevel attribute) NO_PROVIDER_ID (galaxy.openid.providers.OpenIDProviders attribute) NO_TOOL (galaxy.model.Dataset.conversion_messages attribute) (galaxy.model.DatasetInstance.conversion_messages attribute) NoConverterException Node (class in galaxy.util.jstree) (class in galaxy.visualization.data_providers.phyloviz.baseparser) node() (galaxy.containers.docker_model.DockerService property) (galaxy.containers.docker_model.DockerTask property) (galaxy.containers.docker_swarm.DockerSwarmInterface method) node_edge_dataprovider() (galaxy.datatypes.graph.Sif method) (galaxy.datatypes.graph.Xgmml method) node_inspect() (galaxy.containers.docker_swarm.DockerSwarmAPIInterface method) (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) node_ls() (galaxy.containers.docker_swarm.DockerSwarmAPIInterface method) (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) node_ps() (galaxy.containers.docker_swarm.DockerSwarmAPIInterface method) (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) node_spec_option_map (galaxy.containers.docker_swarm.DockerSwarmAPIInterface attribute) node_tasks() (galaxy.containers.docker_swarm.DockerSwarmInterface method) node_update() (galaxy.containers.docker_swarm.DockerSwarmAPIInterface method) (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) NoDefault (class in galaxy.util.pastescript.serve) NodeProxyLauncher (class in galaxy.web.proxy) nodes() (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) (galaxy.containers.docker_swarm.DockerSwarmInterface method) nodes_active() (galaxy.containers.docker_swarm.DockerSwarmInterface method) nodes_active_by_constraints() (galaxy.containers.docker_swarm.DockerSwarmInterface method) nodes_in_state() (galaxy.containers.docker_swarm.DockerSwarmInterface method) NON_DATA_CONNECTION (galaxy.model.WorkflowStepConnection attribute) non_data_connection() (galaxy.model.WorkflowStepConnection property) non_private_roles (galaxy.model.User attribute) (galaxy.model.UserRoleAssociation attribute) (tool_shed.webapp.model.UserRoleAssociation attribute) non_ready_jobs() (galaxy.managers.histories.HistoryManager method) non_ready_states (galaxy.model.Dataset attribute) (galaxy.model.Job attribute) non_shed_tool_panel_configs() (galaxy.tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager property) non_terminal_states (galaxy.model.WorkflowInvocation attribute) non_terminal_tasks() (galaxy.containers.docker_model.DockerNode property) nonce (galaxy.authnz.psa_authnz.Storage attribute) NONCHANGING_WORDS (galaxy.util.inflection.Inflector attribute) NoneDataset (class in galaxy.model.none_like) NoopHandler (class in galaxy.jobs.manager) NoOpLazyProcess (class in galaxy.util.lazy_process) NoopManager (class in galaxy.jobs.manager) NoopQueue (class in galaxy.jobs) NoOptionsValidator (class in galaxy.tools.parameters.validation) NoProviderAvailable NoQuotaAgent (class in galaxy.quota) NoReplacement (class in galaxy.workflow.modules) normalize_input_connections_to_list() (galaxy.workflow.refactor.execute.WorkflowRefactorExecutor static method) normalize_workflow_format() (galaxy.managers.workflows.WorkflowContentsManager method) nose_config_and_run() (in module galaxy_test.driver.driver_util) not_implemented() (galaxy.webapps.base.controller.BaseAPIController method) NotFoundCommand (class in galaxy.util.pastescript.serve) NotImplemented NotLoggedInException NotTested (class in tool_shed.utility_containers) now() (in module galaxy.model.database_heartbeat) (in module galaxy.model.mapping) (in module galaxy.model.migrate.versions.0001_initial_tables) (in module galaxy.model.migrate.versions.0002_metadata_file_table) (in module galaxy.model.migrate.versions.0003_security_and_libraries) (in module galaxy.model.migrate.versions.0008_galaxy_forms) (in module galaxy.model.migrate.versions.0010_hda_display_at_authz_table) (in module galaxy.model.migrate.versions.0011_v0010_mysql_index_fix) (in module galaxy.model.migrate.versions.0012_user_address) (in module galaxy.model.migrate.versions.0014_pages) (in module galaxy.model.migrate.versions.0022_visualization_tables) (in module galaxy.model.migrate.versions.0026_cloud_tables) (in module galaxy.model.migrate.versions.0027_request_events) (in module galaxy.model.migrate.versions.0029_user_actions) (in module galaxy.model.migrate.versions.0037_samples_library) (in module galaxy.model.migrate.versions.0038_add_inheritable_column_to_library_template_assoc_tables) (in module galaxy.model.migrate.versions.0041_workflow_invocation) (in module galaxy.model.migrate.versions.0042_workflow_invocation_fix) (in module galaxy.model.migrate.versions.0045_request_type_permissions_table) (in module galaxy.model.migrate.versions.0049_api_keys_table) (in module galaxy.model.migrate.versions.0050_drop_cloud_tables) (in module galaxy.model.migrate.versions.0052_sample_dataset_table) (in module galaxy.model.migrate.versions.0061_tasks) (in module galaxy.model.migrate.versions.0062_user_openid_table) (in module galaxy.model.migrate.versions.0063_sequencer_table) (in module galaxy.model.migrate.versions.0064_add_run_and_sample_run_association_tables) (in module galaxy.model.migrate.versions.0066_deferred_job_and_transfer_job_tables) (in module galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services) (in module galaxy.model.migrate.versions.0080_quota_tables) (in module galaxy.model.migrate.versions.0082_add_tool_shed_repository_table) (in module galaxy.model.migrate.versions.0087_tool_id_guid_map_table) (in module galaxy.model.migrate.versions.0091_add_tool_version_tables) (in module galaxy.model.migrate.versions.0098_genome_index_tool_data_table) (in module galaxy.model.migrate.versions.0099_add_tool_dependency_table) (in module galaxy.model.migrate.versions.0105_add_cleanup_event_table) (in module galaxy.model.migrate.versions.0109_add_repository_dependency_tables) (in module galaxy.model.migrate.versions.0112_add_data_manager_history_association_and_data_manager_job_association_tables) (in module galaxy.model.migrate.versions.0120_dataset_collections) (in module galaxy.model.migrate.versions.0124_job_state_history) (in module galaxy.model.migrate.versions.0136_collection_and_workflow_state) (in module galaxy.model.migrate.versions.0139_add_history_dataset_association_history_table) (in module galaxy.model.migrate.versions.0144_add_cleanup_event_user_table) (in module galaxy.model.migrate.versions.0149_dynamic_tools) (in module galaxy.model.migrate.versions.0151_add_worker_process) (in module galaxy.model.migrate.versions.0154_created_from_basename) (in module galaxy.model.migrate.versions.0155_job_galaxy_version) (in module galaxy.model.migrate.versions.0156_add_interactivetools) (in module galaxy.model.migrate.versions.0158_workflow_reports) (in module galaxy.model.migrate.versions.0164_page_format) (in module galaxy.model.migrate.versions.0165_add_content_update_time) (in module galaxy.model.migrate.versions.0171_schemaorg_metadata) (in module galaxy.model.migrate.versions.0172_it_entrypoint_requires_domain) (in module galaxy.model.orm.now) (in module galaxy.model.tool_shed_install.mapping) (in module tool_shed.webapp.model) (in module tool_shed.webapp.model.mapping) (in module tool_shed.webapp.model.migrate.versions.0001_initial_tables) (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.0008_add_repository_metadata_table) (in module tool_shed.webapp.model.migrate.versions.0011_add_tool_versions_column) NOW() (in module tool_shed.webapp.model.migrate.versions.0013_add_review_tables) now() (in module tool_shed.webapp.model.migrate.versions.0015_add_api_keys_table) (in module tool_shed.webapp.model.migrate.versions.0019_add_skip_tool_test_table_and_test_install_error_column) NOW() (in module tool_shed.webapp.model.migrate.versions.0022_add_repository_admin_roles) now() (in module tool_shed.webapp.model.migrate.versions.0024_password_reset) (in module tool_shed.webapp.model.migrate.versions.0025_session_timeout) Nrrd (class in galaxy.datatypes.images) NTriples (class in galaxy.datatypes.triples) nullable_basestring() (galaxy.managers.base.ModelValidator method) NullClientTestConfig (class in galaxy.tool_util.verify.interactor) NullContainer (class in galaxy.tool_util.deps.container_classes) NullContainerFinder (class in galaxy.tool_util.deps.containers) NullDatasetPathRewriter (class in galaxy.job_execution.datasets) NullDependency (class in galaxy.tool_util.deps.resolvers) NullDependencyManager (class in galaxy.tool_util.deps) NullErrorPlugin (class in galaxy.tools.error_reports) NullJobInstrumenter (class in galaxy.job_metrics) NullToolOutputActionOption (class in galaxy.tool_util.parser.output_actions) NullToolProvidedMetadata (class in galaxy.tool_util.provided_metadata) NullToolTagManager (class in galaxy.tools.toolbox.tags) NullTourCallback (class in galaxy.selenium.navigates_galaxy) NullWatcher (class in galaxy.util.watcher) num_page_links (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.web.legacy_framework.grids.Grid attribute) num_rows_per_page (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.page.ItemSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid 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.CategoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) numeric_metrics (galaxy.model.Job attribute) (galaxy.model.Task attribute) numeric_revision (tool_shed.webapp.model.RepositoryMetadata attribute)

O

OBFS (class in galaxy.datatypes.molecules) object_id() (galaxy.model.store.discover.JsonCollectedDatasetMatch property) object_key (galaxy.model.store.DirectoryImportModelStore1901 attribute) (galaxy.model.store.DirectoryImportModelStoreLatest attribute) object_key() (galaxy.model.store.ModelImportStore property) object_store (galaxy.model.Dataset attribute) object_store() (galaxy.jobs.JobWrapper property) object_store_id (galaxy.model.Dataset attribute) (galaxy.model.Job attribute) (galaxy.model.MetadataFile attribute) object_to_string() (in module galaxy.util) ObjectAttributeInvalidException ObjectAttributeMissingException ObjectImportTracker (class in galaxy.model.store) ObjectInvalid ObjectNotFound ObjectStore (class in galaxy.objectstore) ObjectStorePopulator (class in galaxy.objectstore) ObjectUploadTarget (class in galaxy.tool_util.cwl.util) Obo (class in galaxy.datatypes.text) odict (class in galaxy.util.odict) OIDC (class in galaxy.webapps.galaxy.controllers.authnz) oidlog() (in module galaxy.openid.openid_manager) OK (galaxy.model.Dataset.conversion_messages attribute) (galaxy.model.Dataset.states attribute) (galaxy.model.DatasetCollection.populated_states attribute) (galaxy.model.DatasetInstance.conversion_messages attribute) (galaxy.model.DatasetInstance.states attribute) (galaxy.model.DatasetInstance.validated_states attribute) (galaxy.model.DeferredJob.states attribute) (galaxy.model.ImplicitCollectionJobs.populated_states attribute) (galaxy.model.Job.states attribute) (galaxy.model.Task.states attribute) (galaxy.model.tool_shed_install.ToolDependency.states attribute) (galaxy.model.tool_shed_install.ToolShedRepository.states attribute) ok (galaxy.model.view.HistoryDatasetCollectionJobStateSummary attribute) ok_to_display() (galaxy.model.security.GalaxyRBACAgent method) ok_to_edit_metadata() (galaxy.model.DatasetInstance method) Oligos (class in galaxy.datatypes.mothur) on_any_event() (galaxy.tools.toolbox.watcher.ToolFileEventHandler method) (galaxy.util.watcher.EventHandler method) on_response() (galaxy.queue_worker.ControlTask method) on_text_for_names() (in module galaxy.tools.actions) on_the_fly_config() (in module galaxy.authnz.psa_authnz) one() (galaxy.managers.base.ModelManager method) op() (galaxy.containers.docker_model.DockerServiceConstraint property) open() (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method) (galaxy.util.pastescript.serve.LazyWriter method) open_data_file() (galaxy.visualization.data_providers.genome.BamDataProvider method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) (galaxy.visualization.data_providers.genome.IntervalIndexDataProvider method) (galaxy.visualization.data_providers.genome.RawVcfDataProvider method) (galaxy.visualization.data_providers.genome.TabixDataProvider method) open_folder() (tool_shed.webapp.controllers.repository.RepositoryController method) open_in_workflow_editor() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) open_in_workflow_run() (galaxy_test.selenium.test_workflow_run.WorkflowRunTestCase method) open_logs() (galaxy.util.heartbeat.Heartbeat method) open_or_build_maf_index() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) open_recipe_file() (in module galaxy.tool_util.deps.mulled.get_tests) open_repository_files_folder() (in module tool_shed.util.shed_util_common) open_tar() (galaxy.util.compression_utils.CompressedFile method) open_zip() (galaxy.util.compression_utils.CompressedFile method) OpenID (class in galaxy.webapps.galaxy.controllers.openid) openid_auth() (galaxy.webapps.galaxy.controllers.openid.OpenID method) openid_process() (galaxy.webapps.galaxy.controllers.openid.OpenID method) OpenIDManager (class in galaxy.openid.openid_manager) OpenIDProvider (class in galaxy.openid.providers) OpenIDProviders (class in galaxy.openid.providers) OpenObject (class in galaxy.visualization.plugins.utils) operation (galaxy.model.Quota attribute) operations (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.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageListGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationListGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid 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.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.DockerImageGrid attribute) (tool_shed.grids.repository_grids.EmailAlertsRepositoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesReadyForReviewGrid 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) option() (galaxy.config.config_manage.OptionValue property) option_map (galaxy.containers.ContainerInterface attribute) (galaxy.containers.docker.DockerCLIInterface attribute) (galaxy.containers.docker_swarm.DockerSwarmCLIInterface attribute)

option_type (in module galaxy.tool_util.parser.output_actions) optional (galaxy.workflow.modules.InputParameterModule attribute) (galaxy.workflow.refactor.schema.AddInputAction attribute) optional() (in module galaxy.dependencies) optional_headers (galaxy.datatypes.speech.BPF attribute) optional_param() (in module galaxy.workflow.modules) options() (galaxy.auth.util.Authenticator property) (galaxy.util.jstree.Path property) (galaxy.webapps.galaxy.api.authenticate.AuthenticationController method) (galaxy_test.base.instrument.StructuredTestDataPlugin method) OptionValue (class in galaxy.config.config_manage) order_components_for_installation() (galaxy.tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) order_contents_on (galaxy.managers.containers.DatasetCollectionAsContainerManagerMixin attribute) (galaxy.managers.containers.LibraryFolderAsContainerManagerMixin attribute) order_id (galaxy.model.LibraryDataset attribute) (galaxy.model.LibraryFolder attribute) order_index (galaxy.model.ImplicitCollectionJobsJobAssociation attribute) (galaxy.model.StoredWorkflowMenuEntry attribute) (galaxy.model.WorkflowStep attribute) (galaxy.workflow.refactor.schema.RefactorActionExecutionMessage attribute) (galaxy.workflow.refactor.schema.StepReferenceByOrderIndex attribute) order_repositories_for_installation() (galaxy.tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager method) order_workflow_steps() (in module galaxy.workflow.steps) order_workflow_steps_with_levels() (in module galaxy.workflow.steps) ordered_dump() (in module galaxy.util.yaml_util) ordered_load() (in module galaxy.util.yaml_util) OrderedLoader (class in galaxy.util.yaml_util) OrderedSet (class in galaxy.util.oset) orient_block_by_region() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) OSW (class in galaxy.datatypes.binary) Otu (class in galaxy.datatypes.mothur) output (galaxy.workflow.refactor.schema.ConnectAction attribute) (galaxy.workflow.refactor.schema.DisconnectAction attribute) (galaxy.workflow.refactor.schema.UpdateOutputLabelAction attribute) output() (galaxy.managers.pages.PageContentProcessor method) output_associations() (galaxy.model.WorkflowInvocation property) output_collection_def() (galaxy.job_execution.output_collect.JobContext method) (galaxy.job_execution.output_collect.SessionlessJobContext method) output_connections (galaxy.model.WorkflowStep attribute) output_dataset_collection_instances (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.Job attribute) output_dataset_collections (galaxy.model.DatasetCollection attribute) (galaxy.model.Job attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowInvocationStep attribute) output_datasets (galaxy.model.Job attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowInvocationStep attribute) output_def() (galaxy.job_execution.output_collect.JobContext method) (galaxy.job_execution.output_collect.SessionlessJobContext method) output_extra_files_rewrite() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) output_hid() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) output_label (galaxy.workflow.refactor.schema.RefactorActionExecutionMessage attribute) (galaxy.workflow.refactor.schema.UpdateOutputLabelAction attribute) output_library_datasets (galaxy.model.Job attribute) output_name (galaxy.model.PostJobAction attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowOutput attribute) (galaxy.model.WorkflowStepConnection attribute) (galaxy.workflow.refactor.schema.OutputReferenceByLabel attribute) (galaxy.workflow.refactor.schema.OutputReferenceByOrderIndex attribute) (galaxy.workflow.refactor.schema.RefactorActionExecutionMessage attribute) output_names() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) output_path_rewrite() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) output_paths() (galaxy.jobs.SharedComputeEnvironment method) output_properties() (in module galaxy.tool_util.cwl.util) output_step (galaxy.model.WorkflowStepConnection attribute) output_step_id (galaxy.model.WorkflowStepConnection attribute) output_to_cwl_json() (in module galaxy.tool_util.cwl.util) output_value (galaxy.model.WorkflowInvocationStep attribute) output_values (galaxy.model.WorkflowInvocation attribute) OutputCollections (class in galaxy.tools.actions) OutputParameterJSONTool (class in galaxy.tools) OutputReferenceByLabel (class in galaxy.workflow.refactor.schema) OutputReferenceByOrderIndex (class in galaxy.workflow.refactor.schema) outputs() (galaxy.webapps.galaxy.api.jobs.JobController method) outputs_directory() (galaxy.jobs.JobWrapper property) OutputsDict (class in galaxy.tool_util.verify.interactor) OutputsToWorkingDirectoryPathRewriter (class in galaxy.job_execution.datasets) Owl (class in galaxy.datatypes.xml) OwnableManagerMixin (class in galaxy.managers.secured) owner (galaxy.model.tool_shed_install.ToolShedRepository attribute) owner_tags (galaxy.model.StoredWorkflow attribute) OwnerAnnotationColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.web.legacy_framework.grids) OwnerColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.web.legacy_framework.grids) OxliBinary (class in galaxy.datatypes.binary) OxliCountGraph (class in galaxy.datatypes.binary) OxliGraphLabels (class in galaxy.datatypes.binary) OxliNodeGraph (class in galaxy.datatypes.binary) OxliStopTags (class in galaxy.datatypes.binary) OxliSubset (class in galaxy.datatypes.binary) OxliTagSet (class in galaxy.datatypes.binary)

P

Package (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler) package() (galaxy.tool_util.deps.mulled.util.Target property) package_gff_feature() (in module galaxy.visualization.data_providers.genome) package_lapack_repository_long_description (in module tool_shed.test.functional.test_1420_tool_dependency_environment_inheritance) package_name() (galaxy.tool_util.deps.mulled.util.Target property) package_specifier() (galaxy.tool_util.deps.conda_util.CondaTarget property) package_tool() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) packages() (galaxy.tool_util.deps.requirements.ToolRequirements property) pad() (galaxy.util.pastescript.serve.Command method) Paf (class in galaxy.datatypes.text) Page (class in galaxy.model) page (galaxy.model.PageAnnotationAssociation attribute) (galaxy.model.PageRatingAssociation attribute) (galaxy.model.PageRevision attribute) (galaxy.model.PageUserShareAssociation attribute) page_id (galaxy.model.PageAnnotationAssociation attribute) (galaxy.model.PageRatingAssociation attribute) (galaxy.model.PageRevision attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.PageUserShareAssociation attribute) PageAllPublishedGrid (class in galaxy.webapps.galaxy.controllers.page) PageAnnotationAssociation (class in galaxy.model) PageApiTestCase (class in galaxy_test.api.test_pages) PageContentProcessor (class in galaxy.managers.pages) PageController (class in galaxy.webapps.galaxy.controllers.page) PageDeserializer (class in galaxy.managers.pages) PageListGrid (class in galaxy.webapps.galaxy.controllers.page) PageListGrid.URLColumn (class in galaxy.webapps.galaxy.controllers.page) PageManager (class in galaxy.managers.pages) PageRatingAssociation (class in galaxy.model) PageRevision (class in galaxy.model) PageRevisionsApiTestCase (class in galaxy_test.api.test_page_revisions) PageRevisionsController (class in galaxy.webapps.galaxy.api.page_revisions) PageRevisionView (class in galaxy.model.search) pages (galaxy.model.PageAnnotationAssociation attribute) (galaxy.model.PageRatingAssociation attribute) (galaxy.model.PageTagAssociation attribute) pages_shared_by_others (galaxy.model.User attribute) PagesController (class in galaxy.webapps.galaxy.api.pages) PageSelectionGrid (class in galaxy.webapps.galaxy.controllers.page) PageSerializer (class in galaxy.managers.pages) PageSource (class in galaxy.tool_util.parser.interface) PagesSource (class in galaxy.tool_util.parser.interface) PagesTestCase (class in galaxy_test.selenium.test_pages) PageTagAssociation (class in galaxy.model) PageUserShareAssociation (class in galaxy.model) PageView (class in galaxy.model.search) pair_identifiers() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method) PairedDatasetCollectionType (class in galaxy.model.dataset_collections.types.paired) PairwiseDistanceMatrix (class in galaxy.datatypes.mothur) PAM (class in galaxy.auth.providers.pam_auth) panel_entry_per_tool() (in module galaxy.tool_shed.util.tool_util) panel_items() (galaxy.tools.toolbox.panel.HasPanelItems method) (galaxy.tools.toolbox.panel.ToolPanelElements method) (galaxy.tools.toolbox.panel.ToolSection method) (galaxy.tools.toolbox.ToolSection method) panel_items_iter() (galaxy.tools.toolbox.panel.HasPanelItems method) ParallelismInfo (class in galaxy.tool_util.parser.xml) param_combinations() (galaxy.tools.parameters.meta.WorkflowParameterExpansion property) param_filename (galaxy.model.Job attribute) (galaxy.model.Task attribute) param_keys() (galaxy.tools.parameters.meta.WorkflowParameterExpansion property) param_names() (galaxy.tools.test.ParamContext method) (galaxy.tools.test.RootParamContext method) ParamContext (class in galaxy.tools.test) parameter_type (galaxy.workflow.modules.InputParameterModule attribute) parameter_value (galaxy.model.WorkflowRequestInputStepParameter attribute) parameters (galaxy.model.Job attribute) parameters_display() (galaxy.webapps.galaxy.api.jobs.JobController method) ParameterValueError ParamikoShell (class in galaxy.jobs.runners.util.cli.shell.rsh) ParamKey (class in galaxy.tools.parameters.meta) ParamMessage (class in galaxy.web_stack.message) ParamModifierParser (class in galaxy.visualization.plugins.config_parser) ParamParser (class in galaxy.visualization.plugins.config_parser) Params (class in galaxy.util) params (galaxy.model.DeferredJob attribute) (galaxy.model.Job attribute) (galaxy.model.TransferJob attribute) (galaxy.model.UserAction attribute) params() (galaxy.tools.parameters.wrapped.WrappedParameters property) (galaxy.web_stack.message.ParamMessage property) params_from_strings() (galaxy.tools.Tool method) params_to_strings() (galaxy.tools.Tool method) params_with_missing_data_table_entry() (galaxy.tools.Tool property) params_with_missing_index_file() (galaxy.tools.Tool property) ParamsWithSpecs (class in galaxy.util) ParamValueFilter (class in galaxy.tools.parameters.dynamic_options) ParamValueToolOutputActionOptionFilter (class in galaxy.tool_util.parser.output_actions) ParamXml (class in galaxy.datatypes.proteomics) parent (galaxy.model.ExtendedMetadataIndex attribute) (galaxy.model.LibraryFolder attribute) (galaxy.model.Tag attribute) parent() (galaxy.datatypes.metadata.MetadataCollection property) (galaxy.model.metadata.MetadataCollection property) parent_hda (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) parent_id (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryFolder attribute) (galaxy.model.Tag attribute) (galaxy.model.tool_shed_install.ToolVersionAssociation attribute) (tool_shed.webapp.model.Tag attribute) parent_ldda (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) parent_library() (galaxy.model.LibraryFolder property) parent_path() (galaxy.tool_util.deps.conda_util.CondaContext property) (galaxy.tool_util.deps.installable.InstallableContext property) parent_tool_association (galaxy.model.tool_shed_install.ToolVersion attribute) parent_workflow_id (galaxy.model.Workflow attribute) parent_workflow_input_connections (galaxy.model.WorkflowStep attribute) parent_workflow_invocation (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute) parent_workflow_invocation_association (galaxy.model.WorkflowInvocation attribute) parent_workflow_steps (galaxy.model.Workflow attribute) Parquet (class in galaxy.datatypes.binary) parse() (galaxy.tools.SetParamAction static method) (galaxy.tools.Tool method) (galaxy.tools.TracksterConfig static method) (galaxy.visualization.plugins.config_parser.DataSourceParser method) (galaxy.visualization.plugins.config_parser.ParamModifierParser method) (galaxy.visualization.plugins.config_parser.ParamParser method) parse_action_module() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_args() (galaxy.util.pastescript.serve.Command method) parse_auth_results() (in module galaxy.auth.util) parse_bool() (galaxy.managers.base.ModelFilterParser method) parse_bytesize() (in module galaxy.util.bytesize) parse_cast_attribute() (in module galaxy.tool_util.parser.output_actions) parse_citation() (galaxy.managers.citations.CitationsManager method) (in module galaxy.managers.citations) parse_cols_arg() (in module galaxy.tools.util.galaxyops) parse_column_at_index() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) parse_column_definitions() (galaxy.tools.parameters.dynamic_options.DynamicOptions method) parse_column_spec() (galaxy.tools.data.RefgenieToolDataTable method) (galaxy.tools.data.TabularToolDataTable method) parse_columns_from_line() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) parse_command() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) (galaxy.tools.ExpressionTool method) (galaxy.tools.Tool method) parse_compare_type() (in module galaxy.tool_util.parser.output_actions) parse_config() (galaxy.visualization.plugins.resource_parser.ResourceParser method) parse_config_xml() (in module galaxy.objectstore.azure_blob) (in module galaxy.objectstore.irods) (in module galaxy.objectstore.pithos) (in module galaxy.objectstore.s3) parse_configs() (galaxy.dependencies.ConditionalDependencies method) parse_containers_config() (in module galaxy.containers) parse_conversion_tuples() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) parse_creator() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_date() (galaxy.managers.base.ModelFilterParser method) parse_description() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_destination_params() (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.chronos.ChronosJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.pbs.PBSJobRunner method) parse_display() (galaxy.tool_util.parser.interface.PageSource method) (galaxy.tool_util.parser.xml.XmlPageSource method) parse_display_interface() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_docker_env_pass_through() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) parse_dynamic_options() (in module galaxy.tools.parameters.basic) parse_dynamic_options_elem() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) parse_edam_operations() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_edam_topics() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_entry_point() (galaxy.visualization.plugins.config_parser.VisualizationsConfigParser method) parse_environment_variables() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) (galaxy.tools.ExpressionTool method) (galaxy.tools.Tool method) parse_error_level() (galaxy.tool_util.parser.xml.StdioParser method) parse_expression() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_external_id() (in module galaxy.jobs.runners.util.external) parse_failure_reason() (galaxy.jobs.runners.util.cli.job.BaseJobExec method) (galaxy.jobs.runners.util.cli.job.lsf.LSF method) parse_file() (galaxy.visualization.plugins.config_parser.VisualizationsConfigParser method) parse_file_fields() (galaxy.tools.data.RefgenieToolDataTable method) (galaxy.tools.data.TabularToolDataTable method) (galaxy.tools.parameters.dynamic_options.DynamicOptions method) parse_filter() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) (galaxy.managers.base.ModelFilterParser method) parse_filter_params() (galaxy.webapps.base.controller.BaseController method) parse_filters() (galaxy.managers.base.ModelFilterParser method) (in module galaxy.util.search) parse_gff3_attributes() (in module galaxy.datatypes.util.gff_util) parse_gff_attributes() (in module galaxy.datatypes.util.gff_util) parse_help() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) (galaxy.tools.Tool method) parse_hidden() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_home_target() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_id() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_id_list() (galaxy.managers.base.ModelFilterParser method) parse_input_elem() (galaxy.tools.Tool method) parse_input_pages() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_input_sources() (galaxy.tool_util.parser.cwl.CwlPageSource method) (galaxy.tool_util.parser.interface.PageSource method) (galaxy.tool_util.parser.xml.XmlPageSource method) (galaxy.tool_util.parser.yaml.YamlPageSource method) parse_input_type() (galaxy.tool_util.parser.xml.XmlInputSource method) (galaxy.tool_util.parser.yaml.YamlInputSource method) parse_inputs() (galaxy.tools.DataSourceTool method) (galaxy.tools.Tool method) parse_int() (in module galaxy.util) parse_int_list() (galaxy.managers.base.ModelFilterParser method) parse_interactivetool() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_interpreter() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_is_multi_byte() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_label() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) parse_license() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_limit_offset() (galaxy.webapps.base.controller.BaseController method) parse_model_class() (galaxy.visualization.plugins.config_parser.DataSourceParser method) parse_name() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) (galaxy.tools.parameters.basic.ToolParameter static method) parse_nested_inputs_source() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) (galaxy.tool_util.parser.yaml.YamlInputSource method) parse_non_hex_float() (in module galaxy.util) parse_optional() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) parse_order_by() (galaxy.managers.histories.HistoryManager method) (galaxy.managers.history_contents.HistoryContentsManager method) parse_outputs() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) (galaxy.tools.ExpressionTool method) (galaxy.tools.Tool method) parse_package_elem() (in module galaxy.tool_shed.util.tool_dependency_util) parse_parallelism() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_param_elem() (galaxy.tools.Tool method) parse_param_type() (galaxy.visualization.plugins.config_parser.ParamParser method) parse_parameter() (galaxy.visualization.plugins.resource_parser.ResourceParser method) parse_parameter_default() (galaxy.visualization.plugins.resource_parser.ResourceParser method) parse_parameter_dictionary() (galaxy.visualization.plugins.resource_parser.ResourceParser method) parse_parameter_modifiers() (galaxy.visualization.plugins.resource_parser.ResourceParser method) parse_port_text() (in module galaxy.tool_util.deps.docker_util) parse_profile() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_provided_metadata_file() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_provided_metadata_style() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_python_template_version() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_redirect_url() (galaxy.tools.Tool method) parse_redirect_url_params_elem() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_refresh() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_repository_dependency_tuple() (in module galaxy.util.tool_shed.common_util) parse_request_param_translation_elem() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_require_login() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_requirements_and_containers() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_requirements_from_dict() (in module galaxy.tool_util.deps.requirements) parse_requirements_from_xml() (in module galaxy.tool_util.deps.requirements) parse_resource_parameters() (in module galaxy.util) parse_row() (galaxy.datatypes.util.gff_util.GFFIntervalToBEDReaderWrapper method) (galaxy.datatypes.util.gff_util.GFFReaderWrapper method) parse_sanitize() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_sanitizer_elem() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) parse_search_kwds() (in module galaxy.workflow.trs_proxy) parse_single_status() (galaxy.jobs.runners.util.cli.job.BaseJobExec method) (galaxy.jobs.runners.util.cli.job.lsf.LSF method) (galaxy.jobs.runners.util.cli.job.slurm.Slurm method) (galaxy.jobs.runners.util.cli.job.torque.Torque method) parse_species_option() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) parse_static_options() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) (galaxy.tool_util.parser.yaml.YamlInputSource method) parse_status() (galaxy.jobs.runners.util.cli.job.BaseJobExec method) (galaxy.jobs.runners.util.cli.job.lsf.LSF method) (galaxy.jobs.runners.util.cli.job.slurm.Slurm method) (galaxy.jobs.runners.util.cli.job.slurm_torque.SlurmTorque method) (galaxy.jobs.runners.util.cli.job.torque.Torque method) parse_stdio() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) (galaxy.tools.Tool method) parse_stdio_exit_codes() (galaxy.tool_util.parser.xml.StdioParser method) parse_stdio_regexes() (galaxy.tool_util.parser.xml.StdioParser method) parse_strict_shell() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_tags() (galaxy.model.tags.TagHandler method) parse_tags_list() (galaxy.model.tags.TagHandler method) parse_test_input_source() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) (galaxy.tool_util.parser.yaml.YamlInputSource method) parse_tests() (galaxy.visualization.plugins.config_parser.DataSourceParser method) (in module galaxy.tools.test) parse_tests_to_dict() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_tmp_directory_vars() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) parse_tmp_target() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_to_params() (galaxy.visualization.plugins.config_parser.DataSourceParser method) parse_tool_module() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_tool_provided_metadata() (in module galaxy.tool_util.provided_metadata) parse_tool_type() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) parse_type_id_list() (galaxy.managers.history_contents.HistoryContentsFilters method) parse_validator_elems() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) parse_value() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) parse_vars() (galaxy.util.pastescript.serve.Command method) parse_version() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_version_command() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_version_command_interpreter() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_visualization() (galaxy.visualization.plugins.config_parser.VisualizationsConfigParser method) parse_when_input_sources() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) (galaxy.tool_util.parser.yaml.YamlInputSource method) parse_xml() (galaxy.objectstore.azure_blob.AzureBlobObjectStore class method) (galaxy.objectstore.BaseObjectStore class method) (galaxy.objectstore.cloud.Cloud class method) (galaxy.objectstore.DiskObjectStore class method) (galaxy.objectstore.DistributedObjectStore class method) (galaxy.objectstore.HierarchicalObjectStore class method) (galaxy.objectstore.irods.IRODSObjectStore class method) (galaxy.objectstore.pithos.PithosObjectStore class method) (galaxy.objectstore.s3.S3ObjectStore class method) (in module galaxy.util) (in module galaxy.util.tool_shed.xml_util) parse_xml_string() (in module galaxy.util) parse_xrefs() (galaxy.tool_util.parser.xml.XmlToolSource method) (galaxy.tool_util.parser.yaml.YamlToolSource method) parse_yaml() (in module galaxy.jobs.dynamic_tool_destination) parsed_filter (galaxy.managers.base.ModelFilterParser attribute) (in module galaxy.managers.base) parseData() (galaxy.visualization.data_providers.phyloviz.newickparser.Newick_Parser method) parseFile() (galaxy.visualization.data_providers.phyloviz.baseparser.Base_Parser method) (galaxy.visualization.data_providers.phyloviz.newickparser.Newick_Parser method) (galaxy.visualization.data_providers.phyloviz.nexusparser.Nexus_Parser method) (galaxy.visualization.data_providers.phyloviz.phyloxmlparser.Phyloxml_Parser method) parseNexus() (galaxy.visualization.data_providers.phyloviz.nexusparser.Nexus_Parser method) parseNode() (galaxy.visualization.data_providers.phyloviz.newickparser.Newick_Parser method) (galaxy.visualization.data_providers.phyloviz.phyloxmlparser.Phyloxml_Parser method) parser (galaxy.util.pastescript.serve.ServeCommand attribute) ParsingException partial (galaxy.authnz.psa_authnz.Storage attribute) PassedTest (class in tool_shed.utility_containers) passes_filters() (galaxy.managers.history_contents.HistoryContentsManager static method) password (galaxy.model.User attribute) (tool_shed.webapp.model.User attribute) PasswordField (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) PasswordResetToken (class in galaxy.model) (class in tool_shed.webapp.model) PasteApplicationStack (class in galaxy.web_stack) patch() (galaxy_test.base.api.ApiTestInteractor method) Path (class in galaxy.util.jstree) path (galaxy.model.ExtendedMetadataIndex attribute) (galaxy.model.TransferJob attribute) (galaxy.web.framework.base.Request attribute) path() (galaxy.files.FileSourcePath property) (galaxy.model.store.discover.DiscoveredFile property) (galaxy.model.store.discover.DiscoveredFileError property) (galaxy.tool_util.verify.test_data.FileDataResolver method) (galaxy.util.jstree.Path property) path_or_uri_to_uri() (in module galaxy.tool_util.cwl.util) paths_and_modtimes() (galaxy.tool_util.parser.interface.ToolSource method) (galaxy.tool_util.parser.ToolSource method) paths_as_file() (galaxy.tools.wrappers.HasDatasets method) paths_to_check_against_root (galaxy.config.BaseAppConfiguration attribute) (galaxy.config.GalaxyAppConfiguration attribute) paths_to_resolve() (galaxy.config.schema.AppSchema property) pause() (galaxy.jobs.JobWrapper method) PAUSED (galaxy.model.Dataset.states attribute) (galaxy.model.DatasetInstance.states attribute) (galaxy.model.Job.states attribute) paused (galaxy.model.view.HistoryDatasetCollectionJobStateSummary attribute) paused_jobs() (galaxy.model.History property)

PauseModule (class in galaxy.workflow.modules) Pbed (class in galaxy.datatypes.genetics) pbkdf2_bin() (in module galaxy.security.passwords) Pbm (class in galaxy.datatypes.images) PBSJobRunner (class in galaxy.jobs.runners.pbs) Pcd (class in galaxy.datatypes.images) Pcx (class in galaxy.datatypes.images) PDB (class in galaxy.datatypes.molecules) PDBQT (class in galaxy.datatypes.molecules) Pdf (class in galaxy.datatypes.images) peek() (galaxy.model.DatasetInstance property) peek_size (galaxy.datatypes.tabular.BaseCSV attribute) PEFF (class in galaxy.datatypes.proteomics) PENDING (galaxy.model.Dataset.conversion_messages attribute) (galaxy.model.DatasetInstance.conversion_messages attribute) PepList (class in galaxy.datatypes.proteomics) PepXml (class in galaxy.datatypes.proteomics) PepXmlReport (class in galaxy.datatypes.proteomics) per_month_all() (galaxy.webapps.reports.controllers.jobs.Jobs method) (galaxy.webapps.reports.controllers.workflows.Workflows method) per_month_in_error() (galaxy.webapps.reports.controllers.jobs.Jobs method) per_tool() (galaxy.webapps.reports.controllers.jobs.Jobs method) per_user() (galaxy.webapps.reports.controllers.jobs.Jobs method) (galaxy.webapps.reports.controllers.workflows.Workflows method) per_workflow() (galaxy.webapps.reports.controllers.workflows.Workflows method) perform_import() (galaxy.model.store.ModelImportStore method) perform_upload() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) perform_upload_of_pasted_content() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) permission_failed_error_class (galaxy.managers.rbac_secured.AccessDatasetRBACPermission attribute) (galaxy.managers.rbac_secured.ManageDatasetRBACPermission attribute) (galaxy.managers.rbac_secured.RBACPermission attribute) PermissionProvider (class in galaxy.job_execution.output_collect) (class in galaxy.model.store.discover) permissions() (galaxy.job_execution.output_collect.PermissionProvider property) (galaxy.model.store.discover.PermissionProvider property) (galaxy.webapps.galaxy.controllers.history.HistoryController method) permissions_class (galaxy.managers.rbac_secured.DatasetRBACPermission attribute) (galaxy.managers.rbac_secured.RBACPermission attribute) permitted_actions (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance attribute) (galaxy.model.Library attribute) (galaxy.security.RBACAgent attribute) (tool_shed.webapp.security.RBACAgent attribute) persist() (galaxy.tools.cache.ToolDocumentCache method) persist_cache() (galaxy.tools.ToolBox method) persist_elements_to_folder() (in module galaxy.model.store.discover) persist_elements_to_hdca() (in module galaxy.model.store.discover) persist_extra_files() (in module galaxy.model.store.discover) persist_hdas() (in module galaxy.model.store.discover) persist_object() (galaxy.job_execution.output_collect.JobContext method) (galaxy.model.store.discover.ModelPersistenceContext method) (galaxy.model.store.discover.SessionlessModelPersistenceContext method) persist_session() (galaxy.openid.openid_manager.OpenIDManager method) persist_target_to_export_store() (in module galaxy.model.store.discover) persist_uploads() (in module galaxy.tools.actions.upload_common) PersistentToolTagManager (class in galaxy.tools.toolbox.tags) Pgm (class in galaxy.datatypes.images) PHAR (class in galaxy.datatypes.molecules) Phe (class in galaxy.datatypes.genetics) Pheno (class in galaxy.datatypes.genetics) phone (galaxy.model.UserAddress attribute) Phylip (class in galaxy.datatypes.phylip) PhyloTree (class in galaxy.visualization.data_providers.phyloviz.baseparser) phyloviz() (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) PhylovizDataProvider (class in galaxy.visualization.data_providers.phyloviz) Phyloxml (class in galaxy.datatypes.xml) Phyloxml_Parser (class in galaxy.visualization.data_providers.phyloviz.phyloxmlparser) pick_a_cycle() (galaxy.util.topsort.CycleError method) pickle_SafeStringWrapper() (in module galaxy.util.object_wrapper) pid (galaxy.model.TransferJob attribute) (galaxy.model.WorkerProcess attribute) Pileup (class in galaxy.datatypes.tabular) PithosObjectStore (class in galaxy.objectstore.pithos) placeholderRenderForEdit() (in module galaxy.managers.pages) placeholderRenderForSave() (in module galaxy.managers.pages) placement (galaxy.tours.TourStep attribute) placement_option_map (galaxy.containers.docker_swarm.DockerSwarmAPIInterface attribute) PlantTribesKsComponents (class in galaxy.datatypes.plant_tribes) plugin (galaxy.model.DeferredJob attribute) (galaxy.model.JobMetricNumeric attribute) (galaxy.model.JobMetricText attribute) (galaxy.model.TaskMetricNumeric attribute) (galaxy.model.TaskMetricText attribute) plugin() (galaxy.auth.util.Authenticator property) plugin_source_from_dict() (in module galaxy.util.plugin_config) plugin_source_from_path() (in module galaxy.util.plugin_config) plugin_type (galaxy.auth.providers.alwaysreject.AlwaysReject attribute) (galaxy.auth.providers.ldap_ad.ActiveDirectory attribute) (galaxy.auth.providers.ldap_ad.LDAP attribute) (galaxy.auth.providers.localdb.LocalDB attribute) (galaxy.auth.providers.pam_auth.PAM attribute) (galaxy.files.sources.dropbox.DropboxFilesSource attribute) (galaxy.files.sources.galaxy.LibraryImportFilesSource attribute) (galaxy.files.sources.galaxy.UserFtpFilesSource attribute) (galaxy.files.sources.galaxy.UserLibraryImportFilesSource attribute) (galaxy.files.sources.posix.PosixFilesSource attribute) (galaxy.files.sources.s3.S3FilesSource attribute) (galaxy.files.sources.webdav.WebDavFilesSource attribute) (galaxy.job_metrics.instrumenters.cgroup.CgroupPlugin attribute) (galaxy.job_metrics.instrumenters.collectl.CollectlPlugin attribute) (galaxy.job_metrics.instrumenters.core.CorePlugin attribute) (galaxy.job_metrics.instrumenters.cpuinfo.CpuInfoPlugin attribute) (galaxy.job_metrics.instrumenters.env.EnvPlugin attribute) (galaxy.job_metrics.instrumenters.hostname.HostnamePlugin attribute) (galaxy.job_metrics.instrumenters.meminfo.MemInfoPlugin attribute) (galaxy.job_metrics.instrumenters.uname.UnamePlugin attribute) (galaxy.tools.error_reports.plugins.email.EmailPlugin attribute) (galaxy.tools.error_reports.plugins.github.GithubPlugin attribute) (galaxy.tools.error_reports.plugins.gitlab.GitLabPlugin attribute) (galaxy.tools.error_reports.plugins.influxdb.InfluxDBPlugin attribute) (galaxy.tools.error_reports.plugins.json.JsonPlugin attribute) (galaxy.tools.error_reports.plugins.sentry.SentryPlugin attribute) (galaxy.workflow.reports.generators.markdown.MarkdownWorkflowMarkdownReportGeneratorPlugin attribute) (galaxy.workflow.schedulers.core.CoreWorkflowSchedulingPlugin attribute) plugin_type() (galaxy.auth.providers.AuthProvider property) (galaxy.job_metrics.instrumenters.InstrumentPlugin property) (galaxy.tools.error_reports.plugins.ErrorPlugin property) (galaxy.workflow.reports.generators.WorkflowReportGeneratorPlugin property) (galaxy.workflow.schedulers.WorkflowSchedulingPlugin property) PluginConfigSource (class in galaxy.util.plugin_config) plugins() (galaxy.webapps.galaxy.api.remote_files.RemoteFilesAPIController method) plugins_dict() (in module galaxy.util.plugin_config) plugins_to_dict() (galaxy.files.ConfiguredFileSources method) PluginsController (class in galaxy.webapps.galaxy.api.plugins) pluralize() (galaxy.util.inflection.Inflector method) PLURALIZE_RULES (galaxy.util.inflection.Inflector attribute) Ply (class in galaxy.datatypes.constructive_solid_geometry) PlyAscii (class in galaxy.datatypes.constructive_solid_geometry) PlyBinary (class in galaxy.datatypes.constructive_solid_geometry) Png (class in galaxy.datatypes.images) poll (galaxy.jobs.runners.pulsar.PulsarMQJobRunner attribute) poll_active_workflow_ids() (galaxy.model.WorkflowInvocation static method) poll_unhandled_workflow_ids() (galaxy.model.WorkflowInvocation static method) pool_members() (galaxy.web_stack.ApplicationStack method) (galaxy.web_stack.UWSGIApplicationStack method) (galaxy.web_stack.WeblessApplicationStack method) pool_name() (galaxy.web_stack.ApplicationStack property) pop() (galaxy.model.custom_types.MutationDict method) (galaxy.model.custom_types.MutationList method) (galaxy.util.oset.OrderedSet method) pop_tool_ids() (in module galaxy.tool_util.deps.views) popitem() (galaxy.util.odict.odict method) populate() (galaxy.model.dataset_collections.builder.BoundCollectionBuilder method) populate_api_routes() (in module galaxy.webapps.galaxy.buildapp) populate_collection_elements() (galaxy.model.store.discover.ModelPersistenceContext method) populate_config_args() (in module galaxy.util.script) populate_containers_dict_for_new_install() (tool_shed.galaxy_install.dependency_display.DependencyDisplayer method) populate_containers_dict_from_repository_metadata() (tool_shed.galaxy_install.dependency_display.DependencyDisplayer method) populate_data_for_step() (galaxy.workflow.render.WorkflowCanvas method) populate_model() (galaxy.tools.Tool method) populate_module_and_state() (in module galaxy.workflow.modules) populate_options() (galaxy.main.GalaxyConfigBuilder class method) populate_repository_dependencies_container() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) populate_repository_dependency_objects_for_processing() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) populate_resource_parameters() (galaxy.tools.Tool method) populate_tool_dependencies_dicts() (tool_shed.galaxy_install.dependency_display.DependencyDisplayer method) populate_tool_shed_info() (galaxy.tools.Tool method) populated() (galaxy.model.DatasetCollection property) (galaxy.model.DatasetCollectionInstance property) populated_optimized() (galaxy.model.DatasetCollection property) populated_state (galaxy.model.DatasetCollection attribute) (galaxy.model.ImplicitCollectionJobs attribute) populated_state_message (galaxy.model.DatasetCollection attribute) PopulatedDisplayApplicationLink (class in galaxy.datatypes.display_applications.application) port (galaxy.model.InteractiveToolEntryPoint attribute) port() (galaxy.containers.ContainerPort property) (galaxy.web.proxy.ProxyMapping property) portable (galaxy.metadata.PortableDirectoryMetadataGenerator attribute) PortableDirectoryMetadataGenerator (class in galaxy.metadata) ports() (galaxy.containers.Container property) (galaxy.containers.docker_model.DockerContainer property) (galaxy.containers.docker_model.DockerService property) Position (class in galaxy.workflow.refactor.schema) position (galaxy.model.WorkflowStep attribute) (galaxy.workflow.refactor.schema.AddInputAction attribute) (galaxy.workflow.refactor.schema.AddStepAction attribute) (galaxy.workflow.refactor.schema.ExtractInputAction attribute) (galaxy.workflow.refactor.schema.ExtractUntypedParameter attribute) (galaxy.workflow.refactor.schema.UpdateStepPositionAction attribute) PosixFilesSource (class in galaxy.files.sources.posix) POSSIBLE_PARAMETER_TYPES (galaxy.workflow.modules.InputParameterModule attribute) possible_subcommands (galaxy.util.pastescript.serve.ServeCommand attribute) post() (galaxy_test.base.api.ApiTestInteractor method) post_authentication() (galaxy.openid.providers.OpenIDProvider method) post_execute_commands() (galaxy.job_metrics.JobInstrumenter method) (galaxy.job_metrics.NullJobInstrumenter method) post_execute_instrument() (galaxy.job_metrics.instrumenters.cgroup.CgroupPlugin method) (galaxy.job_metrics.instrumenters.collectl.CollectlPlugin method) (galaxy.job_metrics.instrumenters.core.CorePlugin method) (galaxy.job_metrics.instrumenters.env.EnvPlugin method) (galaxy.job_metrics.instrumenters.InstrumentPlugin method) post_job_action (galaxy.model.PostJobActionAssociation attribute) post_job_action_id (galaxy.model.PostJobActionAssociation attribute) post_job_actions (galaxy.model.Job attribute) (galaxy.model.WorkflowStep attribute) post_task() (galaxy.jobs.runners.godocker.GodockerJobRunner method) postal_code (galaxy.model.UserAddress attribute) postclick (galaxy.tours.TourStep attribute) postfork_functions (galaxy.web_stack.UWSGIApplicationStack attribute) postfork_setup() (in module galaxy.webapps.galaxy.buildapp) PostgresqlArchive (class in galaxy.datatypes.binary) PostJobAction (class in galaxy.model) (class in tool_shed.webapp.model) PostJobActionAssociation (class in galaxy.model) Pphe (class in galaxy.datatypes.genetics) Ppm (class in galaxy.datatypes.images) PQP (class in galaxy.datatypes.binary) PQR (class in galaxy.datatypes.molecules) pre_execute_commands() (galaxy.job_metrics.JobInstrumenter method) (galaxy.job_metrics.NullJobInstrumenter method) pre_execute_instrument() (galaxy.job_metrics.instrumenters.collectl.CollectlPlugin method) (galaxy.job_metrics.instrumenters.core.CorePlugin method) (galaxy.job_metrics.instrumenters.cpuinfo.CpuInfoPlugin method) (galaxy.job_metrics.instrumenters.env.EnvPlugin method) (galaxy.job_metrics.instrumenters.hostname.HostnamePlugin method) (galaxy.job_metrics.instrumenters.InstrumentPlugin method) (galaxy.job_metrics.instrumenters.meminfo.MemInfoPlugin method) (galaxy.job_metrics.instrumenters.uname.UnamePlugin method) precache() (galaxy.tool_util.deps.DependencyManager property) preclick (galaxy.tours.TourStep attribute) precreate_dataset_collection() (galaxy.managers.collections.DatasetCollectionManager method) precreate_dataset_collection_instance() (galaxy.managers.collections.DatasetCollectionManager method) prefer_template_database (galaxy_test.driver.integration_util.IntegrationInstance attribute) preferences (galaxy.model.User attribute) (galaxy.schema.BootstrapAdminUser attribute) preferences() (galaxy.files.DictFileSourcesUserContext property) (galaxy.files.ProvidesUserFileSourcesUserContext property) (galaxy.managers.users.UserManager method) prefix() (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver property) PrefixFilter (class in galaxy.config.config_manage) prepare() (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter method) (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) prepare_display() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) prepare_export() (galaxy_test.base.populators.BaseDatasetPopulator method) prepare_for_install() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) prepare_input_files_cmd (galaxy.model.Task attribute) prepare_job() (galaxy.jobs.runners.BaseJobRunner method) prepare_multi_history_view() (galaxy_test.selenium.test_history_multi_view.HistoryMultiViewTestCase method) prepare_step() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager.StepManager method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertDirectoryExecutable method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertDirectoryExists method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertFileExecutable method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertFileExists method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.Autoconf method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.ChangeDirectory method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.Chmod method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadBinary method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadByUrl method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadFile method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MakeDirectory method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MakeInstall method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MoveDirectoryFiles method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MoveFile method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.RecipeStep method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.RegexReplace method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetEnvironment method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetEnvironmentForInstall method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupPerlEnvironment method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupPythonEnvironment method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupREnvironment method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupRubyEnvironment method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupVirtualEnv method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.ShellCommand method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.TemplateCommand method) preparing() (galaxy.model.JobExportHistoryArchive property) preparing_display() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) prepend_anaconda_url() (in module galaxy.tool_util.deps.mulled.get_tests) prepend_timeout_message() (galaxy.selenium.has_driver.HasDriver method) preprocess_volumes() (in module galaxy.tool_util.deps.container_classes) pretty() (galaxy.util.jstree.JSTree method) pretty_print_json() (in module galaxy.util) pretty_print_time_interval() (in module galaxy.util) pretty_print_xml() (in module galaxy.util) pretty_stack() (in module galaxy.model.orm.engine_factory) prev_session_id (galaxy.model.GalaxySession attribute) (tool_shed.webapp.model.GalaxySession attribute) preview_repository_in_tool_shed() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) preview_tools_in_changeset() (tool_shed.webapp.controllers.repository.RepositoryController method) previous_changeset_revisions() (tool_shed.webapp.controllers.repository.RepositoryController method) primary_file_name (galaxy.datatypes.data.Data attribute) primitive_parsers (galaxy.visualization.plugins.resource_parser.ResourceParser attribute) print_nonsleeping() (galaxy.util.heartbeat.Heartbeat method) print_versioned_deps() (in module galaxy.tool_util.deps.brew_exts) priority_list (in module galaxy.jobs.dynamic_tool_destination) PRIVATE (galaxy.model.Role.types attribute) private (tool_shed.webapp.model.ComponentReview attribute) (tool_shed.webapp.model.Repository attribute) private_component_reviews (tool_shed.webapp.model.RepositoryReview attribute) private_id (galaxy.model.Role attribute) (tool_shed.webapp.model.Role attribute) private_role() (galaxy.managers.users.UserManager method) privately_share_dataset() (galaxy.model.security.GalaxyRBACAgent method) ProBam (class in galaxy.datatypes.binary) ProBed (class in galaxy.datatypes.interval) process() (galaxy.datatypes.metadata.Statement class method) (galaxy.model.metadata.Statement class method) (galaxy.model.search.SearchQuery method) process_action_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_actions_group_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_actions_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_batch_requests() (galaxy.web.framework.middleware.batch.BatchMiddleware method) process_bind_param() (galaxy.model.custom_types.JSONType method) (galaxy.model.custom_types.MetadataType method) (galaxy.model.custom_types.TrimmedString method) (galaxy.model.custom_types.UUIDType method) process_config() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_data() (galaxy.visualization.data_providers.basic.BaseDataProvider method) (galaxy.visualization.data_providers.genome.BamDataProvider method) (galaxy.visualization.data_providers.genome.BedDataProvider method) (galaxy.visualization.data_providers.genome.ChromatinInteractionsDataProvider method) (galaxy.visualization.data_providers.genome.ENCODEPeakDataProvider method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) (galaxy.visualization.data_providers.genome.GtfTabixDataProvider method) (galaxy.visualization.data_providers.genome.IntervalDataProvider method) (galaxy.visualization.data_providers.genome.IntervalIndexDataProvider method) (galaxy.visualization.data_providers.genome.RawGFFDataProvider method) (galaxy.visualization.data_providers.genome.VcfDataProvider method) process_definition() (galaxy.tool_util.cwl.schema.SchemaLoader method) process_install_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_json() (galaxy.tool_util.deps.mulled.mulled_search.GitHubSearch method) process_key() (in module galaxy.tools.parameters.meta) process_move() (galaxy.tools.data_manager.manager.DataManager method) process_object() (galaxy.tool_util.cwl.schema.RawProcessReference property) process_package_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_repository_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_result() (galaxy.tools.data_manager.manager.DataManager method) process_result_value() (galaxy.model.custom_types.JSONType method) (galaxy.model.custom_types.MetadataType method) (galaxy.model.custom_types.UUIDType method) process_split_file() (galaxy.datatypes.sequence.BaseFastq static method) process_tag_set() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager.TagManager method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Install method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Package method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.ReadMe method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.RecipeTag method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Repository method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.SetEnvironment method) process_task() (galaxy.queue_worker.GalaxyQueueWorker method) process_value_translation() (galaxy.tools.data_manager.manager.DataManager method) produce_k8s_job_prefix() (in module galaxy.jobs.runners.util.pykube_util) produce_outputs() (galaxy.tools.ApplyRulesTool method) (galaxy.tools.BuildListCollectionTool method) (galaxy.tools.DatabaseOperationTool method) (galaxy.tools.ExtractDatasetCollectionTool method) (galaxy.tools.FilterDatasetsTool method) (galaxy.tools.FilterFromFileTool method) (galaxy.tools.FlattenTool method) (galaxy.tools.MergeCollectionTool method) (galaxy.tools.RelabelFromFileTool method) (galaxy.tools.SortTool method) (galaxy.tools.TagFromFileTool method) (galaxy.tools.UnzipCollectionTool method) (galaxy.tools.ZipCollectionTool method) produces_collections_with_unknown_structure() (galaxy.tools.Tool property) produces_entry_points (galaxy.tools.InteractiveTool attribute) (galaxy.tools.Tool attribute) produces_real_jobs (galaxy.tools.actions.DefaultToolAction attribute) (galaxy.tools.actions.history_imp_exp.ExportHistoryToolAction attribute) (galaxy.tools.actions.history_imp_exp.ImportHistoryToolAction attribute) (galaxy.tools.actions.metadata.SetMetadataToolAction attribute) (galaxy.tools.actions.model_operations.ModelOperationToolAction attribute) (galaxy.tools.actions.upload.BaseUploadToolAction attribute) ProfileMiddleware (class in galaxy.web.framework.middleware.profile) PROGRESS (galaxy.model.TransferJob.states attribute) prohibited_middleware (galaxy.web_stack.ApplicationStack attribute) (galaxy.web_stack.UWSGIApplicationStack attribute) prop() (galaxy.tool_util.deps.container_classes.Container method) ProteomicsXml (class in galaxy.datatypes.proteomics) protocol (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.tool_util.deps.container_resolvers.mulled.MulledDockerContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.MulledSingularityContainerResolver attribute) (galaxy.web.framework.base.Request attribute) protocol() (galaxy.containers.ContainerPort property) prototype() (galaxy.model.dataset_collections.registry.DatasetCollectionTypesRegistry method) prototype_elements() (galaxy.model.dataset_collections.types.paired.PairedDatasetCollectionType method) ProtXML (class in galaxy.datatypes.proteomics) ProtXmlReport (class in galaxy.datatypes.proteomics) provenance_item_class (galaxy.webapps.galaxy.api.provenance.HDAProvenanceController attribute) (galaxy.webapps.galaxy.api.provenance.LDDAProvenanceController attribute) provenance_item_id (galaxy.webapps.galaxy.api.provenance.HDAProvenanceController attribute) (galaxy.webapps.galaxy.api.provenance.LDDAProvenanceController attribute) provider (galaxy.model.CloudAuthz attribute) (galaxy.model.CustosAuthnzToken attribute) (galaxy.model.UserAuthnzToken attribute) ProvidesAppContext (class in galaxy.managers.context) ProvidesHistoryContext (class in galaxy.managers.context) ProvidesUserContext (class in galaxy.managers.context) ProvidesUserFileSourcesUserContext (class in galaxy.files) proxy_ipc() (in module galaxy.web.proxy) proxy_launcher() (galaxy.web.proxy.ProxyManager method) ProxyIpc (class in galaxy.web.proxy) ProxyLauncher (class in galaxy.web.proxy) ProxyManager (class in galaxy.web.proxy) ProxyMapping (class in galaxy.web.proxy) ProxyRequests (class in galaxy.web.proxy) prune_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) prune_invalid_repository_dependencies() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) prune_repository_dependencies() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) pruneLD() (in module galaxy.datatypes.converters.pbed_ldreduced_converter) ps() (galaxy.containers.docker.DockerAPIInterface method) (galaxy.containers.docker.DockerCLIInterface method) PSAAssociation (class in galaxy.model) PSAAuthnz (class in galaxy.authnz.psa_authnz) PSACode (class in galaxy.model) PSANonce (class in galaxy.model) PSAPartial (class in galaxy.model) Psd (class in galaxy.datatypes.images) PSMS (class in galaxy.datatypes.proteomics) pstats_as_html() (in module galaxy.web.framework.middleware.profile) public_actions (galaxy.jobs.actions.post.ActionBox attribute) PublicURLColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.web.legacy_framework.grids) publish (galaxy.managers.workflows.WorkflowCreateOptions attribute) publish() (galaxy.managers.sharable.SharableModelManager method) publish_current_history() (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase method) publish_history() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) publish_port_list_required (galaxy.containers.ContainerInterface attribute) (galaxy.containers.docker_swarm.DockerSwarmInterface attribute) published (galaxy.model.History attribute) (galaxy.model.Page attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.Visualization attribute) published() (galaxy.webapps.galaxy.api.histories.HistoriesController method) published_grid_search_for() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) published_list_grid (galaxy.webapps.galaxy.controllers.history.HistoryController attribute) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController attribute) pull() (galaxy.tool_util.deps.container_resolvers.mulled.MulledDockerContainerResolver method) (galaxy.tool_util.deps.container_resolvers.mulled.MulledSingularityContainerResolver method) pull_mulled_singularity_command() (in module galaxy.tool_util.deps.singularity_util) pull_policy() (in module galaxy.jobs.runners.util.pykube_util) pull_repository() (in module galaxy.tool_shed.util.hg_util) (in module tool_shed.util.hg_util) PulsarEmbeddedJobRunner (class in galaxy.jobs.runners.pulsar) PulsarEmbeddedMQJobRunner (class in galaxy.jobs.runners.pulsar) PulsarLegacyJobRunner (class in galaxy.jobs.runners.pulsar) PulsarMQJobRunner (class in galaxy.jobs.runners.pulsar) PulsarObjectStore (class in galaxy.objectstore.pulsar) PulsarRESTJobRunner (class in galaxy.jobs.runners.pulsar) purgable (galaxy.model.Dataset attribute) PurgableDeserializerMixin (class in galaxy.managers.deletable) PurgableFiltersMixin (class in galaxy.managers.deletable) PurgableManagerMixin (class in galaxy.managers.deletable) PurgableSerializerMixin (class in galaxy.managers.deletable) purge() (galaxy.managers.datasets.DatasetAssociationManager method) (galaxy.managers.datasets.DatasetManager method) (galaxy.managers.deletable.PurgableManagerMixin method) (galaxy.managers.hdas.HDAManager method) (galaxy.managers.histories.HistoryManager method) (galaxy.managers.users.UserManager method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) purge_async() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) purge_category() (tool_shed.webapp.controllers.admin.AdminController method) purge_deleted_datasets() (galaxy.webapps.galaxy.controllers.history.HistoryController method) purge_group() (tool_shed.util.admin_util.Admin method) purge_operation (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) (tool_shed.util.admin_util.Admin attribute) (tool_shed.webapp.controllers.admin.AdminController attribute) purge_repository() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) purge_role() (tool_shed.util.admin_util.Admin method) purge_usage_from_quota() (galaxy.model.HistoryDatasetAssociation method) purge_user() (tool_shed.util.admin_util.Admin method) purged (galaxy.model.Dataset attribute) (galaxy.model.History attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.Library attribute) (galaxy.model.LibraryDataset attribute) (galaxy.model.LibraryFolder attribute) (galaxy.model.MetadataFile attribute) (galaxy.model.User attribute) (galaxy.model.UserAddress attribute) (tool_shed.webapp.model.User attribute) purged_history_associations (galaxy.model.Dataset attribute) PurgedColumn (class in galaxy.web.framework.helpers.grids) put() (galaxy.jobs.handler.DefaultJobDispatcher method) (galaxy.jobs.handler.JobHandlerQueue method) (galaxy.jobs.handler.JobHandlerStopQueue method) (galaxy.jobs.NoopQueue method) (galaxy.jobs.runners.BaseJobRunner method) (galaxy_test.base.api.ApiTestInteractor method) put_stop() (galaxy.jobs.NoopQueue method) pykube_client_from_dict() (in module galaxy.jobs.runners.util.pykube_util) PythonObjectParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata)

Q

QC (galaxy.tool_util.parser.stdio.StdioErrorLevel attribute) QCML (class in galaxy.datatypes.proteomics) qp() (galaxy.datatypes.display_applications.parameters.DisplayDataValueWrapper property) (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper property) quality_check() (galaxy.datatypes.sequence.BaseFastq static method) (galaxy.datatypes.sequence.FastqSanger static method) QualityScore (class in galaxy.datatypes.qualityscore) QualityScore454 (class in galaxy.datatypes.qualityscore) QualityScoreIllumina (class in galaxy.datatypes.qualityscore) QualityScoreSolexa (class in galaxy.datatypes.qualityscore) QualityScoreSOLiD (class in galaxy.datatypes.qualityscore) Quantile (class in galaxy.datatypes.mothur) quay_versions() (in module galaxy.tool_util.deps.mulled.util) QuaySearch (class in galaxy.tool_util.deps.mulled.mulled_search) query() (galaxy.jobs.rule_helper.RuleHelper method) (galaxy.managers.base.ModelManager method) (galaxy.model.search.GalaxySearchEngine method) (galaxy.model.store.SessionlessContext method) query_associated() (galaxy.managers.base.ModelManager method) query_proxy() (galaxy.web.proxy.ProxyManager method) queue() (galaxy.workflow.scheduling_manager.WorkflowSchedulingManager method) queue_history_export() (galaxy.webapps.base.controller.ExportsHistoryMixin method) queue_history_import() (galaxy.webapps.base.controller.ImportsHistoryMixin method) queue_job() (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.chronos.ChronosJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.condor.CondorJobRunner method) (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) (galaxy.jobs.runners.godocker.GodockerJobRunner method) (galaxy.jobs.runners.kubernetes.KubernetesJobRunner method) (galaxy.jobs.runners.local.LocalJobRunner method) (galaxy.jobs.runners.pbs.PBSJobRunner method) (galaxy.jobs.runners.tasks.TaskedJobRunner method)

QUEUED (galaxy.model.Dataset.states attribute) (galaxy.model.DatasetInstance.states attribute) (galaxy.model.DeferredJob.states attribute) (galaxy.model.Job.states attribute) (galaxy.model.Task.states attribute) queued (galaxy.model.view.HistoryDatasetCollectionJobStateSummary attribute) Quota (class in galaxy.model) quota (galaxy.model.DefaultQuotaAssociation attribute) (galaxy.model.GroupQuotaAssociation attribute) (galaxy.model.UserQuotaAssociation attribute) quota() (galaxy.managers.users.UserManager method) quota_amount() (galaxy.model.HistoryDatasetAssociation method) quota_id (galaxy.model.DefaultQuotaAssociation attribute) (galaxy.model.GroupQuotaAssociation attribute) (galaxy.model.UserQuotaAssociation attribute) quota_list_grid (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) QuotaAPIController (class in galaxy.webapps.galaxy.api.quotas) QuotaListGrid (class in galaxy.webapps.galaxy.controllers.admin) QuotaListGrid.AmountColumn (class in galaxy.webapps.galaxy.controllers.admin) QuotaListGrid.DescriptionColumn (class in galaxy.webapps.galaxy.controllers.admin) QuotaListGrid.GroupsColumn (class in galaxy.webapps.galaxy.controllers.admin) QuotaListGrid.NameColumn (class in galaxy.webapps.galaxy.controllers.admin) QuotaListGrid.StatusColumn (class in galaxy.webapps.galaxy.controllers.admin) QuotaListGrid.UsersColumn (class in galaxy.webapps.galaxy.controllers.admin) QuotaParamParser (class in galaxy.web.params) quotas (galaxy.model.Group attribute) (galaxy.model.User attribute) quotas_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) quote_first_command_arg() (galaxy.util.pastescript.serve.Command method) quote_plus_string() (in module galaxy.datatypes.display_applications.application)

R

raise_filter_err() (galaxy.managers.base.ModelFilterParser method) RangeParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) rank_collection_type() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) rank_type_plugin() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) Rast (class in galaxy.datatypes.images) RatableDeserializerMixin (class in galaxy.managers.ratable) RatableFilterMixin (class in galaxy.managers.ratable) RatableManagerMixin (class in galaxy.managers.ratable) RatableSerializerMixin (class in galaxy.managers.ratable) rate() (galaxy.managers.ratable.RatableManagerMixin method) rate_async() (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) rate_item() (galaxy.model.item_attrs.UsesItemRatings method) (tool_shed.webapp.util.ratings_util.ItemRatings method) rate_repository() (tool_shed.webapp.controllers.repository.RepositoryController method) rating (galaxy.model.HistoryDatasetAssociationRatingAssociation attribute) (galaxy.model.HistoryDatasetCollectionRatingAssociation attribute) (galaxy.model.HistoryRatingAssociation attribute) (galaxy.model.LibraryDatasetCollectionRatingAssociation attribute) (galaxy.model.PageRatingAssociation attribute) (galaxy.model.StoredWorkflowRatingAssociation attribute) (galaxy.model.VisualizationRatingAssociation attribute) (tool_shed.webapp.model.ComponentReview attribute) (tool_shed.webapp.model.RepositoryRatingAssociation attribute) (tool_shed.webapp.model.RepositoryReview attribute) rating() (galaxy.managers.ratable.RatableManagerMixin method) rating_assoc (galaxy.managers.histories.HistoryManager attribute) (galaxy.managers.pages.PageManager attribute) (galaxy.managers.ratable.RatableManagerMixin attribute) (galaxy.managers.visualizations.VisualizationManager attribute) rating_mapping() (in module galaxy.model.mapping) ratings (galaxy.model.History attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetCollectionAssociation attribute) (galaxy.model.Page attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.Visualization attribute) (tool_shed.webapp.model.Repository attribute) ratings() (galaxy.managers.ratable.RatableManagerMixin method) ratings_avg() (galaxy.managers.ratable.RatableManagerMixin method) ratings_count() (galaxy.managers.ratable.RatableManagerMixin method) raw_document_loader() (galaxy.tool_util.cwl.schema.SchemaLoader property) raw_element_identifiers() (galaxy.model.store.discover.JsonCollectedDatasetMatch property) raw_help() (galaxy.tools.Tool property) raw_library_contents_create() (galaxy_test.base.populators.LibraryPopulator method) raw_metadata() (in module galaxy.tool_util.deps.conda_compat) raw_param_dict() (galaxy.model.Job method) raw_process_reference() (galaxy.tool_util.cwl.schema.ResolvedProcessDefinition property) (galaxy.tool_util.cwl.schema.SchemaLoader method) raw_process_reference_for_object() (galaxy.tool_util.cwl.schema.SchemaLoader method) raw_set_dataset_state() (galaxy.model.DatasetInstance method) raw_tool_xml_tree() (in module galaxy.tool_util.loader) raw_xml_tree() (in module galaxy.util.xml_macros) RawBedDataProvider (class in galaxy.visualization.data_providers.genome) RawGFFDataProvider (class in galaxy.visualization.data_providers.genome) RawObjectWrapper (class in galaxy.tools.wrappers) RawProcessReference (class in galaxy.tool_util.cwl.schema) RawVcfDataProvider (class in galaxy.visualization.data_providers.genome) RawWorkflowDescription (class in galaxy.managers.workflows) RBACAgent (class in galaxy.security) (class in tool_shed.webapp.security) RBACPermission (class in galaxy.managers.rbac_secured) RBACPermissionFailedException RData (class in galaxy.datatypes.binary) Rdf (class in galaxy.datatypes.triples) reactivate_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) read_build_sites() (in module galaxy.util) READ_CHUNK_SIZE (galaxy.webapps.galaxy.api.uploads.UploadsAPIController attribute) read_config() (tool_shed.util.hgweb_config.HgWebConfigManager method) read_dbnames() (in module galaxy.util.dbkeys) read_exit_code() (galaxy.jobs.runners.JobState method) read_exit_code_from() (in module galaxy.job_execution.output_collect) read_file() (galaxy.util.properties.NicerConfigParser method) read_only (galaxy.tool_util.deps.container_resolvers.ContainerResolver attribute) (galaxy.tool_util.deps.resolvers.DependencyResolver attribute) read_pidfile() (in module galaxy.util.pastescript.serve) read_unordered_gtf() (in module galaxy.datatypes.util.gff_util) readable_output() (in module galaxy.tool_util.deps.mulled.mulled_search) readline() (galaxy.tools.exception_handling.UCSCOutWrapper method) (galaxy.util.ucsc.UCSCOutWrapper method) readlines() (galaxy.datatypes.dataproviders.base.DataProvider method) ReadMe (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler) (class in tool_shed.utility_containers.utility_container_manager) READY (galaxy.model.WorkflowInvocation.states attribute) (galaxy.model.WorkflowInvocationStep.states attribute) ready() (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter method) (galaxy.model.JobExportHistoryArchive property) (galaxy.webapps.galaxy.controllers.interactive_environments.InteractiveEnvironmentsController method) ready_galaxy_markdown_for_export() (in module galaxy.managers.markdown_util) ready_galaxy_markdown_for_import() (in module galaxy.managers.markdown_util) ready_name_for_url() (in module galaxy.util) ready_states (galaxy.model.Dataset attribute) realize_to() (galaxy.files.sources.FilesSource method) (galaxy.files.sources.posix.PosixFilesSource method) realpath() (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method) rebuild() (galaxy.tools.cache.ToolShedRepositoryCache method) rebuild_toolbox_search_index() (in module galaxy.queue_worker) recalculate_user_disk_usage() (in module galaxy.queue_worker) recipe_cellar_path() (in module galaxy.tool_util.deps.brew_exts) recipe_present() (galaxy.tool_util.deps.mulled.mulled_search.GitHubSearch method) RecipeContext (class in galaxy.tool_util.deps.brew_exts) RecipeStep (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) RecipeTag (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler) reclaim_ownership() (galaxy.jobs.JobWrapper method) recommended (galaxy.managers.licenses.LicenseMetadataModel attribute) reconfigure_watcher() (in module galaxy.queue_worker) record_pid() (galaxy.util.pastescript.serve.ServeCommand method) recover() (galaxy.jobs.handler.DefaultJobDispatcher method) (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.chronos.ChronosJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.condor.CondorJobRunner method) (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) (galaxy.jobs.runners.godocker.GodockerJobRunner method) (galaxy.jobs.runners.kubernetes.KubernetesJobRunner method) (galaxy.jobs.runners.local.LocalJobRunner method) (galaxy.jobs.runners.pbs.PBSJobRunner method) (galaxy.jobs.runners.tasks.TaskedJobRunner method) recover_mapping() (galaxy.workflow.modules.InputModule method) (galaxy.workflow.modules.PauseModule method) (galaxy.workflow.modules.WorkflowModule method) recover_state() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) RecursiveNone (class in galaxy.model.none_like) redirect() (galaxy.authnz.psa_authnz.Strategy method) (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) redirect_aware_commmunicate() (in module galaxy.util.commands) redirecting_io() (in module galaxy.util.commands) reduce_block_by_primary_genome() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) refactor() (galaxy.managers.workflows.WorkflowContentsManager method) (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) (galaxy.workflow.refactor.execute.WorkflowRefactorExecutor method) refactor_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method) RefactorActionExecution (class in galaxy.workflow.refactor.schema) RefactorActionExecutionMessage (class in galaxy.workflow.refactor.schema) RefactorActionExecutionMessageTypeEnum (class in galaxy.workflow.refactor.schema) RefactorActions (class in galaxy.workflow.refactor.schema) RefactorRequest (class in galaxy.managers.workflows) RefactorResponse (class in galaxy.managers.workflows) RefactorResponse.Config (class in galaxy.managers.workflows) reference (galaxy.managers.licenses.LicenseMetadataModel attribute) reference() (galaxy.visualization.genomes.Genomes method) referenceNumber (galaxy.managers.licenses.LicenseMetadataModel attribute) referer (galaxy.model.GalaxySession attribute) (tool_shed.webapp.model.GalaxySession attribute) RefgenieToolDataTable (class in galaxy.tools.data) refresh() (in module tool_shed.test.base.test_db_util) refresh_expiration_time (galaxy.model.CustosAuthnzToken attribute) refresh_token (galaxy.model.CustosAuthnzToken attribute) RefTaxonomy (class in galaxy.datatypes.mothur) regenerate_imported_metadata_if_needed() (galaxy.tools.SetMetadataTool method) regenerate_primary_file() (galaxy.datatypes.assembly.Velvet method) (galaxy.datatypes.genetics.IdeasPre method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.genetics.Rgenetics method) (galaxy.datatypes.ngsindex.BowtieIndex method) (galaxy.datatypes.text.SnpSiftDbNSFP method) regenerate_statistics() (tool_shed.webapp.controllers.admin.AdminController method) regex_line_dataprovider() (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.data.Text method) (galaxy.datatypes.tabular.Sam method) RegexCollectedDatasetMatch (class in galaxy.model.store.discover) RegexLineDataProvider (class in galaxy.datatypes.dataproviders.line) RegexpFilter (class in galaxy.tools.parameters.dynamic_options) RegexReplace (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) RegexSubprocessDataProvider (class in galaxy.datatypes.dataproviders.external) RegexValidator (class in galaxy.tools.parameters.validation) RegionAlignment (class in galaxy.datatypes.util.maf_utilities) (class in galaxy.tools.util.maf_utilities) register() (galaxy.managers.users.UserManager method) (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) (galaxy.tools.toolbox.lineages.factory.LineageMap method) (galaxy.tools.toolbox.lineages.LineageMap method) register_and_change_password() (galaxy_test.selenium.test_change_password.ChangePasswordTestCase method) register_cleanup_file_attribute() (galaxy.jobs.runners.AsynchronousJobState method) register_container_information() (galaxy.job_execution.ports.JobPortsView method) (galaxy.job_execution.ports.view.JobPortsView method) register_exception() (galaxy.tool_util.verify.script.Results method) register_func() (galaxy.web_stack.message.ApplicationStackMessageDispatcher method) register_job_data() (in module galaxy_test.base.instrument) register_message_handler() (galaxy.web_stack.ApplicationStack method) (galaxy.web_stack.MessageApplicationStack method) register_postfork_function() (galaxy.web_stack.ApplicationStack class method) (galaxy.web_stack.UWSGIApplicationStack class method) (in module galaxy.web_stack) register_result() (galaxy.tool_util.verify.script.Results method) register_signals() (in module galaxy.main) register_sniffable_binary_format() (galaxy.datatypes.binary.Binary static method) register_tool() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) register_unsniffable_binary_ext() (galaxy.datatypes.binary.Binary static method) register_version() (galaxy.tools.toolbox.lineages.interface.ToolLineage method) (galaxy.tools.toolbox.lineages.ToolLineage method) REGISTERED (galaxy.model.DefaultQuotaAssociation.types attribute) registered_users() (galaxy.webapps.reports.controllers.users.Users method) registered_users_per_month() (galaxy.webapps.reports.controllers.users.Users method) RegistrationTestCase (class in galaxy_test.selenium.test_registration) Registry (class in galaxy.datatypes.registry) (class in galaxy.tool_shed.tool_shed_registry) (class in tool_shed.repository_registry) (class in tool_shed.repository_types.registry) registry (galaxy.webapps.galaxy.api.tours.FastAPITours attribute) reimport_history() (galaxy_test.base.populators.BaseDatasetPopulator method) reindex_tool_search() (galaxy.config.ConfiguresGalaxyMixin method) reinstall_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) RelabelFromFileTool (class in galaxy.tools) RelationBuilder (class in tool_shed.dependencies.repository.relation_builder) relativize_symlinks() (in module galaxy.util) release() (galaxy.util.filelock.FileLock method) relink_initialworkdir() (in module galaxy.tool_util.cwl.cwltool_deps) reload() (galaxy.datatypes.display_applications.application.DisplayApplication method) (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.display_applications.DisplayApplicationsController method) (galaxy.webapps.galaxy.api.tool_data.ToolData method) (galaxy.webapps.galaxy.api.tools.ToolsController method) reload_config_options() (in module galaxy.config) reload_core_config() (in module galaxy.queue_worker) reload_data_managers() (in module galaxy.queue_worker) reload_dependency_manager() (galaxy.tools.toolbox.base.BaseGalaxyToolBox method) (galaxy.tools.toolbox.BaseGalaxyToolBox method) reload_display_application() (in module galaxy.queue_worker) reload_display_applications() (galaxy.datatypes.registry.Registry method) reload_from_files() (galaxy.tools.data.ToolDataTable method) reload_genomes() (galaxy.visualization.genomes.Genomes method) reload_job_rules() (in module galaxy.queue_worker) reload_sanitize_allowlist() (galaxy.config.GalaxyAppConfiguration method) (in module galaxy.queue_worker) reload_tables() (galaxy.tools.data.ToolDataTableManager method) reload_tool() (in module galaxy.queue_worker) reload_tool_by_id() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) reload_tool_data_table() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) reload_tool_data_tables() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) (in module galaxy.queue_worker) reload_toolbox() (galaxy.webapps.galaxy.api.configuration.ConfigurationController method) (in module galaxy.queue_worker) reload_tour() (in module galaxy.queue_worker) reloadable_options() (galaxy.config.schema.AppSchema property) remappable() (galaxy.model.Job method) remote_addr (galaxy.model.GalaxySession attribute) (tool_shed.webapp.model.GalaxySession attribute) remote_host (galaxy.model.GalaxySession attribute) (galaxy.web.framework.base.Request attribute) (tool_shed.webapp.model.GalaxySession attribute) remote_hostname (galaxy.web.framework.base.Request attribute) remote_port (galaxy.web.framework.base.Request attribute) remote_repository_url (tool_shed.webapp.model.Repository attribute) RemoteFilesAPIController (class in galaxy.webapps.galaxy.api.remote_files) RemoteShell (class in galaxy.jobs.runners.util.cli.shell.rsh) RemoteUser (class in galaxy.web.framework.middleware.remoteuser) (class in tool_shed.webapp.framework.middleware.remoteuser) remove() (galaxy.managers.interactivetool.InteractiveToolSqlite method) (galaxy.model.custom_types.MutationList method) (galaxy.model.PSAAssociation class method) remove_category_entry() (tool_shed.repository_registry.Registry method) remove_dir() (in module galaxy.tool_shed.util.basic_util) remove_display_app() (galaxy.datatypes.data.Data method) remove_entry() (galaxy.tools.data.ToolDataTable method) (tool_shed.repository_registry.Registry method) remove_entry_from_installed_repository_dependencies_of_installed_repositories() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) remove_entry_from_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) remove_entry_from_installed_tool_dependencies_of_installed_repositories() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) remove_entry_from_repository_dependencies_of_installed_repositories() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) remove_entry_from_runtime_tool_dependencies_of_installed_tool_dependencies() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) remove_entry_from_tool_dependencies_of_installed_repositories() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) remove_entry_point() (galaxy.managers.interactivetool.InteractiveToolManager method) (galaxy.managers.interactivetool.InteractiveToolSqlite method) remove_entry_points() (galaxy.managers.interactivetool.InteractiveToolManager method) remove_favorite() (galaxy.webapps.galaxy.api.users.UserAPIController method) remove_file() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Repository method) (in module tool_shed.util.hg_util) remove_from_cache() (galaxy.tools.Tool method) remove_from_data_manager() (galaxy.tool_shed.galaxy_install.tools.data_manager.DataManagerHandler method) remove_from_key_rd_dicts() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) remove_from_shed_tool_config() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) remove_item_tag() (galaxy.model.tags.TagHandler method) remove_key() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataCollection method) remove_manager() (galaxy.tools.data_manager.manager.DataManagers method) remove_port_from_tool_shed_url() (in module galaxy.util.tool_shed.common_util) remove_protocol_and_port_from_tool_shed_url() (in module galaxy.util.tool_shed.common_util) remove_protocol_and_user_from_clone_url() (in module galaxy.util.tool_shed.common_util) remove_protocol_from_tool_shed_url() (in module galaxy.util.tool_shed.common_util) remove_protocol_from_url() (in module galaxy.util) remove_repository_contents() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) remove_repository_dependency() (tool_shed.utility_containers.utility_container_manager.Folder method) remove_repository_dependency_reference_to_self() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) remove_repository_registry_entry() (tool_shed.webapp.api.repositories.RepositoriesController method) remove_tag_async() (galaxy.webapps.galaxy.controllers.tag.TagsController method) remove_tags_from_list() (galaxy.model.tags.TagHandler method) remove_temp_index_file() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) remove_tool_by_id() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) remove_tool_dependency() (in module galaxy.tool_shed.util.tool_dependency_util) remove_tool_dependency_installation_directory() (in module galaxy.tool_shed.util.tool_dependency_util) remove_unused_dependency_paths() (galaxy.tool_util.deps.views.DependencyResolversView method) remove_version_from_guid() (in module galaxy.util.tool_version) RemoveColumnsRuleDefinition (class in galaxy.util.rules_dsl) RemoveTagDatasetAction (class in galaxy.jobs.actions.post) RemoveUnlabeledWorkflowOutputs (class in galaxy.workflow.refactor.schema) RemoveValueFilter (class in galaxy.tools.parameters.dynamic_options) rename() (galaxy.webapps.galaxy.controllers.history.HistoryController method) rename_async() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) rename_group() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (tool_shed.util.admin_util.Admin method) rename_history() (galaxy_test.base.populators.BaseDatasetPopulator method) rename_quota() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) rename_role() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (tool_shed.util.admin_util.Admin method) renamed_options (galaxy.config.BaseAppConfiguration attribute) (galaxy.config.GalaxyAppConfiguration attribute) RenameDatasetAction (class in galaxy.jobs.actions.post) RenamedTemporaryFile (class in galaxy.util.renamed_temporary_file) render() (galaxy.visualization.plugins.plugin.VisualizationPlugin method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) render_html() (galaxy.authnz.psa_authnz.Strategy method) render_saved() (galaxy.visualization.plugins.plugin.VisualizationPlugin method) reopen_ro() (galaxy.tools.cache.ToolDocumentCache method) repair_methods() (galaxy.datatypes.data.Data method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.tabular.Pileup method) Repeat (class in galaxy.tools.parameters.grouping) replace_elements_in_collection() (galaxy.model.dataset_collections.builder.CollectionBuilder method) replace_failed_elements() (galaxy.model.DatasetCollection method) replace_request_syntax_sugar() (in module galaxy.model.store.discover) replace_tool() (galaxy.tools.toolbox.panel.ToolPanelElements method) REPLACEMENT_PARAMETERS (galaxy.model.WorkflowRequestInputParameter.types attribute) repo_files_directory() (galaxy.model.tool_shed_install.ToolShedRepository method) REPO_INSTALL (galaxy.selenium.navigates_galaxy.WAIT_TYPES attribute) repo_path() (galaxy.model.tool_shed_install.ToolShedRepository method) (tool_shed.webapp.model.Repository method) RepoManager (class in tool_shed.managers.repositories) Report (class in galaxy.webapps.reports.controllers.root) (class in galaxy.workflow.refactor.schema) report (galaxy.workflow.refactor.schema.UpdateReportAction attribute) report() (galaxy_test.base.instrument.StructuredTestDataPlugin method) ReportQueryBuilder (class in galaxy.webapps.reports.controllers.query) reports_config (galaxy.model.Workflow attribute) ReportsWebApplication (class in galaxy.webapps.reports.buildapp) RepoSearch (class in tool_shed.webapp.search.repo_search) repositories (tool_shed.webapp.model.Category attribute) (tool_shed.webapp.model.Role attribute) repositories_by_user_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) repositories_i_can_administer_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) repositories_i_own_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) repositories_in_category_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) repositories_missing_tool_test_components_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) repositories_ready_for_review_grid (tool_shed.webapp.controllers.repository_review.RepositoryReviewController attribute) repositories_reviewed_by_me_grid (tool_shed.webapp.controllers.repository_review.RepositoryReviewController attribute) repositories_with_invalid_tools_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) repositories_with_no_tool_tests_grid (tool_shed.webapp.controllers.repository_review.RepositoryReviewController attribute) repositories_with_reviews_grid (tool_shed.webapp.controllers.repository_review.RepositoryReviewController attribute) repositories_without_reviews_grid (tool_shed.webapp.controllers.repository_review.RepositoryReviewController attribute) RepositoriesByUserGrid (class in tool_shed.grids.repository_grids) RepositoriesController (class in tool_shed.webapp.api.repositories) RepositoriesICanAdministerGrid (class in tool_shed.grids.repository_grids) RepositoriesInCategoryGrid (class in tool_shed.grids.repository_grids) RepositoriesInstalledException RepositoriesIOwnGrid (class in tool_shed.grids.repository_grids) RepositoriesMissingToolTestComponentsGrid (class in tool_shed.grids.repository_grids) RepositoriesReadyForReviewGrid (class in tool_shed.grids.repository_review_grids) RepositoriesReviewedByMeGrid (class in tool_shed.grids.repository_review_grids) RepositoriesWithInvalidToolsGrid (class in tool_shed.grids.repository_grids) RepositoriesWithInvalidToolsGrid.InvalidToolConfigColumn (class in tool_shed.grids.repository_grids) RepositoriesWithNoToolTestsGrid (class in tool_shed.grids.repository_review_grids) RepositoriesWithoutReviewsGrid (class in tool_shed.grids.repository_review_grids) RepositoriesWithReviewsGrid (class in tool_shed.grids.repository_review_grids) RepositoriesWithReviewsGrid.ApprovedColumn (class in tool_shed.grids.repository_review_grids) RepositoriesWithReviewsGrid.RatingColumn (class in tool_shed.grids.repository_review_grids) RepositoriesWithReviewsGrid.ReviewersColumn (class in tool_shed.grids.repository_review_grids) RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn (class in tool_shed.grids.repository_review_grids) RepositoriesWithReviewsGrid.WithReviewsRevisionColumn (class in tool_shed.grids.repository_review_grids) Repository (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler) (class in tool_shed.webapp.model) repository (galaxy.model.tool_shed_install.RepositoryDependency attribute) (galaxy.model.tool_shed_install.RepositoryRepositoryDependencyAssociation attribute) (tool_shed.webapp.model.RepositoryCategoryAssociation 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) repository_dependencies() (galaxy.model.tool_shed_install.ToolShedRepository property) (tool_shed.webapp.api.repository_revisions.RepositoryRevisionsController method) (tool_shed.webapp.model.RepositoryMetadata property) repository_dependencies_being_installed() (galaxy.model.tool_shed_install.ToolShedRepository property) repository_dependencies_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) repository_dependencies_missing_or_being_installed() (galaxy.model.tool_shed_install.ToolShedRepository property) repository_dependencies_with_installation_errors() (galaxy.model.tool_shed_install.ToolShedRepository property) repository_dependency (galaxy.model.tool_shed_install.RepositoryRepositoryDependencyAssociation attribute) repository_dependency_id (galaxy.model.tool_shed_install.RepositoryRepositoryDependencyAssociation attribute) repository_dependency_needed_only_for_compiling_tool_dependency() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) repository_grid (tool_shed.webapp.controllers.admin.AdminController attribute) (tool_shed.webapp.controllers.repository.RepositoryController attribute) repository_id (tool_shed.webapp.model.RepositoryCategoryAssociation attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) (tool_shed.webapp.model.RepositoryRatingAssociation attribute) (tool_shed.webapp.model.RepositoryReview attribute) (tool_shed.webapp.model.RepositoryRoleAssociation attribute) repository_ids_for_setting_metadata() (tool_shed.webapp.api.repositories.RepositoriesController method) repository_installation_status_updates() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) repository_is_new() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) repository_long_description (in module tool_shed.test.functional.test_0010_repository_with_tool_dependencies) (in module tool_shed.test.functional.test_0400_repository_component_reviews) (in module tool_shed.test.functional.test_0410_repository_component_review_access_control) (in module tool_shed.test.functional.test_0480_tool_dependency_xml_verification) repository_metadata (tool_shed.webapp.model.RepositoryReview attribute) repository_metadata_grid (tool_shed.webapp.controllers.admin.AdminController attribute) (tool_shed.webapp.controllers.repository.RepositoryController attribute) repository_review (tool_shed.webapp.model.ComponentReview attribute) repository_review_id (tool_shed.webapp.model.ComponentReview attribute) repository_reviews_by_user() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method) repository_reviews_by_user_grid (tool_shed.webapp.controllers.repository_review.RepositoryReviewController attribute) repository_was_previously_installed() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) RepositoryCategoryAssociation (class in tool_shed.webapp.model) RepositoryController (class in tool_shed.webapp.controllers.repository) RepositoryDependenciesGrid (class in tool_shed.grids.repository_grids) RepositoryDependenciesGrid.RequiredRepositoryColumn (class in tool_shed.grids.repository_grids) RepositoryDependency (class in galaxy.model.tool_shed_install) (class in tool_shed.utility_containers.utility_container_manager) RepositoryDependencyAttributeHandler (class in tool_shed.dependencies.attribute_handlers) RepositoryDependencyInstallManager (class in galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager) RepositoryGrid (class in tool_shed.grids.repository_grids) RepositoryGrid.CategoryColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.DeprecatedColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.DescriptionColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.EmailAlertsColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.EmailColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.HeadsColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.LatestInstallableRevisionColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.MetadataRevisionColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.NameColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.RepositoryCategoryColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.TipRevisionColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.TypeColumn (class in tool_shed.grids.repository_grids) RepositoryGrid.UserColumn (class in tool_shed.grids.repository_grids) RepositoryGridFilterManager (class in tool_shed.grids.repository_grid_filter_manager) RepositoryInstallationError (class in tool_shed.utility_containers) RepositoryMetadata (class in tool_shed.webapp.model) RepositoryMetadataGrid (class in tool_shed.grids.admin_grids) (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.ChangesetRevisionColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.DatatypesColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.DeletedColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.DeprecatedColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.DownloadableColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.HasRepositoryDependenciesColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.IdColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.IncludesDatatypesColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.IncludesToolDependenciesColumn (class in tool_shed.grids.repository_grids)

RepositoryMetadataGrid.IncludesToolsColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.IncludesWorkflowsColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.MaliciousColumn (class in tool_shed.grids.admin_grids) (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.NameColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.OwnerColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.RepositoryNameColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.RepositoryOwnerColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.RepositoryTypeColumn (class in tool_shed.grids.repository_grids) RepositoryMetadataGrid.RevisionColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.ToolsColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataGrid.WorkflowsColumn (class in tool_shed.grids.admin_grids) RepositoryMetadataManager (class in tool_shed.metadata.repository_metadata_manager) RepositoryRatingAssociation (class in tool_shed.webapp.model) RepositoryRepositoryDependencyAssociation (class in galaxy.model.tool_shed_install) RepositoryReview (class in tool_shed.webapp.model) RepositoryReviewController (class in tool_shed.webapp.controllers.repository_review) RepositoryReviewsByUserGrid (class in tool_shed.grids.repository_review_grids) RepositoryReviewsByUserGrid.RatingColumn (class in tool_shed.grids.repository_review_grids) RepositoryReviewsByUserGrid.RepositoryDescriptionColumn (class in tool_shed.grids.repository_review_grids) RepositoryReviewsByUserGrid.RepositoryNameColumn (class in tool_shed.grids.repository_review_grids) RepositoryReviewsByUserGrid.RevisionColumn (class in tool_shed.grids.repository_review_grids) RepositoryRevisionsController (class in tool_shed.webapp.api.repository_revisions) RepositoryRoleAssociation (class in tool_shed.webapp.model) RepositorySuccessfulInstallation (class in tool_shed.utility_containers) RepositorySuiteDefinition (class in tool_shed.repository_types.repository_suite_definition) RepositoryWithDependencyRevisions (class in tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions) RepoWeighting (class in tool_shed.webapp.search.repo_search) RepresentById (class in galaxy.model) Request (class in galaxy.web.framework.base) request() (galaxy.webapps.galaxy.api.toolshed.ToolShedController method) request_data() (galaxy.authnz.psa_authnz.Strategy method) request_host() (galaxy.authnz.psa_authnz.Strategy method) RequestIDMiddleware (class in galaxy.web.framework.middleware.request_id) RequestParameterInvalidException RequestParameterMissingException require_admin() (in module galaxy.web) (in module galaxy.web.framework.decorators) require_admin_message() (in module galaxy.web.framework.decorators) require_admin_user (galaxy_test.api.test_workflows.AdminWorkflowsApiTestCase attribute) require_dataset_ok (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.FilterEmptyDatasetsTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) require_file() (in module galaxy.tools.test) require_login() (in module galaxy.web) (in module galaxy.web.framework.decorators) require_uwsgi (galaxy_test.driver.integration_util.IntegrationInstance attribute) required_args (galaxy.util.pastescript.serve.Command attribute) required_module (galaxy.files.sources.dropbox.DropboxFilesSource attribute) (galaxy.files.sources.s3.S3FilesSource attribute) (galaxy.files.sources.webdav.WebDavFilesSource attribute) required_package (galaxy.files.sources.dropbox.DropboxFilesSource attribute) (galaxy.files.sources.s3.S3FilesSource attribute) (galaxy.files.sources.webdav.WebDavFilesSource attribute) required_repositories (galaxy.model.tool_shed_install.ToolShedRepository attribute) requirement_to_recipe() (in module galaxy.tool_util.deps.brew_util) RequirementMapping (class in galaxy.tool_util.deps.resolvers) requirements() (galaxy.webapps.galaxy.api.tools.ToolsController method) requirements_to_conda_targets() (in module galaxy.tool_util.deps.conda_util) requirements_to_dependencies() (galaxy.tool_util.deps.DependencyManager method) requirements_to_mulled_targets() (in module galaxy.tool_util.deps.mulled.mulled_build_tool) requirements_to_recipe_contexts() (in module galaxy.tool_util.deps.brew_util) requirements_to_recipes() (in module galaxy.tool_util.deps.brew_util) RequirementSpecification (class in galaxy.tool_util.deps.requirements) requires_admin (galaxy_test.selenium.framework.TestWithSeleniumMixin attribute) (galaxy_test.selenium.test_admin_app.AdminAppTestCase attribute) (galaxy_test.selenium.test_library_contents.LibraryContentsTestCase attribute) (galaxy_test.selenium.test_library_landing.LibraryLandingTestCase attribute) (galaxy_test.selenium.test_library_to_collections.LibraryToCollectionsTestCase attribute) requires_config_file (galaxy.util.pastescript.serve.ServeCommand attribute) requires_containerization() (galaxy.jobs.JobWrapper property) requires_dataset_id() (galaxy.datatypes.metadata.MetadataCollection property) (galaxy.model.metadata.MetadataCollection property) requires_dataset_metadata (galaxy.tools.parameters.validation.MetadataInDataTableColumnValidator attribute) (galaxy.tools.parameters.validation.MetadataInFileColumnValidator attribute) (galaxy.tools.parameters.validation.MetadataInRangeValidator attribute) (galaxy.tools.parameters.validation.MetadataNotInDataTableColumnValidator attribute) (galaxy.tools.parameters.validation.MetadataValidator attribute) (galaxy.tools.parameters.validation.UnspecifiedBuildValidator attribute) (galaxy.tools.parameters.validation.Validator attribute) requires_domain (galaxy.model.InteractiveToolEntryPoint attribute) requires_galaxy_python_environment() (galaxy.tools.Tool property) requires_js_runtime (galaxy.tools.ExpressionTool attribute) requires_prior_installation_of() (galaxy.model.tool_shed_install.ToolShedRepository property) requires_setting_metadata (galaxy.tools.SetMetadataTool attribute) (galaxy.tools.Tool attribute) requires_setting_metadata() (galaxy.jobs.JobWrapper property) RequiresGalaxyEnvironmentContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit) RequiresGalaxyEnvironmentSingularityContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit) rerun() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) reselect_tool_panel_section() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) resend_activation_email (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) resend_activation_email() (galaxy.webapps.galaxy.controllers.user.User method) resend_verification() (galaxy.webapps.galaxy.controllers.user.User method) reset() (galaxy.managers.pages.PageContentProcessor method) reset_all_metadata() (tool_shed.webapp.controllers.repository.RepositoryController method) reset_all_metadata_on_installed_repository() (galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) reset_all_metadata_on_repository_in_tool_shed() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) reset_all_tool_versions() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) reset_driver_and_session() (galaxy_test.selenium.framework.TestWithSeleniumMixin method) reset_installed_repository_metadata() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) reset_metadata_on_installed_repositories() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) reset_metadata_on_my_writable_repositories_in_tool_shed() (tool_shed.webapp.controllers.repository.RepositoryController method) reset_metadata_on_repositories() (tool_shed.webapp.api.repositories.RepositoriesController method) reset_metadata_on_repository() (tool_shed.webapp.api.repositories.RepositoriesController method) reset_metadata_on_selected_installed_repositories() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) reset_metadata_on_selected_repositories() (galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) reset_metadata_on_selected_repositories_in_tool_shed() (tool_shed.webapp.controllers.admin.AdminController method) reset_password() (galaxy.webapps.galaxy.controllers.user.User method) (tool_shed.webapp.controllers.user.User method) reset_previously_installed_repository() (galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) reset_repository_metadata() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) reset_request_query_counts() (in module galaxy.model.orm.engine_factory) reset_status() (galaxy.tools.cache.ToolCache method) reset_tags() (galaxy.tools.toolbox.tags.AbstractToolTagManager method) (galaxy.tools.toolbox.tags.NullToolTagManager method) (galaxy.tools.toolbox.tags.PersistentToolTagManager method) reset_tokens (galaxy.model.User attribute) reset_tool_data_tables() (galaxy.tool_shed.tools.data_table_manager.ShedToolDataTableManager method) reset_user_password() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (tool_shed.util.admin_util.Admin method) resolution_cache() (galaxy.tool_util.deps.containers.ContainerFinder method) ResolutionCache (class in galaxy.tool_util.deps.container_resolvers) resolvable() (galaxy.tool_util.deps.requirements.ToolRequirements property) resolve() (galaxy.tool_util.deps.container_resolvers.ContainerResolver method) (galaxy.tool_util.deps.container_resolvers.explicit.ExplicitContainerResolver method) (galaxy.tool_util.deps.container_resolvers.explicit.ExplicitSingularityContainerResolver method) (galaxy.tool_util.deps.container_resolvers.explicit.FallbackContainerResolver method) (galaxy.tool_util.deps.container_resolvers.explicit.MappingContainerResolver method) (galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledDockerContainerResolver method) (galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledSingularityContainerResolver method) (galaxy.tool_util.deps.container_resolvers.mulled.CachedMulledDockerContainerResolver method) (galaxy.tool_util.deps.container_resolvers.mulled.CachedMulledSingularityContainerResolver method) (galaxy.tool_util.deps.container_resolvers.mulled.MulledDockerContainerResolver method) (galaxy.tool_util.deps.containers.ContainerFinder method) (galaxy.tool_util.deps.containers.ContainerRegistry method) (galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages.HomebrewToolShedDependencyResolver method) (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method) (galaxy.tool_util.deps.resolvers.DependencyResolver method) (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependencyResolver method) (galaxy.tool_util.deps.resolvers.homebrew.HomebrewDependencyResolver method) (galaxy.tool_util.deps.resolvers.lmod.LmodDependencyResolver method) (galaxy.tool_util.deps.resolvers.modules.ModuleDependencyResolver method) (galaxy.tool_util.deps.views.ContainerResolutionView method) (galaxy.webapps.galaxy.api.container_resolution.ContainerResolutionAPIController method) resolve_all() (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method) (galaxy.tool_util.deps.resolvers.MultipleDependencyResolver method) resolve_and_validate_document() (in module galaxy.tool_util.cwl.cwltool_deps) resolve_dependencies() (galaxy.tool_util.deps.container_classes.Container property) resolve_invocation_markdown() (in module galaxy.managers.markdown_util) resolve_path() (galaxy.config.BaseAppConfiguration method) (in module galaxy.webapps.reports.config) resolve_toolbox() (galaxy.tool_util.deps.views.ContainerResolutionView method) (galaxy.webapps.galaxy.api.container_resolution.ContainerResolutionAPIController method) resolve_toolbox_with_install() (galaxy.webapps.galaxy.api.container_resolution.ContainerResolutionAPIController method) resolve_with_install() (galaxy.webapps.galaxy.api.container_resolution.ContainerResolutionAPIController method) ResolvedContainerDescription (class in galaxy.tool_util.deps.containers) ResolvedProcessDefinition (class in galaxy.tool_util.cwl.schema) resolver_dependency() (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) resolver_msg() (galaxy.tool_util.deps.resolvers.Dependency property) (galaxy.tool_util.deps.resolvers.NullDependency property) resolver_requirements() (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) resolver_type (galaxy.tool_util.deps.container_resolvers.explicit.ExplicitContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.ExplicitSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.FallbackContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.FallbackNoRequirementsContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.FallbackNoRequirementsSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.FallbackSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.MappingContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.RequiresGalaxyEnvironmentContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.RequiresGalaxyEnvironmentSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledDockerContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.CachedMulledDockerContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.CachedMulledSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.MulledDockerContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.MulledSingularityContainerResolver attribute) (galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages.HomebrewToolShedDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.homebrew.HomebrewDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.lmod.LmodDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.modules.ModuleDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.tool_shed_packages.ToolShedPackageDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages.UnlinkedToolShedPackageDependencyResolver attribute) resolver_type() (galaxy.tool_util.deps.container_resolvers.ContainerResolver property) resolves_simple_dependencies (galaxy.tool_util.deps.resolvers.DependencyResolver attribute) (galaxy.tool_util.deps.resolvers.tool_shed_packages.ToolShedPackageDependencyResolver attribute) RESOURCE_PARAMETERS (galaxy.model.WorkflowRequestInputParameter.types attribute) resource_parameters() (galaxy.model.WorkflowInvocation property) ResourceParser (class in galaxy.visualization.plugins.resource_parser) resources_option_map (galaxy.containers.docker_swarm.DockerSwarmAPIInterface attribute) Response (class in galaxy.web.framework.base) response() (galaxy.util.zipstream.ZipstreamWrapper method) restart() (galaxy_test.driver.integration_util.IntegrationInstance method) restart_policy_option_map (galaxy.containers.docker_swarm.DockerSwarmAPIInterface attribute) restart_with_monitor() (galaxy.util.pastescript.serve.ServeCommand method) restart_with_reloader() (galaxy.util.pastescript.serve.ServeCommand method) RestGolangProxyIpc (class in galaxy.web.proxy) restore_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) restore_text() (galaxy.tools.parameters.sanitize.ToolParameterSanitizer method) (in module galaxy.util) restrict_job_name_length (galaxy.jobs.runners.drmaa.DRMAAJobRunner attribute) (galaxy.jobs.runners.slurm.SlurmJobRunner attribute) restrict_on_connections (galaxy.workflow.refactor.schema.AddInputAction attribute) restrict_test() (in module galaxy.selenium.toolbox.filters) restrictions (galaxy.workflow.refactor.schema.AddInputAction attribute) RESUBMITTED (galaxy.model.Job.states attribute) resubmitted (galaxy.model.view.HistoryDatasetCollectionJobStateSummary attribute) result_processor() (galaxy.model.custom_types.GalaxyLargeBinary method) Results (class in galaxy.tool_util.verify.script) resume() (galaxy.model.Job method) (galaxy.webapps.galaxy.api.jobs.JobController method) resume_paused_jobs() (galaxy.model.History method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) resume_watching() (galaxy.util.watcher.BaseWatcher method) retag_async() (galaxy.webapps.galaxy.controllers.tag.TagsController method) retry_call_during_transitions() (in module galaxy.selenium.navigates_galaxy) retry_during_transitions() (in module galaxy.selenium.navigates_galaxy) return_action() (galaxy.workflow.refactor.schema.Action class method) return_code (galaxy.util.pastescript.serve.Command attribute) reverse() (galaxy.util.odict.odict method) reversed_lower_upper_bounded_changelog() (in module galaxy.tool_shed.util.hg_util) (in module tool_shed.util.hg_util) reversed_upper_bounded_changelog() (in module galaxy.tool_shed.util.hg_util) (in module tool_shed.util.hg_util) ReverseSortColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.web.legacy_framework.grids) review_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) review_tool_migration_stages() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) reviewed_repositories_i_own() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method) reviewed_repositories_i_own_grid (tool_shed.webapp.controllers.repository_review.RepositoryReviewController attribute) ReviewedRepositoriesIOwnGrid (class in tool_shed.grids.repository_review_grids) reviewers (tool_shed.webapp.model.Repository attribute) reviews (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) revision() (tool_shed.webapp.model.Repository method) revision_update_available() (galaxy.model.tool_shed_install.ToolShedRepository property) revisions (galaxy.model.Page attribute) (galaxy.model.Visualization attribute) revoke() (galaxy.managers.rbac_secured.AccessDatasetRBACPermission method) (galaxy.managers.rbac_secured.ManageDatasetRBACPermission method) (galaxy.managers.rbac_secured.RBACPermission method) revoke_write_access() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) rewrite() (galaxy.tool_util.provided_metadata.BaseToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.LegacyToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.ToolProvidedMetadata method) rewrite_content_for_export() (galaxy.managers.pages.PageManager method) rewrite_content_for_import() (galaxy.managers.pages.PageManager method) rewrite_dataset_path() (galaxy.job_execution.datasets.DatasetPathRewriter method) (galaxy.job_execution.datasets.NullDatasetPathRewriter method) (galaxy.job_execution.datasets.OutputsToWorkingDirectoryPathRewriter method) (galaxy.job_execution.datasets.TaskPathRewriter method) RexpBase (class in galaxy.datatypes.genetics) Rgb (class in galaxy.datatypes.images) rgConv() (in module galaxy.datatypes.converters.lped_to_fped_converter) (in module galaxy.datatypes.converters.lped_to_pbed_converter) (in module galaxy.datatypes.converters.pbed_to_lped_converter) Rgenetics (class in galaxy.datatypes.genetics) rgFeatureList (class in galaxy.datatypes.genetics) rgSampleList (class in galaxy.datatypes.genetics) rgTabList (class in galaxy.datatypes.genetics) RMA6 (class in galaxy.datatypes.binary) RNADotPlotMatrix (class in galaxy.datatypes.sequence) Roadmaps (class in galaxy.datatypes.assembly) Role (class in galaxy.model) (class in tool_shed.webapp.model) role (galaxy.model.DatasetPermissions attribute) (galaxy.model.DefaultHistoryPermissions attribute) (galaxy.model.DefaultUserPermissions attribute) (galaxy.model.GroupRoleAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationPermissions attribute) (galaxy.model.LibraryDatasetPermissions attribute) (galaxy.model.LibraryFolderPermissions attribute) (galaxy.model.LibraryPermissions attribute) (galaxy.model.UserRoleAssociation attribute) (tool_shed.webapp.model.GroupRoleAssociation attribute) (tool_shed.webapp.model.RepositoryRoleAssociation attribute) (tool_shed.webapp.model.UserRoleAssociation attribute) Role.types (class in galaxy.model) role_id (galaxy.model.DatasetPermissions attribute) (galaxy.model.DefaultHistoryPermissions attribute) (galaxy.model.DefaultUserPermissions attribute) (galaxy.model.GroupRoleAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationPermissions attribute) (galaxy.model.LibraryDatasetPermissions attribute) (galaxy.model.LibraryFolderPermissions attribute) (galaxy.model.LibraryPermissions attribute) (galaxy.model.UserRoleAssociation attribute) (tool_shed.webapp.model.GroupRoleAssociation attribute) (tool_shed.webapp.model.RepositoryRoleAssociation attribute) (tool_shed.webapp.model.UserRoleAssociation attribute) role_list_grid (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) (tool_shed.util.admin_util.Admin attribute) (tool_shed.webapp.controllers.admin.AdminController attribute) role_manager (galaxy.webapps.galaxy.api.roles.FastAPIRoles attribute) role_search_option (galaxy.auth.providers.ldap_ad.LDAP attribute) role_to_model() (in module galaxy.webapps.galaxy.api.roles) RoleAPIController (class in galaxy.webapps.galaxy.api.roles) RoleDefinitionModel (class in galaxy.managers.roles) RoleGrid (class in tool_shed.grids.admin_grids) RoleGrid.DescriptionColumn (class in tool_shed.grids.admin_grids) RoleGrid.GroupsColumn (class in tool_shed.grids.admin_grids) RoleGrid.NameColumn (class in tool_shed.grids.admin_grids) RoleGrid.RepositoriesColumn (class in tool_shed.grids.admin_grids) RoleGrid.StatusColumn (class in tool_shed.grids.admin_grids) RoleGrid.TypeColumn (class in tool_shed.grids.admin_grids) RoleGrid.UsersColumn (class in tool_shed.grids.admin_grids) RoleListGrid (class in galaxy.webapps.galaxy.controllers.admin) RoleListGrid.DescriptionColumn (class in galaxy.webapps.galaxy.controllers.admin) RoleListGrid.GroupsColumn (class in galaxy.webapps.galaxy.controllers.admin) RoleListGrid.NameColumn (class in galaxy.webapps.galaxy.controllers.admin) RoleListGrid.StatusColumn (class in galaxy.webapps.galaxy.controllers.admin) RoleListGrid.TypeColumn (class in galaxy.webapps.galaxy.controllers.admin) RoleListGrid.UsersColumn (class in galaxy.webapps.galaxy.controllers.admin) RoleListModel (class in galaxy.webapps.galaxy.api.roles) RoleManager (class in galaxy.managers.roles) RoleModel (class in galaxy.managers.roles) roles (galaxy.model.Group attribute) (galaxy.model.User attribute) (tool_shed.webapp.model.Repository attribute) roles() (tool_shed.util.admin_util.Admin method) roles_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) RolesApiTestCase (class in galaxy_test.api.test_roles) root (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) Root (in module galaxy.webapps.base.controller) root_container_class (galaxy.managers.history_contents.HistoryContentsManager attribute) root_folder (galaxy.model.Library attribute) root_folder_id (galaxy.model.Library attribute) RootController (class in galaxy.webapps.galaxy.controllers.root) RootParamContext (class in galaxy.tools.test) roundify() (in module galaxy.util) rst_invalid() (in module galaxy.tool_util.linters.help) rst_to_html() (in module galaxy.util) rule_builder_add_regex_groups() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_add_regex_replacement() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_add_value() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_concatenate_columns() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_enter_source_text() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_filter_count() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_remove_columns() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_rule_editor() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_set_collection_name() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_set_extension() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_set_mapping() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_set_source() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_sort() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_split_columns() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_builder_swap_columns() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) rule_class (in module galaxy.util.rules_dsl) rule_type (galaxy.util.rules_dsl.AddColumnBasenameRuleDefinition attribute) (galaxy.util.rules_dsl.AddColumnConcatenateRuleDefinition attribute) (galaxy.util.rules_dsl.AddColumnGroupTagValueRuleDefinition attribute) (galaxy.util.rules_dsl.AddColumnMetadataRuleDefinition attribute) (galaxy.util.rules_dsl.AddColumnRegexRuleDefinition attribute) (galaxy.util.rules_dsl.AddColumnRownumRuleDefinition attribute) (galaxy.util.rules_dsl.AddColumnSubstrRuleDefinition attribute) (galaxy.util.rules_dsl.AddColumnValueRuleDefinition attribute) (galaxy.util.rules_dsl.AddFilterCompareRuleDefinition attribute) (galaxy.util.rules_dsl.AddFilterCountRuleDefinition attribute) (galaxy.util.rules_dsl.AddFilterEmptyRuleDefinition attribute) (galaxy.util.rules_dsl.AddFilterMatchesRuleDefinition attribute) (galaxy.util.rules_dsl.AddFilterRegexRuleDefinition attribute) (galaxy.util.rules_dsl.RemoveColumnsRuleDefinition attribute) (galaxy.util.rules_dsl.SortRuleDefinition attribute) (galaxy.util.rules_dsl.SplitColumnsRuleDefinition attribute) (galaxy.util.rules_dsl.SwapColumnsRuleDefinition attribute) rule_type() (galaxy.util.rules_dsl.BaseRuleDefinition property) RuleHelper (class in galaxy.jobs.rule_helper) rules() (galaxy.util.rules_dsl.RuleSet property) RuleSet (class in galaxy.util.rules_dsl) RulesListToolParameter (class in galaxy.tools.parameters.basic) RuleValidator (class in galaxy.jobs.dynamic_tool_destination) run() (galaxy.containers.docker.DockerAPIInterface method) (galaxy.containers.docker.DockerCLIInterface method) (galaxy.job_metrics.collectl.cli.CollectlCli method) (galaxy.jobs.transfer_manager.TransferManager method) (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader.AsynchronousReader method) (galaxy.util.heartbeat.Heartbeat method) (galaxy.util.pastescript.serve.Command method) (galaxy.util.pastescript.serve.NotFoundCommand method) (galaxy_test.driver.driver_util.TestDriver method) (in module galaxy.util.pastescript.serve) (in module galaxy_ext.expressions.handle_job) (in module galaxy_test.base.nose_util) run_collection_creates_list() (galaxy_test.base.populators.BaseDatasetPopulator method) run_exit_code_from_file() (galaxy_test.base.populators.BaseDatasetPopulator method) run_in_container() (galaxy.containers.ContainerInterface method) (galaxy.containers.docker.DockerInterface method) (galaxy.containers.docker_swarm.DockerSwarmInterface method) run_next() (galaxy.jobs.runners.BaseJobRunner method) run_sniffers_raw() (in module galaxy.datatypes.sniff) run_stats() (galaxy.webapps.reports.controllers.home.HomePage method) run_tests() (in module galaxy.tool_util.verify.script) run_tool() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) (galaxy_test.base.populators.BaseDatasetPopulator method) run_tool_payload() (galaxy_test.base.populators.BaseDatasetPopulator method) run_tour() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) run_tour_step() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) run_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method) RunJobsSummary (class in galaxy_test.api.test_workflow_extraction) (class in galaxy_test.base.populators) runner_name (galaxy.jobs.runners.chronos.ChronosJobRunner attribute) (galaxy.jobs.runners.cli.ShellJobRunner attribute) (galaxy.jobs.runners.condor.CondorJobRunner attribute) (galaxy.jobs.runners.drmaa.DRMAAJobRunner attribute) (galaxy.jobs.runners.godocker.GodockerJobRunner attribute) (galaxy.jobs.runners.kubernetes.KubernetesJobRunner attribute) (galaxy.jobs.runners.local.LocalJobRunner attribute) (galaxy.jobs.runners.pbs.PBSJobRunner attribute) (galaxy.jobs.runners.slurm.SlurmJobRunner attribute) (galaxy.jobs.runners.tasks.TaskedJobRunner attribute) (galaxy.jobs.runners.univa.UnivaJobRunner attribute) (galaxy.model.Job attribute) (galaxy.model.Task attribute) RUNNER_PARAM_SPEC (galaxy.jobs.runners.chronos.ChronosJobRunner attribute) RUNNER_PARAM_SPEC_KEY (galaxy.jobs.runners.chronos.ChronosJobRunner attribute) runner_states (galaxy.jobs.runners.JobState attribute) RunnerParams (class in galaxy.jobs.runners) RUNNING (galaxy.model.Dataset.states attribute) (galaxy.model.DatasetInstance.states attribute) (galaxy.model.DeferredJob.states attribute) (galaxy.model.Job.states attribute) (galaxy.model.Task.states attribute) (galaxy.model.TransferJob.states attribute) running (galaxy.model.view.HistoryDatasetCollectionJobStateSummary attribute) running() (galaxy.jobs.runners.AsynchronousJobState property) (galaxy.model.Job property) (galaxy.util.lazy_process.LazyProcess property) (galaxy.util.lazy_process.NoOpLazyProcess property) runtime_to_json() (in module galaxy.tools.parameters.basic) runtime_to_object() (in module galaxy.tools.parameters.basic) runtime_value (galaxy.model.WorkflowStepInput attribute) RuntimeContext (class in galaxy.tool_util.cwl.cwltool_deps) RuntimeValue (class in galaxy.tools.parameters.basic) RunToolException

S

S3FilesSource (class in galaxy.files.sources.s3) S3ObjectStore (class in galaxy.objectstore.s3) sa_session (galaxy.model.PSAAssociation attribute) (galaxy.model.PSACode attribute) (galaxy.model.PSANonce attribute) (galaxy.model.PSAPartial attribute) (galaxy.model.UserAuthnzToken attribute) sa_session() (galaxy.managers.context.ProvidesAppContext property) (galaxy.model.database_heartbeat.DatabaseHeartbeat property) (galaxy.model.security.GalaxyRBACAgent property) (galaxy.model.security.HostAgent property) (galaxy.tool_shed.galaxy_install.migrate.common.MigrateToolsApplication property) (galaxy.tools.Tool property) (galaxy.tools.toolbox.base.BaseGalaxyToolBox property) (galaxy.tools.toolbox.BaseGalaxyToolBox property) (tool_shed.repository_registry.Registry property) (tool_shed.webapp.security.CommunityRBACAgent property) (tool_shed.webapp.util.shed_statistics.ShedCounter property) Sabund (class in galaxy.datatypes.mothur) safe_contains() (in module galaxy.util.path) safe_dumps() (in module galaxy.util.json) safe_makedirs() (in module galaxy.util.path) safe_relpath() (in module galaxy.util.path) safe_str_cmp() (in module galaxy.util) safe_update (in module galaxy.tools) safe_walk() (in module galaxy.util.path) SafeJsonEncoder (class in galaxy.model.custom_types) safemembers() (galaxy.util.compression_utils.CompressedFile method) SafeStringWrapper (class in galaxy.util.object_wrapper) Sakura (class in galaxy.datatypes.images) salt (galaxy.model.PSANonce attribute) Sam (class in galaxy.datatypes.tabular) SamDataProvider (class in galaxy.visualization.data_providers.genome) sample_destination() (galaxy.config.config_manage.App property) samtools_dataprovider() (galaxy.datatypes.binary.Bam method) SamtoolsDataProvider (class in galaxy.datatypes.dataproviders.dataset) sanitize_allowlist() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) sanitize_for_filename() (in module galaxy.util) sanitize_html() (in module galaxy.util.sanitize_html) sanitize_lists_to_string() (in module galaxy.util) (in module galaxy.util.object_wrapper) sanitize_param() (galaxy.tools.parameters.sanitize.ToolParameterSanitizer method) (in module galaxy.util) sanitize_text() (galaxy.tools.parameters.sanitize.ToolParameterSanitizer method) (in module galaxy.util) save() (galaxy.managers.interactivetool.InteractiveToolSqlite method) (galaxy.model.PSAAssociation method) (galaxy.model.PSACode method) (galaxy.model.PSANonce method) (galaxy.model.PSAPartial method) (galaxy.model.UserAuthnzToken method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) save_entry_point() (galaxy.managers.interactivetool.InteractiveToolManager method) (galaxy.managers.interactivetool.InteractiveToolSqlite method) save_form_definition() (galaxy.webapps.galaxy.controllers.forms.Forms method) save_new_revision() (galaxy.managers.pages.PageManager method) save_to_step() (galaxy.workflow.modules.InputModule method) (galaxy.workflow.modules.InputParameterModule method) (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) save_visualization() (galaxy.webapps.base.controller.UsesVisualizationMixin method) save_widget_field() (galaxy.webapps.base.controller.UsesFormDefinitionsMixin method) save_workflow_as() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) saved() (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) SavedHistoriesTestCase (class in galaxy_test.selenium.test_histories_list) Sbml (class in galaxy.datatypes.xml) ScannerError scatter_type (galaxy.model.WorkflowStepInput attribute) Scf (class in galaxy.datatypes.binary) schedule() (galaxy.workflow.schedulers.ActiveWorkflowSchedulingPlugin method) (galaxy.workflow.schedulers.core.CoreWorkflowSchedulingPlugin method) SCHEDULED (galaxy.model.WorkflowInvocation.states attribute) (galaxy.model.WorkflowInvocationStep.states attribute) scheduler (galaxy.model.WorkflowInvocation attribute) Schema (class in galaxy.config.schema) schema() (galaxy.config.config_manage.App property) schema_path() (galaxy.config.config_manage.App property) SchemaLoader (class in galaxy.tool_util.cwl.schema) scheme (galaxy.tool_util.locations.dockstore.DockStoreResolver attribute) (galaxy.tool_util.locations.file.HttpToolResolver attribute) (galaxy.tool_util.locations.http.HttpsToolResolver attribute) (galaxy.tool_util.locations.http.HttpToolResolver attribute) scheme() (galaxy.tool_util.locations.ToolLocationResolver property) ScIdx (class in galaxy.datatypes.interval) screenshot() (galaxy.selenium.context.GalaxySeleniumContext method) ScriptVisualizationPlugin (class in galaxy.visualization.plugins.plugin) SDF (class in galaxy.datatypes.molecules) search() (galaxy.datatypes.sniff.FilePrefix method) (galaxy.model.search.HistoryDatasetView method) (galaxy.model.search.HistoryView method) (galaxy.model.search.JobView method) (galaxy.model.search.LibraryDatasetDatasetView method) (galaxy.model.search.LibraryDatasetView method) (galaxy.model.search.LibraryFolderView method) (galaxy.model.search.LibraryView method) (galaxy.model.search.PageRevisionView method) (galaxy.model.search.PageView method) (galaxy.model.search.ToolView method) (galaxy.model.search.ViewQueryBaseClass method) (galaxy.model.search.WorkflowView method) (galaxy.tools.search.ToolBoxSearch method) (galaxy.webapps.galaxy.api.jobs.JobController method) (tool_shed.webapp.search.repo_search.RepoSearch method) (tool_shed.webapp.search.tool_search.ToolSearch method) search_for_valid_tools() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) search_ids_names() (in module tool_shed.util.search_util) search_ids_versions() (in module tool_shed.util.search_util) search_names_versions() (in module tool_shed.util.search_util) search_repository() (galaxy.tool_util.deps.mulled.mulled_search.QuaySearch method) search_repository_metadata() (in module tool_shed.util.search_util) search_str() (galaxy.datatypes.sniff.FilePrefix method) SearchApiTestCase (class in galaxy_test.api.test_search) SearchController (class in galaxy.webapps.galaxy.api.search) SearchGuiArchive (class in galaxy.datatypes.binary) SearchQuery (class in galaxy.model.search) SecondaryStructureMap (class in galaxy.datatypes.mothur) seconds_since_created() (galaxy.model.UsesCreateAndUpdateTime property) seconds_since_updated() (galaxy.model.UsesCreateAndUpdateTime property) seconds_to_str() (in module galaxy.job_metrics.formatting) secret (galaxy.model.PSAAssociation attribute) Section (class in galaxy.tools.parameters.grouping) secure() (galaxy.managers.folders.FolderManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.managers.library_datasets.LibraryDatasetsManager method) SecureShell (class in galaxy.jobs.runners.util.cli.shell.rsh) security_check() (galaxy.webapps.base.controller.SharableItemSecurityMixin method) (in module galaxy.managers.base) seeAlso (galaxy.managers.licenses.LicenseMetadataModel attribute) SELECT (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute) select2_set_value() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) select_day() (galaxy.webapps.reports.controllers.query.ReportQueryBuilder method) select_dropdown_item() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) select_files_to_delete() (tool_shed.webapp.controllers.repository.RepositoryController method) select_filter() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) select_month() (galaxy.webapps.reports.controllers.query.ReportQueryBuilder method) select_previous_review() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method) SelectField (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) selector() (galaxy.selenium.components.Component property) (galaxy.selenium.components.SelectorTemplate property) selector_is_displayed() (galaxy.selenium.has_driver.HasDriver method) SelectorTemplate (class in galaxy.selenium.components) SelectParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) SelectTagParameter (class in galaxy.tools.parameters.basic) SelectToolParameter (class in galaxy.tools.parameters) (class in galaxy.tools.parameters.basic) SelectToolParameterWrapper (class in galaxy.tools.wrappers) SelectToolParameterWrapper.SelectToolParameterFieldWrapper (class in galaxy.tools.wrappers) selenium_test() (in module galaxy_test.selenium.framework) selenium_to_requests_cookies() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) SeleniumSessionDatasetCollectionPopulator (class in galaxy_test.selenium.framework) SeleniumSessionDatasetPopulator (class in galaxy_test.selenium.framework) SeleniumSessionGetPostMixin (class in galaxy_test.selenium.framework) SeleniumSessionWorkflowPopulator (class in galaxy_test.selenium.framework) SeleniumTestCase (class in galaxy_test.selenium.framework) self_handler_tags() (galaxy.web_stack.handlers.ConfiguresHandlers property) send() (galaxy.managers.cloud.CloudManager method) (galaxy.webapps.galaxy.api.cloud.CloudController method) send_activation_email() (galaxy.managers.users.UserManager method) send_backspace() (galaxy.selenium.has_driver.HasDriver method) send_control_task() (galaxy.queue_worker.GalaxyQueueWorker method) (in module galaxy.queue_worker) send_database_heartbeat() (galaxy.model.database_heartbeat.DatabaseHeartbeat method) send_enter() (galaxy.selenium.has_driver.HasDriver method) send_escape() (galaxy.selenium.has_driver.HasDriver method) send_file() (in module galaxy.web.framework.base) send_local_control_task() (galaxy.queue_worker.GalaxyQueueWorker method) (in module galaxy.queue_worker) send_mail() (in module galaxy.util) send_message() (galaxy.web_stack.ApplicationStack method) (galaxy.web_stack.MessageApplicationStack method) (galaxy.web_stack.transport.ApplicationStackTransport method) (galaxy.web_stack.transport.UWSGIFarmMessageTransport method) send_message_to_repository_owner() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) send_redirect() (galaxy.web.framework.base.Response method) send_report() (galaxy.tools.errors.ErrorReporter method) send_reset_email() (galaxy.managers.users.UserManager method) send_subscription_email() (galaxy.managers.users.UserManager method) send_task() (galaxy.queue_worker.ControlTask method) send_to_owner() (tool_shed.webapp.controllers.repository.RepositoryController method) Sentry (class in galaxy.web.framework.middleware.sentry) sentry_dsn_public() (galaxy.config.CommonConfigurationMixin property) (galaxy.webapps.reports.config.Configuration property) SentryPlugin (class in galaxy.tools.error_reports.plugins.sentry) sep() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SimpleComputeEnvironment method) Sequence (class in galaxy.datatypes.sequence) sequence_regexp (galaxy.datatypes.sequence.DotBracket attribute) Sequences (class in galaxy.datatypes.assembly) sequences() (galaxy.webapps.galaxy.api.genomes.GenomesController method) SequenceSplitLocations (class in galaxy.datatypes.sequence) SerializationOptions (class in galaxy.model) serialize() (galaxy.managers.base.ModelSerializer method) (galaxy.managers.datasets.DatasetAssociationSerializer method) (galaxy.managers.hdas.HDASerializer method) (galaxy.managers.histories.HistoryExportView method) (galaxy.managers.library_datasets.LibraryDatasetsManager method) (galaxy.managers.users.CurrentUserSerializer method) (galaxy.model.Dataset method) (galaxy.model.DatasetCollection method) (galaxy.model.DatasetCollectionElement method) (galaxy.model.DatasetHash method) (galaxy.model.DatasetInstance method) (galaxy.model.History method) (galaxy.model.HistoryDatasetAssociation method) (galaxy.model.HistoryDatasetCollectionAssociation method) (galaxy.model.ImplicitCollectionJobs method) (galaxy.model.Job method) (galaxy.model.Library method) (galaxy.model.LibraryDataset method) (galaxy.model.LibraryDatasetDatasetAssociation method) (galaxy.model.LibraryFolder method) (galaxy.model.MetadataFile method) serialize_annotation() (galaxy.managers.annotatable.AnnotatableSerializerMixin method) serialize_community_rating() (galaxy.managers.ratable.RatableSerializerMixin method) serialize_contents() (galaxy.managers.histories.HistorySerializer method) serialize_contents_active() (galaxy.managers.histories.HistorySerializer method) serialize_contents_states() (galaxy.managers.histories.HistorySerializer method) serialize_current_anonymous_user() (galaxy.managers.users.CurrentUserSerializer method) serialize_dataset_association_roles() (galaxy.managers.datasets.DatasetAssociationManager method) serialize_date() (galaxy.managers.base.ModelSerializer method) serialize_display_apps() (galaxy.managers.hdas.HDASerializer method) serialize_elements() (galaxy.managers.hdcas.DCSerializer method) serialize_extra_files_path() (galaxy.managers.datasets.DatasetSerializer method) serialize_file_name() (galaxy.managers.datasets.DatasetSerializer method) serialize_files() (galaxy.model.SerializationOptions method) (galaxy.model.store.DirectoryModelExportStore method) serialize_history_state() (galaxy.managers.histories.HistorySerializer method) serialize_id() (galaxy.managers.base.ModelSerializer method) serialize_id_or_skip() (galaxy.managers.history_contents.HistoryContentsSerializer method) serialize_job_state_summary() (galaxy.managers.hdcas.HDCASerializer method) serialize_object() (galaxy.managers.hdcas.DCESerializer method) serialize_old_display_applications() (galaxy.managers.hdas.HDASerializer method) serialize_permissions() (galaxy.managers.datasets.DatasetSerializer method) serialize_state_counts() (galaxy.managers.histories.HistorySerializer method) serialize_state_ids() (galaxy.managers.histories.HistorySerializer method) serialize_tags() (galaxy.managers.taggable.TaggableSerializerMixin method) serialize_title() (galaxy.managers.sharable.SharableModelSerializer method) serialize_to_view() (galaxy.managers.base.ModelSerializer method) serialize_type_id() (galaxy.managers.base.ModelSerializer method) serialize_urls() (galaxy.managers.hdas.HDASerializer method) serialize_user_rating() (galaxy.managers.ratable.RatableSerializerMixin method) serialize_username_and_slug() (galaxy.managers.sharable.SharableModelSerializer method) serialize_users_shared_with() (galaxy.managers.sharable.SharableModelSerializer method) serialize_visualization_links() (galaxy.managers.hdas.HDASerializer method) serialize_workflow_invocation() (galaxy.managers.workflows.WorkflowsManager method) serialize_workflow_invocations() (galaxy.managers.workflows.WorkflowsManager method) serializer (galaxy.webapps.base.controller.SharableMixin attribute) serve_ready_history_export() (galaxy.webapps.base.controller.ExportsHistoryMixin method) ServeCommand (class in galaxy.util.pastescript.serve) server_name (galaxy.model.WorkerProcess attribute) server_name() (galaxy.model.database_heartbeat.DatabaseHeartbeat property) server_name_template (galaxy.web_stack.ApplicationStack attribute) (galaxy.web_stack.UWSGIApplicationStack attribute) server_starttime (in module galaxy.web.framework.base) server_url (galaxy.model.PSAAssociation attribute) (galaxy.model.PSANonce attribute) ServesTemplatesPluginMixin (class in galaxy.visualization.plugins.plugin) service() (galaxy.containers.docker_model.DockerTask property) (galaxy.containers.docker_swarm.DockerSwarmInterface method) service_create() (galaxy.containers.docker_swarm.DockerSwarmAPIInterface method) (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) service_inspect() (galaxy.containers.docker_swarm.DockerSwarmAPIInterface method) (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) service_ls() (galaxy.containers.docker_swarm.DockerSwarmAPIInterface method) (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) service_mode_option_map (galaxy.containers.docker_swarm.DockerSwarmAPIInterface attribute) service_ps() (galaxy.containers.docker_swarm.DockerSwarmAPIInterface method) (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) service_rm() (galaxy.containers.docker_swarm.DockerSwarmAPIInterface method) (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) service_tasks() (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) (galaxy.containers.docker_swarm.DockerSwarmInterface method) services() (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) (galaxy.containers.docker_swarm.DockerSwarmInterface method) services_clean() (galaxy.containers.docker_swarm.DockerSwarmInterface method) services_completed() (galaxy.containers.docker_swarm.DockerSwarmInterface method) services_in_state() (galaxy.containers.docker_swarm.DockerSwarmInterface method) services_terminal() (galaxy.containers.docker_swarm.DockerSwarmInterface method) services_waiting() (galaxy.containers.docker_swarm.DockerSwarmInterface method) services_waiting_by_constraints() (galaxy.containers.docker_swarm.DockerSwarmInterface method) session (galaxy.web.framework.base.DefaultWebTransaction attribute) session() (galaxy.managers.base.ModelManager method) (galaxy.managers.rbac_secured.RBACPermission method) Session() (galaxy.model.base.ModelMapping property) session_csrf_token() (galaxy.webapps.base.webapp.GalaxyWebTransaction property) session_get() (galaxy.authnz.psa_authnz.Strategy method) session_id (galaxy.model.Event attribute) (galaxy.model.GalaxySessionToHistoryAssociation attribute) (galaxy.model.Job attribute) (galaxy.model.UserAction attribute) session_key (galaxy.model.GalaxySession attribute) (tool_shed.webapp.model.GalaxySession attribute) session_pop() (galaxy.authnz.psa_authnz.Strategy method) session_set() (galaxy.authnz.psa_authnz.Strategy method) SessionlessContext (class in galaxy.model.store) SessionlessJobContext (class in galaxy.job_execution.output_collect) SessionlessModelPersistenceContext (class in galaxy.model.store.discover) SessionRequestContext (class in galaxy.work.context) set() (galaxy.managers.datasets.DatasetRBACPermissions method) (galaxy.managers.rbac_secured.DatasetRBACPermission method) (galaxy.tools.cache.ToolDocumentCache method) (galaxy.tools.data.ToolDataTableManager method) set_accessible_async() (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) set_add_to_tool_panel_attribute_for_tool() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) set_all_dataset_permissions() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) set_all_library_permissions() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) set_allow_push() (tool_shed.webapp.model.Repository method) set_amount() (galaxy.model.Quota method) set_api_key() (galaxy.webapps.galaxy.api.users.UserAPIController method) set_as_current() (galaxy.webapps.galaxy.controllers.history.HistoryController method) set_attribute_metadata() (galaxy.datatypes.interval.Gff method) set_basename_and_derived_properties() (in module galaxy.tool_util.cwl.util) set_basic_defaults() (in module galaxy.jobs.splitters.basic) set_changeset_revision() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) set_check_interval() (galaxy.model.DeferredJob method) set_collection_elements() (galaxy.managers.collections.DatasetCollectionManager method) (in module galaxy.model.dataset_collections.builder) set_command_line() (galaxy.model.Job method) (galaxy.model.Task method) set_compute_environment() (galaxy.tools.evaluation.ToolEvaluator method) set_container() (galaxy.jobs.JobWrapper method) set_content_type() (galaxy.web.framework.base.Response method) set_cookie() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) set_copied_from_job_id() (galaxy.model.Job method) set_cors_allow() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) set_cors_headers() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) set_cors_origin() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) set_cpus() (galaxy.containers.docker_model.DockerService method) set_created_from_basename() (galaxy.model.DatasetInstance method) set_current() (galaxy.managers.histories.HistoryManager method) set_current_by_id() (galaxy.managers.histories.HistoryManager method) set_dataset_matcher_factory() (in module galaxy.tools.parameters.dataset_matcher) set_dataset_permission() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) set_dataset_permissions() (galaxy.model.security.HostAgent method) set_dataset_state() (galaxy.model.DatasetInstance method) set_datasets_metadata() (galaxy.model.store.discover.ModelPersistenceContext static method) set_datatypes_registry() (in module galaxy.model) set_dbkey() (galaxy.model.DatasetInstance method) set_default_hda_permissions() (galaxy.job_execution.output_collect.PermissionProvider method) (galaxy.model.store.discover.PermissionProvider method) set_default_values() (galaxy.datatypes.registry.Registry method) set_defaults() (galaxy.jobs.runners.JobState method) set_dependencies() (galaxy.model.Job method) set_destination_conf_dicts() (galaxy.job_metrics.JobMetrics method) set_destination_conf_element() (galaxy.job_metrics.JobMetrics method) set_destination_conf_file() (galaxy.job_metrics.JobMetrics method) set_destination_instrumenter() (galaxy.job_metrics.JobMetrics method) set_disk_usage() (galaxy.model.GalaxySession method) (galaxy.model.User method) (tool_shed.webapp.model.User method) set_edit() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) set_email_alerts() (tool_shed.webapp.controllers.repository.RepositoryController method) set_enabled_container_types() (galaxy.tool_util.deps.DependencyManager method) set_entity_group_associations() (galaxy.model.security.GalaxyRBACAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) set_entity_role_associations() (galaxy.model.security.GalaxyRBACAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) set_entity_user_associations() (galaxy.model.security.GalaxyRBACAgent method) (tool_shed.webapp.security.CommunityRBACAgent method) set_environment() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.SetEnvironment method) set_external_id() (galaxy.jobs.JobWrapper method) set_extra_data() (galaxy.model.UserAuthnzToken method) set_extra_files_path() (galaxy.model.Dataset method) set_favorite() (galaxy.webapps.galaxy.api.users.UserAPIController method) set_file_name() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) set_filter() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase method) (tool_shed.grids.repository_grid_filter_manager.RepositoryGridFilterManager method) set_filter_dependencies_needed_for_compiling() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) set_final_state() (galaxy.model.Job method) set_form_value() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) set_from_dict() (galaxy.model.DatasetCollection method) (galaxy.model.DatasetCollectionInstance method) set_handler() (galaxy.model.Job method) (galaxy.model.WorkflowInvocation method) set_history() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) (galaxy.work.context.WorkRequestContext method) set_history_annotation() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) set_id() (galaxy.model.Task method) set_image() (galaxy.containers.docker_model.DockerService method) set_image_paths() (in module galaxy.tool_shed.util.shed_util_common) (in module tool_shed.util.shed_util_common) set_imported() (galaxy.model.Job method) set_index_file() (galaxy.datatypes.binary.CRAM method) set_info() (galaxy.model.Job method) (galaxy.model.LibraryDataset method) (galaxy.model.Task method) set_information() (galaxy.webapps.galaxy.api.users.UserAPIController method) set_initial_metadata() (galaxy.datatypes.constructive_solid_geometry.Vtk method) set_input_datasets() (galaxy.model.Job method) set_input_library_datasets() (galaxy.model.Job method) set_item() (galaxy.model.HistoryDatasetAssociationRatingAssociation method) (galaxy.model.HistoryDatasetCollectionRatingAssociation method) (galaxy.model.HistoryRatingAssociation method) (galaxy.model.ItemRatingAssociation method) (galaxy.model.LibraryDatasetCollectionRatingAssociation method) (galaxy.model.PageRatingAssociation method) (galaxy.model.StoredWorkflowRatingAssociation method) (galaxy.model.VisualizationRatingAssociation method) (tool_shed.webapp.model.ItemRatingAssociation method) (tool_shed.webapp.model.RepositoryRatingAssociation method) set_item_extended_metadata_obj() (galaxy.webapps.base.controller.UsesExtendedMetadataMixin method) set_job() (galaxy.model.Task method) set_job_destination() (galaxy.jobs.JobWrapper method) set_job_runner_external_id() (galaxy.model.Task method) set_job_runner_external_pid() (galaxy.metadata.MetadataCollectionStrategy method) set_kwopts_name() (galaxy.containers.ContainerInterface method) set_labels_for_constraints() (galaxy.containers.docker_model.DockerNode method) set_last_check() (galaxy.model.DeferredJob method) set_library_item_permission() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) set_log_handler() (in module galaxy.util.script) set_malicious() (tool_shed.webapp.controllers.repository.RepositoryController method) set_max_optional_metadata_filesize() (galaxy.datatypes.data.Data method) set_message() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) set_meta() (galaxy.datatypes.anvio.AnvioDB method) (galaxy.datatypes.assembly.Velvet method) (galaxy.datatypes.binary.Anndata method) (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.binary.Bcf method) (galaxy.datatypes.binary.Biom2 method) (galaxy.datatypes.binary.BlibSQlite method) (galaxy.datatypes.binary.Cel method) (galaxy.datatypes.binary.ChiraSQLite method) (galaxy.datatypes.binary.CRAM method) (galaxy.datatypes.binary.CuffDiffSQlite method) (galaxy.datatypes.binary.DlibSQlite method) (galaxy.datatypes.binary.ElibSQlite method) (galaxy.datatypes.binary.Fast5Archive method) (galaxy.datatypes.binary.GAFASQLite method) (galaxy.datatypes.binary.GeminiSQLite method) (galaxy.datatypes.binary.IdpDB method) (galaxy.datatypes.binary.Loom method) (galaxy.datatypes.binary.MzSQlite method) (galaxy.datatypes.binary.NcbiTaxonomySQlite method) (galaxy.datatypes.binary.OSW method) (galaxy.datatypes.binary.PostgresqlArchive method) (galaxy.datatypes.binary.PQP method) (galaxy.datatypes.binary.SearchGuiArchive method) (galaxy.datatypes.binary.SQlite method) (galaxy.datatypes.binary.SQmass method) (galaxy.datatypes.constructive_solid_geometry.Ply method) (galaxy.datatypes.constructive_solid_geometry.Vtk method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.data.Text method) (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.genetics.IdeasPre method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.genetics.Rgenetics method) (galaxy.datatypes.interval.Bed method) (galaxy.datatypes.interval.BedStrict method) (galaxy.datatypes.interval.CustomTrack method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Gff3 method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.Wiggle method) (galaxy.datatypes.media.Audio method) (galaxy.datatypes.media.Video method) (galaxy.datatypes.media.Wav method) (galaxy.datatypes.microarrays.Gal method) (galaxy.datatypes.microarrays.Gpr method) (galaxy.datatypes.molecules.CML method) (galaxy.datatypes.molecules.DRF method) (galaxy.datatypes.molecules.FPS method) (galaxy.datatypes.molecules.InChI method) (galaxy.datatypes.molecules.MOL method) (galaxy.datatypes.molecules.MOL2 method) (galaxy.datatypes.molecules.PDB method) (galaxy.datatypes.molecules.PQR method) (galaxy.datatypes.molecules.SDF method) (galaxy.datatypes.molecules.SMILES method) (galaxy.datatypes.mothur.AlignCheck method) (galaxy.datatypes.mothur.CountTable method) (galaxy.datatypes.mothur.DistanceMatrix method) (galaxy.datatypes.mothur.Group method) (galaxy.datatypes.mothur.GroupAbund method) (galaxy.datatypes.mothur.Otu method) (galaxy.datatypes.mothur.PairwiseDistanceMatrix method) (galaxy.datatypes.mothur.SffFlow method) (galaxy.datatypes.msa.InfernalCM method) (galaxy.datatypes.msa.MauveXmfa method) (galaxy.datatypes.msa.Stockholm_1_0 method) (galaxy.datatypes.phylip.Phylip method) (galaxy.datatypes.plant_tribes.PlantTribesKsComponents method) (galaxy.datatypes.proteomics.Dta method) (galaxy.datatypes.proteomics.Dta2d method) (galaxy.datatypes.proteomics.Edta method) (galaxy.datatypes.qualityscore.QualityScoreSOLiD method) (galaxy.datatypes.sequence.BaseFastq method) (galaxy.datatypes.sequence.csFasta method) (galaxy.datatypes.sequence.DotBracket method) (galaxy.datatypes.sequence.Fastg method) (galaxy.datatypes.sequence.Maf method) (galaxy.datatypes.sequence.MafCustomTrack method) (galaxy.datatypes.sequence.Sequence method) (galaxy.datatypes.speech.BPF method) (galaxy.datatypes.tabular.BaseCSV method) (galaxy.datatypes.tabular.BaseVcf method) (galaxy.datatypes.tabular.CMAP method) (galaxy.datatypes.tabular.ConnectivityTable method) (galaxy.datatypes.tabular.Eland method) (galaxy.datatypes.tabular.MatrixMarket method) (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.SraManifest method) (galaxy.datatypes.tabular.Tabular method) (galaxy.datatypes.tabular.TabularData method) (galaxy.datatypes.tabular.VcfGz method) (galaxy.datatypes.text.Arff method) (galaxy.datatypes.text.Biom1 method) (galaxy.datatypes.text.ExpressionJson method) (galaxy.datatypes.text.ImgtJson method) (galaxy.datatypes.text.Ipynb method) (galaxy.datatypes.text.SnpEffDb method) (galaxy.datatypes.text.SnpSiftDbNSFP method) (galaxy.datatypes.xml.Dzi method) (galaxy.model.DatasetInstance method) set_meta_with_tool_provided() (in module galaxy.metadata.set_metadata) set_metadata() (galaxy.managers.datasets.DatasetAssociationManager method) (galaxy.model.DatasetInstance method) (in module galaxy.metadata.set_metadata) (in module galaxy_ext.metadata.set_metadata) set_metadata_defaults() (galaxy.tools.actions.DefaultToolAction method) set_metadata_portable() (in module galaxy.metadata.set_metadata) set_metadata_requires_flush() (galaxy.model.DatasetInstance property) set_name() (galaxy.model.LibraryDataset method) set_object_store_id() (galaxy.objectstore.ObjectStorePopulator method) set_only_if_compiling_contained_td() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) set_output_datasets() (galaxy.model.Job method) set_output_library_datasets() (galaxy.model.Job method) set_param_filename() (galaxy.model.Job method) set_parameters() (galaxy.model.Job method) (galaxy.model.Task method) set_params() (galaxy.model.Job method) set_parent() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataCollection method) set_password() (galaxy.webapps.galaxy.api.users.UserAPIController method) set_password_cleartext() (galaxy.model.User method) (tool_shed.webapp.model.User method) set_peek() (galaxy.datatypes.annotation.Augustus method) (galaxy.datatypes.annotation.SnapHmm method) (galaxy.datatypes.anvio.AnvioComposite method) (galaxy.datatypes.binary.Ab1 method) (galaxy.datatypes.binary.Anndata method) (galaxy.datatypes.binary.BafTar method) (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.binary.BigWig method) (galaxy.datatypes.binary.Binary method) (galaxy.datatypes.binary.Biom2 method) (galaxy.datatypes.binary.Cel method) (galaxy.datatypes.binary.CompressedArchive method) (galaxy.datatypes.binary.CompressedZipArchive method) (galaxy.datatypes.binary.Cool method) (galaxy.datatypes.binary.CRAM method) (galaxy.datatypes.binary.CuffDiffSQlite method) (galaxy.datatypes.binary.Dcd method) (galaxy.datatypes.binary.ExcelXls method) (galaxy.datatypes.binary.Fast5Archive method) (galaxy.datatypes.binary.GeminiSQLite method) (galaxy.datatypes.binary.GmxBinary method) (galaxy.datatypes.binary.H5 method) (galaxy.datatypes.binary.ICM method) (galaxy.datatypes.binary.IdpDB method) (galaxy.datatypes.binary.Loom method) (galaxy.datatypes.binary.MCool method) (galaxy.datatypes.binary.NcbiTaxonomySQlite method) (galaxy.datatypes.binary.NetCDF method) (galaxy.datatypes.binary.PostgresqlArchive method) (galaxy.datatypes.binary.Scf method) (galaxy.datatypes.binary.SearchGuiArchive method) (galaxy.datatypes.binary.Sff method) (galaxy.datatypes.binary.SQlite method) (galaxy.datatypes.binary.Sra method) (galaxy.datatypes.binary.TwoBit method) (galaxy.datatypes.binary.Vel method) (galaxy.datatypes.blast.BlastXml method) (galaxy.datatypes.blast.LastDb method) (galaxy.datatypes.constructive_solid_geometry.Ply method) (galaxy.datatypes.constructive_solid_geometry.Vtk method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.data.Text method) (galaxy.datatypes.genetics.RexpBase method) (galaxy.datatypes.genetics.SNPMatrix method) (galaxy.datatypes.gis.Shapefile method) (galaxy.datatypes.graph.Sif method) (galaxy.datatypes.graph.Xgmml method) (galaxy.datatypes.images.Gmaj method) (galaxy.datatypes.images.Image method) (galaxy.datatypes.images.Laj method) (galaxy.datatypes.microarrays.GenericMicroarrayFile method) (galaxy.datatypes.molecules.CML method) (galaxy.datatypes.molecules.GenericMolFile method) (galaxy.datatypes.molecules.grd method) (galaxy.datatypes.molecules.grdtgz method) (galaxy.datatypes.molecules.InChI method) (galaxy.datatypes.molecules.OBFS method) (galaxy.datatypes.molecules.PDB method) (galaxy.datatypes.molecules.PDBQT method) (galaxy.datatypes.molecules.PHAR method) (galaxy.datatypes.molecules.PQR method) (galaxy.datatypes.molecules.SMILES method) (galaxy.datatypes.msa.Hmmer method) (galaxy.datatypes.msa.HmmerPress method) (galaxy.datatypes.msa.InfernalCM method) (galaxy.datatypes.msa.MauveXmfa method) (galaxy.datatypes.msa.Stockholm_1_0 method) (galaxy.datatypes.neo4j.Neo4j method) (galaxy.datatypes.ngsindex.BowtieIndex method) (galaxy.datatypes.phylip.Phylip method) (galaxy.datatypes.plant_tribes.PlantTribesKsComponents method) (galaxy.datatypes.plant_tribes.Smat method) (galaxy.datatypes.proteomics.MascotDat method) (galaxy.datatypes.proteomics.Mgf method) (galaxy.datatypes.proteomics.MzTab method) (galaxy.datatypes.proteomics.MzTab2 method) (galaxy.datatypes.proteomics.ProteomicsXml method) (galaxy.datatypes.proteomics.SPLib method) (galaxy.datatypes.proteomics.SPLibNoIndex method) (galaxy.datatypes.proteomics.ThermoRAW method) (galaxy.datatypes.sequence.Fastg method) (galaxy.datatypes.sequence.Maf method) (galaxy.datatypes.sequence.RNADotPlotMatrix method) (galaxy.datatypes.sequence.Sequence method) (galaxy.datatypes.sequence.SequenceSplitLocations method) (galaxy.datatypes.tabular.TabularData method) (galaxy.datatypes.text.Arff method) (galaxy.datatypes.text.Biom1 method) (galaxy.datatypes.text.GeoJson method) (galaxy.datatypes.text.Html method) (galaxy.datatypes.text.ImgtJson method) (galaxy.datatypes.text.Ipynb method) (galaxy.datatypes.text.Json method) (galaxy.datatypes.text.Obo method) (galaxy.datatypes.tracks.UCSCTrackHub method) (galaxy.datatypes.triples.HDT method) (galaxy.datatypes.triples.Jsonld method) (galaxy.datatypes.triples.N3 method) (galaxy.datatypes.triples.NTriples method) (galaxy.datatypes.triples.Rdf method) (galaxy.datatypes.triples.Triples method) (galaxy.datatypes.triples.Turtle method) (galaxy.datatypes.xml.CisML method) (galaxy.datatypes.xml.Dzi method) (galaxy.datatypes.xml.GenericXml method) (galaxy.datatypes.xml.MEMEXml method) (galaxy.datatypes.xml.Owl method) (galaxy.datatypes.xml.Phyloxml method) (galaxy.datatypes.xml.Sbml method) (galaxy.model.DatasetInstance method) set_permission_roles() (galaxy.managers.libraries.LibraryManager method) set_permissions() (galaxy.webapps.galaxy.api.folders.FoldersController method) (galaxy.webapps.galaxy.api.libraries.LibrariesController method) (galaxy.webapps.galaxy.api.users.UserAPIController method) (galaxy_test.base.populators.LibraryPopulator method) set_permissions_old() (galaxy.webapps.galaxy.api.libraries.LibrariesController method) set_position() (galaxy.datatypes.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.RegionAlignment method) set_post_job_actions() (galaxy.model.Job method) set_postfork_server_name() (galaxy.web_stack.ApplicationStack method) set_prepare_input_files_cmd() (galaxy.model.Task method) set_prior_installation_required() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) set_private() (galaxy.managers.rbac_secured.AccessDatasetRBACPermission method) set_private_to_one_user() (galaxy.managers.datasets.DatasetRBACPermissions method) set_public_username() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) set_public_with_single_manager() (galaxy.managers.datasets.DatasetRBACPermissions method) set_quota_default() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) set_random_password() (galaxy.model.User method) set_range() (galaxy.datatypes.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.RegionAlignment method) set_relative_install_dir() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) set_repository() (galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) set_repository_attributes() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) set_repository_clone_url() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) set_repository_deprecated() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) set_repository_files_dir() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) set_repository_malicious() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) set_repository_metadata() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) set_repository_metadata_due_to_new_tip() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) set_runner() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) set_runner_external_id() (galaxy.model.Job method) set_runner_name() (galaxy.model.Job method) set_session_id() (galaxy.model.Job method) set_size() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) set_slug() (galaxy.managers.sharable.SharableModelManager method) set_slug_async() (galaxy.webapps.base.controller.SharableMixin method) set_state() (galaxy.model.Job method) (galaxy.model.Task method) set_streams() (galaxy.model.JobLike method) set_structure_metadata() (galaxy.datatypes.constructive_solid_geometry.Vtk method) set_tags() (galaxy.managers.taggable.TaggableManagerMixin method) set_tags_from_list() (galaxy.model.tags.TagHandler method) (galaxy.webapps.base.controller.UsesTagsMixin method) set_target() (galaxy.web_stack.message.ApplicationStackMessage property) set_task_runner_external_id() (galaxy.model.Task method) set_task_runner_name() (galaxy.model.Task method) set_text_element() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase static method) set_tool_dependency_attributes() (in module galaxy.tool_shed.util.tool_dependency_util) set_tool_id() (galaxy.model.Job method) set_tool_version() (galaxy.model.Job method) set_toolbox_filters() (galaxy.webapps.galaxy.api.users.UserAPIController method) set_total_size() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) set_transaction_factory() (galaxy.web.framework.base.WebApplication method) set_user() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) (galaxy.work.context.WorkRequestContext method) set_user_id() (galaxy.model.Job method) set_validated_state() (in module galaxy.metadata.set_metadata) set_workflow_menu() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) set_working_directory() (galaxy.model.Task method) setdefault() (galaxy.util.odict.odict method) SetEnvironment (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler) SetEnvironmentForInstall (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) SetMetadataAction (class in galaxy.jobs.actions.post) SetMetadataTool (class in galaxy.tools) SetMetadataToolAction (class in galaxy.tools.actions.metadata) SetParamAction (class in galaxy.tools) SETTING_METADATA (galaxy.model.Dataset.states attribute) (galaxy.model.DatasetInstance.states attribute) SETTING_TOOL_VERSIONS (galaxy.model.tool_shed_install.ToolShedRepository.installation_status attribute) settings (galaxy.datatypes.dataproviders.base.DataProvider attribute) (galaxy.datatypes.dataproviders.base.FilteredDataProvider attribute) (galaxy.datatypes.dataproviders.base.LimitedOffsetDataProvider attribute) (galaxy.datatypes.dataproviders.base.MultiSourceDataProvider attribute) (galaxy.datatypes.dataproviders.chunk.Base64ChunkDataProvider attribute) (galaxy.datatypes.dataproviders.chunk.ChunkDataProvider attribute) (galaxy.datatypes.dataproviders.column.ColumnarDataProvider attribute) (galaxy.datatypes.dataproviders.column.DictDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.BigWigDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.ConvertedDatasetDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.DatasetColumnarDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.DatasetDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.DatasetDictDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.DatasetSubprocessDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.FastaDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.GenomicRegionDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.IntervalDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.SQliteDataDictProvider attribute) (galaxy.datatypes.dataproviders.dataset.SQliteDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.SQliteDataTableProvider attribute) (galaxy.datatypes.dataproviders.dataset.TwoBitFastaDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.WiggleDataProvider attribute) (galaxy.datatypes.dataproviders.external.GzipDataProvider attribute) (galaxy.datatypes.dataproviders.external.RegexSubprocessDataProvider attribute) (galaxy.datatypes.dataproviders.external.SubprocessDataProvider attribute) (galaxy.datatypes.dataproviders.external.TempfileDataProvider attribute) (galaxy.datatypes.dataproviders.external.URLDataProvider attribute) (galaxy.datatypes.dataproviders.hierarchy.HierarchalDataProvider attribute) (galaxy.datatypes.dataproviders.hierarchy.XMLDataProvider attribute) (galaxy.datatypes.dataproviders.line.BlockDataProvider attribute) (galaxy.datatypes.dataproviders.line.FilteredLineDataProvider attribute) (galaxy.datatypes.dataproviders.line.RegexLineDataProvider attribute) (galaxy.datatypes.graph.SIFGraphDataProvider attribute) (galaxy.datatypes.graph.XGMMLGraphDataProvider attribute) setUp() (galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase method) (galaxy_test.api.test_datasets.DatasetsApiTestCase method) (galaxy_test.api.test_histories.ImportExportHistoryTestCase method) (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) (galaxy_test.api.test_history_contents_provenance.TestProvenance method) (galaxy_test.api.test_jobs.JobsApiTestCase method) (galaxy_test.api.test_libraries.LibrariesApiTestCase method) (galaxy_test.api.test_roles.RolesApiTestCase method) (galaxy_test.api.test_tools.ToolsTestCase method) (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) (galaxy_test.api.test_webhooks.WebhooksApiTestCase method) (galaxy_test.api.test_workflow_extraction.WorkflowExtractionApiTestCase method) (galaxy_test.api.test_workflows.BaseWorkflowsApiTestCase method) (galaxy_test.api.test_workflows_from_yaml.WorkflowsFromYamlApiTestCase method) (galaxy_test.base.testcase.FunctionalTestCase method) setup() (galaxy_test.driver.driver_util.TestDriver method) setUp() (galaxy_test.driver.integration_util.IntegrationInstance method) (galaxy_test.selenium.framework.SeleniumTestCase method) (galaxy_test.selenium.test_tool_describing_tours.ToolDescribingToursTestCase method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) setup() (tool_shed.test.functional_tests.ToolShedTestDriver method) setup_driver_and_session() (galaxy_test.selenium.framework.TestWithSeleniumMixin method) setup_external_metadata() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.metadata.ExtendedDirectoryMetadataGenerator method) (galaxy.metadata.MetadataCollectionStrategy method) (galaxy.metadata.PortableDirectoryMetadataGenerator method) setup_fetch_to_folder() (galaxy_test.base.populators.LibraryPopulator method) setup_galaxy_config() (in module galaxy_test.driver.driver_util) setup_global_logger() (in module galaxy.tool_util.verify.script) setup_history_for_export_testing() (galaxy_test.base.populators.BaseDatasetPopulator method) setup_i18n() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) setup_input_connections_by_name() (galaxy.model.WorkflowStep method) setup_job() (galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper method) (galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper method) setup_keep_outdir() (in module galaxy_test.base.env) setup_logging() (galaxy.main.GalaxyConfigBuilder method) SETUP_NEEDED (galaxy.openid.openid_manager.OpenIDManager attribute) setup_proxy() (galaxy.web.proxy.ProxyManager method) setup_selenium() (galaxy_test.selenium.framework.TestWithSeleniumMixin method) setup_shared_state() (galaxy_test.selenium.framework.SharedStateSeleniumTestCase method) (galaxy_test.selenium.test_custom_builds.CustomBuildsTestcase method) (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase method) setup_two_users_with_one_shared_history() (galaxy_test.selenium.test_history_sharing.HistorySharingTestCase method) setup_volumes() (galaxy.jobs.runners.kubernetes.KubernetesJobRunner method) setup_with_driver() (galaxy_test.selenium.framework.SharedStateSeleniumTestCase method) (galaxy_test.selenium.framework.TestWithSeleniumMixin method) (galaxy_test.selenium.test_library_landing.LibraryLandingTestCase method) setUpClass() (galaxy_test.base.testcase.FunctionalTestCase class method) (galaxy_test.driver.integration_util.IntegrationInstance class method) SetupPerlEnvironment (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) SetupPythonEnvironment (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) SetupREnvironment (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) SetupRubyEnvironment (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) SetupVirtualEnv (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) Sf3 (class in galaxy.datatypes.proteomics) Sff (class in galaxy.datatypes.binary) SffFlow (class in galaxy.datatypes.mothur) sha() (in module galaxy.util.hash_util) sha1() (in module galaxy.util.hash_util) Shapefile (class in galaxy.datatypes.gis) sharable_owner() (tool_shed.webapp.controllers.repository.RepositoryController method) sharable_repository() (tool_shed.webapp.controllers.repository.RepositoryController method) sharable_repository_revision() (tool_shed.webapp.controllers.repository.RepositoryController method) SharableItemSecurityMixin (class in galaxy.webapps.base.controller) SharableMixin (class in galaxy.webapps.base.controller) SharableModelDeserializer (class in galaxy.managers.sharable) SharableModelFilters (class in galaxy.managers.sharable) SharableModelManager (class in galaxy.managers.sharable) SharableModelSerializer (class in galaxy.managers.sharable) share() (galaxy.webapps.base.controller.SharableMixin method) (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) share_history_with_user() (galaxy_test.selenium.test_history_sharing.HistorySharingTestCase method) share_restricted() (galaxy.webapps.galaxy.controllers.history.HistoryController method) share_with() (galaxy.managers.sharable.SharableModelManager method) shared_list_grid (galaxy.webapps.galaxy.controllers.history.HistoryController attribute) shared_state_in_error (galaxy_test.selenium.framework.SharedStateSeleniumTestCase attribute) shared_state_initialized (galaxy_test.selenium.framework.SharedStateSeleniumTestCase attribute) shared_with_me() (galaxy.webapps.galaxy.api.histories.HistoriesController method) SharedComputeEnvironment (class in galaxy.jobs) SharedHistoryListGrid (class in galaxy.webapps.galaxy.controllers.history) SharedHistoryListGrid.DatasetsByStateColumn (class in galaxy.webapps.galaxy.controllers.history) SharedHistoryListGrid.SharedByColumn (class in galaxy.webapps.galaxy.controllers.history) SharedStateSeleniumTestCase (class in galaxy_test.selenium.framework) SHARING (galaxy.model.Role.types attribute) sharing() (galaxy.webapps.base.controller.SharableMixin method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) sharing_roles() (galaxy.managers.users.UserManager method) SharingStatusColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.web.legacy_framework.grids) shed_config_filename() (galaxy.model.tool_shed_install.ToolShedRepository property) SHED_SEARCH (galaxy.selenium.navigates_galaxy.WAIT_TYPES attribute) shed_tool_conf (galaxy.managers.workflows.WorkflowCreateOptions attribute) shed_tool_data_path() (tool_shed.webapp.config.ToolShedAppConfiguration property) ShedCounter (class in tool_shed.webapp.util.shed_statistics) ShedToolDataTableManager (class in galaxy.tool_shed.tools.data_table_manager) ShedToolStatic (class in galaxy.webapps.galaxy.controllers.shed_tool_static) ShedTwillTestCase (class in tool_shed.test.base.twilltestcase) shell (galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledDockerContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.CachedMulledDockerContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.CachedMulledSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.MulledDockerContainerResolver attribute) shell() (galaxy.jobs.JobWrapper property) (galaxy.tool_util.deps.container_classes.Container property) (in module galaxy.util.commands) shell_commands() (galaxy.tool_util.deps.resolvers.ContainerDependency property) (galaxy.tool_util.deps.resolvers.Dependency method) (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependency method) (galaxy.tool_util.deps.resolvers.NullDependency method) (galaxy.tool_util.deps.resolvers.resolver_mixins.HomebrewDependency method) shell_process() (in module galaxy.util.commands) ShellCommand (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) ShellJobRunner (class in galaxy.jobs.runners.cli) short_name() (galaxy.tool_util.deps.requirements.RequirementSpecification property) should_burst() (galaxy.jobs.rule_helper.RuleHelper method) show() (galaxy.tool_util.deps.views.ContainerResolutionView method) (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.container_resolution.ContainerResolutionAPIController method) (galaxy.webapps.galaxy.api.dataset_collections.DatasetCollectionsController method) (galaxy.webapps.galaxy.api.datasets.DatasetsController method) (galaxy.webapps.galaxy.api.dynamic_tools.DynamicToolsController method) (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method) (galaxy.webapps.galaxy.api.folders.FoldersController method) (galaxy.webapps.galaxy.api.forms.FormDefinitionAPIController method) (galaxy.webapps.galaxy.api.genomes.GenomesController method) (galaxy.webapps.galaxy.api.group_roles.GroupRolesAPIController method) (galaxy.webapps.galaxy.api.group_users.GroupUsersAPIController method) (galaxy.webapps.galaxy.api.groups.GroupAPIController method) (galaxy.webapps.galaxy.api.histories.HistoriesController method) (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method) (galaxy.webapps.galaxy.api.item_tags.BaseItemTagsController method) (galaxy.webapps.galaxy.api.jobs.FastAPIJobs method) (galaxy.webapps.galaxy.api.jobs.JobController method) (galaxy.webapps.galaxy.api.libraries.LibrariesController method) (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method) (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method) (galaxy.webapps.galaxy.api.pages.PagesController method) (galaxy.webapps.galaxy.api.plugins.PluginsController method) (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method) (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method) (galaxy.webapps.galaxy.api.roles.FastAPIRoles method) (galaxy.webapps.galaxy.api.roles.RoleAPIController method) (galaxy.webapps.galaxy.api.tool_data.ToolData method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) (galaxy.webapps.galaxy.api.tools.ToolsController method) (galaxy.webapps.galaxy.api.tours.FastAPITours method) (galaxy.webapps.galaxy.api.tours.ToursController method) (galaxy.webapps.galaxy.api.users.UserAPIController method) (galaxy.webapps.galaxy.api.visualizations.VisualizationsController method) (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) (tool_shed.webapp.api.categories.CategoriesController method) (tool_shed.webapp.api.groups.GroupsController method) (tool_shed.webapp.api.repositories.RepositoriesController method) (tool_shed.webapp.api.repository_revisions.RepositoryRevisionsController method) (tool_shed.webapp.api.users.UsersController method)

show_dependencies() (galaxy.tool_util.deps.views.DependencyResolversView method) show_dynamic_tool() (galaxy_test.base.populators.BaseDatasetPopulator method) show_error_message() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) show_field() (galaxy.webapps.galaxy.api.tool_data.ToolData method) show_in_tool_panel() (galaxy.model.StoredWorkflow method) show_invocation() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) show_invocation_report() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) show_invocation_report_pdf() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) show_item_checkboxes (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.web.legacy_framework.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.TracksterSelectionGrid attribute) (tool_shed.grids.repository_grids.DockerImageGrid attribute) show_job_lock() (galaxy.webapps.galaxy.api.jobs.JobController method) show_jobs_summary() (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method) show_ldda() (galaxy_test.base.populators.LibraryPopulator method) show_library_item() (galaxy.model.security.GalaxyRBACAgent method) show_message() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) show_ok_message() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) show_params() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) show_pdf() (galaxy.webapps.galaxy.api.pages.PagesController method) show_roles() (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method) (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method) show_status() (galaxy.util.pastescript.serve.ServeCommand method) show_storage() (galaxy.webapps.galaxy.api.datasets.DatasetsController method) show_tools() (tool_shed.webapp.api.repositories.RepositoriesController method) show_version() (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method) show_versions() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) show_warn_message() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) showforms() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) shrink_and_unicodify() (in module galaxy.util) shrink_stream_by_size() (in module galaxy.util) shrink_string_by_size() (in module galaxy.util) shutdown() (galaxy.app.UniverseApplication method) (galaxy.config_watchers.ConfigWatchers method) (galaxy.jobs.handler.DefaultJobDispatcher method) (galaxy.jobs.handler.JobHandler method) (galaxy.jobs.handler.JobHandlerQueue method) (galaxy.jobs.handler.JobHandlerStopQueue method) (galaxy.jobs.manager.JobManager method) (galaxy.jobs.manager.NoopHandler method) (galaxy.jobs.NoopQueue method) (galaxy.jobs.runners.AsynchronousJobRunner method) (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.local.LocalJobRunner method) (galaxy.jobs.transfer_manager.TransferManager method) (galaxy.model.database_heartbeat.DatabaseHeartbeat method) (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.DistributedObjectStore method) (galaxy.objectstore.irods.IRODSObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.pulsar.PulsarObjectStore method) (galaxy.objectstore.s3.S3ObjectStore method) (galaxy.queue_worker.GalaxyQueueWorker method) (galaxy.tool_shed.galaxy_install.migrate.common.MigrateToolsApplication method) (galaxy.tool_shed.galaxy_install.update_repository_manager.UpdateRepositoryManager method) (galaxy.tools.toolbox.watcher.ToolConfWatcher method) (galaxy.util.heartbeat.Heartbeat method) (galaxy.util.lazy_process.LazyProcess method) (galaxy.util.lazy_process.NoOpLazyProcess method) (galaxy.util.watcher.BaseWatcher method) (galaxy.util.watcher.NullWatcher method) (galaxy.web.proxy.ProxyManager method) (galaxy.web_stack.ApplicationStack method) (galaxy.web_stack.MessageApplicationStack method) (galaxy.web_stack.transport.ApplicationStackTransport method) (galaxy.web_stack.transport.UWSGIFarmMessageTransport method) (galaxy.web_stack.UWSGIApplicationStack method) (galaxy.webapps.reports.app.UniverseApplication method) (galaxy.workflow.schedulers.core.CoreWorkflowSchedulingPlugin method) (galaxy.workflow.schedulers.WorkflowSchedulingPlugin method) (galaxy.workflow.scheduling_manager.WorkflowRequestMonitor method) (galaxy.workflow.scheduling_manager.WorkflowSchedulingManager method) (tool_shed.webapp.app.UniverseApplication method) shutdown_monitor() (galaxy.util.monitors.Monitors method) SHUTDOWN_MSG (galaxy.web_stack.transport.ApplicationStackTransport attribute) Sif (class in galaxy.datatypes.graph) SIFGraphDataProvider (class in galaxy.datatypes.graph) SignOutTestCase (class in galaxy_test.selenium.test_sign_out) simple_mapping() (in module galaxy.model.mapping) simple_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method) SimpleComputeEnvironment (class in galaxy.jobs) SimpleGraph (class in galaxy.util.simplegraph) SimpleGraphEdge (class in galaxy.util.simplegraph) SimpleGraphNode (class in galaxy.util.simplegraph) SimpleTextToolParameter (class in galaxy.tools.parameters.basic) SINGLE_CHAR_ABBR (galaxy.managers.histories.HistorySerializer attribute) (galaxy.managers.pages.PageSerializer attribute) (galaxy.managers.sharable.SharableModelManager attribute) (galaxy.managers.sharable.SharableModelSerializer attribute) (galaxy.managers.visualizations.VisualizationSerializer attribute) SingleTagContentsParser (class in galaxy.webapps.galaxy.controllers.workflow) singularity_container_test() (in module galaxy.tool_util.deps.mulled.mulled_update_singularity_containers) singularity_search() (in module galaxy.tool_util.deps.mulled.mulled_search) SingularityContainer (class in galaxy.tool_util.deps.container_classes) singularize() (galaxy.util.inflection.Inflector method) SINGULARIZE_RULES (galaxy.util.inflection.Inflector attribute) site (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization attribute) sites (galaxy.model.security.HostAgent attribute) size() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method) size_string() (in module galaxy.tool_shed.util.basic_util) size_to_bytes() (in module galaxy.util) sizzle_presence_of_selector() (in module galaxy.selenium.sizzle) sizzle_selector_clickable() (in module galaxy.selenium.sizzle) SizzleLoadingTestCase (class in galaxy_test.selenium.test_sizzle_loading) skip() (galaxy.managers.base.ModelSerializer method) skip_count() (galaxy.tool_util.verify.script.Results property) skip_if_github_down() (in module galaxy_test.base.populators) skip_if_github_workflow() (in module galaxy_test.driver.integration_util) skip_if_jenkins() (in module galaxy_test.driver.integration_util) skip_if_site_down() (in module galaxy_test.base.populators) skip_if_toolshed_down() (in module galaxy_test.base.populators) skip_unless_amqp() (in module galaxy_test.driver.integration_util) skip_unless_docker() (in module galaxy_test.driver.integration_util) skip_unless_executable() (in module galaxy_test.driver.integration_util) skip_unless_fixed_port() (in module galaxy_test.driver.integration_util) skip_unless_kubernetes() (in module galaxy_test.driver.integration_util) skip_unless_postgres() (in module galaxy_test.driver.integration_util) skip_without_datatype() (in module galaxy_test.base.populators) skip_without_tool() (in module galaxy_test.base.populators) SkipAttribute skipped() (in module galaxy.tools.util.galaxyops) slash_join() (in module galaxy.files.sources) sleep() (galaxy.tool_shed.galaxy_install.update_repository_manager.Sleeper method) (galaxy.util.sleeper.Sleeper method) sleep_for() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) sleep_for_seconds() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) Sleeper (class in galaxy.tool_shed.galaxy_install.update_repository_manager) (class in galaxy.util.sleeper) slice_collections() (galaxy.model.dataset_collections.matching.MatchingCollections method) sliced_collection_type() (galaxy.model.dataset_collections.structure.Leaf method) slot() (galaxy.containers.docker_model.DockerTask property) slug (galaxy.model.History attribute) (galaxy.model.Page attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.Visualization attribute) Slurm (class in galaxy.jobs.runners.util.cli.job.slurm) SlurmJobRunner (class in galaxy.jobs.runners.slurm) SlurmTorque (class in galaxy.jobs.runners.util.cli.job.slurm_torque) smart_str() (in module galaxy.util) SmartComponent (class in galaxy.selenium.smart_components) SmartTarget (class in galaxy.selenium.smart_components) Smat (class in galaxy.datatypes.plant_tribes) SMILES (class in galaxy.datatypes.molecules) SnapHmm (class in galaxy.datatypes.annotation) snapshot() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) (galaxy_test.selenium.framework.TestWithSeleniumMixin method) sniff() (galaxy.datatypes.annotation.Augustus method) (galaxy.datatypes.annotation.SnapHmm method) (galaxy.datatypes.assembly.Amos method) (galaxy.datatypes.assembly.Roadmaps method) (galaxy.datatypes.assembly.Sequences method) (galaxy.datatypes.binary.Anndata method) (galaxy.datatypes.binary.BafTar method) (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.binary.BamInputSorted method) (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.binary.BamQuerynameSorted method) (galaxy.datatypes.binary.Bcf method) (galaxy.datatypes.binary.BcfUncompressed method) (galaxy.datatypes.binary.BigWig method) (galaxy.datatypes.binary.Biom2 method) (galaxy.datatypes.binary.BlibSQlite method) (galaxy.datatypes.binary.Cel method) (galaxy.datatypes.binary.ChiraSQLite method) (galaxy.datatypes.binary.CompressedZipArchive method) (galaxy.datatypes.binary.Cool method) (galaxy.datatypes.binary.CRAM method) (galaxy.datatypes.binary.CuffDiffSQlite method) (galaxy.datatypes.binary.DAA method) (galaxy.datatypes.binary.Dcd method) (galaxy.datatypes.binary.DlibSQlite method) (galaxy.datatypes.binary.DMND method) (galaxy.datatypes.binary.ElibSQlite method) (galaxy.datatypes.binary.ExcelXls method) (galaxy.datatypes.binary.Fast5Archive method) (galaxy.datatypes.binary.Fast5ArchiveBz2 method) (galaxy.datatypes.binary.Fast5ArchiveGz method) (galaxy.datatypes.binary.GAFASQLite method) (galaxy.datatypes.binary.GeminiSQLite method) (galaxy.datatypes.binary.GmxBinary method) (galaxy.datatypes.binary.H5 method) (galaxy.datatypes.binary.ICM method) (galaxy.datatypes.binary.Idat method) (galaxy.datatypes.binary.IdpDB method) (galaxy.datatypes.binary.Loom method) (galaxy.datatypes.binary.MCool method) (galaxy.datatypes.binary.Meryldb method) (galaxy.datatypes.binary.MzSQlite method) (galaxy.datatypes.binary.NcbiTaxonomySQlite method) (galaxy.datatypes.binary.NetCDF method) (galaxy.datatypes.binary.OSW method) (galaxy.datatypes.binary.OxliCountGraph method) (galaxy.datatypes.binary.OxliGraphLabels method) (galaxy.datatypes.binary.OxliNodeGraph method) (galaxy.datatypes.binary.OxliStopTags method) (galaxy.datatypes.binary.OxliSubset method) (galaxy.datatypes.binary.OxliTagSet method) (galaxy.datatypes.binary.Parquet method) (galaxy.datatypes.binary.PostgresqlArchive method) (galaxy.datatypes.binary.PQP method) (galaxy.datatypes.binary.RData method) (galaxy.datatypes.binary.RMA6 method) (galaxy.datatypes.binary.SearchGuiArchive method) (galaxy.datatypes.binary.Sff method) (galaxy.datatypes.binary.SQlite method) (galaxy.datatypes.binary.SQmass method) (galaxy.datatypes.binary.Sra method) (galaxy.datatypes.binary.TwoBit method) (galaxy.datatypes.binary.Vel method) (galaxy.datatypes.binary.WiffTar method) (galaxy.datatypes.binary.Xlsx method) (galaxy.datatypes.blast.BlastXml method) (galaxy.datatypes.constructive_solid_geometry.Ply method) (galaxy.datatypes.constructive_solid_geometry.Vtk method) (galaxy.datatypes.data.Newick method) (galaxy.datatypes.data.Nexus method) (galaxy.datatypes.genetics.AllegroLOD method) (galaxy.datatypes.genetics.DataIn method) (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.genetics.GenotypeMatrix method) (galaxy.datatypes.genetics.MarkerMap method) (galaxy.datatypes.genetics.SNPMatrix method) (galaxy.datatypes.graph.Sif method) (galaxy.datatypes.graph.Xgmml method) (galaxy.datatypes.images.Gifti method) (galaxy.datatypes.images.Gmaj method) (galaxy.datatypes.images.Image method) (galaxy.datatypes.images.Nifti1 method) (galaxy.datatypes.images.Nifti2 method) (galaxy.datatypes.images.Pdf method) (galaxy.datatypes.images.Tck method) (galaxy.datatypes.images.Trk method) (galaxy.datatypes.interval.BedStrict method) (galaxy.datatypes.interval.ChromatinInteractions method) (galaxy.datatypes.interval.CustomTrack method) (galaxy.datatypes.interval.ENCODEPeak method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.ScIdx method) (galaxy.datatypes.interval.Wiggle method) (galaxy.datatypes.media.Flv method) (galaxy.datatypes.media.Mkv method) (galaxy.datatypes.media.Mp3 method) (galaxy.datatypes.media.Mp4 method) (galaxy.datatypes.media.Mpg method) (galaxy.datatypes.media.Wav method) (galaxy.datatypes.microarrays.Gal method) (galaxy.datatypes.microarrays.Gpr method) (galaxy.datatypes.molecules.CML method) (galaxy.datatypes.molecules.FPS method) (galaxy.datatypes.molecules.InChI method) (galaxy.datatypes.molecules.MOL2 method) (galaxy.datatypes.molecules.PDB method) (galaxy.datatypes.molecules.PDBQT method) (galaxy.datatypes.molecules.PQR method) (galaxy.datatypes.molecules.SDF method) (galaxy.datatypes.mothur.Axes method) (galaxy.datatypes.mothur.Frequency method) (galaxy.datatypes.mothur.LaneMask method) (galaxy.datatypes.mothur.LowerTriangleDistanceMatrix method) (galaxy.datatypes.mothur.Oligos method) (galaxy.datatypes.mothur.Otu method) (galaxy.datatypes.mothur.PairwiseDistanceMatrix method) (galaxy.datatypes.mothur.Quantile method) (galaxy.datatypes.mothur.RefTaxonomy method) (galaxy.datatypes.mothur.SecondaryStructureMap method) (galaxy.datatypes.mothur.SquareDistanceMatrix method) (galaxy.datatypes.msa.Hmmer method) (galaxy.datatypes.msa.InfernalCM method) (galaxy.datatypes.msa.MauveXmfa method) (galaxy.datatypes.msa.Stockholm_1_0 method) (galaxy.datatypes.phylip.Phylip method) (galaxy.datatypes.plant_tribes.PlantTribesKsComponents method) (galaxy.datatypes.plant_tribes.Smat method) (galaxy.datatypes.proteomics.Dta2d method) (galaxy.datatypes.proteomics.Edta method) (galaxy.datatypes.proteomics.Kroenik method) (galaxy.datatypes.proteomics.MascotDat method) (galaxy.datatypes.proteomics.Mgf method) (galaxy.datatypes.proteomics.Ms2 method) (galaxy.datatypes.proteomics.Msp method) (galaxy.datatypes.proteomics.MzTab method) (galaxy.datatypes.proteomics.PEFF method) (galaxy.datatypes.proteomics.PepList method) (galaxy.datatypes.proteomics.PSMS method) (galaxy.datatypes.proteomics.SPLib method) (galaxy.datatypes.proteomics.ThermoRAW method) (galaxy.datatypes.qualityscore.QualityScore454 method) (galaxy.datatypes.qualityscore.QualityScoreSOLiD method) (galaxy.datatypes.sequence.Axt method) (galaxy.datatypes.sequence.BaseFastq method) (galaxy.datatypes.sequence.csFasta method) (galaxy.datatypes.sequence.DotBracket method) (galaxy.datatypes.sequence.Fasta method) (galaxy.datatypes.sequence.Fastg method) (galaxy.datatypes.sequence.Genbank method) (galaxy.datatypes.sequence.Lav method) (galaxy.datatypes.sequence.Maf method) (galaxy.datatypes.sequence.MemePsp method) (galaxy.datatypes.sequence.RNADotPlotMatrix method) (galaxy.datatypes.sequence.SequenceSplitLocations method) (galaxy.datatypes.speech.BPF method) (galaxy.datatypes.speech.TextGrid method) (galaxy.datatypes.tabular.BaseCSV method) (galaxy.datatypes.tabular.BaseVcf method) (galaxy.datatypes.tabular.CMAP method) (galaxy.datatypes.tabular.ConnectivityTable method) (galaxy.datatypes.tabular.Eland method) (galaxy.datatypes.tabular.ElandMulti method) (galaxy.datatypes.tabular.MatrixMarket method) (galaxy.datatypes.tabular.Pileup method) (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.VcfGz method) (galaxy.datatypes.text.Arff method) (galaxy.datatypes.text.Biom1 method) (galaxy.datatypes.text.GeoJson method) (galaxy.datatypes.text.Gfa1 method) (galaxy.datatypes.text.Gfa2 method) (galaxy.datatypes.text.Html method) (galaxy.datatypes.text.ImgtJson method) (galaxy.datatypes.text.Ipynb method) (galaxy.datatypes.text.IQTree method) (galaxy.datatypes.text.Json method) (galaxy.datatypes.text.Obo method) (galaxy.datatypes.text.Paf method) (galaxy.datatypes.tracks.UCSCTrackHub method) (galaxy.datatypes.triples.HDT method) (galaxy.datatypes.triples.Jsonld method) (galaxy.datatypes.triples.N3 method) (galaxy.datatypes.triples.NTriples method) (galaxy.datatypes.triples.Rdf method) (galaxy.datatypes.triples.Triples method) (galaxy.datatypes.triples.Turtle method) (galaxy.datatypes.xml.CisML method) (galaxy.datatypes.xml.GenericXml method) (galaxy.datatypes.xml.MEMEXml method) sniff_prefix() (galaxy.datatypes.annotation.SnapHmm method) (galaxy.datatypes.assembly.Amos method) (galaxy.datatypes.assembly.Roadmaps method) (galaxy.datatypes.assembly.Sequences method) (galaxy.datatypes.binary.BigWig method) (galaxy.datatypes.binary.DAA method) (galaxy.datatypes.binary.DMND method) (galaxy.datatypes.binary.GmxBinary method) (galaxy.datatypes.binary.NetCDF method) (galaxy.datatypes.binary.Parquet method) (galaxy.datatypes.binary.RMA6 method) (galaxy.datatypes.binary.Sff method) (galaxy.datatypes.binary.Sra method) (galaxy.datatypes.binary.TwoBit method) (galaxy.datatypes.blast.BlastXml method) (galaxy.datatypes.constructive_solid_geometry.Ply method) (galaxy.datatypes.constructive_solid_geometry.Vtk method) (galaxy.datatypes.data.Nexus method) (galaxy.datatypes.genetics.AllegroLOD method) (galaxy.datatypes.genetics.DataIn method) (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.genetics.GenotypeMatrix method) (galaxy.datatypes.genetics.MarkerMap method) (galaxy.datatypes.images.Gifti method) (galaxy.datatypes.images.Nifti1 method) (galaxy.datatypes.images.Nifti2 method) (galaxy.datatypes.images.Tck method) (galaxy.datatypes.images.Trk method) (galaxy.datatypes.interval.Bed method) (galaxy.datatypes.interval.CustomTrack method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Gff3 method) (galaxy.datatypes.interval.Gtf method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.ScIdx method) (galaxy.datatypes.interval.Wiggle method) (galaxy.datatypes.microarrays.Gal method) (galaxy.datatypes.microarrays.Gpr method) (galaxy.datatypes.molecules.CML method) (galaxy.datatypes.molecules.FPS method) (galaxy.datatypes.molecules.InChI method) (galaxy.datatypes.molecules.MOL2 method) (galaxy.datatypes.molecules.PDB method) (galaxy.datatypes.molecules.PDBQT method) (galaxy.datatypes.molecules.PQR method) (galaxy.datatypes.molecules.SDF method) (galaxy.datatypes.mothur.Axes method) (galaxy.datatypes.mothur.Frequency method) (galaxy.datatypes.mothur.GroupAbund method) (galaxy.datatypes.mothur.LaneMask method) (galaxy.datatypes.mothur.LowerTriangleDistanceMatrix method) (galaxy.datatypes.mothur.Oligos method) (galaxy.datatypes.mothur.Otu method) (galaxy.datatypes.mothur.PairwiseDistanceMatrix method) (galaxy.datatypes.mothur.Quantile method) (galaxy.datatypes.mothur.RefTaxonomy method) (galaxy.datatypes.mothur.Sabund method) (galaxy.datatypes.mothur.SecondaryStructureMap method) (galaxy.datatypes.mothur.SquareDistanceMatrix method) (galaxy.datatypes.msa.Hmmer method) (galaxy.datatypes.msa.Hmmer2 method) (galaxy.datatypes.msa.Hmmer3 method) (galaxy.datatypes.msa.InfernalCM method) (galaxy.datatypes.msa.MauveXmfa method) (galaxy.datatypes.msa.Stockholm_1_0 method) (galaxy.datatypes.phylip.Phylip method) (galaxy.datatypes.plant_tribes.Smat method) (galaxy.datatypes.proteomics.Dta2d method) (galaxy.datatypes.proteomics.Edta method) (galaxy.datatypes.proteomics.Kroenik method) (galaxy.datatypes.proteomics.Ms2 method) (galaxy.datatypes.proteomics.Msp method) (galaxy.datatypes.proteomics.MzTab method) (galaxy.datatypes.proteomics.PEFF method) (galaxy.datatypes.proteomics.PepList method) (galaxy.datatypes.proteomics.ProteomicsXml method) (galaxy.datatypes.proteomics.PSMS method) (galaxy.datatypes.proteomics.SPLib method) (galaxy.datatypes.qualityscore.QualityScore454 method) (galaxy.datatypes.qualityscore.QualityScoreSOLiD method) (galaxy.datatypes.sequence.Axt method) (galaxy.datatypes.sequence.BaseFastq method) (galaxy.datatypes.sequence.csFasta method) (galaxy.datatypes.sequence.DotBracket method) (galaxy.datatypes.sequence.Fasta method) (galaxy.datatypes.sequence.Fastg method) (galaxy.datatypes.sequence.Genbank method) (galaxy.datatypes.sequence.Lav method) (galaxy.datatypes.sequence.Maf method) (galaxy.datatypes.sequence.MemePsp method) (galaxy.datatypes.sequence.SequenceSplitLocations method) (galaxy.datatypes.tabular.CMAP method) (galaxy.datatypes.tabular.ConnectivityTable method) (galaxy.datatypes.tabular.Eland method) (galaxy.datatypes.tabular.ElandMulti method) (galaxy.datatypes.tabular.MatrixMarket method) (galaxy.datatypes.tabular.Pileup method) (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.Vcf method) (galaxy.datatypes.text.Arff method) (galaxy.datatypes.text.Biom1 method) (galaxy.datatypes.text.GeoJson method) (galaxy.datatypes.text.Gfa1 method) (galaxy.datatypes.text.Gfa2 method) (galaxy.datatypes.text.Html method) (galaxy.datatypes.text.ImgtJson method) (galaxy.datatypes.text.Ipynb method) (galaxy.datatypes.text.IQTree method) (galaxy.datatypes.text.Json method) (galaxy.datatypes.text.Obo method) (galaxy.datatypes.text.Paf method) (galaxy.datatypes.triples.Jsonld method) (galaxy.datatypes.triples.NTriples method) (galaxy.datatypes.triples.Rdf method) (galaxy.datatypes.triples.Turtle method) (galaxy.datatypes.xml.CisML method) (galaxy.datatypes.xml.Dzi method) (galaxy.datatypes.xml.GenericXml method) (galaxy.datatypes.xml.MEMEXml method) (galaxy.datatypes.xml.Owl method) (galaxy.datatypes.xml.Phyloxml method) (galaxy.datatypes.xml.Sbml method) sniff_relaxed_interleaved() (galaxy.datatypes.phylip.Phylip method) sniff_strict_interleaved() (galaxy.datatypes.phylip.Phylip method) sniff_strict_sequential() (galaxy.datatypes.phylip.Phylip method) sniff_table_names() (galaxy.datatypes.binary.SQlite method) sniff_with_cls() (in module galaxy.datatypes.sniff) sniffers() (galaxy.webapps.galaxy.api.datatypes.DatatypesController method) SnpEffDb (class in galaxy.datatypes.text) SNPMatrix (class in galaxy.datatypes.genetics) SnpSiftDbNSFP (class in galaxy.datatypes.text) Snptest (class in galaxy.datatypes.genetics) social_auth (galaxy.model.User attribute) socket (galaxy.model.TransferJob attribute) sort() (galaxy.job_execution.output_collect.DatasetCollector method) (galaxy.web.framework.helpers.grids.BooleanColumn method) (galaxy.web.framework.helpers.grids.CommunityRatingColumn method) (galaxy.web.framework.helpers.grids.DateTimeColumn method) (galaxy.web.framework.helpers.grids.GridColumn method) (galaxy.web.framework.helpers.grids.IntegerColumn method) (galaxy.web.framework.helpers.grids.OwnerColumn method) (galaxy.web.framework.helpers.grids.ReverseSortColumn method) (galaxy.web.framework.helpers.grids.TextColumn method) (galaxy.web.legacy_framework.grids.BooleanColumn method) (galaxy.web.legacy_framework.grids.CommunityRatingColumn method) (galaxy.web.legacy_framework.grids.DateTimeColumn method) (galaxy.web.legacy_framework.grids.GridColumn method) (galaxy.web.legacy_framework.grids.IntegerColumn method) (galaxy.web.legacy_framework.grids.OwnerColumn method) (galaxy.web.legacy_framework.grids.ReverseSortColumn method) (galaxy.web.legacy_framework.grids.TextColumn method) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid.DeletedColumn method) (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid.HistoryColumn method) sort_block_components_by_block() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) sort_by_attr() (galaxy.model.security.GalaxyRBACAgent method) (in module galaxy.webapps.base.controller) (in module tool_shed.webapp.model) sort_flag (galaxy.datatypes.binary.BamInputSorted attribute) (galaxy.datatypes.binary.BamNative attribute) (galaxy.datatypes.binary.BamQuerynameSorted attribute) SortByColumnFilter (class in galaxy.tools.parameters.dynamic_options) sorter() (in module galaxy.webapps.reports.controllers.jobs) SortRuleDefinition (class in galaxy.util.rules_dsl) SortTool (class in galaxy.tools) source (galaxy.model.DatasetSourceHash attribute) source() (galaxy.util.plugin_config.PluginConfigSource property) source_dataset_chain() (galaxy.model.DatasetInstance property) source_environment() (galaxy.tool_util.deps.container_classes.Container property) source_library_dataset() (galaxy.model.DatasetInstance property) source_path() (galaxy.tool_util.parser.cwl.CwlToolSource property) (galaxy.tool_util.parser.interface.ToolSource property) (galaxy.tool_util.parser.ToolSource property) (galaxy.tool_util.parser.xml.XmlToolSource property) (galaxy.tool_util.parser.yaml.YamlToolSource property) source_uri (galaxy.model.DatasetSource attribute) sources (galaxy.model.Dataset attribute) sources() (galaxy.model.store.discover.JsonCollectedDatasetMatch property) SpalnNuclDb (class in galaxy.datatypes.spaln) SpalnProtDb (class in galaxy.datatypes.spaln) spdxUrl (galaxy.managers.licenses.LicenseMetadataModel attribute) spec() (galaxy.datatypes.metadata.MetadataCollection property) (galaxy.model.metadata.MetadataCollection property) SpecificationAwareDependencyResolver (class in galaxy.tool_util.deps.resolvers) SpecificationPatternDependencyResolver (class in galaxy.tool_util.deps.resolvers) specified_date() (galaxy.webapps.reports.controllers.users.Users method) specified_date_handler() (galaxy.webapps.reports.controllers.jobs.Jobs method) (galaxy.webapps.reports.controllers.workflows.Workflows method) specified_date_list_grid (galaxy.webapps.reports.controllers.jobs.Jobs attribute) (galaxy.webapps.reports.controllers.workflows.Workflows attribute) specified_month() (galaxy.webapps.reports.controllers.users.Users method) specified_month_all() (galaxy.webapps.reports.controllers.jobs.Jobs method) specified_month_in_error() (galaxy.webapps.reports.controllers.jobs.Jobs method) SpecifiedDateListGrid (class in galaxy.webapps.reports.controllers.jobs) (class in galaxy.webapps.reports.controllers.workflows) SpecifiedDateListGrid.CreateTimeColumn (class in galaxy.webapps.reports.controllers.jobs) (class in galaxy.webapps.reports.controllers.workflows) SpecifiedDateListGrid.EmailColumn (class in galaxy.webapps.reports.controllers.jobs) (class in galaxy.webapps.reports.controllers.workflows) SpecifiedDateListGrid.JobIdColumn (class in galaxy.webapps.reports.controllers.jobs) SpecifiedDateListGrid.SpecifiedDateColumn (class in galaxy.webapps.reports.controllers.jobs) (class in galaxy.webapps.reports.controllers.workflows) SpecifiedDateListGrid.StateColumn (class in galaxy.webapps.reports.controllers.jobs) SpecifiedDateListGrid.ToolColumn (class in galaxy.webapps.reports.controllers.jobs) SpecifiedDateListGrid.UserColumn (class in galaxy.webapps.reports.controllers.jobs) (class in galaxy.webapps.reports.controllers.workflows) SpecifiedDateListGrid.WorkflowNameColumn (class in galaxy.webapps.reports.controllers.workflows) specifies_version() (galaxy.tool_util.deps.requirements.RequirementSpecification property) SPLib (class in galaxy.datatypes.proteomics) SPLibNoIndex (class in galaxy.datatypes.proteomics) SplicedAlignment (class in galaxy.datatypes.util.maf_utilities) (class in galaxy.tools.util.maf_utilities) split() (galaxy.datatypes.data.Text class method) (galaxy.datatypes.molecules.CML class method) (galaxy.datatypes.molecules.FPS class method) (galaxy.datatypes.molecules.MOL2 class method) (galaxy.datatypes.molecules.OBFS method) (galaxy.datatypes.molecules.SDF class method) (galaxy.datatypes.msa.Stockholm_1_0 class method) (galaxy.datatypes.sequence.Alignment method) (galaxy.datatypes.sequence.BaseFastq class method) (galaxy.datatypes.sequence.Fasta class method) (galaxy.datatypes.sequence.Sequence method) split_constraint_string() (galaxy.containers.docker_model.DockerServiceConstraint static method) split_container_name() (in module galaxy.tool_util.deps.mulled.util) split_dataset_collection_instance() (in module galaxy.model.dataset_collections.subcollections) split_output_name() (galaxy.tool_util.parser.output_objects.ToolOutputCollectionPart static method) (galaxy.tool_util.parser.ToolOutputCollectionPart static method) split_params() (in module galaxy.jobs.runners.util.cli) split_tag() (in module galaxy.tool_util.deps.mulled.util) SplitColumnsRuleDefinition (class in galaxy.util.rules_dsl) splitLinebyWhitespaces() (galaxy.visualization.data_providers.phyloviz.nexusparser.Nexus_Parser method) SQLDebugMiddleware (class in galaxy.web.framework.middleware.sqldebug) SQlite (class in galaxy.datatypes.binary) sqlite_datadictprovider() (galaxy.datatypes.binary.SQlite method) sqlite_dataprovider() (galaxy.datatypes.binary.SQlite method) sqlite_datatableprovider() (galaxy.datatypes.binary.SQlite method) SQliteDataDictProvider (class in galaxy.datatypes.dataproviders.dataset) SQliteDataProvider (class in galaxy.datatypes.dataproviders.dataset) SQliteDataTableProvider (class in galaxy.datatypes.dataproviders.dataset) SqliteProxyIpc (class in galaxy.web.proxy) SQmass (class in galaxy.datatypes.binary) SquareDistanceMatrix (class in galaxy.datatypes.mothur) Sra (class in galaxy.datatypes.binary) SraManifest (class in galaxy.datatypes.tabular) src_merge() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) src_split() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) stage() (galaxy.tool_util.client.staging.StagingInterace method) stage_addition() (galaxy.model.History method) stage_data_async() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) stage_data_in_history() (in module galaxy.tool_util.verify.interactor) stage_inputs() (in module galaxy_test.base.populators) stage_rules_example() (in module galaxy_test.base.populators) StagingInterace (class in galaxy.tool_util.client.staging) standard_filters (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.UserListGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) standard_parser() (galaxy.util.pastescript.serve.Command class method) start() (galaxy.authnz.psa_authnz.Strategy method) (galaxy.config_watchers.ConfigWatchers method) (galaxy.datatypes.util.maf_utilities.SplicedAlignment property) (galaxy.jobs.handler.JobHandler method) (galaxy.jobs.handler.JobHandlerQueue method) (galaxy.jobs.handler.JobHandlerStopQueue method) (galaxy.jobs.manager.JobManager method) (galaxy.jobs.manager.NoopHandler method) (galaxy.model.database_heartbeat.DatabaseHeartbeat method) (galaxy.tools.toolbox.watcher.ToolConfWatcher method) (galaxy.tools.util.maf_utilities.SplicedAlignment property) (galaxy.util.watcher.BaseWatcher method) (galaxy.util.watcher.NullWatcher method) (galaxy.web_stack.ApplicationStack method) (galaxy.web_stack.MessageApplicationStack method) (galaxy.web_stack.transport.ApplicationStackTransport method) (galaxy.web_stack.transport.UWSGIFarmMessageTransport method) (galaxy.web_stack.UWSGIApplicationStack method) (galaxy.webapps.reports.controllers.jobs.Timer method) (galaxy.workflow.scheduling_manager.WorkflowRequestMonitor method) start_cache_monitor() (galaxy.objectstore.s3.S3ObjectStore method) start_if_needed() (galaxy.web_stack.transport.ApplicationStackTransport method) start_monitoring() (galaxy.util.monitors.Monitors method) start_process() (galaxy.util.lazy_process.LazyProcess method) (galaxy.util.lazy_process.NoOpLazyProcess method) startswith() (galaxy.datatypes.sniff.FilePrefix method) startswith_bytes() (galaxy.datatypes.sniff.FilePrefix method) startup() (galaxy.workflow.schedulers.core.CoreWorkflowSchedulingPlugin method) (galaxy.workflow.schedulers.WorkflowSchedulingPlugin method) state (galaxy.model.Dataset attribute) (galaxy.model.DeferredJob attribute) (galaxy.model.Job attribute) (galaxy.model.JobStateHistory attribute) (galaxy.model.Task attribute) (galaxy.model.TransferJob attribute) (galaxy.model.UserAddress attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowInvocationStep attribute) state() (galaxy.containers.docker_model.DockerNode property) (galaxy.containers.docker_model.DockerService property) (galaxy.containers.docker_model.DockerTask property) (galaxy.model.DatasetCollection property) (galaxy.model.DatasetCollectionInstance property) (galaxy.model.DatasetInstance property) state_counts() (galaxy.managers.history_contents.HistoryContentsManager method) state_history (galaxy.model.Job attribute) StateColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.web.legacy_framework.grids) Statement (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) StaticFileVisualizationPlugin (class in galaxy.visualization.plugins.plugin) StaticValueFilter (class in galaxy.tools.parameters.dynamic_options) StatisticsTracker (class in galaxy.job_metrics.collectl.stats) StatsdMiddleware (class in galaxy.web.framework.middleware.statsd) StatsdStructuredExecutionTimer (class in galaxy.app) status (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) status_code (galaxy.exceptions.ActionInputError attribute) (galaxy.exceptions.AdminRequiredException attribute) (galaxy.exceptions.AuthenticationFailed attribute) (galaxy.exceptions.AuthenticationRequired attribute) (galaxy.exceptions.ConfigDoesNotAllowException attribute) (galaxy.exceptions.ConfigurationError attribute) (galaxy.exceptions.Conflict attribute) (galaxy.exceptions.DeprecatedMethod attribute) (galaxy.exceptions.DuplicatedIdentifierException attribute) (galaxy.exceptions.DuplicatedSlugException attribute) (galaxy.exceptions.InconsistentDatabase attribute) (galaxy.exceptions.InsufficientPermissionsException attribute) (galaxy.exceptions.InternalServerError attribute) (galaxy.exceptions.InvalidFileFormatError attribute) (galaxy.exceptions.ItemAccessibilityException attribute) (galaxy.exceptions.ItemOwnershipException attribute) (galaxy.exceptions.MalformedContents attribute) (galaxy.exceptions.MalformedId attribute) (galaxy.exceptions.MessageException attribute) (galaxy.exceptions.NotImplemented attribute) (galaxy.exceptions.ObjectAttributeInvalidException attribute) (galaxy.exceptions.ObjectAttributeMissingException attribute) (galaxy.exceptions.ObjectNotFound attribute) (galaxy.exceptions.RequestParameterInvalidException attribute) (galaxy.exceptions.RequestParameterMissingException attribute) (galaxy.exceptions.ToolExecutionError attribute) (galaxy.exceptions.ToolInputsNotReadyException attribute) (galaxy.exceptions.ToolMetaParameterException attribute) (galaxy.exceptions.ToolMissingException attribute) (galaxy.exceptions.UnknownContentsType attribute) (galaxy.exceptions.UserActivationRequiredException attribute) stderr() (galaxy.model.JobLike property) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) StdFsAccess (class in galaxy.tool_util.cwl.cwltool_deps) StdioErrorLevel (class in galaxy.tool_util.parser.stdio) StdioParser (class in galaxy.tool_util.parser.xml) stdout() (galaxy.model.JobLike property) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) step (galaxy.workflow.refactor.schema.FillStepDefaultsAction attribute) (galaxy.workflow.refactor.schema.UpdateStepLabelAction attribute) (galaxy.workflow.refactor.schema.UpdateStepPositionAction attribute) (galaxy.workflow.refactor.schema.UpgradeSubworkflowAction attribute) (galaxy.workflow.refactor.schema.UpgradeToolAction attribute) step_by_index() (galaxy.model.Workflow method) step_by_label() (galaxy.model.Workflow method) step_count (galaxy.model.Workflow attribute) step_invocation_for_label() (galaxy.model.WorkflowInvocation method) step_invocation_for_step_id() (galaxy.model.WorkflowInvocation method) step_invocations_by_step_id() (galaxy.model.WorkflowInvocation method) step_label (galaxy.workflow.refactor.schema.RefactorActionExecutionMessage attribute) STEP_PARAMETERS (galaxy.model.WorkflowRequestInputParameter.types attribute) step_state_to_tool_state() (galaxy.workflow.modules.InputModule method) (galaxy.workflow.modules.InputParameterModule method) (galaxy.workflow.modules.WorkflowModule method) step_states (galaxy.model.WorkflowInvocation attribute) step_states_by_step_id() (galaxy.model.WorkflowInvocation method) STEP_TYPE_TO_INPUT_TYPE (galaxy.model.WorkflowStep attribute) StepManager (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager) StepReferenceByLabel (class in galaxy.workflow.refactor.schema) StepReferenceByOrderIndex (class in galaxy.workflow.refactor.schema) steps (galaxy.model.Workflow attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.tours.TourDetails attribute) steps_by_id() (galaxy.model.Workflow property) STL (class in galaxy.datatypes.constructive_solid_geometry) Stockholm_1_0 (class in galaxy.datatypes.msa) stop() (galaxy.jobs.handler.DefaultJobDispatcher method) (galaxy.jobs.manager.JobManager method) (galaxy.jobs.manager.NoopManager method) (galaxy.managers.interactivetool.InteractiveToolManager method) (galaxy.managers.jobs.JobManager method) (galaxy.webapps.reports.controllers.jobs.Timer method) stop_creating_job() (galaxy.managers.datasets.DatasetAssociationManager method) stop_daemon() (galaxy.util.pastescript.serve.ServeCommand method) stop_entry_point() (galaxy.webapps.galaxy.api.tool_entry_points.ToolEntryPointsAPIController method) stop_err() (in module galaxy.datatypes.converters.fastqsolexa_to_fasta_converter) (in module galaxy.datatypes.converters.fastqsolexa_to_qual_converter) (in module galaxy.datatypes.converters.interval_to_bed_converter) (in module galaxy.datatypes.converters.interval_to_bedstrict_converter) stop_if_unneeded() (galaxy.web_stack.transport.ApplicationStackTransport method) stop_job() (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.chronos.ChronosJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.condor.CondorJobRunner method) (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) (galaxy.jobs.runners.godocker.GodockerJobRunner method) (galaxy.jobs.runners.kubernetes.KubernetesJobRunner method) (galaxy.jobs.runners.local.LocalJobRunner method) (galaxy.jobs.runners.pbs.PBSJobRunner method) (galaxy.jobs.runners.tasks.TaskedJobRunner method) (in module galaxy.jobs.runners.util.pykube_util) stop_monitoring() (galaxy.util.monitors.Monitors method) stop_servers() (galaxy_test.driver.driver_util.TestDriver method) STOP_SIGNAL (galaxy.jobs.handler.JobHandlerQueue attribute) (galaxy.jobs.handler.JobHandlerStopQueue attribute) STOPPED (galaxy.model.Job.states attribute) STOPPING (galaxy.model.Job.states attribute) StorableObject (class in galaxy.model) Storage (class in galaxy.authnz.psa_authnz) store() (galaxy.model.PSAAssociation class method) store_by() (galaxy.model.Dataset property) store_jobtemplate() (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) store_type (galaxy.objectstore.azure_blob.AzureBlobObjectStore attribute) (galaxy.objectstore.cloud.Cloud attribute) (galaxy.objectstore.DiskObjectStore attribute) (galaxy.objectstore.DistributedObjectStore attribute) (galaxy.objectstore.HierarchicalObjectStore attribute) (galaxy.objectstore.irods.IRODSObjectStore attribute) (galaxy.objectstore.pithos.PithosObjectStore attribute) (galaxy.objectstore.s3.S3ObjectStore attribute) (galaxy.objectstore.s3.SwiftObjectStore attribute) stored_list_grid (galaxy.webapps.galaxy.controllers.history.HistoryController attribute) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController attribute) stored_workflow (galaxy.model.StoredWorkflowAnnotationAssociation attribute) (galaxy.model.StoredWorkflowMenuEntry attribute) (galaxy.model.StoredWorkflowRatingAssociation attribute) (galaxy.model.StoredWorkflowUserShareAssociation attribute) (galaxy.model.Workflow attribute) stored_workflow() (galaxy.managers.workflows.CreatedWorkflow property) stored_workflow_id (galaxy.model.StoredWorkflowAnnotationAssociation attribute) (galaxy.model.StoredWorkflowMenuEntry attribute) (galaxy.model.StoredWorkflowRatingAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.StoredWorkflowUserShareAssociation attribute) (galaxy.model.Workflow attribute) stored_workflow_menu_entries (galaxy.model.User attribute) stored_workflows (galaxy.model.StoredWorkflowAnnotationAssociation attribute) (galaxy.model.StoredWorkflowRatingAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.User attribute) StoredWorkflow (class in galaxy.model) StoredWorkflowAllPublishedGrid (class in galaxy.webapps.galaxy.controllers.workflow) StoredWorkflowAnnotationAssociation (class in galaxy.model) (class in tool_shed.webapp.model) StoredWorkflowListGrid (class in galaxy.webapps.galaxy.controllers.workflow) StoredWorkflowListGrid.StepsColumn (class in galaxy.webapps.galaxy.controllers.workflow) StoredWorkflowMenuEntry (class in galaxy.model) StoredWorkflowRatingAssociation (class in galaxy.model) StoredWorkflowTagAssociation (class in galaxy.model) StoredWorkflowUserShareAssociation (class in galaxy.model) str_to_bytes() (in module galaxy.jobs.dynamic_tool_destination) Strategy (class in galaxy.authnz.psa_authnz) stream_dataset_collection() (in module galaxy.managers.hdcas) stream_template_mako() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) stream_to_file() (in module galaxy.datatypes.sniff) stream_to_open_named_file() (in module galaxy.datatypes.sniff) stream_url_to_file() (in module galaxy.datatypes.sniff) strict_shell() (galaxy.jobs.JobWrapper property) strict_width (galaxy.datatypes.tabular.CSV attribute) (galaxy.datatypes.tabular.TSV attribute) string_as_bool() (in module galaxy.util) string_as_bool_or_none() (in module galaxy.util) string_io() (galaxy.datatypes.sniff.FilePrefix method) string_standard_ops() (galaxy.managers.base.ModelFilterParser method) string_to_object() (in module galaxy.util) StringFunctionFilter (class in galaxy.tool_util.parser.output_actions) stringify() (in module galaxy.tool_shed.util.basic_util) stringify_dictionary_keys() (in module galaxy.util) strip_control_characters() (in module galaxy.util) strip_path() (in module galaxy.tool_shed.util.basic_util) stripwd() (in module galaxy.model.orm.engine_factory) structure() (galaxy.model.dataset_collections.matching.MatchingCollections property) structure_regexp (galaxy.datatypes.sequence.DotBracket attribute) (galaxy.datatypes.tabular.ConnectivityTable attribute) StructuredExecutionTimer (class in galaxy.util) StructuredTestDataPlugin (class in galaxy_test.base.instrument) stub_label() (galaxy.tools.toolbox.panel.ToolPanelElements method) stub_tool() (galaxy.tools.toolbox.panel.ToolPanelElements method) stub_workflow() (galaxy.tools.toolbox.panel.ToolPanelElements method) style (galaxy.managers.workflows.RefactorRequest attribute) stylesheet_link() (in module galaxy.web.framework.helpers.tags) subcollection_mapping_type() (galaxy.model.dataset_collections.matching.MatchingCollections method) subcollection_type_description() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) subcontainer_class (galaxy.managers.containers.ContainerManagerMixin attribute) (galaxy.managers.containers.DatasetCollectionAsContainerManagerMixin attribute) (galaxy.managers.containers.LibraryFolderAsContainerManagerMixin attribute) (galaxy.managers.history_contents.HistoryContentsManager attribute) subcontainer_class_manager_class (galaxy.managers.history_contents.HistoryContentsManager attribute) subcontainer_class_type_name (galaxy.managers.history_contents.HistoryContentsManager attribute) subcontainers() (galaxy.managers.containers.ContainerManagerMixin method) (galaxy.managers.history_contents.HistoryContentsManager method) submission_params() (in module galaxy.jobs.runners.util.condor) submit() (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.util.cli.job.BaseJobExec method) (galaxy.jobs.runners.util.cli.job.lsf.LSF method) (galaxy.jobs.runners.util.cli.job.slurm.Slurm method) (galaxy.jobs.runners.util.cli.job.torque.Torque method) submit_form() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) submit_login() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) submit_report() (galaxy.tools.error_reports.ErrorPlugin method) (galaxy.tools.error_reports.NullErrorPlugin method) (galaxy.tools.error_reports.plugins.email.EmailPlugin method) (galaxy.tools.error_reports.plugins.ErrorPlugin method) (galaxy.tools.error_reports.plugins.github.GithubPlugin method) (galaxy.tools.error_reports.plugins.gitlab.GitLabPlugin method) (galaxy.tools.error_reports.plugins.influxdb.InfluxDBPlugin method) (galaxy.tools.error_reports.plugins.json.JsonPlugin method) (galaxy.tools.error_reports.plugins.sentry.SentryPlugin method) subprocess() (galaxy.datatypes.dataproviders.external.SubprocessDataProvider method) SubprocessDataProvider (class in galaxy.datatypes.dataproviders.external) subset (galaxy.model.HistoryDatasetAssociationSubset attribute) subtype (galaxy.datatypes.constructive_solid_geometry.Ply attribute) (galaxy.datatypes.constructive_solid_geometry.PlyAscii attribute) (galaxy.datatypes.constructive_solid_geometry.PlyBinary attribute) (galaxy.datatypes.constructive_solid_geometry.Vtk attribute) (galaxy.datatypes.constructive_solid_geometry.VtkAscii attribute) (galaxy.datatypes.constructive_solid_geometry.VtkBinary attribute) subworkflow (galaxy.model.WorkflowStep attribute) subworkflow_id (galaxy.model.WorkflowStep attribute) subworkflow_invocation (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute) subworkflow_invocation_id (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute) subworkflow_invocations (galaxy.model.WorkflowInvocation attribute) SubWorkflowModule (class in galaxy.workflow.modules) SUCCESS (galaxy.openid.openid_manager.OpenIDManager attribute) success_count() (galaxy.tool_util.verify.script.Results property) sudo_popen() (in module galaxy.jobs.runners.util.sudo) suggestions (galaxy.workflow.refactor.schema.AddInputAction attribute) sum_job_runtime() (galaxy.jobs.rule_helper.RuleHelper method) summarize() (in module galaxy.workflow.extract) summarize_condor_log() (in module galaxy.jobs.runners.util.condor) summarize_destination_params() (in module galaxy.managers.jobs) summarize_instance_history_on_error() (in module galaxy_test.base.populators) summarize_invocation_jobs() (in module galaxy.managers.jobs) summarize_job_metrics() (in module galaxy.managers.jobs) summarize_job_parameters() (in module galaxy.managers.jobs) summarize_jobs_to_dict() (in module galaxy.managers.jobs) summarize_requirements() (galaxy.tool_util.deps.views.DependencyResolversView method) summarize_toolbox() (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) summarize_tools() (galaxy.tool_util.deps.views.DependencyResolversView method) Summary (class in galaxy.datatypes.mothur) summary (galaxy.util.pastescript.serve.ServeCommand attribute) supported_display_apps (galaxy.datatypes.data.Data attribute) supported_field_types (galaxy.model.FormDefinition attribute) supports_docker() (galaxy.jobs.rule_helper.RuleHelper method) supports_test_data_download() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi property) supports_volumes (galaxy.containers.ContainerInterface attribute) (galaxy.containers.docker_swarm.DockerSwarmInterface attribute) SwapColumnsRuleDefinition (class in galaxy.util.rules_dsl) sweepster() (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) SwiftObjectStore (class in galaxy.objectstore.s3) switch_to_history() (galaxy.webapps.galaxy.controllers.history.HistoryController method) switch_to_main_panel() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) sync_database_with_file_system() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.SyncDatabase method) SyncDatabase (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler) synchronized() (in module galaxy.util) synopsis (galaxy.model.Library attribute) System (class in galaxy.webapps.reports.controllers.system) SYSTEM (galaxy.model.Role.types attribute) system_user_pwent() (galaxy.model.User method)

T

TabixDataProvider (class in galaxy.visualization.data_providers.genome) table (galaxy.model.APIKeys attribute) (galaxy.model.CloudAuthz attribute) (galaxy.model.CustosAuthnzToken attribute) (galaxy.model.DataManagerHistoryAssociation attribute) (galaxy.model.DataManagerJobAssociation attribute) (galaxy.model.Dataset attribute) (galaxy.model.DatasetCollection attribute) (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.DatasetHash attribute) (galaxy.model.DatasetPermissions attribute) (galaxy.model.DatasetSource attribute) (galaxy.model.DatasetSourceHash attribute) (galaxy.model.DefaultHistoryPermissions attribute) (galaxy.model.DefaultQuotaAssociation attribute) (galaxy.model.DefaultUserPermissions attribute) (galaxy.model.DeferredJob attribute) (galaxy.model.DynamicTool attribute) (galaxy.model.Event attribute) (galaxy.model.ExtendedMetadata attribute) (galaxy.model.ExtendedMetadataIndex attribute) (galaxy.model.FormDefinition attribute) (galaxy.model.FormDefinitionCurrent attribute) (galaxy.model.FormValues attribute) (galaxy.model.GalaxySession attribute) (galaxy.model.GalaxySessionToHistoryAssociation attribute) (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.Group attribute) (galaxy.model.GroupQuotaAssociation attribute) (galaxy.model.GroupRoleAssociation attribute) (galaxy.model.History attribute) (galaxy.model.HistoryAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization attribute) (galaxy.model.HistoryDatasetAssociationHistory attribute) (galaxy.model.HistoryDatasetAssociationRatingAssociation attribute) (galaxy.model.HistoryDatasetAssociationSubset attribute) (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetCollectionRatingAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryRatingAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.HistoryUserShareAssociation attribute) (galaxy.model.ImplicitCollectionJobs attribute) (galaxy.model.ImplicitCollectionJobsJobAssociation attribute) (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) (galaxy.model.ImplicitlyCreatedDatasetCollectionInput attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.Job attribute) (galaxy.model.JobContainerAssociation attribute) (galaxy.model.JobExportHistoryArchive attribute) (galaxy.model.JobExternalOutputMetadata attribute) (galaxy.model.JobImportHistoryArchive attribute) (galaxy.model.JobMetricNumeric attribute) (galaxy.model.JobMetricText attribute) (galaxy.model.JobParameter attribute) (galaxy.model.JobStateHistory attribute) (galaxy.model.JobToImplicitOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetAssociation attribute) (galaxy.model.JobToInputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetCollectionElementAssociation attribute) (galaxy.model.JobToInputLibraryDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToOutputLibraryDatasetAssociation attribute) (galaxy.model.Library attribute) (galaxy.model.LibraryDataset attribute) (galaxy.model.LibraryDatasetCollectionAnnotationAssociation attribute) (galaxy.model.LibraryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetCollectionRatingAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationPermissions attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) (galaxy.model.LibraryDatasetPermissions attribute) (galaxy.model.LibraryFolder attribute) (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryFolderPermissions attribute) (galaxy.model.LibraryInfoAssociation attribute) (galaxy.model.LibraryPermissions attribute) (galaxy.model.MetadataFile attribute) (galaxy.model.Page attribute) (galaxy.model.PageAnnotationAssociation attribute) (galaxy.model.PageRatingAssociation attribute) (galaxy.model.PageRevision attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.PageUserShareAssociation attribute) (galaxy.model.PasswordResetToken attribute) (galaxy.model.PostJobAction attribute) (galaxy.model.PostJobActionAssociation attribute) (galaxy.model.PSAAssociation attribute) (galaxy.model.PSACode attribute) (galaxy.model.PSANonce attribute) (galaxy.model.PSAPartial attribute) (galaxy.model.Quota attribute) (galaxy.model.Role attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.StoredWorkflowAnnotationAssociation attribute) (galaxy.model.StoredWorkflowMenuEntry attribute) (galaxy.model.StoredWorkflowRatingAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.StoredWorkflowUserShareAssociation attribute) (galaxy.model.Tag attribute) (galaxy.model.Task attribute) (galaxy.model.TaskMetricNumeric attribute) (galaxy.model.TaskMetricText attribute) (galaxy.model.tool_shed_install.MigrateTools attribute) (galaxy.model.tool_shed_install.RepositoryDependency attribute) (galaxy.model.tool_shed_install.RepositoryRepositoryDependencyAssociation attribute) (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.model.tool_shed_install.ToolVersion attribute) (galaxy.model.tool_shed_install.ToolVersionAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.TransferJob attribute) (galaxy.model.User attribute) (galaxy.model.UserAction attribute) (galaxy.model.UserAddress attribute) (galaxy.model.UserAuthnzToken attribute) (galaxy.model.UserGroupAssociation attribute) (galaxy.model.UserPreference attribute) (galaxy.model.UserQuotaAssociation attribute) (galaxy.model.UserRoleAssociation attribute) (galaxy.model.Visualization attribute) (galaxy.model.VisualizationAnnotationAssociation attribute) (galaxy.model.VisualizationRatingAssociation attribute) (galaxy.model.VisualizationRevision attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.VisualizationUserShareAssociation attribute) (galaxy.model.WorkerProcess attribute) (galaxy.model.Workflow attribute) (galaxy.model.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.WorkflowOutput attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.model.WorkflowRequestInputStepParameter attribute) (galaxy.model.WorkflowRequestStepState attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowStep attribute) (galaxy.model.WorkflowStepAnnotationAssociation attribute) (galaxy.model.WorkflowStepConnection attribute) (galaxy.model.WorkflowStepInput attribute) (galaxy.model.WorkflowStepTagAssociation attribute) (tool_shed.webapp.model.APIKeys attribute) (tool_shed.webapp.model.Category attribute) (tool_shed.webapp.model.Component 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.PasswordResetToken attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.RepositoryCategoryAssociation attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) (tool_shed.webapp.model.RepositoryRatingAssociation attribute) (tool_shed.webapp.model.RepositoryReview attribute) (tool_shed.webapp.model.RepositoryRoleAssociation attribute) (tool_shed.webapp.model.Role attribute) (tool_shed.webapp.model.Tag attribute) (tool_shed.webapp.model.User attribute) (tool_shed.webapp.model.UserGroupAssociation attribute) (tool_shed.webapp.model.UserRoleAssociation attribute) Tabular (class in galaxy.datatypes.tabular) TabularData (class in galaxy.datatypes.tabular) TabularToolDataField (class in galaxy.tools.data) TabularToolDataTable (class in galaxy.tools.data) Tag (class in galaxy.model) (class in tool_shed.webapp.model) tag (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.WorkflowStepTagAssociation attribute) (galaxy.tool_util.parser.output_actions.BooleanFilter attribute) (galaxy.tool_util.parser.output_actions.ColumnReplaceFilter attribute) (galaxy.tool_util.parser.output_actions.ColumnStripFilter attribute) (galaxy.tool_util.parser.output_actions.DatatypeIsInstanceToolOutputActionConditionalWhen attribute) (galaxy.tool_util.parser.output_actions.FormatToolOutputAction attribute) (galaxy.tool_util.parser.output_actions.FromDataTableOutputActionOption attribute) (galaxy.tool_util.parser.output_actions.FromFileToolOutputActionOption attribute) (galaxy.tool_util.parser.output_actions.FromParamToolOutputActionOption attribute) (galaxy.tool_util.parser.output_actions.InsertColumnToolOutputActionOptionFilter attribute) (galaxy.tool_util.parser.output_actions.MetadataToolOutputAction attribute) (galaxy.tool_util.parser.output_actions.MetadataValueFilter attribute) (galaxy.tool_util.parser.output_actions.MultipleSplitterFilter attribute) (galaxy.tool_util.parser.output_actions.NullToolOutputActionOption attribute) (galaxy.tool_util.parser.output_actions.ParamValueToolOutputActionOptionFilter attribute) (galaxy.tool_util.parser.output_actions.StringFunctionFilter attribute) (galaxy.tool_util.parser.output_actions.ToolOutputAction attribute) (galaxy.tool_util.parser.output_actions.ToolOutputActionConditional attribute) (galaxy.tool_util.parser.output_actions.ToolOutputActionConditionalWhen attribute) (galaxy.tool_util.parser.output_actions.ToolOutputActionGroup attribute) (galaxy.tool_util.parser.output_actions.ToolOutputActionOption attribute) (galaxy.tool_util.parser.output_actions.ToolOutputActionOptionFilter attribute) (galaxy.tool_util.parser.output_actions.ValueToolOutputActionConditionalWhen attribute) tag_assoc (galaxy.managers.hdas.HDAManager attribute) (galaxy.managers.hdcas.HDCAManager attribute) (galaxy.managers.histories.HistoryManager attribute) (galaxy.managers.pages.PageManager attribute) (galaxy.managers.taggable.TaggableManagerMixin attribute) (galaxy.managers.visualizations.VisualizationManager attribute) tag_autocomplete_data() (galaxy.webapps.galaxy.controllers.tag.TagsController method) tag_handler() (galaxy.job_execution.output_collect.JobContext property) (galaxy.model.store.discover.ModelPersistenceContext property) (galaxy.model.store.discover.SessionlessModelPersistenceContext property) tag_id (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.WorkflowStepTagAssociation attribute) tag_list() (galaxy.model.store.discover.JsonCollectedDatasetMatch property) tag_mapping() (in module galaxy.model.mapping) TagAttributeHandler (class in tool_shed.dependencies.tool.tag_attribute_handler) TagDatasetAction (class in galaxy.jobs.actions.post) TagFromFileTool (class in galaxy.tools) TaggableDeserializerMixin (class in galaxy.managers.taggable) TaggableFilterMixin (class in galaxy.managers.taggable) TaggableManagerMixin (class in galaxy.managers.taggable) TaggableSerializerMixin (class in galaxy.managers.taggable) tagged_histories (galaxy.model.Tag attribute) tagged_history_dataset_associations (galaxy.model.Tag attribute) tagged_history_dataset_collections (galaxy.model.Tag attribute) tagged_item_class (galaxy.webapps.galaxy.api.item_tags.HistoryContentTagsController attribute) (galaxy.webapps.galaxy.api.item_tags.HistoryTagsController attribute) (galaxy.webapps.galaxy.api.item_tags.WorkflowTagsController attribute) tagged_item_id (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.item_tags.HistoryContentTagsController attribute) (galaxy.webapps.galaxy.api.item_tags.HistoryTagsController attribute) (galaxy.webapps.galaxy.api.item_tags.WorkflowTagsController attribute) tagged_library_dataset_collections (galaxy.model.Tag attribute) tagged_library_dataset_dataset_associations (galaxy.model.Tag attribute) tagged_pages (galaxy.model.Tag attribute) tagged_tools (galaxy.model.Tag attribute) tagged_visualizations (galaxy.model.Tag attribute) tagged_workflow_steps (galaxy.model.Tag attribute) tagged_workflows (galaxy.model.Tag attribute) tagging_add() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) TagHandler (class in galaxy.model.tags) TagManager (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager) tags (galaxy.model.History attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.Page attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.Visualization attribute) (galaxy.model.WorkflowStep attribute) (galaxy.tours.TourCore attribute) tags_used() (galaxy.managers.users.UserManager method) TagsController (class in galaxy.webapps.galaxy.api.tags) (class in galaxy.webapps.galaxy.controllers.tag) takes_config_file (galaxy.util.pastescript.serve.Command attribute) (galaxy.util.pastescript.serve.ServeCommand attribute) TandemXML (class in galaxy.datatypes.proteomics) tap_path() (galaxy.tool_util.deps.brew_exts.RecipeContext property) tar_export_directory() (in module galaxy.model.store) Target (class in galaxy.selenium.components) (class in galaxy.tool_util.deps.mulled.util) target (galaxy.web_stack.message.JobHandlerMessage attribute) (galaxy.web_stack.message.WorkflowSchedulingMessage attribute) target() (galaxy.web_stack.message.ApplicationStackMessage property) target_galaxy_version() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi property) target_history() (galaxy.model.store.ModelImportStore method) target_if_active() (galaxy.managers.interactivetool.InteractiveToolManager method) target_url_parts() (in module galaxy_test.base.env) TarModelExportStore (class in galaxy.model.store) Task (class in galaxy.model) task (galaxy.model.TaskMetricNumeric attribute) (galaxy.model.TaskMetricText attribute) task() (galaxy.web_stack.message.TaskMessage property) Task.states (class in galaxy.model) task_add() (galaxy.containers.docker_model.DockerNode method) (galaxy.containers.docker_model.DockerService method) task_count() (galaxy.containers.docker_model.DockerNode property) (galaxy.containers.docker_model.DockerService property) task_id (galaxy.model.TaskMetricNumeric attribute) (galaxy.model.TaskMetricText attribute) task_inspect() (galaxy.containers.docker_swarm.DockerSwarmAPIInterface method) (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) task_ls() (galaxy.containers.docker_swarm.DockerSwarmAPIInterface method) task_runner_external_id (galaxy.model.Task attribute) task_runner_name (galaxy.model.Task attribute) task_suspend() (galaxy.jobs.runners.godocker.GodockerJobRunner method) task_template_option_map (galaxy.containers.docker_swarm.DockerSwarmAPIInterface attribute) TaskedJobRunner (class in galaxy.jobs.runners.tasks) TaskMessage (class in galaxy.web_stack.message) TaskMetricNumeric (class in galaxy.model) TaskMetricText (class in galaxy.model) TaskPathRewriter (class in galaxy.job_execution.datasets) tasks (galaxy.model.Job attribute) tasks() (galaxy.containers.docker_model.DockerNode property) (galaxy.containers.docker_model.DockerService property) TaskWrapper (class in galaxy.jobs) Taxonomy (class in galaxy.datatypes.tabular) TaxonomySummary (class in galaxy.datatypes.mothur) Tck (class in galaxy.datatypes.images) TdfTar (class in galaxy.datatypes.binary) tear_down() (galaxy_test.driver.driver_util.TestDriver method) tear_down_driver() (galaxy_test.selenium.framework.TestWithSeleniumMixin method) tear_down_selenium() (galaxy_test.selenium.framework.TestWithSeleniumMixin method) tearDown() (galaxy_test.base.api.UsesApiTestCaseMixin method) (galaxy_test.selenium.framework.SeleniumTestCase method) tearDownClass() (galaxy_test.base.testcase.FunctionalTestCase class method) (galaxy_test.driver.integration_util.IntegrationInstance class method) temp_config_dir() (galaxy_test.driver.integration_util.IntegrationInstance class method) temp_directory() (galaxy.model.JobExportHistoryArchive property) TempfileDataProvider (class in galaxy.datatypes.dataproviders.external) TempFileHandler (class in galaxy.datatypes.util.maf_utilities) (class in galaxy.tools.util.maf_utilities) template (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryInfoAssociation attribute) (galaxy.web.legacy_framework.grids.Grid attribute) (tool_shed.grids.repository_grids.CategoryGrid 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) template() (galaxy.webapps.base.controller.JSAppLauncher method) template_context (galaxy.webapps.base.webapp.GalaxyWebTransaction attribute) template_macro_params() (in module galaxy.tool_util.loader) (in module galaxy.util.xml_macros) TEMPLATE_PATHS_CONFIG (galaxy.visualization.plugins.registry.VisualizationsRegistry attribute) TemplateCommand (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) terminal() (galaxy.containers.docker_model.DockerService property) (galaxy.containers.docker_model.DockerTask property) terminal_states (galaxy.containers.docker_model.DockerTask attribute) (galaxy.model.Dataset attribute) (galaxy.model.Job attribute) (galaxy.model.TransferJob attribute) test_0000_create_or_login_admin_user() (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository method) (tool_shed.test.functional.test_0070_invalid_tool.TestBismarkRepository method) (tool_shed.test.functional.test_1070_invalid_tool.TestFreebayesRepository method) (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies method) (tool_shed.test.functional.test_1100_install_updated_repository_dependencies.TestRepositoryDependencies method) test_0000_initiate_users() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) (tool_shed.test.functional.test_0020_basic_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies method) (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_0080_advanced_circular_dependencies.TestRepositoryCircularDependencies method) (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain method) (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies method) (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners.TestRepositoryMultipleOwners method) (tool_shed.test.functional.test_0130_datatype_converters.TestDatatypeConverters method) (tool_shed.test.functional.test_0140_tool_help_images.TestToolHelpImages method) (tool_shed.test.functional.test_0150_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_0160_circular_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_0170_complex_prior_installation_required.TestComplexPriorInstallation method) (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) (tool_shed.test.functional.test_0310_hg_api_features.TestHgWebFeatures method) (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) (tool_shed.test.functional.test_0410_repository_component_review_access_control.TestRepositoryComponentReviews method) (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs method) (tool_shed.test.functional.test_0430_browse_utilities.TestToolShedBrowseUtilities method) (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole method) (tool_shed.test.functional.test_0540_get_all_metadata_from_api.TestGetAllMetadata method) (tool_shed.test.functional.test_0550_metadata_updated_dependencies.TestGetUpdatedMetadata method) (tool_shed.test.functional.test_1000_install_basic_repository.BasicToolShedFeatures method) (tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies.ToolWithToolDependencies method) (tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies.ToolWithRepositoryDependencies method) (tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions.RepositoryWithDependencyRevisions method) (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners method) (tool_shed.test.functional.test_1150_datatype_converters.TestDatatypeConverters method) (tool_shed.test.functional.test_1160_tool_help_images.TestToolHelpImages method) (tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1190_complex_prior_installation_required.TestComplexPriorInstallation method) (tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository.UninstallingAndReinstallingRepositories method) (tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies.UninstallingAndReinstallingRepositories method) (tool_shed.test.functional.test_1220_uninstall_reinstall_repository_with_repository_dependencies.UninstallingAndReinstallingRepositories method) (tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions.UninstallingAndReinstallingRepositories method) (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) (tool_shed.test.functional.test_1410_update_manager.TestUpdateManager method) (tool_shed.test.functional.test_1450_installing_datatypes_sniffers.TestInstallDatatypesSniffers method) (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository method) test_0000_initiate_users_and_category() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) (tool_shed.test.functional.test_0480_tool_dependency_xml_verification.TestDependencyDefinitionValidation method) (tool_shed.test.functional.test_1420_tool_dependency_environment_inheritance.TestEnvironmentInheritance method) (tool_shed.test.functional.test_1430_repair_installed_repository.TestRepairRepository method) (tool_shed.test.functional.test_1440_missing_env_sh_files.TestMissingEnvSh method) (tool_shed.test.functional.test_1460_data_managers.TestDataManagers method) test_0005_create_and_populate_column_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies method) (tool_shed.test.functional.test_1100_install_updated_repository_dependencies.TestRepositoryDependencies method) test_0005_create_bed_to_gff_repository() (tool_shed.test.functional.test_0130_datatype_converters.TestDatatypeConverters method) (tool_shed.test.functional.test_1150_datatype_converters.TestDatatypeConverters method) test_0005_create_bwa_base_repository() (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain method) test_0005_create_bwa_package_repository() (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies method) (tool_shed.test.functional.test_0540_get_all_metadata_from_api.TestGetAllMetadata method) (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0005_create_categories() (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) test_0005_create_category() (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository method) (tool_shed.test.functional.test_0020_basic_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies method) (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies method) test_0005_create_category_and_repository() (tool_shed.test.functional.test_0070_invalid_tool.TestBismarkRepository method) test_0005_create_column_maker_repository() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0005_create_column_repository() (tool_shed.test.functional.test_0080_advanced_circular_dependencies.TestRepositoryCircularDependencies method) test_0005_create_convert_repository() (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_0080_advanced_circular_dependencies.TestRepositoryCircularDependencies method) (tool_shed.test.functional.test_0150_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_0160_circular_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) (tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) test_0005_create_datatypes_repository() (tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners.TestRepositoryMultipleOwners method) (tool_shed.test.functional.test_0430_browse_utilities.TestToolShedBrowseUtilities method) (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners method) test_0005_create_filter_repository() (tool_shed.test.functional.test_1430_repair_installed_repository.TestRepairRepository method) test_0005_create_filtering_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) (tool_shed.test.functional.test_0310_hg_api_features.TestHgWebFeatures method) (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole method) (tool_shed.test.functional.test_1410_update_manager.TestUpdateManager method) (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository method) test_0005_create_freebayes_repository() (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies method) test_0005_create_htseq_count_repository() (tool_shed.test.functional.test_0140_tool_help_images.TestToolHelpImages method) (tool_shed.test.functional.test_1160_tool_help_images.TestToolHelpImages method) test_0005_create_lapack_repository() (tool_shed.test.functional.test_1420_tool_dependency_environment_inheritance.TestEnvironmentInheritance method) test_0005_create_libx11_repository() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) test_0005_create_matplotlib_repository() (tool_shed.test.functional.test_0170_complex_prior_installation_required.TestComplexPriorInstallation method) (tool_shed.test.functional.test_1190_complex_prior_installation_required.TestComplexPriorInstallation method) test_0005_create_package_repository() (tool_shed.test.functional.test_1440_missing_env_sh_files.TestMissingEnvSh method) test_0005_create_repository() (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs method) test_0005_create_repository_without_categories() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0005_create_tool_dependency_repository() (tool_shed.test.functional.test_0480_tool_dependency_xml_verification.TestDependencyDefinitionValidation method) test_0005_ensure_existence_of_repository_and_category() (tool_shed.test.functional.test_1070_invalid_tool.TestFreebayesRepository method) test_0005_ensure_repositories_and_categories_exist() (tool_shed.test.functional.test_1000_install_basic_repository.BasicToolShedFeatures method) (tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies.ToolWithToolDependencies method) (tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies.ToolWithRepositoryDependencies method) (tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions.RepositoryWithDependencyRevisions method) (tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository.UninstallingAndReinstallingRepositories method) (tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies.UninstallingAndReinstallingRepositories method) (tool_shed.test.functional.test_1220_uninstall_reinstall_repository_with_repository_dependencies.UninstallingAndReinstallingRepositories method) (tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions.UninstallingAndReinstallingRepositories method) (tool_shed.test.functional.test_1450_installing_datatypes_sniffers.TestInstallDatatypesSniffers method) test_0005_freebayes_repository() (tool_shed.test.functional.test_0550_metadata_updated_dependencies.TestGetUpdatedMetadata method) test_0005_grant_reviewer_role() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) (tool_shed.test.functional.test_0410_repository_component_review_access_control.TestRepositoryComponentReviews method) test_0010_browse_tool_shed() (tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies.ToolWithToolDependencies method) (tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies.ToolWithRepositoryDependencies method) (tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions.RepositoryWithDependencyRevisions method) (tool_shed.test.functional.test_1070_invalid_tool.TestFreebayesRepository method) test_0010_browse_tool_sheds() (tool_shed.test.functional.test_1000_install_basic_repository.BasicToolShedFeatures method) test_0010_clone() (tool_shed.test.functional.test_0310_hg_api_features.TestHgWebFeatures method) test_0010_create_and_populate_convert_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies method) (tool_shed.test.functional.test_1100_install_updated_repository_dependencies.TestRepositoryDependencies method) test_0010_create_atlas_repository() (tool_shed.test.functional.test_1420_tool_dependency_environment_inheritance.TestEnvironmentInheritance method) test_0010_create_bwa_base_repository() (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies method) (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0010_create_bwa_color_repository() (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain method) test_0010_create_bwa_package_repository() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0010_create_categories() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0010_create_column_repository() (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_0150_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_0160_circular_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) (tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1430_repair_installed_repository.TestRepairRepository method) test_0010_create_convert_chars_repository() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0010_create_convert_repository() (tool_shed.test.functional.test_0540_get_all_metadata_from_api.TestGetAllMetadata method) test_0010_create_data_manager_repository() (tool_shed.test.functional.test_1460_data_managers.TestDataManagers method) test_0010_create_emboss_5_0_0_repository() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) test_0010_create_emboss_5_repository() (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) test_0010_create_emboss_datatypes_repository_and_upload_tarball() (tool_shed.test.functional.test_0020_basic_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies method) test_0010_create_emboss_repository() (tool_shed.test.functional.test_0430_browse_utilities.TestToolShedBrowseUtilities method) test_0010_create_filter_repository() (tool_shed.test.functional.test_1440_missing_env_sh_files.TestMissingEnvSh method) test_0010_create_freebayes_repository() (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies method) (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0010_create_freebayes_repository_and_upload_tool_xml() (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository method) test_0010_create_numpy_repository() (tool_shed.test.functional.test_0170_complex_prior_installation_required.TestComplexPriorInstallation method) (tool_shed.test.functional.test_1190_complex_prior_installation_required.TestComplexPriorInstallation method) test_0010_create_repositories_from_0000_series() (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) test_0010_create_samtools_repository() (tool_shed.test.functional.test_0550_metadata_updated_dependencies.TestGetUpdatedMetadata method) test_0010_install_datatype_converter_to_galaxy() (tool_shed.test.functional.test_1150_datatype_converters.TestDatatypeConverters method) test_0010_install_datatypes_repository() (tool_shed.test.functional.test_1450_installing_datatypes_sniffers.TestInstallDatatypesSniffers method) test_0010_install_emboss_repository() (tool_shed.test.functional.test_1220_uninstall_reinstall_repository_with_repository_dependencies.UninstallingAndReinstallingRepositories method) (tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions.UninstallingAndReinstallingRepositories method) test_0010_install_filtering_repository() (tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository.UninstallingAndReinstallingRepositories method) (tool_shed.test.functional.test_1410_update_manager.TestUpdateManager method) test_0010_install_filtering_to_galaxy() (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository method) test_0010_install_freebayes_repository() (tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies.UninstallingAndReinstallingRepositories method) test_0010_load_tool_page() (tool_shed.test.functional.test_0140_tool_help_images.TestToolHelpImages method) (tool_shed.test.functional.test_1160_tool_help_images.TestToolHelpImages method) test_0010_populate_tool_dependency_repository() (tool_shed.test.functional.test_0480_tool_dependency_xml_verification.TestDependencyDefinitionValidation method) test_0010_upload_new_file_to_repository() (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs method) test_0010_verify_datatypes_repository() (tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners.TestRepositoryMultipleOwners method) (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners method) test_0010_verify_repository_admin_role_exists() (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole method) test_0010_verify_repository_review_components() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) (tool_shed.test.functional.test_0410_repository_component_review_access_control.TestRepositoryComponentReviews method) test_0010_verify_tool_and_datatype() (tool_shed.test.functional.test_0130_datatype_converters.TestDatatypeConverters method) test_0015_browse_test_0000_category() (tool_shed.test.functional.test_1000_install_basic_repository.BasicToolShedFeatures method) test_0015_create_and_upload_dependency_files() (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies method) test_0015_create_bzlib_repository() (tool_shed.test.functional.test_1420_tool_dependency_environment_inheritance.TestEnvironmentInheritance method) test_0015_create_column_repository() (tool_shed.test.functional.test_0540_get_all_metadata_from_api.TestGetAllMetadata method) test_0015_create_complex_repository_dependency() (tool_shed.test.functional.test_0170_complex_prior_installation_required.TestComplexPriorInstallation method) (tool_shed.test.functional.test_1190_complex_prior_installation_required.TestComplexPriorInstallation method) test_0015_create_datatypes_0020_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0015_create_dependency_on_convert_chars() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0015_create_dependency_on_datatypes_repository() (tool_shed.test.functional.test_0430_browse_utilities.TestToolShedBrowseUtilities method) test_0015_create_emboss_5_repository() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) test_0015_create_emboss_6_repository() (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) test_0015_create_emboss_datatypes_repository() (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0015_create_filtering_repository() (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies method) (tool_shed.test.functional.test_0160_circular_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_0550_metadata_updated_dependencies.TestGetUpdatedMetadata method) (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies method) (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) test_0015_create_repositories_from_0010_series() (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) test_0015_create_repository() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) (tool_shed.test.functional.test_0410_repository_component_review_access_control.TestRepositoryComponentReviews method) test_0015_create_repository_dependency() (tool_shed.test.functional.test_0150_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1430_repair_installed_repository.TestRepairRepository method) test_0015_create_tool_dependency_repositories() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0015_create_tool_repository() (tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners.TestRepositoryMultipleOwners method) (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners method) test_0015_generate_complex_repository_dependency_invalid_shed_url() (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies method) (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0015_install_and_uninstall_column_repository() (tool_shed.test.functional.test_1100_install_updated_repository_dependencies.TestRepositoryDependencies method) test_0015_install_emboss_repository() (tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies.ToolWithRepositoryDependencies method) (tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions.RepositoryWithDependencyRevisions method) test_0015_install_filter_repository() (tool_shed.test.functional.test_1440_missing_env_sh_files.TestMissingEnvSh method) test_0015_install_freebayes_repository() (tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies.ToolWithToolDependencies method) (tool_shed.test.functional.test_1070_invalid_tool.TestFreebayesRepository method) test_0015_load_user_view_page() (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs method) test_0015_uninstall_and_verify_tool_panel_section() (tool_shed.test.functional.test_1150_datatype_converters.TestDatatypeConverters method) test_0015_uninstall_emboss_repository() (tool_shed.test.functional.test_1220_uninstall_reinstall_repository_with_repository_dependencies.UninstallingAndReinstallingRepositories method) (tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions.UninstallingAndReinstallingRepositories method) test_0015_uninstall_filtering_repository() (tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository.UninstallingAndReinstallingRepositories method) test_0015_uninstall_freebayes_repository() (tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies.UninstallingAndReinstallingRepositories method) test_0015_update_repository() (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository method) test_0015_upload_dependency_xml_if_needed() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0015_upload_missing_tool_data_table_conf_file() (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository method) test_0015_upload_readme_file() (tool_shed.test.functional.test_1410_update_manager.TestUpdateManager method) test_0015_verify_datatypes_count() (tool_shed.test.functional.test_1450_installing_datatypes_sniffers.TestInstallDatatypesSniffers method) test_0015_verify_datatypes_in_datatypes_repository() (tool_shed.test.functional.test_0020_basic_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies method) test_0015_verify_repository_role_association() (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole method) test_0015_verify_tool_panel_display() (tool_shed.test.functional.test_0130_datatype_converters.TestDatatypeConverters method) test_0020_check_for_displayed_update() (tool_shed.test.functional.test_1410_update_manager.TestUpdateManager method) test_0020_check_repository_dependency() (tool_shed.test.functional.test_0550_metadata_updated_dependencies.TestGetUpdatedMetadata method) test_0020_create_boost_repository() (tool_shed.test.functional.test_1420_tool_dependency_environment_inheritance.TestEnvironmentInheritance method) test_0020_create_dependency_on_freebayes() (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies method) test_0020_create_emboss_0020_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0020_create_emboss_5_repository_and_upload_files() (tool_shed.test.functional.test_0020_basic_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies method) test_0020_create_emboss_datatypes_repository() (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) test_0020_create_emboss_repository() (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0020_create_repositories_from_0020_series() (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) test_0020_create_repository_dependencies() (tool_shed.test.functional.test_0080_advanced_circular_dependencies.TestRepositoryCircularDependencies method) (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies method) test_0020_create_repository_dependency() (tool_shed.test.functional.test_0160_circular_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_0540_get_all_metadata_from_api.TestGetAllMetadata method) (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) test_0020_create_tool_dependency_repository() (tool_shed.test.functional.test_0430_browse_utilities.TestToolShedBrowseUtilities method) test_0020_deactivate_datatypes_repository() (tool_shed.test.functional.test_1450_installing_datatypes_sniffers.TestInstallDatatypesSniffers method) test_0020_edit_repository() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0020_generate_complex_repository_dependency_invalid_repository_name() (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies method) (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0020_get_repository_updates() (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository method) test_0020_install_column_repository() (tool_shed.test.functional.test_1430_repair_installed_repository.TestRepairRepository method) test_0020_install_convert_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0020_install_data_manager_repository() (tool_shed.test.functional.test_1460_data_managers.TestDataManagers method) test_0020_install_repositories() (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies method) test_0020_load_repository_view_page() (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs method) test_0020_populate_complex_dependency_test_1_0460() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0020_preview_filtering_repository() (tool_shed.test.functional.test_1000_install_basic_repository.BasicToolShedFeatures method) test_0020_reinstall_emboss_repository() (tool_shed.test.functional.test_1220_uninstall_reinstall_repository_with_repository_dependencies.UninstallingAndReinstallingRepositories method) (tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions.UninstallingAndReinstallingRepositories method) test_0020_reinstall_filtering_repository() (tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository.UninstallingAndReinstallingRepositories method) test_0020_reinstall_freebayes_repository() (tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies.UninstallingAndReinstallingRepositories method) test_0020_rename_repository() (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole method) test_0020_review_initial_revision_data_types() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0020_review_repository() (tool_shed.test.functional.test_0410_repository_component_review_access_control.TestRepositoryComponentReviews method) test_0020_upload_dependency_xml() (tool_shed.test.functional.test_1100_install_updated_repository_dependencies.TestRepositoryDependencies method) test_0020_upload_missing_sample_loc_file() (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository method) test_0020_upload_updated_tool_dependency_to_package_x11() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) test_0020_verify_dependency_metadata() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0020_verify_generated_dependency() (tool_shed.test.functional.test_0170_complex_prior_installation_required.TestComplexPriorInstallation method) (tool_shed.test.functional.test_1190_complex_prior_installation_required.TestComplexPriorInstallation method) test_0020_verify_installed_repository_metadata() (tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies.ToolWithToolDependencies method) (tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies.ToolWithRepositoryDependencies method) test_0020_verify_missing_tool_dependency() (tool_shed.test.functional.test_1440_missing_env_sh_files.TestMissingEnvSh method) test_0020_verify_repository_dependency() (tool_shed.test.functional.test_0150_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation method) test_0020_verify_tool_repository() (tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners.TestRepositoryMultipleOwners method) (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners method) test_0025_browse_custom_datatypes() (tool_shed.test.functional.test_0430_browse_utilities.TestToolShedBrowseUtilities method) test_0025_change_repository_category() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0025_check_admin_role_name() (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole method) test_0025_create_dependency_on_filtering() (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies method) (tool_shed.test.functional.test_0080_advanced_circular_dependencies.TestRepositoryCircularDependencies method) test_0025_create_emboss_datatypes_0030_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0025_create_emboss_repository() (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) test_0025_create_filtering_repository() (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0025_create_numpy_repository() (tool_shed.test.functional.test_1420_tool_dependency_environment_inheritance.TestEnvironmentInheritance method) test_0025_create_repositories_from_0030_series() (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) test_0025_create_repository_dependency() (tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners.TestRepositoryMultipleOwners method) (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners method) test_0025_deactivate_datatypes_repository() (tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies.ToolWithRepositoryDependencies method) test_0025_deactivate_emboss_repository() (tool_shed.test.functional.test_1220_uninstall_reinstall_repository_with_repository_dependencies.UninstallingAndReinstallingRepositories method) (tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions.UninstallingAndReinstallingRepositories method) test_0025_deactivate_filtering_repository() (tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository.UninstallingAndReinstallingRepositories method) test_0025_deactivate_freebayes_repository() (tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies.UninstallingAndReinstallingRepositories method) test_0025_delete_repository_dependency() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0025_generate_and_upload_repository_dependencies_xml() (tool_shed.test.functional.test_0020_basic_repository_dependencies.TestBasicRepositoryDependencies method) test_0025_generate_complex_repository_dependency_invalid_owner_name() (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies method) (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0025_generate_repository_dependency_with_invalid_url() (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies method) test_0025_install_column_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) (tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation method) test_0025_install_filtering_repository() (tool_shed.test.functional.test_1000_install_basic_repository.BasicToolShedFeatures method) test_0025_install_freebayes_repository() (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies method) test_0025_install_matplotlib_repository() (tool_shed.test.functional.test_1190_complex_prior_installation_required.TestComplexPriorInstallation method) test_0025_load_view_page_for_previous_revision() (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs method) test_0025_populate_complex_dependency_test_2_0460() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0025_reactivate_datatypes_repository() (tool_shed.test.functional.test_1450_installing_datatypes_sniffers.TestInstallDatatypesSniffers method) test_0025_uninstall_column_repository() (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies method) test_0025_uninstall_filter_repository() (tool_shed.test.functional.test_1430_repair_installed_repository.TestRepairRepository method) test_0025_uninstall_repository() (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository method) test_0025_update_dependent_repositories() (tool_shed.test.functional.test_0550_metadata_updated_dependencies.TestGetUpdatedMetadata method) test_0025_upload_malformed_tool_dependency_xml() (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository method) test_0025_upload_updated_tool_dependency_to_package_emboss() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) test_0025_verify_datatype_review() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0025_verify_dependency_json() (tool_shed.test.functional.test_0540_get_all_metadata_from_api.TestGetAllMetadata method) test_0025_verify_installed_repository_metadata() (tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions.RepositoryWithDependencyRevisions method) test_0025_verify_repository_dependency() (tool_shed.test.functional.test_0160_circular_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1100_install_updated_repository_dependencies.TestRepositoryDependencies method) (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) test_0025_verify_repository_review() (tool_shed.test.functional.test_0410_repository_component_review_access_control.TestRepositoryComponentReviews method) test_0025_verify_sample_files() (tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies.ToolWithToolDependencies method) test_0030_browse_tools() (tool_shed.test.functional.test_0430_browse_utilities.TestToolShedBrowseUtilities method) test_0030_browse_with_other_user() (tool_shed.test.functional.test_0410_repository_component_review_access_control.TestRepositoryComponentReviews method) test_0030_create_bwa_package_repository() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0030_create_emboss_5_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0030_create_freebayes_repository() (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0030_create_rdkit_repository() (tool_shed.test.functional.test_1420_tool_dependency_environment_inheritance.TestEnvironmentInheritance method) test_0030_create_repositories_from_0040_series() (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) test_0030_deactivate_convert_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0030_generate_complex_repository_dependency_invalid_changeset_revision() (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies method) (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0030_generate_repository_dependencies_for_emboss_5() (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) test_0030_generate_repository_dependency_with_invalid_name() (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies method) test_0030_grant_write_access() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0030_install_filtering_repository() (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) test_0030_install_filtering_repository_again() (tool_shed.test.functional.test_1000_install_basic_repository.BasicToolShedFeatures method) test_0030_load_sharable_url_with_invalid_changeset_revision() (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs method) test_0030_populate_complex_dependency_test_3_0460() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0030_reactivate_datatypes_repository() (tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies.ToolWithRepositoryDependencies method) test_0030_reactivate_emboss_repository() (tool_shed.test.functional.test_1220_uninstall_reinstall_repository_with_repository_dependencies.UninstallingAndReinstallingRepositories method) (tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions.UninstallingAndReinstallingRepositories method) test_0030_reactivate_filtering_repository() (tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository.UninstallingAndReinstallingRepositories method) test_0030_reactivate_freebayes_repository() (tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies.UninstallingAndReinstallingRepositories method) test_0030_reinstall_column_repository() (tool_shed.test.functional.test_1100_install_updated_repository_dependencies.TestRepositoryDependencies method) test_0030_reinstall_repository() (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository method) test_0030_review_initial_revision_functional_tests() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0030_uninstall_convert_repository() (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies method) test_0030_uninstall_datatypes_repository() (tool_shed.test.functional.test_1450_installing_datatypes_sniffers.TestInstallDatatypesSniffers method) test_0030_uninstall_filtering_repository() (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies method) test_0030_upload_invalid_tool_dependency_xml() (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository method) test_0030_upload_updated_tool_dependency_to_emboss_5_repository() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) test_0030_verify_access_denied() (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole method) test_0030_verify_data_manager_tool() (tool_shed.test.functional.test_1460_data_managers.TestDataManagers method) test_0030_verify_emboss_5_dependencies() (tool_shed.test.functional.test_0020_basic_repository_dependencies.TestBasicRepositoryDependencies method) test_0030_verify_installation_order() (tool_shed.test.functional.test_1170_prior_installation_required.TestSimplePriorInstallation method) (tool_shed.test.functional.test_1190_complex_prior_installation_required.TestComplexPriorInstallation method) test_0030_verify_repository_dependencies() (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies method) (tool_shed.test.functional.test_0080_advanced_circular_dependencies.TestRepositoryCircularDependencies method) test_0035_browse_repository_dependencies() (tool_shed.test.functional.test_0430_browse_utilities.TestToolShedBrowseUtilities method) test_0035_create_and_upload_dependency_definitions() (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain method) test_0035_create_bismark_repository() (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0035_create_bwa_base_repository() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0035_create_emboss_6_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0035_create_repositories_for_url_upload() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0035_create_repositories_from_0050_series() (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) test_0035_create_repositories_from_0060_series() (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) test_0035_generate_complex_repository_dependency() (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies method) test_0035_generate_repository_dependencies_for_emboss_6() (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) test_0035_generate_repository_dependency_with_invalid_owner() (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies method) test_0035_generate_valid_complex_repository_dependency() (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0035_grant_admin_role() (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole method) test_0035_grant_write_access_to_other_user() (tool_shed.test.functional.test_0410_repository_component_review_access_control.TestRepositoryComponentReviews method) test_0035_install_rdkit_2012_12_repository() (tool_shed.test.functional.test_1420_tool_dependency_environment_inheritance.TestEnvironmentInheritance method) test_0035_load_sharable_url_with_invalid_repository_name() (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs method) test_0035_modify_package_x11_repository_type() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) test_0035_reactivate_convert_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0035_reactivate_filtering_repository() (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies method) test_0035_reinstall_column_repository() (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies method) test_0035_reinstall_datatypes_repository() (tool_shed.test.functional.test_1450_installing_datatypes_sniffers.TestInstallDatatypesSniffers method) test_0035_upload_filtering_1_1_0() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0035_upload_valid_tool_dependency_xml() (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository method) test_0035_verify_absence_of_ghosts() (tool_shed.test.functional.test_1470_updating_installed_repositories.TestUpdateInstalledRepository method) test_0035_verify_functional_test_review() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0035_verify_installation_order() (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) test_0035_verify_installed_repository_metadata() (tool_shed.test.functional.test_1000_install_basic_repository.BasicToolShedFeatures method) test_0035_verify_repository_metadata() (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies method) (tool_shed.test.functional.test_0080_advanced_circular_dependencies.TestRepositoryCircularDependencies method) test_0040_browse_tool_dependencies() (tool_shed.test.functional.test_0430_browse_utilities.TestToolShedBrowseUtilities method) test_0040_create_and_upload_dependency_definitions() (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0040_create_dependency_on_bwa_package_repository() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0040_create_emboss_0030_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0040_deactivate_all_repositories() (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) test_0040_deactivate_column_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0040_generate_repository_dependency_on_emboss_5() (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) test_0040_generate_repository_dependency_with_invalid_changeset_revision() (tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies.TestBasicRepositoryDependencies method) (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies method) test_0040_generate_tool_dependency() (tool_shed.test.functional.test_0100_complex_repository_dependencies.TestComplexRepositoryDependencies method) test_0040_load_sharable_url_with_invalid_owner() (tool_shed.test.functional.test_0420_citable_urls_for_repositories.TestRepositoryCitableURLs method) test_0040_modify_package_emboss_repository_type() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) test_0040_reinstall_convert_repository() (tool_shed.test.functional.test_1090_repository_dependency_handling.TestRepositoryDependencies method) test_0040_rename_repository_as_repository_admin() (tool_shed.test.functional.test_0530_repository_admin_feature.TestRepositoryAdminRole method) test_0040_review_readme() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0040_uninstall_freebayes_repository() (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies method) test_0040_update_tool_repository() (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0040_url_upload_to_complex_test() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0040_verify_data_manager_data_table() (tool_shed.test.functional.test_1460_data_managers.TestDataManagers method) test_0040_verify_env_sh_contents() (tool_shed.test.functional.test_1420_tool_dependency_environment_inheritance.TestEnvironmentInheritance method) test_0040_verify_repository() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0040_verify_repository_dependencies() (tool_shed.test.functional.test_0090_tool_search.TestRepositoryCircularDependenciesAgain method) test_0040_verify_repository_dependency() (tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners.TestRepositoryMultipleOwners method) (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners method) test_0040_verify_repository_metadata() (tool_shed.test.functional.test_0020_basic_repository_dependencies.TestBasicRepositoryDependencies method) test_0040_verify_test_user_3_can_browse_reviews() (tool_shed.test.functional.test_0410_repository_component_review_access_control.TestRepositoryComponentReviews method) test_0040_verify_tool_dependencies() (tool_shed.test.functional.test_0010_repository_with_tool_dependencies.TestFreebayesRepository method) (tool_shed.test.functional.test_0040_repository_circular_dependencies.TestRepositoryCircularDependencies method) test_0045_alter_repository_states() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0045_create_repository_dependencies_for_0030() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0045_deactivate_convert_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0045_deactivate_filtering_repository() (tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies.TestInstallingCircularDependencies method) test_0045_generate_repository_dependency_on_emboss_6() (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) test_0045_install_base_repository() (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0045_install_blastxml_to_top_descr() (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners method) test_0045_install_repository_with_invalid_repository_dependency() (tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency.TestBasicRepositoryDependencies method) test_0045_reactivate_filter_repository() (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) test_0045_reset_repository_metadata() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) test_0045_url_upload_to_complex_test() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0045_verify_browse_review_with_write_access() (tool_shed.test.functional.test_0410_repository_component_review_access_control.TestRepositoryComponentReviews method) test_0045_verify_dependency_metadata() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0045_verify_readme_review() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0045_verify_repository_dependencies() (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0050_create_freebayes_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0050_create_repositories_for_simple_dependencies() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0050_delete_complex_repository_dependency() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0050_display_repository_tip_file() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0050_reactivate_column_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0050_reset_emboss_5_metadata() (tool_shed.test.functional.test_0470_tool_dependency_repository_type.TestEnvironmentInheritance method) test_0050_review_repository_dependencies() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0050_verify_installed_repositories() (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0050_verify_reinstallation_order() (tool_shed.test.functional.test_1180_circular_prior_installation_required.TestSimplePriorInstallation method) test_0050_verify_repository_dependency_revisions() (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) test_0050_verify_repository_installation() (tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners.TestInstallRepositoryMultipleOwners method) test_0050_verify_tool_dependencies() (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0055_create_bwa_tool_dependency_repository() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0055_create_filtering_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0055_install_column_repository() (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0055_populate_repository_dependency_test_1_0460() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0055_reactivate_convert_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0055_upload_filtering_txt_file() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0055_verify_complex_tool_dependency() (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0055_verify_repository_dependency_review() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0055_verify_repository_metadata() (tool_shed.test.functional.test_0030_repository_dependency_revisions.TestRepositoryDependencyRevisions method) (tool_shed.test.functional.test_0050_circular_dependencies_4_levels.TestRepositoryCircularDependenciesToNLevels method) test_0060_create_dependency_structure() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0060_delete_bwa_tool_dependency_definition() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0060_install_emboss_repository() (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0060_populate_repository_dependency_test_2_0460() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0060_review_tool_dependencies() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0060_uninstall_column_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0060_upload_filtering_test_data() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0060_verify_tool_dependency_uninstallation() (tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies.TestInstallingComplexRepositoryDependencies method) test_0065_create_convert_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0065_deactivate_datatypes_repository() (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0065_populate_repository_dependency_test_3_0460() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0065_reinstall_column_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0065_reupload_bwa_tool_dependency_definition() (tool_shed.test.functional.test_0440_deleting_dependency_definitions.TestDeletedDependencies method) test_0065_upload_filtering_2_2_0() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0065_verify_tool_dependency_review() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0070_create_column_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0070_create_repositories_for_url_upload() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0070_review_tools() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0070_uninstall_convert_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0070_uninstall_emboss_repository() (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0070_verify_filtering_repository() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0075_create_emboss_datatypes_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0075_install_freebayes_repository() (tool_shed.test.functional.test_1050_circular_dependencies_4_levels.TestInstallRepositoryCircularDependencies method) test_0075_uninstall_column_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0075_upload_readme_txt_file() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0075_url_upload_to_complex_test() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0075_verify_tools_review() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0080_create_emboss_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0080_delete_readme_txt_file() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0080_reinstall_convert_repository() (tool_shed.test.functional.test_1080_advanced_circular_dependency_installation.TestRepositoryDependencies method) test_0080_review_workflows() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0080_url_upload_to_complex_test() (tool_shed.test.functional.test_0460_upload_to_repository.TestAutomaticDependencyRevision method) test_0085_create_filtering_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0085_search_for_valid_filter_tool() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0085_verify_workflows_review() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0090_create_freebayes_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0090_upload_readme_file() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0090_verify_repository_metadata() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0095_create_bismark_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0095_review_new_changeset_readme_component() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0095_verify_reserved_repository_name_handling() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0100_create_and_upload_dependency_definitions() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0100_verify_readme_review() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0100_verify_reserved_username_handling() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0105_contact_repository_owner() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0105_create_filtering_repository() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0105_upload_test_data() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0110_delete_filtering_repository() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0110_reset_metadata_on_all_repositories() (tool_shed.test.functional.test_0300_reset_all_metadata.TestResetAllRepositoryMetadata method) test_0110_review_new_changeset_functional_tests() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0115_undelete_filtering_repository() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0115_verify_functional_tests_review() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0120_enable_email_notifications() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0120_upload_new_tool_version() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0125_review_new_changeset_functional_tests() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0125_upload_new_readme_file() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0130_verify_handling_of_invalid_characters() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0135_api_get_repositories_in_category() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_0135_verify_review_for_new_version() (tool_shed.test.functional.test_0400_repository_component_reviews.TestRepositoryComponentReviews method) test_0140_view_invalid_changeset() (tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures method) test_400_on_delete_invalid_page_id() (galaxy_test.api.test_pages.PageApiTestCase method) test_400_on_invalid_embedded_content() (galaxy_test.api.test_pages.PageApiTestCase method) test_400_on_invalid_id_encoding() (galaxy_test.api.test_pages.PageApiTestCase method) test_400_on_invalid_id_encoding_markdown() (galaxy_test.api.test_pages.PageApiTestCase method) test_400_on_invalid_markdown_call() (galaxy_test.api.test_pages.PageApiTestCase method) test_400_on_invalid_workflow_id() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_403_if_create_revision_on_unowned_page() (galaxy_test.api.test_page_revisions.PageRevisionsApiTestCase method) test_403_on_delete_unowned_page() (galaxy_test.api.test_pages.PageApiTestCase method) test_403_on_unowner_show() (galaxy_test.api.test_pages.PageApiTestCase method) test_404_on_unknown_license() (galaxy_test.api.test_licenses.LicensesApiTestCase method) test_404_route() (galaxy_test.api.test_api_batch.ApiBatchTestCase method) test_9900_install_all_missing_repositories() (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) test_9905_reset_metadata_on_all_repositories() (tool_shed.test.functional.test_1300_reset_all_metadata.TestResetInstalledRepositoryMetadata method) test_admin_data_manager() (galaxy_test.selenium.test_admin_app.AdminAppTestCase method) test_admin_dependencies_display() (galaxy_test.selenium.test_admin_app.AdminAppTestCase method) test_admin_jobs_display() (galaxy_test.selenium.test_admin_app.AdminAppTestCase method) test_admin_only() (galaxy_test.api.test_tool_data.ToolDataApiTestCase method) test_admin_server_display() (galaxy_test.selenium.test_admin_app.AdminAppTestCase method) test_admin_toolshed() (galaxy_test.selenium.test_admin_app.AdminAppTestCase method) test_admin_update() (galaxy_test.api.test_users.UsersApiTestCase method) test_admin_user_configuration() (galaxy_test.api.test_configuration.ConfigurationApiTestCase method) test_admin_user_display() (galaxy_test.selenium.test_admin_app.AdminAppTestCase method) test_advanced_search() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) test_anon_can_download_public_workflow() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_anon_history_after_registration() (galaxy_test.selenium.test_anon_history.AnonymousHistoriesTestCase method) test_anon_history_landing() (galaxy_test.selenium.test_anon_history.AnonymousHistoriesTestCase method) test_anon_history_upload() (galaxy_test.selenium.test_anon_history.AnonymousHistoriesTestCase method) test_anonymous_published() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_api_key() (galaxy_test.selenium.test_personal_information.ManageInformationTestCase method) test_apply_rules_1() (galaxy_test.api.test_tools.ToolsTestCase method) test_apply_rules_2() (galaxy_test.api.test_tools.ToolsTestCase method) test_apply_rules_3() (galaxy_test.api.test_tools.ToolsTestCase method) test_apply_rules_4() (galaxy_test.api.test_tools.ToolsTestCase method) test_apply_rules_5() (galaxy_test.api.test_tools.ToolsTestCase method) test_apply_rules_6() (galaxy_test.api.test_tools.ToolsTestCase method) test_assign_column_pja() (galaxy_test.api.test_workflows.ChangeDatatypeTestCase method) test_auth() (galaxy_test.api.test_authenticate.AuthenticationApiTestCase method) test_bad_emails() (galaxy_test.selenium.test_registration.RegistrationTestCase method) test_bad_usernames() (galaxy_test.selenium.test_registration.RegistrationTestCase method) test_bam_state_regression() (galaxy_test.api.test_tools.ToolsTestCase method) test_basics() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_bibtex_rendering() (galaxy_test.selenium.test_tool_form.ToolFormTestCase method) test_build_add() (galaxy_test.selenium.test_custom_builds.CustomBuildsTestcase method) test_build_delete() (galaxy_test.selenium.test_custom_builds.CustomBuildsTestcase method) test_build_list_and_show_items() (galaxy_test.selenium.test_collection_builders.CollectionBuildersTestCase method) test_build_list_simple_hidden() (galaxy_test.selenium.test_collection_builders.CollectionBuildersTestCase method) test_build_pair_simple_hidden() (galaxy_test.selenium.test_collection_builders.CollectionBuildersTestCase method) test_build_paired_list_show_original() (galaxy_test.selenium.test_collection_builders.CollectionBuildersTestCase method) test_build_paired_list_simple() (galaxy_test.selenium.test_collection_builders.CollectionBuildersTestCase method) test_build_simple_list_via_rules_hidden() (galaxy_test.selenium.test_collection_builders.CollectionBuildersTestCase method) test_cancel_new_workflow_when_history_deleted() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_cancel_ready_workflow_when_history_deleted() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_cancel_workflow_invocation() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_cannot_create_page_with_invalid_content_format() (galaxy_test.api.test_pages.PageApiTestCase method) test_cannot_create_pages_with_same_slug() (galaxy_test.api.test_pages.PageApiTestCase method) test_cannot_download_private_workflow() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_cannot_map_over_incompatible_collections() (galaxy_test.api.test_tools.ToolsTestCase method) test_cannot_run_against_other_users_history() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_cannot_run_inaccessible_workflow() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_cannot_show_private_workflow() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_change_datatype_collection_map_over() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_change_email() (galaxy_test.selenium.test_personal_information.ManageInformationTestCase method) test_change_password() (galaxy_test.selenium.test_change_password.ChangePasswordTestCase method) test_clean_anon_history_after_logout() (galaxy_test.selenium.test_anon_history.AnonymousHistoriesTestCase method) test_click_error() (galaxy_test.selenium.test_navigates_galaxy.NavigatesGalaxySeleniumTestCase method) test_collection_contents_invalid_collection() (galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase method) test_collection_contents_limit_offset() (galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase method) test_collection_contents_security() (galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase method) test_collection_input() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_collection_operation_collection_input_permissions() (galaxy_test.api.test_tools.ToolsTestCase method) test_collection_operation_dataset_input_permissions() (galaxy_test.api.test_tools.ToolsTestCase method) test_collection_operations() (galaxy_test.selenium.test_history_panel_collections.HistoryPanelCollectionsTestCase method) test_collection_parameter() (galaxy_test.api.test_tools.ToolsTestCase method) test_column_legal_values() (galaxy_test.api.test_tools.ToolsTestCase method) test_combined_mapping_and_subcollection_mapping() (galaxy_test.api.test_tools.ToolsTestCase method) test_comma_separated_columns() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_common_problems() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_composite_datatype() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_composite_datatype_fetch() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_composite_datatype_isatab() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_composite_datatype_posix_lines() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_composite_datatype_space_to_tab() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_composite_datatype_stage_fetch() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_composite_datatype_stage_upload1() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_conditional_ints() (galaxy_test.api.test_workflows_from_yaml.WorkflowsFromYamlApiTestCase method) test_converter_present_after_toolbox_reload() (galaxy_test.api.test_datatypes.DatatypesApiTestCase method) test_converters() (galaxy_test.api.test_datatypes.DatatypesApiTestCase method) test_copy_hdca() (galaxy_test.selenium.test_history_copy_elements.HistoryCopyElementsTestCase method) test_copy_history() (galaxy_test.selenium.test_history_multi_view.HistoryMultiViewTestCase method) test_core_galaxy_ui() (galaxy_test.selenium.test_stock_tours.TestStockToursTestCase method) test_core_history() (galaxy_test.selenium.test_stock_tours.TestStockToursTestCase method) test_core_scratchbook() (galaxy_test.selenium.test_stock_tours.TestStockToursTestCase method) test_create() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) (galaxy_test.api.test_page_revisions.PageRevisionsApiTestCase method) (galaxy_test.api.test_pages.PageApiTestCase method) (galaxy_test.api.test_visualizations.VisualizationsApiTestCase method) test_create_anonymous_fails() (galaxy_test.api.test_histories.HistoriesApiTestCase method) test_create_api_key() (galaxy_test.api.test_users.UsersApiTestCase method) test_create_dataset() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_create_dataset_denied() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_create_dataset_in_folder() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_create_dataset_in_subfolder() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_create_datasets_in_folder_from_collection() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_create_datasets_in_library_from_collection() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_create_fails_with_bad_slug() (galaxy_test.api.test_visualizations.VisualizationsApiTestCase method) test_create_fails_with_invalid_config() (galaxy_test.api.test_visualizations.VisualizationsApiTestCase method) test_create_fails_without_title() (galaxy_test.api.test_visualizations.VisualizationsApiTestCase method) test_create_from_report() (galaxy_test.api.test_pages.PageApiTestCase method) test_create_history() (galaxy_test.api.test_histories.HistoriesApiTestCase method) test_create_invalid_params() (galaxy_test.api.test_roles.RolesApiTestCase method) test_create_list_from_history() (galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase method) test_create_list_of_existing_pairs() (galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase method) test_create_list_of_new_pairs() (galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase method) test_create_new() (galaxy_test.selenium.test_library_landing.LibraryLandingTestCase method) test_create_new_close() (galaxy_test.selenium.test_library_landing.LibraryLandingTestCase method) test_create_new_old_slides_next() (galaxy_test.selenium.test_history_multi_view.HistoryMultiViewTestCase method) test_create_only_admin() (galaxy_test.api.test_roles.RolesApiTestCase method) test_create_pair_from_history() (galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase method) test_create_private_library_permissions() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_create_tag() (galaxy_test.api.test_histories.HistoriesApiTestCase method) test_create_valid() (galaxy_test.api.test_roles.RolesApiTestCase method) test_csv_fetch() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_csv_sniff_fetch() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_csv_upload() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_csv_upload_auto() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_currect_password_incorrect() (galaxy_test.selenium.test_change_password.ChangePasswordTestCase method) test_data() (galaxy.tool_util.verify.interactor.ToolTestDescription method) (galaxy.webapps.galaxy.api.tools.ToolsController method) test_data_column_input_editing() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_data_download() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) (galaxy.webapps.galaxy.api.tools.ToolsController method) test_data_input() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_data_iter() (in module galaxy.tool_util.verify.interactor) test_data_path() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) (galaxy.tools.Tool method) (galaxy.webapps.galaxy.api.tools.ToolsController method) test_data_source_ok_request() (galaxy_test.api.test_tools.ToolsTestCase method) test_data_source_sniff_fastqsanger() (galaxy_test.api.test_tools.ToolsTestCase method) test_data_sources_block_file_parameters() (galaxy_test.api.test_tools.ToolsTestCase method) test_data_table_requirement_annotated() (galaxy_test.api.test_tools.ToolsTestCase method) test_dataset_change_dbkey() (galaxy_test.selenium.test_history_dataset_state.HistoryDatasetStateTestCase method) test_dataset_collection_create_from_exisiting_datasets_with_new_tags() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_dataset_collection_creation_on_contents() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_dataset_collection_creation_on_typed_contents() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_dataset_collection_hide_originals() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_dataset_state() (galaxy_test.selenium.test_history_dataset_state.HistoryDatasetStateTestCase method) test_dce_submission_security() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_default_identifier_source_map_over() (galaxy_test.api.test_tools.ToolsTestCase method) test_defaults_editor() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_delete() (galaxy_test.api.test_histories.HistoriesApiTestCase method) (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) (galaxy_test.api.test_libraries.LibrariesApiTestCase method) (galaxy_test.api.test_pages.PageApiTestCase method) (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_delete_and_undelete_history() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) test_delete_and_undelete_multiple_histories() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) test_delete_dataset() (galaxy_test.selenium.test_library_contents.LibraryContentsTestCase method) test_delete_history() (galaxy_test.selenium.test_history_multi_view.HistoryMultiViewTestCase method) test_delete_intermediate_datasets_pja_1() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_delete_user() (galaxy_test.api.test_users.UsersApiTestCase method) test_deleting_output_keep_running_until_all_deleted() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_detect_datatype_of_dataset_in_folder() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_display() (galaxy_test.api.test_datasets.DatasetsApiTestCase method) test_download() (galaxy_test.selenium.test_workflow_management.WorkflowManagementTestCase method) test_download_field_file() (galaxy_test.api.test_tool_data.ToolDataApiTestCase method) test_dynamic_list_output() (galaxy_test.api.test_tools.ToolsTestCase method) test_dynamic_list_output_datasets_in_failed_state() (galaxy_test.api.test_tools.ToolsTestCase method) test_dynamic_parameter_error_handling() (galaxy_test.api.test_tools.ToolsTestCase method) test_dynamic_tool_1() (galaxy_test.api.test_tools.ToolsTestCase method) test_dynamic_tool_from_path() (galaxy_test.api.test_tools.ToolsTestCase method) test_dynamic_tool_no_id() (galaxy_test.api.test_tools.ToolsTestCase method) test_edit_annotation() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_edit_name() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_editor_duplicate_node() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_editor_embed_workflow() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_editor_invalid_tool_state() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_editor_tool_upgrade() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_editor_tool_upgrade_message() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_empty_create() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_empty_file_data_column_specified() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_empty_list_mapping() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_empty_list_reduction() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_enforces_unique_names() (galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase method) test_error_outputs_with_purged_inputs() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_errors() (galaxy_test.api.test_api_batch.ApiBatchTestCase method) test_execution_with_custom_invocation_report() (galaxy_test.selenium.test_workflow_run.WorkflowRunTestCase method) test_execution_with_multiple_inputs() (galaxy_test.selenium.test_workflow_run.WorkflowRunTestCase method) test_execution_with_rules() (galaxy_test.selenium.test_workflow_run.WorkflowRunTestCase method) test_execution_with_tool_upgrade() (galaxy_test.selenium.test_workflow_run.WorkflowRunTestCase method) test_existing_connections() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_export() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_export_editor() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_export_editor_collection_type_source() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_export_editor_filtered_outputs() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_export_editor_filtered_outputs_exception_handling() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_export_editor_subworkflow_collection_type_source() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_export_format2() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_export_invocation_bco() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_expression_tool_map_over() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_extract_copied_mapping_from_history() (galaxy_test.api.test_workflow_extraction.WorkflowExtractionApiTestCase method) test_extract_copied_mapping_from_history_reimported() (galaxy_test.api.test_workflow_extraction.WorkflowExtractionApiTestCase method) test_extract_from_history() (galaxy_test.api.test_workflow_extraction.WorkflowExtractionApiTestCase method) test_extract_mapping_workflow_from_history() (galaxy_test.api.test_workflow_extraction.WorkflowExtractionApiTestCase method) test_extract_reduction_from_history() (galaxy_test.api.test_workflow_extraction.WorkflowExtractionApiTestCase method) test_extract_with_copied_inputs() (galaxy_test.api.test_workflow_extraction.WorkflowExtractionApiTestCase method) test_extract_with_copied_inputs_reimported() (galaxy_test.api.test_workflow_extraction.WorkflowExtractionApiTestCase method) test_extract_with_mapped_output_collections() (galaxy_test.api.test_workflow_extraction.WorkflowExtractionApiTestCase method) test_extract_workflow_with_output_collections() (galaxy_test.api.test_workflow_extraction.WorkflowExtractionApiTestCase method) test_extract_workflows_with_dataset_collections() (galaxy_test.api.test_workflow_extraction.WorkflowExtractionApiTestCase method) test_favorites() (galaxy_test.api.test_users.UsersApiTestCase method) test_fetch_bagit_archive_to_folder() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_fetch_bam_file() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_fetch_bam_file_from_url_with_extension_set() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_fetch_compressed_auto_decompress_target() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_fetch_compressed_default() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_fetch_compressed_with_auto() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_fetch_compressed_with_explicit_type() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_fetch_failed_validation() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_fetch_metadata() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_fetch_posix_unaltered() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_fetch_post_lines_option() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_fetch_post_lines_trailing_if_to_posix() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_fetch_post_lines_trailing_off_by_default() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_fetch_single_url_to_folder() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_fetch_single_url_with_invalid_datatype() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_fetch_tab_to_space() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_fetch_tab_to_space_off_by_default() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_fetch_upload_to_folder() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_fetch_url_archive_to_folder() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_fetch_zip_to_folder() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_files (galaxy.datatypes.genetics.LinkageStudies attribute) test_filter_failed_list() (galaxy_test.api.test_tools.ToolsTestCase method) test_filter_failed_list_paired() (galaxy_test.api.test_tools.ToolsTestCase method) test_filter_failed_mapping() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_full_index() (galaxy_test.api.test_datatypes.DatatypesApiTestCase method) test_galaxy_expression_metadata() (galaxy_test.api.test_tools.ToolsTestCase method) test_galaxy_expression_tool_simple() (galaxy_test.api.test_tools.ToolsTestCase method) test_galaxy_expression_tool_simplest() (galaxy_test.api.test_tools.ToolsTestCase method) test_generate_tour_no_data() (galaxy_test.selenium.test_tool_describing_tours.ToolDescribingToursTestCase method) test_generate_tour_with_data() (galaxy_test.selenium.test_tool_describing_tours.ToolDescribingToursTestCase method) test_get_all() (galaxy_test.api.test_webhooks.WebhooksApiTestCase method) test_get_data() (galaxy_test.api.test_webhooks.WebhooksApiTestCase method) test_get_license() (galaxy_test.api.test_licenses.LicensesApiTestCase method) test_get_tool_predictions() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_group_tag_selection() (galaxy_test.api.test_tools.ToolsTestCase method) test_group_tag_selection_multiple() (galaxy_test.api.test_tools.ToolsTestCase method) test_guess_derived_permissions() (galaxy_test.api.test_tools.ToolsTestCase method) test_guess_derived_permissions_collections() (galaxy_test.api.test_tools.ToolsTestCase method) test_hda_copy() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_hda_security() (galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase method) test_hdca_copy() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_hdca_copy_and_elements() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_hdca_from_inaccessible_library_datasets() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_hdca_from_library_datasets() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_hidden_param_in_workflow() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_histories_list() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) test_history() (galaxy_test.base.populators.BaseDatasetPopulator method) test_history_grid_histories() (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase method) test_history_grid_search_advanced() (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase method) test_history_grid_search_standard() (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase method) test_history_grid_sort_by_name() (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase method) test_history_grid_sort_by_owner() (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase method) test_history_grid_tag_click() (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase method) test_history_panel_annotations_change() (galaxy_test.selenium.test_history_panel.HistoryPanelTestCase method) test_history_panel_landing_state() (galaxy_test.selenium.test_history_panel.HistoryPanelTestCase method) test_history_panel_rename() (galaxy_test.selenium.test_history_panel.HistoryPanelTestCase method) test_history_panel_tags_change() (galaxy_test.selenium.test_history_panel.HistoryPanelTestCase method) test_history_publish() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) test_history_rename_cancel_with_escape() (galaxy_test.selenium.test_history_panel.HistoryPanelTestCase method) test_history_rename_confirm_with_click() (galaxy_test.selenium.test_history_panel.HistoryPanelTestCase method) test_history_structure() (galaxy_test.selenium.test_history_structure.HistoryStructureTestCase method) test_history_switch() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) test_history_tags_and_annotations_buttons() (galaxy_test.selenium.test_history_panel.HistoryPanelTestCase method) test_history_view() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) test_identifier_in_actions() (galaxy_test.api.test_tools.ToolsTestCase method) test_identifier_in_map() (galaxy_test.api.test_tools.ToolsTestCase method) test_identifier_in_multiple_reduce() (galaxy_test.api.test_tools.ToolsTestCase method) test_identifier_map_over_input_in_conditional() (galaxy_test.api.test_tools.ToolsTestCase method) test_identifier_map_over_multiple_input_in_conditional() (galaxy_test.api.test_tools.ToolsTestCase method) test_identifier_map_over_multiple_input_in_conditional_new_payload_form() (galaxy_test.api.test_tools.ToolsTestCase method) test_identifier_multiple_in_conditional() (galaxy_test.api.test_tools.ToolsTestCase method) test_identifier_multiple_reduce_in_conditional() (galaxy_test.api.test_tools.ToolsTestCase method) test_identifier_multiple_reduce_in_repeat() (galaxy_test.api.test_tools.ToolsTestCase method) test_identifier_multiple_reduce_in_repeat_new_payload_form() (galaxy_test.api.test_tools.ToolsTestCase method) test_identifier_outside_map() (galaxy_test.api.test_tools.ToolsTestCase method) test_identifier_single_in_repeat() (galaxy_test.api.test_tools.ToolsTestCase method) test_identifier_with_data_collection() (galaxy_test.api.test_tools.ToolsTestCase method) test_identifier_with_multiple_normal_datasets() (galaxy_test.api.test_tools.ToolsTestCase method) test_image_upload_auto() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_implicit_connections() (galaxy_test.api.test_workflows_from_yaml.WorkflowsFromYamlApiTestCase method) test_implicit_conversion_and_reduce() (galaxy_test.api.test_tools.ToolsTestCase method) test_implicit_conversion_and_reduce_invalid_param() (galaxy_test.api.test_tools.ToolsTestCase method) test_implicit_reduce_with_mapping() (galaxy_test.api.test_tools.ToolsTestCase method) test_import_1901_histories() (galaxy_test.api.test_histories.ImportExportHistoryTestCase method) test_import_annotations() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_import_dataset_from_history() (galaxy_test.selenium.test_library_contents.LibraryContentsTestCase method) test_import_dataset_from_path() (galaxy_test.selenium.test_library_contents.LibraryContentsTestCase method) test_import_deprecated() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_import_export() (galaxy_test.api.test_histories.ImportExportHistoryTestCase method) test_import_export_collection() (galaxy_test.api.test_histories.ImportExportHistoryTestCase method) test_import_export_dynamic() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_import_export_dynamic_tools() (galaxy_test.api.test_workflows.AdminWorkflowsApiTestCase method) test_import_export_failed_job() (galaxy_test.api.test_histories.ImportExportHistoryTestCase method) test_import_export_include_deleted() (galaxy_test.api.test_histories.ImportExportHistoryTestCase method) test_import_export_nested_collection() (galaxy_test.api.test_histories.ImportExportHistoryTestCase method) test_import_export_with_runtime_inputs() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_import_from_url() (galaxy_test.selenium.test_workflow_management.WorkflowManagementTestCase method) test_import_metadata_regeneration() (galaxy_test.api.test_histories.ImportExportHistoryTestCase method) test_import_missing_tool() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_import_no_tool_id() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_import_paired_collection() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_import_published() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_import_subworkflows() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_import_tools_requires_admin() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_index() (galaxy.tool_util.verify.script.TestReference property) (galaxy_test.api.test_datasets.DatasetsApiTestCase method) (galaxy_test.api.test_datatypes.DatatypesApiTestCase method) (galaxy_test.api.test_jobs.JobsApiTestCase method) (galaxy_test.api.test_licenses.LicensesApiTestCase method) (galaxy_test.api.test_pages.PageApiTestCase method) (galaxy_test.api.test_tools.ToolsTestCase method) (galaxy_test.api.test_tours.TourApiTestCase method) (galaxy_test.api.test_users.UsersApiTestCase method) (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_index_and_show() (galaxy_test.api.test_visualizations.VisualizationsApiTestCase method) test_index_date_filter() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_index_deleted() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_index_does_not_show_unavailable_pages() (galaxy_test.api.test_pages.PageApiTestCase method) test_index_hda_all_details() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_index_hda_detail_by_id() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_index_hda_summary() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_index_hidden() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_index_history() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_index_multiple_states_filter() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_index_only_self_for_nonadmins() (galaxy_test.api.test_users.UsersApiTestCase method) test_index_order() (galaxy_test.api.test_histories.HistoriesApiTestCase method) test_index_search() (galaxy_test.selenium.test_workflow_management.WorkflowManagementTestCase method) test_index_state_filter() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_index_upload_only() (galaxy_test.api.test_datatypes.DatatypesApiTestCase method) test_information() (galaxy_test.api.test_users.UsersApiTestCase method) test_inputs_to_steps() (galaxy_test.api.test_workflows_from_yaml.WorkflowsFromYamlApiTestCase method) test_integer_input() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_invalid_create_multiple_types() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_invalid_keys() (galaxy_test.api.test_histories.HistoriesApiTestCase method) test_invalid_logins() (galaxy_test.selenium.test_login.LoginTestCase method) test_invalid_passwords() (galaxy_test.selenium.test_login.LoginTestCase method) test_invalid_search() (galaxy_test.api.test_datasets.DatasetsApiTestCase method) test_invalid_update_dataset_in_folder() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_invocation_usage() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_invocation_with_collection_mapping() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_invocations_accessible_imported_workflow() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_invocations_accessible_published_workflow() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_invocations_not_accessible_by_different_user_for_published_workflow() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_job_build_for_rerun() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_job_build_for_rerun_list_list() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_job_state_summary_field() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_jobs_summary_implicit_hdca() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_jobs_summary_simple_hdca() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_jupyter_interaction() (galaxy_test.selenium.test_jupyter.JupyterTestCase method) test_jupyter_launch() (galaxy_test.selenium.test_jupyter.JupyterTestCase method) test_landing() (galaxy_test.selenium.test_registration.RegistrationTestCase method) test_ldda_collection_import_to_history() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_ldda_collection_import_to_history_hide_source() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_legacy_upload_unknown_datatype() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_library_copy() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_library_data_param() (galaxy_test.api.test_tools.ToolsTestCase method) test_limiting_collection_rendering() (galaxy_test.selenium.test_history_panel_collections.HistoryPanelCollectionsTestCase method) test_list() (galaxy_test.api.test_tool_data.ToolDataApiTestCase method) test_list_and_show() (galaxy_test.api.test_roles.RolesApiTestCase method) test_list_collection_output() (galaxy_test.api.test_tools.ToolsTestCase method) test_list_collection_output_format_source() (galaxy_test.api.test_tools.ToolsTestCase method) test_list_creation() (galaxy_test.selenium.test_library_to_collections.LibraryToCollectionsTestCase method) test_list_display() (galaxy_test.selenium.test_history_panel_collections.HistoryPanelCollectionsTestCase method) test_list_download() (galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase method) test_list_list_display() (galaxy_test.selenium.test_history_multi_view.HistoryMultiViewTestCase method) (galaxy_test.selenium.test_history_panel_collections.HistoryPanelCollectionsTestCase method) test_list_list_download() (galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase method) test_list_list_list_display() (galaxy_test.selenium.test_history_multi_view.HistoryMultiViewTestCase method) test_list_list_list_download() (galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase method) test_list_pair_download() (galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase method) test_list_paired_display() (galaxy_test.selenium.test_history_panel_collections.HistoryPanelCollectionsTestCase method) test_list_selectable_in_multidata_input() (galaxy_test.api.test_tools.ToolsTestCase method) test_local_test_data_download() (galaxy_test.api.test_galaxy_interactor.GalaxyInteractorBackwardCompatTestCase method) test_logging_in() (galaxy_test.selenium.test_login.LoginTestCase method) test_logout() (galaxy_test.selenium.test_registration.RegistrationTestCase method) test_make_private_and_public() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_malformed_id_if_index_unknown_page() (galaxy_test.api.test_page_revisions.PageRevisionsApiTestCase method) test_map_over_collected_and_individual_datasets() (galaxy_test.api.test_tools.ToolsTestCase method) test_map_over_collection() (galaxy_test.api.test_tools.ToolsTestCase method) test_map_over_collection_output() (galaxy_test.api.test_tools.ToolsTestCase method) test_map_over_collection_structured_like() (galaxy_test.api.test_tools.ToolsTestCase method) test_map_over_collection_type_source() (galaxy_test.api.test_tools.ToolsTestCase method) test_map_over_empty_collection() (galaxy_test.api.test_tools.ToolsTestCase method) test_map_over_nested_collections() (galaxy_test.api.test_tools.ToolsTestCase method) test_map_over_two_collections() (galaxy_test.api.test_tools.ToolsTestCase method) test_map_over_two_collections_unlinked() (galaxy_test.api.test_tools.ToolsTestCase method) test_map_over_with_complex_output_actions() (galaxy_test.api.test_tools.ToolsTestCase method) test_map_over_with_discovered_output_collection_elements() (galaxy_test.api.test_tools.ToolsTestCase method) test_map_over_with_nested_paired_output_format_actions() (galaxy_test.api.test_tools.ToolsTestCase method) test_map_over_with_output_filter_no_filtering() (galaxy_test.api.test_tools.ToolsTestCase method) test_map_over_with_output_filter_on_optional_input() (galaxy_test.api.test_tools.ToolsTestCase method) test_map_over_with_output_filter_one_filtered() (galaxy_test.api.test_tools.ToolsTestCase method) test_map_over_with_output_format_actions() (galaxy_test.api.test_tools.ToolsTestCase method) test_mapping() (galaxy_test.api.test_datatypes.DatatypesApiTestCase method) test_mapping_and_subcollection_mapping() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_mapping_collection_states_running() (galaxy_test.selenium.test_history_panel_collections.HistoryPanelCollectionsTestCase method) test_mapping_collection_states_terminal() (galaxy_test.selenium.test_history_panel_collections.HistoryPanelCollectionsTestCase method) test_missing_tools() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_multi_select_as_list() (galaxy_test.api.test_tools.ToolsTestCase method) test_multi_select_optional() (galaxy_test.api.test_tools.ToolsTestCase method) test_multidata_param() (galaxy_test.api.test_tools.ToolsTestCase method) test_multiple_files_posix_lines() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_multirun_cat1() (galaxy_test.api.test_tools.ToolsTestCase method) test_multirun_in_repeat() (galaxy_test.api.test_tools.ToolsTestCase method) test_multirun_in_repeat_mismatch() (galaxy_test.api.test_tools.ToolsTestCase method) test_multirun_non_data_parameter() (galaxy_test.api.test_tools.ToolsTestCase method) test_multirun_on_multiple_inputs() (galaxy_test.api.test_tools.ToolsTestCase method) test_multirun_on_multiple_inputs_unlinked() (galaxy_test.api.test_tools.ToolsTestCase method) test_name_tags_display() (galaxy_test.selenium.test_history_panel_collections.HistoryPanelCollectionsTestCase method) test_nested_workflow_rerun_with_use_cached_job() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_new_password_password() (galaxy_test.selenium.test_change_password.ChangePasswordTestCase method) test_new_password_same_password() (galaxy_test.selenium.test_change_password.ChangePasswordTestCase method) test_new_password_short() (galaxy_test.selenium.test_change_password.ChangePasswordTestCase method) test_newlines_stage_fetch() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_newlines_stage_fetch_configured() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_no_panel_index() (galaxy_test.api.test_tools.ToolsTestCase method) test_no_password_confirmation() (galaxy_test.selenium.test_change_password.ChangePasswordTestCase method) test_no_unhide_on_error_if_mapped_over() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_non_data_connections() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_nonadmin() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_nonadmin_users_cannot_create_tools() (galaxy_test.api.test_tools.ToolsTestCase method) test_normal_user_configuration() (galaxy_test.api.test_configuration.ConfigurationApiTestCase method) test_normal_user_decode_id() (galaxy_test.api.test_configuration.ConfigurationApiTestCase method) test_not_importable_prevents_import() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_only_own_invocations_indexed_and_accessible() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_optional_workflow_output() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_options() (galaxy_test.selenium.test_history_options.HistoryOptionsTestCase method) test_other_cannot_delete() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_output_collection_states_running() (galaxy_test.selenium.test_history_panel_collections.HistoryPanelCollectionsTestCase method) test_output_collection_states_terminal() (galaxy_test.selenium.test_history_panel_collections.HistoryPanelCollectionsTestCase method) test_outputs() (galaxy_test.api.test_workflows_from_yaml.WorkflowsFromYamlApiTestCase method) test_page_requires_name() (galaxy_test.api.test_pages.PageApiTestCase method) test_page_requires_slug() (galaxy_test.api.test_pages.PageApiTestCase method) test_pagination() (galaxy_test.selenium.test_history_panel_pagination.HistoryPanelPaginationTestCase method) test_pair_download() (galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase method) test_paired_collection_output() (galaxy_test.api.test_tools.ToolsTestCase method) test_paired_display() (galaxy_test.selenium.test_history_panel_collections.HistoryPanelCollectionsTestCase method) test_paired_input_conditional_map_over_nested_collections() (galaxy_test.api.test_tools.ToolsTestCase method) test_paired_input_map_over_nested_collections() (galaxy_test.api.test_tools.ToolsTestCase method) test_parameter_default_rep() (galaxy_test.api.test_workflows_from_yaml.WorkflowsFromYamlApiTestCase method) test_parameter_substitution_sanitization() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_parameter_substitution_validation_value_errors_0() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_parameter_substitution_validation_value_errors_1() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_password_confirmation() (galaxy_test.selenium.test_registration.RegistrationTestCase method) test_pause() (galaxy_test.api.test_workflows_from_yaml.WorkflowsFromYamlApiTestCase method) test_pause_outputs_with_deleted_inputs() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_permanently_delete_history() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) test_pja_import_export() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_placements_from_text_inputs() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_post_lines_trailing() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_post_lines_trailing_off() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_public_name() (galaxy_test.selenium.test_personal_information.ManageInformationTestCase method) test_purge() (galaxy_test.api.test_histories.HistoriesApiTestCase method) (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_purge_history() (galaxy_test.selenium.test_history_multi_view.HistoryMultiViewTestCase method) test_purge_user() (galaxy_test.api.test_users.UsersApiTestCase method) test_purging_output_cleaned_after_ok_run() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_purging_output_keep_running_until_all_purged() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_qc_messages() (galaxy_test.api.test_tools.ToolsTestCase method) test_querystring_params() (galaxy_test.api.test_api_batch.ApiBatchTestCase method) test_rdata_not_decompressed() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_reconnecting_nodes() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_recover_mapping_in_subworkflow() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_reduce_collections() (galaxy_test.api.test_tools.ToolsTestCase method) test_reduce_collections_in_repeat() (galaxy_test.api.test_tools.ToolsTestCase method) test_reduce_collections_in_repeat_legacy() (galaxy_test.api.test_tools.ToolsTestCase method) test_reduce_collections_legacy() (galaxy_test.api.test_tools.ToolsTestCase method) test_reduce_multiple_lists_on_multi_data() (galaxy_test.api.test_tools.ToolsTestCase method) test_refactor() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_refresh_preserves_state() (galaxy_test.selenium.test_history_panel.HistoryPanelTestCase method) test_registration() (galaxy_test.selenium.test_registration.RegistrationTestCase method) test_rename() (galaxy_test.selenium.test_library_landing.LibraryLandingTestCase method) (galaxy_test.selenium.test_workflow_management.WorkflowManagementTestCase method) test_rename_history() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) test_rendering_output_collection_connections() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_rendering_rules_workflow_1() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_rendering_rules_workflow_2() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_rendering_simple_nested_workflow() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_replacement_parameters() (galaxy_test.selenium.test_workflow_run.WorkflowRunTestCase method) test_replacement_parameters_on_subworkflows() (galaxy_test.selenium.test_workflow_run.WorkflowRunTestCase method) test_report_error() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_report_error_anon() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_require_unique_step_labels() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_require_unique_step_uuids() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_requirements() (galaxy_test.api.test_tools.ToolsTestCase method) test_reregister_email_fails() (galaxy_test.selenium.test_registration.RegistrationTestCase method) test_reregister_username_fails() (galaxy_test.selenium.test_registration.RegistrationTestCase method) test_rerun() (galaxy_test.selenium.test_tool_form.ToolFormTestCase method) test_resume_job() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_revision_index() (galaxy_test.api.test_page_revisions.PageRevisionsApiTestCase method) test_rules_example_1_datasets() (galaxy_test.selenium.test_uploads.UploadsTestCase method) test_rules_example_2_list() (galaxy_test.selenium.test_uploads.UploadsTestCase method) test_rules_example_3_list_pairs() (galaxy_test.selenium.test_uploads.UploadsTestCase method) test_rules_example_4_accessions() (galaxy_test.selenium.test_uploads.UploadsTestCase method) test_rules_example_5_matching_collections() (galaxy_test.selenium.test_uploads.UploadsTestCase method) test_rules_example_6_nested_lists() (galaxy_test.selenium.test_uploads.UploadsTestCase method) test_run_add_tag_on_collection_output() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_add_tag_on_mapped_over_collection() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_apply_rules_1() (galaxy_test.selenium.test_tool_form.LoggedInToolFormTestCase method) test_run_apply_rules_2() (galaxy_test.selenium.test_tool_form.LoggedInToolFormTestCase method) test_run_apply_rules_3() (galaxy_test.selenium.test_tool_form.LoggedInToolFormTestCase method) test_run_apply_rules_4() (galaxy_test.selenium.test_tool_form.LoggedInToolFormTestCase method) test_run_apply_rules_tutorial() (galaxy_test.selenium.test_tool_form.LoggedInToolFormTestCase method) test_run_as_invalid_user() (galaxy_test.api.test_framework.ApiFrameworkTestCase method) test_run_as_valid_user() (galaxy_test.api.test_framework.ApiFrameworkTestCase method) test_run_batch() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_batch_inputs() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_build_list_change_datatype_collection_output() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_build_list_delete_intermediate_collection_output() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_build_list_hide_collection_output() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_build_list_rename_collection_output() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_by_versions() (galaxy_test.api.test_tools.ToolsTestCase method) test_run_cat1() (galaxy_test.api.test_tools.ToolsTestCase method) test_run_cat1_listified_param() (galaxy_test.api.test_tools.ToolsTestCase method) test_run_cat1_single_meta_wrapper() (galaxy_test.api.test_tools.ToolsTestCase method) test_run_cat1_use_cached_job() (galaxy_test.api.test_tools.ToolsTestCase method) test_run_cat1_with_two_inputs() (galaxy_test.api.test_tools.ToolsTestCase method) test_run_data() (galaxy_test.selenium.test_tool_form.ToolFormTestCase method) test_run_hide_on_collection_output() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_hide_on_mapped_over_collection() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_remove_tag_on_collection_output() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_rename_based_on_input() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_rename_based_on_input_collection() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_rename_based_on_input_conditional() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_rename_based_on_input_recursive() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_rename_based_on_input_repeat() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_rename_based_on_inputs_on_mapped_over_collection() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_rename_collection_output() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_rename_multiple_outputs() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_rename_on_mapped_over_collection() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_rename_when_resuming_jobs() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_replace_params_by_steps() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_replace_params_by_tool() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_replace_params_by_uuid() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_replace_params_nested() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_replace_params_nested_normalized() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method)

test_run_replace_params_over_default() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_replace_params_over_default_delayed() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_runtime_parameters_after_pause() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_subworkflow_auto_labels() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_subworkflow_replacement_parameters() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_subworkflow_runtime_parameters() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_subworkflow_simple() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_tool_verify_contents_by_peek() (galaxy_test.selenium.test_tool_form.ToolFormTestCase method) test_run_tool_verify_dataset_details() (galaxy_test.selenium.test_tool_form.ToolFormTestCase method) test_run_versioned_tools() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_with_delayed_runtime_pja() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_with_implicit_connection() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_with_int_parameter() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_with_int_parameter_nested() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_with_non_optional_collection_unspecified_fails_invocation() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_with_non_optional_data_unspecified_fails_invocation() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_with_numeric_input_connection() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_with_optional_collection_specified() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_with_optional_collection_unspecified() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_with_optional_data_specified_to_multi_data() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_with_optional_data_unspecified_to_multi_data() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_with_pja() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_with_runtime_pja() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_with_text_input_connection() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_with_validated_parameter_connection_default_values() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_with_validated_parameter_connection_invalid() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_with_validated_parameter_connection_optional() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_workflow() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_workflow_by_index() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_workflow_by_name() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_workflow_by_uuid() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_run_workflow_by_uuid_implicitly() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_runtime_data_column_parameter() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_runtime_inputs() (galaxy_test.api.test_workflows_from_yaml.WorkflowsFromYamlApiTestCase method) test_runtime_parameters_simple() (galaxy_test.selenium.test_workflow_run.WorkflowRunTestCase method) test_save_as() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_search() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_search_by_tag() (galaxy_test.api.test_datasets.DatasetsApiTestCase method) test_search_by_tool_id() (galaxy_test.api.test_datasets.DatasetsApiTestCase method) test_search_cat() (galaxy_test.api.test_tools.ToolsTestCase method) test_search_datasets() (galaxy_test.api.test_datasets.DatasetsApiTestCase method) test_search_delete_hdca_output() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_search_delete_outputs() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_search_favorites() (galaxy_test.api.test_users.UsersApiTestCase method) test_search_grep() (galaxy_test.api.test_tools.ToolsTestCase method) test_search_handle_identifiers() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_search_returns_only_accessible() (galaxy_test.api.test_datasets.DatasetsApiTestCase method) test_search_trimmer() (galaxy_test.api.test_tools.ToolsTestCase method) test_search_with_hdca_list_input() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_search_with_hdca_list_pair_collection_mapped_over_pair_input() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_search_with_hdca_list_pair_input() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_search_with_hdca_pair_input() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_search_workflows() (galaxy_test.api.test_search.SearchApiTestCase method) test_select_legal_values() (galaxy_test.api.test_tools.ToolsTestCase method) test_set_permissions_add_admin_datasets() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_set_permissions_add_admin_history_contents() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_sharing_valid() (galaxy_test.selenium.test_history_sharing.HistorySharingTestCase method) test_sharing_valid_by_id() (galaxy_test.selenium.test_history_sharing.HistorySharingTestCase method) test_sharing_with_invalid_user() (galaxy_test.selenium.test_history_sharing.HistorySharingTestCase method) test_sharing_with_self() (galaxy_test.selenium.test_history_sharing.HistorySharingTestCase method) test_short_password() (galaxy_test.selenium.test_registration.RegistrationTestCase method) test_show() (galaxy_test.api.test_datasets.DatasetsApiTestCase method) (galaxy_test.api.test_jobs.JobsApiTestCase method) (galaxy_test.api.test_pages.PageApiTestCase method) (galaxy_test.api.test_tool_data.ToolDataApiTestCase method) (galaxy_test.api.test_tours.TourApiTestCase method) (galaxy_test.api.test_users.UsersApiTestCase method) test_show_conditional() (galaxy_test.api.test_tools.ToolsTestCase method) test_show_dataset_collection_contents() (galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase method) test_show_details() (galaxy_test.selenium.test_library_contents.LibraryContentsTestCase method) test_show_dynamic_tools() (galaxy_test.api.test_tools.ToolsTestCase method) test_show_error_codes() (galaxy_test.api.test_roles.RolesApiTestCase method) test_show_field() (galaxy_test.api.test_tool_data.ToolDataApiTestCase method) test_show_hda() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_show_history() (galaxy_test.api.test_histories.HistoriesApiTestCase method) test_show_invalid_key_is_400() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_show_most_recently_used() (galaxy_test.api.test_histories.HistoriesApiTestCase method) test_show_multi_data() (galaxy_test.api.test_tools.ToolsTestCase method) test_show_output_collection() (galaxy_test.api.test_tools.ToolsTestCase method) test_show_private_dataset_permissions() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_show_prov() (galaxy_test.api.test_history_contents_provenance.TestProvenance method) test_show_repeat() (galaxy_test.api.test_tools.ToolsTestCase method) test_show_security() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_show_valid() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_show_with_wrong_tool_version_in_tool_id() (galaxy_test.api.test_tools.ToolsTestCase method) test_sign_out() (galaxy_test.selenium.test_sign_out.SignOutTestCase method) test_simple_array() (galaxy_test.api.test_api_batch.ApiBatchTestCase method) test_simple_execution() (galaxy_test.selenium.test_workflow_run.WorkflowRunTestCase method) test_simple_mapping_connections() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_simple_output_actions() (galaxy_test.api.test_workflows_from_yaml.WorkflowsFromYamlApiTestCase method) test_simple_page_creation_edit_and_view() (galaxy_test.selenium.test_pages.PagesTestCase method) test_simple_upload() (galaxy_test.api.test_workflows_from_yaml.WorkflowsFromYamlApiTestCase method) test_sizzle_loads() (galaxy_test.selenium.test_sizzle_loading.SizzleLoadingTestCase method) test_sniffers() (galaxy_test.api.test_datatypes.DatatypesApiTestCase method) test_sort_by_name() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) test_sorting() (galaxy_test.selenium.test_library_landing.LibraryLandingTestCase method) test_stage_object() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_stage_object_fetch() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_standard_search() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) test_step_parameter_inputs() (galaxy_test.selenium.test_workflow_run.WorkflowRunTestCase method) test_sub_folder() (galaxy_test.selenium.test_library_contents.LibraryContentsTestCase method) test_subcollection_mapping() (galaxy_test.api.test_tools.ToolsTestCase method) (galaxy_test.api.test_workflow_extraction.WorkflowExtractionApiTestCase method) test_subcollection_reduction() (galaxy_test.api.test_workflow_extraction.WorkflowExtractionApiTestCase method) test_subworkflow_duplicate() (galaxy_test.api.test_workflows_from_yaml.WorkflowsFromYamlApiTestCase method) test_subworkflow_inputs_optional_editor() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_subworkflow_output_as_output() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_subworkflow_recover_mapping_1() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_subworkflow_recover_mapping_2() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_subworkflow_runtime_parameters() (galaxy_test.selenium.test_workflow_run.WorkflowRunTestCase method) test_subworkflow_simple() (galaxy_test.api.test_workflows_from_yaml.WorkflowsFromYamlApiTestCase method) test_subworkflows_simple() (galaxy_test.selenium.test_workflow_run.WorkflowRunTestCase method) test_switch_history() (galaxy_test.selenium.test_history_multi_view.HistoryMultiViewTestCase method) test_system_details_admin_only() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_tag_auto_propagation() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_tag_change() (galaxy_test.api.test_datasets.DatasetsApiTestCase method) test_tagging() (galaxy_test.selenium.test_workflow_management.WorkflowManagementTestCase method) test_tags() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) test_test_by_versions() (galaxy_test.api.test_tools.ToolsTestCase method) test_test_data_admin_security() (galaxy_test.api.test_tools.ToolsTestCase method) test_test_data_collection_nested() (galaxy_test.api.test_tools.ToolsTestCase method) test_test_data_collection_two_paired() (galaxy_test.api.test_tools.ToolsTestCase method) test_test_data_composite_output() (galaxy_test.api.test_tools.ToolsTestCase method) test_test_data_download() (galaxy_test.api.test_tools.ToolsTestCase method) test_test_data_download_composite() (galaxy_test.api.test_tools.ToolsTestCase method) test_test_data_downloads_security() (galaxy_test.api.test_tools.ToolsTestCase method) test_test_data_filepath_security() (galaxy_test.api.test_tools.ToolsTestCase method) test_test_data_null_boolean_inputs() (galaxy_test.api.test_tools.ToolsTestCase method) test_test_data_yaml_tools() (galaxy_test.api.test_tools.ToolsTestCase method) test_tool_deactivate() (galaxy_test.api.test_tools.ToolsTestCase method) test_tools() (in module galaxy.tool_util.verify.script) test_types_and_mapping() (galaxy_test.api.test_datatypes.DatatypesApiTestCase method) test_unallowed_route() (galaxy_test.api.test_api_batch.ApiBatchTestCase method) test_undelete() (galaxy_test.api.test_histories.HistoriesApiTestCase method) test_undelete_user() (galaxy_test.api.test_users.UsersApiTestCase method) test_unhide_on_error() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_unshared_history_inaccessible() (galaxy_test.selenium.test_history_sharing.HistorySharingTestCase method) test_unsharing() (galaxy_test.selenium.test_history_sharing.HistorySharingTestCase method) test_unzip_collection() (galaxy_test.api.test_tools.ToolsTestCase method) test_unzip_nested() (galaxy_test.api.test_tools.ToolsTestCase method) test_update() (galaxy_test.api.test_histories.HistoriesApiTestCase method) (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) (galaxy_test.api.test_libraries.LibrariesApiTestCase method) (galaxy_test.api.test_tours.TourApiTestCase method) (galaxy_test.api.test_users.UsersApiTestCase method) (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_update_batch() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_update_dataset_collection() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_update_dataset_in_folder() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_update_dataset_tags() (galaxy_test.api.test_libraries.LibrariesApiTestCase method) test_update_datatype() (galaxy_test.api.test_datasets.DatasetsApiTestCase method) test_update_invalid_attribute() (galaxy_test.api.test_histories.HistoriesApiTestCase method) test_update_invalid_types() (galaxy_test.api.test_histories.HistoriesApiTestCase method) test_update_missing_tool() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_update_name() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_update_no_tool_id() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_update_tags() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_update_title() (galaxy_test.api.test_visualizations.VisualizationsApiTestCase method) test_update_type_failures() (galaxy_test.api.test_history_contents.HistoryContentsApiTestCase method) test_upload() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_upload1_paste() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload1_paste_bad_datatype() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_and_validate_invalid() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_and_validate_valid() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_auto_decompress_off() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_bam_file() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_collection() (galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase method) test_upload_collection_failed_expansion_url() (galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase method) test_upload_collection_from_url() (galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase method) test_upload_composite_as_tar() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_composite_as_tar_fetch() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_composite_from_bad_tar() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_dbkey() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_decompress_off_if_compressed_type_selected() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_decompress_off_with_auto_by_default() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_decompresses_if_uncompressed_type_selected() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_deprecated() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_upload_disable_posix_fix() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_force_composite() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_from_404_url() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_from_invalid_url() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_from_valid_url() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_list() (galaxy_test.selenium.test_uploads.UploadsTestCase method) test_upload_multiple_files_1() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_multiple_files_2() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_multiple_files_3() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_multiple_files_no_dbkey() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_multiple_files_space_to_tab() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_multiple_mixed_success() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_nested() (galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase method) test_upload_pair() (galaxy_test.selenium.test_uploads.UploadsTestCase method) test_upload_pair_specify_extension() (galaxy_test.selenium.test_uploads.UploadsTestCase method) test_upload_paired_list() (galaxy_test.selenium.test_uploads.UploadsTestCase method) test_upload_posix_newline_fixes_by_default() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_simplest() (galaxy_test.selenium.test_uploads.UploadsTestCase method) test_upload_specify_ext() (galaxy_test.selenium.test_uploads.UploadsTestCase method) test_upload_specify_ext_all() (galaxy_test.selenium.test_uploads.UploadsTestCase method) test_upload_specify_genome() (galaxy_test.selenium.test_uploads.UploadsTestCase method) test_upload_specify_genome_all() (galaxy_test.selenium.test_uploads.UploadsTestCase method) test_upload_tab_to_space() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_upload_tab_to_space_off_by_default() (galaxy_test.api.test_tools_upload.ToolsUploadTestCase method) test_user_address() (galaxy_test.selenium.test_personal_information.ManageInformationTestCase method) test_user_cannont_run_as() (galaxy_test.api.test_framework.ApiFrameworkTestCase method) test_validated_post_job_action_invalid() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_validated_post_job_action_unvalidated_default() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_validated_post_job_action_validated() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_validation() (galaxy_test.api.test_tools.ToolsTestCase method) test_validation_empty_dataset() (galaxy_test.api.test_tools.ToolsTestCase method) test_validation_in_repeat() (galaxy_test.api.test_tools.ToolsTestCase method) test_value_restriction_with_select_and_text_param() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_verify_dataset_details_tables() (galaxy_test.selenium.test_tool_form.ToolFormTestCase method) test_view() (galaxy_test.selenium.test_workflow_management.WorkflowManagementTestCase method) test_workflow_bookmarking() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) test_workflow_embed_tool() (galaxy_test.api.test_workflows_from_yaml.WorkflowsFromYamlApiTestCase method) test_workflow_flatten() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_flatten_with_mapped_over_execution() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_import_state_validation_1() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_import_tool() (galaxy_test.api.test_workflows_from_yaml.WorkflowsFromYamlApiTestCase method) test_workflow_input_as_output() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_input_mapping() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_invocation_report_1() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_invocation_report_custom() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_list_list_multi_data_map_over() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_map_reduce_pause() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_metadata_validation_0() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_optional_input_filtering() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_optional_input_text_parameter_reevaluation() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_output_dataset() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_output_dataset_collection() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_pause() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_pause_cancel() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_publishing() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_request() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_rerun_with_use_cached_job() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_resume_from_failed_step() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_resume_from_failed_step_with_hdca_input() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_resume_with_mapped_over_input() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_run_apply_rules() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_run_dynamic_output_collections() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_run_dynamic_output_collections_2() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_run_dynamic_output_collections_3() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_run_input_mapping_with_output_collections() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_run_input_mapping_with_subworkflows() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_run_output_collection_mapping() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_run_output_collections() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_run_with_matching_lists() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_run_zip_collections() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_workflow_stability() (galaxy_test.api.test_workflows.WorkflowsApiTestCase method) test_wrong_password() (galaxy_test.selenium.test_login.LoginTestCase method) test_zip_inputs() (galaxy_test.api.test_tools.ToolsTestCase method) test_zip_list_inputs() (galaxy_test.api.test_tools.ToolsTestCase method) TestAutomaticDependencyRevision (class in tool_shed.test.functional.test_0460_upload_to_repository) TestBasicRepositoryDependencies (class in tool_shed.test.functional.test_0020_basic_repository_dependencies) (class in tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies) (class in tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency) TestBasicRepositoryFeatures (class in tool_shed.test.functional.test_0000_basic_repository_features) TestBismarkRepository (class in tool_shed.test.functional.test_0070_invalid_tool) TestCaseGalaxyInteractor (class in galaxy_test.base.interactor) TestCollectionDef (class in galaxy.tool_util.parser.interface) TestCollectionOutputDef (class in galaxy.tool_util.parser.interface) TestComplexPriorInstallation (class in tool_shed.test.functional.test_0170_complex_prior_installation_required) (class in tool_shed.test.functional.test_1190_complex_prior_installation_required) TestComplexRepositoryDependencies (class in tool_shed.test.functional.test_0100_complex_repository_dependencies) TestDataManagers (class in tool_shed.test.functional.test_1460_data_managers) TestDataResolver (class in galaxy.tool_util.verify.test_data) TestDatatypeConverters (class in tool_shed.test.functional.test_0130_datatype_converters) (class in tool_shed.test.functional.test_1150_datatype_converters) TestDeletedDependencies (class in tool_shed.test.functional.test_0440_deleting_dependency_definitions) TestDependencyDefinitionValidation (class in tool_shed.test.functional.test_0480_tool_dependency_xml_verification) TestDriver (class in galaxy_test.driver.driver_util) TestEnvironmentInheritance (class in tool_shed.test.functional.test_0470_tool_dependency_repository_type) (class in tool_shed.test.functional.test_1420_tool_dependency_environment_inheritance) TestException (class in galaxy.tool_util.verify.script) TestFreebayesRepository (class in tool_shed.test.functional.test_0010_repository_with_tool_dependencies) (class in tool_shed.test.functional.test_1070_invalid_tool) TestGetAllMetadata (class in tool_shed.test.functional.test_0540_get_all_metadata_from_api) TestGetUpdatedMetadata (class in tool_shed.test.functional.test_0550_metadata_updated_dependencies) TestHgWebFeatures (class in tool_shed.test.functional.test_0310_hg_api_features) TestInstallDatatypesSniffers (class in tool_shed.test.functional.test_1450_installing_datatypes_sniffers) TestInstallingCircularDependencies (class in tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies) TestInstallingComplexRepositoryDependencies (class in tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies) TestInstallRepositoryCircularDependencies (class in tool_shed.test.functional.test_1050_circular_dependencies_4_levels) TestInstallRepositoryMultipleOwners (class in tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners) TestMissingEnvSh (class in tool_shed.test.functional.test_1440_missing_env_sh_files) TestProvenance (class in galaxy_test.api.test_history_contents_provenance) TestReference (class in galaxy.tool_util.verify.script) TestRepairRepository (class in tool_shed.test.functional.test_1430_repair_installed_repository) TestRepositoryAdminRole (class in tool_shed.test.functional.test_0530_repository_admin_feature) TestRepositoryCircularDependencies (class in tool_shed.test.functional.test_0040_repository_circular_dependencies) (class in tool_shed.test.functional.test_0080_advanced_circular_dependencies) TestRepositoryCircularDependenciesAgain (class in tool_shed.test.functional.test_0090_tool_search) TestRepositoryCircularDependenciesToNLevels (class in tool_shed.test.functional.test_0050_circular_dependencies_4_levels) TestRepositoryCitableURLs (class in tool_shed.test.functional.test_0420_citable_urls_for_repositories) TestRepositoryComponentReviews (class in tool_shed.test.functional.test_0400_repository_component_reviews) (class in tool_shed.test.functional.test_0410_repository_component_review_access_control) TestRepositoryDependencies (class in tool_shed.test.functional.test_1080_advanced_circular_dependency_installation) (class in tool_shed.test.functional.test_1090_repository_dependency_handling) (class in tool_shed.test.functional.test_1100_install_updated_repository_dependencies) TestRepositoryDependencyRevisions (class in tool_shed.test.functional.test_0030_repository_dependency_revisions) TestRepositoryMultipleOwners (class in tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners) TestResetAllRepositoryMetadata (class in tool_shed.test.functional.test_0300_reset_all_metadata) TestResetInstalledRepositoryMetadata (class in tool_shed.test.functional.test_1300_reset_all_metadata) tests() (galaxy.tools.Tool property) tests_summary() (galaxy.webapps.galaxy.api.tools.ToolsController method) TestsDatasets (class in galaxy_test.base.populators) TestSimplePriorInstallation (class in tool_shed.test.functional.test_0150_prior_installation_required) (class in tool_shed.test.functional.test_0160_circular_prior_installation_required) (class in tool_shed.test.functional.test_1170_prior_installation_required) (class in tool_shed.test.functional.test_1180_circular_prior_installation_required) TestSnapshot (class in galaxy_test.selenium.framework) TestStockToursTestCase (class in galaxy_test.selenium.test_stock_tours) TestsTools (class in galaxy_test.api.test_tools) TestToolHelpImages (class in tool_shed.test.functional.test_0140_tool_help_images) (class in tool_shed.test.functional.test_1160_tool_help_images) TestToolShedBrowseUtilities (class in tool_shed.test.functional.test_0430_browse_utilities) TestUpdateInstalledRepository (class in tool_shed.test.functional.test_1470_updating_installed_repositories) TestUpdateManager (class in tool_shed.test.functional.test_1410_update_manager) TestWithSeleniumMixin (class in galaxy_test.selenium.framework) Text (class in galaxy.datatypes.data) (class in galaxy.selenium.components) TEXT (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute) text_data() (galaxy.managers.hdas.HDAManager method) text_metrics (galaxy.model.Job attribute) (galaxy.model.Task attribute) TextArea (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) TextColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.web.legacy_framework.grids) TextField (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) TextGrid (class in galaxy.datatypes.speech) textinsert (galaxy.tours.TourStep attribute) TextToolParameter (class in galaxy.tools.parameters.basic) ThermoRAW (class in galaxy.datatypes.proteomics) thread_is_sleeping() (galaxy.util.heartbeat.Heartbeat method) Tiff (class in galaxy.datatypes.images) time_ago() (in module galaxy.web.framework.helpers) time_elapsed() (galaxy.webapps.reports.controllers.jobs.Timer method) timenow() (in module galaxy.datatypes.converters.lped_to_fped_converter) (in module galaxy.datatypes.converters.lped_to_pbed_converter) (in module galaxy.datatypes.converters.pbed_ldreduced_converter) (in module galaxy.datatypes.converters.pbed_to_lped_converter) timeout_for() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) timeout_multiplier() (galaxy_test.selenium.framework.TestWithSeleniumMixin property) TimeoutAssertionError TimeoutException Timer (class in galaxy.webapps.reports.controllers.jobs) times_downloaded (tool_shed.webapp.model.Repository attribute) timestamp (galaxy.model.PSANonce attribute) timing() (galaxy.web.statsd_client.GalaxyStatsdClient method) tip() (tool_shed.webapp.model.Repository method) tip_has_metadata() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) TipOnly (class in tool_shed.repository_types.metadata) title (galaxy.model.Page attribute) (galaxy.model.PageRevision attribute) (galaxy.model.Visualization attribute) (galaxy.model.VisualizationRevision attribute) (galaxy.tours.TourStep attribute) (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.GroupGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.DatatypesGrid attribute) (tool_shed.grids.repository_grids.DeprecatedRepositoriesIOwnGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithInvalidToolsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesByUserGrid attribute) (tool_shed.grids.repository_grids.RepositoriesICanAdministerGrid attribute) (tool_shed.grids.repository_grids.RepositoriesInCategoryGrid attribute) (tool_shed.grids.repository_grids.RepositoriesIOwnGrid attribute) (tool_shed.grids.repository_grids.RepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithInvalidToolsGrid attribute) (tool_shed.grids.repository_grids.RepositoryDependenciesGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ToolDependenciesGrid attribute) (tool_shed.grids.repository_grids.ToolsGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_grids.ValidRepositoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesReadyForReviewGrid 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) title() (galaxy.tools.parameters.grouping.Repeat property) title_by_index() (galaxy.tools.parameters.grouping.UploadDataset method) title_default (galaxy.tours.TourDetails attribute) title_id (galaxy.webapps.galaxy.controllers.admin.GroupListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.RoleListGrid attribute) (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) title_plural() (galaxy.tools.parameters.grouping.Repeat property) (galaxy.tools.parameters.grouping.Section property) (galaxy.tools.parameters.grouping.UploadDataset property) tmp_dir (galaxy.datatypes.metadata.MetadataTempFile attribute) (galaxy.model.metadata.MetadataTempFile attribute) tmp_dir_creation_statement() (galaxy.jobs.JobWrapper property) tmp_directory() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.JobWrapper method) (galaxy.jobs.SharedComputeEnvironment method) tmp_target() (galaxy.jobs.JobWrapper property) to_archive() (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.data.Data method) (galaxy.tools.Tool method) to_bibtex() (galaxy.managers.citations.BibtexCitation method) (galaxy.managers.citations.DoiCitation method) to_bool() (in module galaxy.util.specs) to_bool_or_none() (in module galaxy.util.specs) to_cwl_job() (in module galaxy.tool_util.cwl) (in module galaxy.tool_util.cwl.representation) to_dataset_instances() (galaxy.tools.wrappers.DatasetListWrapper static method) to_dict() (galaxy.files.ConfiguredFileSources method) (galaxy.files.ConfiguredFileSourcesConfig method) (galaxy.files.sources.BaseFilesSource method) (galaxy.files.sources.FilesSource method) (galaxy.managers.citations.BaseCitation method) (galaxy.model.FormDefinition method) (galaxy.model.HasTags method) (galaxy.model.History method) (galaxy.model.HistoryDatasetAssociation method) (galaxy.model.HistoryDatasetCollectionAssociation method) (galaxy.model.Job method) (galaxy.model.JobExportHistoryArchive method) (galaxy.model.Library method) (galaxy.model.LibraryDataset method) (galaxy.model.LibraryDatasetCollectionAssociation method) (galaxy.model.LibraryDatasetDatasetAssociation method) (galaxy.model.LibraryFolder method) (galaxy.model.Page method) (galaxy.model.PageRevision method) (galaxy.model.StoredWorkflow method) (galaxy.model.tool_shed_install.ToolShedRepository method) (galaxy.model.tool_shed_install.ToolVersion method) (galaxy.model.UserAddress method) (galaxy.model.Workflow method) (galaxy.model.WorkflowInvocation method) (galaxy.model.WorkflowInvocationStep method) (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.cloud.Cloud method) (galaxy.objectstore.ConcreteObjectStore method) (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.DistributedObjectStore method) (galaxy.objectstore.HierarchicalObjectStore method) (galaxy.objectstore.irods.IRODSObjectStore method) (galaxy.objectstore.pithos.PithosObjectStore method) (galaxy.objectstore.s3.S3ObjectStore method) (galaxy.tool_util.deps.dependencies.DependenciesDescription method) (galaxy.tool_util.deps.DependencyManager method) (galaxy.tool_util.deps.NullDependencyManager method) (galaxy.tool_util.deps.requirements.ContainerDescription method) (galaxy.tool_util.deps.requirements.RequirementSpecification method) (galaxy.tool_util.deps.requirements.ToolRequirement method) (galaxy.tool_util.deps.requirements.ToolRequirements method) (galaxy.tool_util.parser.interface.TestCollectionDef method) (galaxy.tool_util.parser.interface.TestCollectionOutputDef method) (galaxy.tool_util.parser.output_collection_def.DatasetCollectionDescription method) (galaxy.tool_util.parser.output_collection_def.FilePatternDatasetCollectionDescription method) (galaxy.tool_util.parser.output_objects.ToolOutput method) (galaxy.tool_util.parser.output_objects.ToolOutputBase method) (galaxy.tool_util.parser.output_objects.ToolOutputCollection method) (galaxy.tool_util.parser.output_objects.ToolOutputCollectionStructure method) (galaxy.tool_util.parser.stdio.ToolStdioExitCode method) (galaxy.tool_util.parser.stdio.ToolStdioRegex method) (galaxy.tool_util.verify.interactor.ToolTestDescription method) (galaxy.tools.data.TabularToolDataField method) (galaxy.tools.data.TabularToolDataTable method) (galaxy.tools.parameters.basic.BaseURLToolParameter method) (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.GenomeBuildParameter method) (galaxy.tools.parameters.basic.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.TextToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.DataCollectionToolParameter method) (galaxy.tools.parameters.DataToolParameter method) (galaxy.tools.parameters.grouping.Conditional method) (galaxy.tools.parameters.grouping.ConditionalWhen method) (galaxy.tools.parameters.grouping.Group method) (galaxy.tools.parameters.grouping.Repeat method) (galaxy.tools.parameters.grouping.Section method) (galaxy.tools.parameters.SelectToolParameter method) (galaxy.tools.Tool method) (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) (galaxy.tools.toolbox.lineages.interface.ToolLineage method) (galaxy.tools.toolbox.lineages.interface.ToolLineageVersion method) (galaxy.tools.toolbox.lineages.ToolLineage method) (galaxy.tools.toolbox.panel.ToolSection method) (galaxy.tools.toolbox.panel.ToolSectionLabel method) (galaxy.tools.toolbox.ToolSection method) (galaxy.tools.toolbox.ToolSectionLabel method) (galaxy.util.dictifiable.Dictifiable method) (galaxy.util.form_builder.AddressField method) (galaxy.util.form_builder.BaseField method) (galaxy.util.form_builder.CheckboxField method) (galaxy.util.form_builder.HistoryField method) (galaxy.util.form_builder.PasswordField method) (galaxy.util.form_builder.SelectField method) (galaxy.util.form_builder.TextArea method) (galaxy.util.form_builder.TextField method) (galaxy.util.form_builder.WorkflowField method) (galaxy.visualization.genomes.Genome method) (galaxy.visualization.plugins.plugin.VisualizationPlugin method) (galaxy.web.form_builder.AddressField method) (galaxy.web.form_builder.BaseField method) (galaxy.web.form_builder.CheckboxField method) (galaxy.web.form_builder.HistoryField method) (galaxy.web.form_builder.PasswordField method) (galaxy.web.form_builder.SelectField method) (galaxy.web.form_builder.TextArea method) (galaxy.web.form_builder.TextField method) (galaxy.web.form_builder.WorkflowField method) (galaxy.webhooks.Webhook method) (galaxy.workflow.modules.InputProxy method) (galaxy.workflow.refactor.schema.Position method) (tool_shed.webapp.model.Repository method) to_dict_time() (galaxy.files.sources.BaseFilesSource method) to_external_value() (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.model.metadata.FileParameter method) (galaxy.model.metadata.MetadataParameter method) to_float_or_none() (in module galaxy.util.specs) to_galaxy_parameters() (in module galaxy.tool_util.cwl) (in module galaxy.tool_util.cwl.representation) to_hda_representative() (galaxy.model.HistoryDatasetCollectionAssociation method) to_history_dataset_association() (galaxy.model.LibraryDatasetDatasetAssociation method) to_html_string() (in module galaxy.tool_shed.util.basic_util) to_js_bool() (in module galaxy.web.framework.helpers) to_JSON() (galaxy.datatypes.metadata.MetadataTempFile method) (galaxy.model.metadata.MetadataTempFile method) to_json() (galaxy.tools.parameters.basic.BaseDataToolParameter method) (galaxy.tools.parameters.basic.BaseJsonToolParameter method) (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.FileToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.LibraryDatasetToolParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.SimpleTextToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.SelectToolParameter method) (galaxy.tools.Tool method) to_JSON_dict() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataCollection method) to_library_dataset_dataset_association() (galaxy.model.HistoryDatasetAssociation method) to_list() (galaxy.tool_util.deps.requirements.ToolRequirements method) to_native() (galaxy.containers.ContainerVolume method) (galaxy.containers.docker_model.DockerVolume method) to_options_list() (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider method) to_param_dict_string() (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.ColorToolParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.LibraryDatasetToolParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.DataToolParameter method) (galaxy.tools.parameters.SelectToolParameter method) to_python() (galaxy.tools.parameters.basic.BaseDataToolParameter method) (galaxy.tools.parameters.basic.BaseJsonToolParameter method) (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.FileToolParameter method) (galaxy.tools.parameters.basic.FloatToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.IntegerToolParameter method) (galaxy.tools.parameters.basic.LibraryDatasetToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) to_safe_string() (galaxy.datatypes.metadata.DictParameter method) (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.model.metadata.DictParameter method) (galaxy.model.metadata.FileParameter method) (galaxy.model.metadata.MetadataParameter method) to_statements() (galaxy.tool_util.deps.brew_exts.EnvAction method) to_str() (galaxy.app.StatsdStructuredExecutionTimer method) (galaxy.util.StructuredExecutionTimer method) to_str_or_none() (in module galaxy.util.specs) to_string() (galaxy.datatypes.metadata.ColumnTypesParameter method) (galaxy.datatypes.metadata.DictParameter method) (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.ListParameter method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.datatypes.metadata.PythonObjectParameter method) (galaxy.datatypes.metadata.SelectParameter method) (galaxy.model.metadata.ColumnTypesParameter method) (galaxy.model.metadata.DictParameter method) (galaxy.model.metadata.FileParameter method) (galaxy.model.metadata.ListParameter method) (galaxy.model.metadata.MetadataParameter method) (galaxy.model.metadata.PythonObjectParameter method) (galaxy.model.metadata.SelectParameter method) (galaxy.tool_util.parser.xml.XmlToolSource method) to_tabix() (in module galaxy.datatypes.converters.interval_to_tabix_converter) to_text() (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.RulesListToolParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.DataCollectionToolParameter method) (galaxy.tools.parameters.DataToolParameter method) (galaxy.tools.parameters.SelectToolParameter method) to_tool_path() (galaxy.tool_util.fetcher.ToolLocationFetcher method) to_unicode() (in module galaxy.web.framework.helpers) to_unit() (galaxy.util.bytesize.ByteSize method) to_xml() (in module galaxy.tool_util.verify.asserts.xml) to_xml_file() (galaxy.datatypes.registry.Registry method) (galaxy.tools.data.ToolDataTableManager method) toJson() (galaxy.visualization.data_providers.phyloviz.baseparser.Base_Parser method) (galaxy.visualization.data_providers.phyloviz.baseparser.Node method) token (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.PasswordResetToken attribute) (galaxy.model.PSAPartial attribute) (tool_shed.webapp.model.PasswordResetToken attribute) tokens (galaxy.model.CloudAuthz attribute) Tool (class in galaxy.tools) (class in tool_shed.utility_containers.utility_container_manager) tool() (galaxy.tool_util.cwl.schema.SchemaLoader method) (galaxy.tool_util.parser.output_actions.ToolOutputAction property) (galaxy.tool_util.parser.output_actions.ToolOutputActionConditional property) (galaxy.tool_util.parser.output_actions.ToolOutputActionGroup property) (galaxy.tool_util.parser.output_actions.ToolOutputActionOption property) (galaxy.tool_util.parser.output_actions.ToolOutputActionOptionFilter property) tool_class (in module galaxy.tools) tool_config_paths() (galaxy.config_watchers.ConfigWatchers property) tool_data_path_files() (galaxy.tools.data.ToolDataPathFiles property) tool_data_paths() (galaxy.config_watchers.ConfigWatchers property) tool_data_table() (galaxy.tools.parameters.dynamic_options.DynamicOptions property) tool_data_table_info() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) tool_data_table_info_1() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) tool_data_table_items() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) tool_dependencies (galaxy.model.tool_shed_install.ToolShedRepository attribute) tool_dependencies_being_installed() (galaxy.model.tool_shed_install.ToolShedRepository property) tool_dependencies_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) tool_dependencies_installed_or_in_error() (galaxy.model.tool_shed_install.ToolShedRepository property) tool_dependencies_missing_or_being_installed() (galaxy.model.tool_shed_install.ToolShedRepository property) tool_dependencies_with_installation_errors() (galaxy.model.tool_shed_install.ToolShedRepository property) tool_dependency_dir() (galaxy.config.ConfiguresGalaxyMixin property) tool_dependency_is_orphan() (tool_shed.galaxy_install.dependency_display.DependencyDisplayer method) tool_directory (galaxy.model.DynamicTool attribute) tool_directory() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) tool_error_messages() (galaxy.webapps.reports.controllers.tools.Tools method) tool_errors (galaxy.model.WorkflowStep attribute) tool_execution_time() (galaxy.webapps.reports.controllers.tools.Tools method) tool_execution_time_per_month() (galaxy.webapps.reports.controllers.tools.Tools method) tool_fail() (in module galaxy.datatypes.util.maf_utilities) (in module galaxy.tools.util.maf_utilities) tool_form_execute() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) tool_form_generate_tour() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) tool_format (galaxy.model.DynamicTool attribute) tool_help() (galaxy.webapps.galaxy.controllers.root.RootController method) tool_id (galaxy.model.DynamicTool attribute) (galaxy.model.Event attribute) (galaxy.model.Job attribute) (galaxy.model.tool_shed_install.ToolVersion attribute) (galaxy.model.tool_shed_install.ToolVersionAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.WorkflowStep attribute) tool_id() (galaxy.tool_util.verify.script.TestException property) (galaxy.tool_util.verify.script.TestReference property) tool_ids() (galaxy.tools.toolbox.lineages.interface.ToolLineage property) (galaxy.tools.toolbox.lineages.ToolLineage property) tool_ids_by_requirements() (galaxy.tool_util.deps.views.DependencyResolversView property) tool_inputs (galaxy.model.WorkflowStep attribute) tool_lineages() (galaxy.webapps.galaxy.api.configuration.ConfigurationController method) tool_open() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) tool_output_to_structure() (in module galaxy.model.dataset_collections.structure) tool_panel_contents() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) tool_panel_section_id (galaxy.managers.workflows.WorkflowCreateOptions attribute) tool_panel_section_mapping (galaxy.managers.workflows.WorkflowCreateOptions attribute) tool_parameter_div() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) tool_parameter_edit_rules() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) tool_path (galaxy.model.DynamicTool attribute) tool_paths() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager property) tool_per_month() (galaxy.webapps.reports.controllers.jobs.Jobs method) tool_port (galaxy.model.InteractiveToolEntryPoint attribute) tool_provided_metadata() (galaxy.tools.Tool method) tool_proxy() (galaxy.tool_util.parser.cwl.CwlToolSource property) (in module galaxy.tool_util.cwl) (in module galaxy.tool_util.cwl.parser) tool_proxy_from_persistent_representation() (in module galaxy.tool_util.cwl) tool_repository_long_description (in module tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners) (in module tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners) (in module tool_shed.test.functional.test_1440_missing_env_sh_files) tool_requirements() (galaxy.tools.Tool property) tool_requirements_status() (galaxy.tools.Tool property) tool_response_to_output() (in module galaxy.tool_util.cwl.util) tool_search() (galaxy.webapps.galaxy.controllers.root.RootController method) tool_set_value() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) tool_shed module tool_shed (galaxy.model.tool_shed_install.ToolShedRepository attribute) tool_shed.dependencies module tool_shed.dependencies.attribute_handlers module tool_shed.dependencies.repository module tool_shed.dependencies.repository.relation_builder module tool_shed.dependencies.tool module tool_shed.dependencies.tool.tag_attribute_handler module tool_shed.galaxy_install module tool_shed.galaxy_install.dependency_display module tool_shed.galaxy_install.grids module tool_shed.galaxy_install.grids.admin_toolshed_grids module tool_shed.galaxy_install.utility_containers module tool_shed.grids module tool_shed.grids.admin_grids module tool_shed.grids.repository_grid_filter_manager module tool_shed.grids.repository_grids module tool_shed.grids.repository_review_grids module tool_shed.grids.util module tool_shed.managers module tool_shed.managers.groups module tool_shed.managers.repositories module tool_shed.metadata module tool_shed.metadata.metadata_generator module tool_shed.metadata.repository_metadata_manager module tool_shed.repository_registry module tool_shed.repository_types module tool_shed.repository_types.metadata module tool_shed.repository_types.registry module tool_shed.repository_types.repository_suite_definition module tool_shed.repository_types.tool_dependency_definition module tool_shed.repository_types.unrestricted module tool_shed.repository_types.util module tool_shed.test module tool_shed.test.base module tool_shed.test.base.common module tool_shed.test.base.test_db_util module tool_shed.test.base.twilltestcase module tool_shed.test.functional module tool_shed.test.functional.test_0000_basic_repository_features module tool_shed.test.functional.test_0010_repository_with_tool_dependencies module tool_shed.test.functional.test_0020_basic_repository_dependencies module tool_shed.test.functional.test_0030_repository_dependency_revisions module tool_shed.test.functional.test_0040_repository_circular_dependencies module tool_shed.test.functional.test_0050_circular_dependencies_4_levels module tool_shed.test.functional.test_0070_invalid_tool module tool_shed.test.functional.test_0080_advanced_circular_dependencies module tool_shed.test.functional.test_0090_tool_search module tool_shed.test.functional.test_0100_complex_repository_dependencies module tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies module tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners module tool_shed.test.functional.test_0130_datatype_converters module tool_shed.test.functional.test_0140_tool_help_images module tool_shed.test.functional.test_0150_prior_installation_required module tool_shed.test.functional.test_0160_circular_prior_installation_required module tool_shed.test.functional.test_0170_complex_prior_installation_required module tool_shed.test.functional.test_0300_reset_all_metadata module tool_shed.test.functional.test_0310_hg_api_features module tool_shed.test.functional.test_0400_repository_component_reviews module tool_shed.test.functional.test_0410_repository_component_review_access_control module tool_shed.test.functional.test_0420_citable_urls_for_repositories module tool_shed.test.functional.test_0430_browse_utilities module tool_shed.test.functional.test_0440_deleting_dependency_definitions module tool_shed.test.functional.test_0460_upload_to_repository module tool_shed.test.functional.test_0470_tool_dependency_repository_type module tool_shed.test.functional.test_0480_tool_dependency_xml_verification module tool_shed.test.functional.test_0530_repository_admin_feature module tool_shed.test.functional.test_0540_get_all_metadata_from_api module tool_shed.test.functional.test_0550_metadata_updated_dependencies module tool_shed.test.functional.test_1000_install_basic_repository module tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies module tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies module tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions module tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies module tool_shed.test.functional.test_1050_circular_dependencies_4_levels module tool_shed.test.functional.test_1070_invalid_tool module tool_shed.test.functional.test_1080_advanced_circular_dependency_installation module tool_shed.test.functional.test_1090_repository_dependency_handling module tool_shed.test.functional.test_1100_install_updated_repository_dependencies module tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies module tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency module tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners module tool_shed.test.functional.test_1150_datatype_converters module tool_shed.test.functional.test_1160_tool_help_images module tool_shed.test.functional.test_1170_prior_installation_required module tool_shed.test.functional.test_1180_circular_prior_installation_required module tool_shed.test.functional.test_1190_complex_prior_installation_required module tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository module tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies module tool_shed.test.functional.test_1220_uninstall_reinstall_repository_with_repository_dependencies module tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions module tool_shed.test.functional.test_1300_reset_all_metadata module tool_shed.test.functional.test_1410_update_manager module tool_shed.test.functional.test_1420_tool_dependency_environment_inheritance module tool_shed.test.functional.test_1430_repair_installed_repository module tool_shed.test.functional.test_1440_missing_env_sh_files module tool_shed.test.functional.test_1450_installing_datatypes_sniffers module tool_shed.test.functional.test_1460_data_managers module tool_shed.test.functional.test_1470_updating_installed_repositories module tool_shed.test.functional_tests module tool_shed.tools module tool_shed.tools.data_table_manager module tool_shed.tools.tool_validator module tool_shed.tools.tool_version_manager module tool_shed.util module tool_shed.util.admin_util module tool_shed.util.basic_util module tool_shed.util.commit_util module tool_shed.util.common_util module tool_shed.util.container_util module tool_shed.util.encoding_util module tool_shed.util.hg_util module tool_shed.util.hgweb_config module tool_shed.util.metadata_util module tool_shed.util.readme_util module tool_shed.util.repository_content_util module tool_shed.util.repository_util module tool_shed.util.review_util module tool_shed.util.search_util module tool_shed.util.shed_index module tool_shed.util.shed_util_common module tool_shed.util.tool_dependency_util module tool_shed.util.tool_util module tool_shed.util.web_util module tool_shed.util.xml_util module tool_shed.utility_containers module tool_shed.utility_containers.utility_container_manager module tool_shed.webapp module tool_shed.webapp.api module tool_shed.webapp.api.authenticate module tool_shed.webapp.api.categories module tool_shed.webapp.api.configuration module tool_shed.webapp.api.groups module tool_shed.webapp.api.repositories module tool_shed.webapp.api.repository_revisions module tool_shed.webapp.api.tools module tool_shed.webapp.api.users module tool_shed.webapp.app module tool_shed.webapp.buildapp module tool_shed.webapp.config module tool_shed.webapp.controllers module tool_shed.webapp.controllers.admin module tool_shed.webapp.controllers.groups module tool_shed.webapp.controllers.hg module tool_shed.webapp.controllers.repository module tool_shed.webapp.controllers.repository_review module tool_shed.webapp.controllers.upload module tool_shed.webapp.controllers.user module tool_shed.webapp.framework module tool_shed.webapp.framework.middleware module tool_shed.webapp.framework.middleware.remoteuser module tool_shed.webapp.model module tool_shed.webapp.model.mapping module tool_shed.webapp.model.migrate module tool_shed.webapp.model.migrate.check module tool_shed.webapp.model.migrate.versions module tool_shed.webapp.model.migrate.versions.0001_initial_tables module tool_shed.webapp.model.migrate.versions.0002_add_tool_suite_column module tool_shed.webapp.model.migrate.versions.0003_review_and_review_association_tables module tool_shed.webapp.model.migrate.versions.0004_repository_tables module tool_shed.webapp.model.migrate.versions.0005_drop_tool_related_tables module tool_shed.webapp.model.migrate.versions.0006_add_email_alerts_column module tool_shed.webapp.model.migrate.versions.0007_add_long_description_times_downloaded_columns module tool_shed.webapp.model.migrate.versions.0008_add_repository_metadata_table module tool_shed.webapp.model.migrate.versions.0009_add_malicious_column module tool_shed.webapp.model.migrate.versions.0010_add_new_repo_alert_column module tool_shed.webapp.model.migrate.versions.0011_add_tool_versions_column module tool_shed.webapp.model.migrate.versions.0012_add_downloadable_column module tool_shed.webapp.model.migrate.versions.0013_add_review_tables module tool_shed.webapp.model.migrate.versions.0014_add_deprecated_column module tool_shed.webapp.model.migrate.versions.0015_add_api_keys_table module tool_shed.webapp.model.migrate.versions.0016_add_do_not_test_tools_functionally_correct_errors_columns module tool_shed.webapp.model.migrate.versions.0017_add_galaxy_utility_columns_to_repository_metadata_table module tool_shed.webapp.model.migrate.versions.0018_add_repository_metadata_flag_columns module tool_shed.webapp.model.migrate.versions.0019_add_skip_tool_test_table_and_test_install_error_column module tool_shed.webapp.model.migrate.versions.0020_add_repository_type_column module tool_shed.webapp.model.migrate.versions.0021_change_repository_type_value module tool_shed.webapp.model.migrate.versions.0022_add_repository_admin_roles module tool_shed.webapp.model.migrate.versions.0023_add_repository_url_and_hompeage_url module tool_shed.webapp.model.migrate.versions.0024_password_reset module tool_shed.webapp.model.migrate.versions.0025_session_timeout module tool_shed.webapp.model.migrate.versions.0026_add_numeric_revision_column module tool_shed.webapp.search module tool_shed.webapp.search.repo_search module tool_shed.webapp.search.tool_search module tool_shed.webapp.security module tool_shed.webapp.util module tool_shed.webapp.util.ratings_util module tool_shed.webapp.util.shed_statistics module tool_shed_decode() (in module galaxy.util.tool_shed.encoding_util) tool_shed_encode() (in module galaxy.util.tool_shed.encoding_util) tool_shed_from_repository_clone_url() (galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) tool_shed_is_this_tool_shed() (in module galaxy.tool_shed.util.shed_util_common) (in module tool_shed.util.shed_util_common) tool_shed_path_name() (galaxy.model.tool_shed_install.ToolShedRepository property) tool_shed_repository (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolVersion attribute) tool_shed_repository() (galaxy.tools.Tool property) tool_shed_repository_id (galaxy.model.tool_shed_install.RepositoryDependency attribute) (galaxy.model.tool_shed_install.RepositoryRepositoryDependencyAssociation attribute) (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolVersion attribute) tool_shed_status (galaxy.model.tool_shed_install.ToolShedRepository attribute) tool_state (galaxy.workflow.refactor.schema.AddStepAction attribute) tool_state_adjustment (galaxy.workflow.refactor.schema.RefactorActionExecutionMessageTypeEnum attribute) tool_stderr (galaxy.model.Job attribute) (galaxy.model.Task attribute) tool_stdout (galaxy.model.Job attribute) (galaxy.model.Task attribute) tool_tag_manager() (in module galaxy.tools.toolbox.tags) tool_type (galaxy.tools.ApplyRulesTool attribute) (galaxy.tools.AsyncDataSourceTool attribute) (galaxy.tools.BuildListCollectionTool attribute) (galaxy.tools.DataDestinationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.ExportHistoryTool attribute) (galaxy.tools.ExpressionTool attribute) (galaxy.tools.ExtractDatasetCollectionTool attribute) (galaxy.tools.FilterEmptyDatasetsTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) (galaxy.tools.FilterFromFileTool attribute) (galaxy.tools.FlattenTool attribute) (galaxy.tools.ImportHistoryTool attribute) (galaxy.tools.InteractiveTool attribute) (galaxy.tools.MergeCollectionTool attribute) (galaxy.tools.OutputParameterJSONTool attribute) (galaxy.tools.RelabelFromFileTool attribute) (galaxy.tools.SetMetadataTool attribute) (galaxy.tools.SortTool attribute) (galaxy.tools.TagFromFileTool attribute) (galaxy.tools.Tool attribute) (galaxy.tools.UnzipCollectionTool attribute) (galaxy.tools.ZipCollectionTool attribute) tool_uuid() (galaxy.model.WorkflowStep property) tool_version (galaxy.model.DynamicTool attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.Job attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.WorkflowStep attribute) (galaxy.workflow.refactor.schema.UpgradeToolAction attribute) tool_version() (galaxy.tool_util.verify.script.TestReference property) tool_version_change (galaxy.workflow.refactor.schema.RefactorActionExecutionMessageTypeEnum attribute) tool_version_list_grid (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) tool_versions (galaxy.model.tool_shed_install.ToolShedRepository attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) tool_versions() (galaxy.tools.Tool property) tool_versions_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) tool_working_directory() (galaxy.jobs.JobWrapper property) ToolAction (class in galaxy.tools.actions) ToolBox (class in galaxy.tools) toolbox_install() (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) toolbox_requirements_status() (galaxy.tool_util.deps.views.DependencyResolversView property) toolbox_uninstall() (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) ToolBoxSearch (class in galaxy.tools.search) ToolCache (class in galaxy.tools.cache) ToolConfRepository (class in galaxy.tools.toolbox.base) ToolConfWatcher (class in galaxy.tools.toolbox.watcher) ToolData (class in galaxy.webapps.galaxy.api.tool_data) ToolDataApiTestCase (class in galaxy_test.api.test_tool_data) ToolDataPathFiles (class in galaxy.tools.data) ToolDataTable (class in galaxy.tools.data) ToolDataTableManager (class in galaxy.tools.data) (in module galaxy.tool_shed.tools.data_table_manager) ToolDependenciesAPIController (class in galaxy.webapps.galaxy.api.tool_dependencies) ToolDependenciesGrid (class in tool_shed.grids.repository_grids) ToolDependenciesGrid.ToolDependencyColumn (class in tool_shed.grids.repository_grids) ToolDependency (class in galaxy.model.tool_shed_install) (class in tool_shed.utility_containers.utility_container_manager) ToolDependency.states (class in galaxy.model.tool_shed_install) ToolDependencyAttributeHandler (class in tool_shed.dependencies.attribute_handlers) ToolDependencyDefinition (class in tool_shed.repository_types.tool_dependency_definition) ToolDependencyInstallationError (class in tool_shed.utility_containers) ToolDependencySuccessfulInstallation (class in tool_shed.utility_containers) ToolDescribingToursTestCase (class in galaxy_test.selenium.test_tool_describing_tours) ToolDocumentCache (class in galaxy.tools.cache) ToolEntryPointsAPIController (class in galaxy.webapps.galaxy.api.tool_entry_points) ToolErrorLog (class in galaxy.tools) ToolEvaluator (class in galaxy.tools.evaluation) ToolExecutionCache (class in galaxy.tools.actions) ToolExecutionError ToolExpressionOutput (class in galaxy.tool_util.parser.output_objects) ToolFileEventHandler (class in galaxy.tools.toolbox.watcher) ToolFilterMixin (class in galaxy.managers.tools) ToolFormTestCase (class in galaxy_test.selenium.test_tool_form) ToolHash (class in galaxy.tools.cache) ToolInfo (class in galaxy.tool_util.deps.dependencies) ToolInputsNotReadyException ToolInputTranslator (class in galaxy.tools.parameters.input_translation) ToolLineage (class in galaxy.tools.toolbox.lineages) (class in galaxy.tools.toolbox.lineages.interface) ToolLineageVersion (class in galaxy.tools.toolbox.lineages.interface) ToolLocationFetcher (class in galaxy.tool_util.fetcher) ToolLocationResolver (class in galaxy.tool_util.locations) ToolMetadataDatasetCollector (class in galaxy.job_execution.output_collect) ToolMetaParameterException ToolMigrationManager (class in galaxy.tool_shed.galaxy_install.tool_migration_manager) ToolMissingException ToolModule (class in galaxy.workflow.modules) ToolNotFoundException ToolOutput (class in galaxy.tool_util.cwl.runnable) (class in galaxy.tool_util.parser.output_objects) ToolOutputAction (class in galaxy.tool_util.parser.output_actions) ToolOutputActionConditional (class in galaxy.tool_util.parser.output_actions) ToolOutputActionConditionalWhen (class in galaxy.tool_util.parser.output_actions) ToolOutputActionGroup (class in galaxy.tool_util.parser.output_actions) ToolOutputActionOption (class in galaxy.tool_util.parser.output_actions) ToolOutputActionOptionFilter (class in galaxy.tool_util.parser.output_actions) ToolOutputBase (class in galaxy.tool_util.parser.output_objects) ToolOutputCollection (class in galaxy.tool_util.parser.output_objects) ToolOutputCollectionPart (class in galaxy.tool_util.parser) (class in galaxy.tool_util.parser.output_objects) ToolOutputCollectionStructure (class in galaxy.tool_util.parser.output_objects) ToolPanelElements (class in galaxy.tools.toolbox.panel) ToolPanelManager (class in galaxy.tool_shed.galaxy_install.tools.tool_panel_manager) ToolParameter (class in galaxy.tools.parameters.basic) ToolParameterSanitizer (class in galaxy.tools.parameters.sanitize) ToolParameterValueWrapper (class in galaxy.tools.wrappers) ToolProvidedMetadata (class in galaxy.tool_util.provided_metadata) ToolProvidedMetadataDatasetCollection (class in galaxy.tool_util.parser.output_collection_def) ToolRecommendations (class in galaxy.tools.recommendations) ToolRequirement (class in galaxy.tool_util.deps.requirements) ToolRequirements (class in galaxy.tool_util.deps.requirements) ToolRequirementsException ToolRunner (class in galaxy.webapps.galaxy.controllers.tool_runner) Tools (class in galaxy.webapps.reports.controllers.tools) tools() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) tools_and_job_state() (galaxy.webapps.reports.controllers.tools.Tools method) tools_and_job_state_per_month() (galaxy.webapps.reports.controllers.tools.Tools method) tools_by_id() (galaxy.tools.ToolBox property) tools_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) tools_post() (galaxy_test.base.populators.BaseDatasetPopulator method) ToolsController (class in galaxy.webapps.galaxy.api.tools) (class in tool_shed.webapp.api.tools) ToolSearch (class in tool_shed.webapp.search.tool_search) ToolSection (class in galaxy.tools.toolbox) (class in galaxy.tools.toolbox.panel) ToolSectionLabel (class in galaxy.tools.toolbox) (class in galaxy.tools.toolbox.panel) ToolsGrid (class in tool_shed.grids.repository_grids) ToolsGrid.ToolsColumn (class in tool_shed.grids.repository_grids) ToolShedAppConfiguration (class in tool_shed.webapp.config) ToolShedAuthenticationController (class in tool_shed.webapp.api.authenticate) ToolShedController (class in galaxy.webapps.galaxy.api.toolshed) ToolShedDependency (class in galaxy.tool_util.deps.resolvers.galaxy_packages) ToolShedPackageDependencyResolver (class in galaxy.tool_util.deps.resolvers.tool_shed_packages) ToolShedRepositoriesController (class in galaxy.webapps.galaxy.api.tool_shed_repositories) ToolShedRepository (class in galaxy.model.tool_shed_install) ToolShedRepository.installation_status (class in galaxy.model.tool_shed_install) ToolShedRepository.states (class in galaxy.model.tool_shed_install) ToolShedRepositoryCache (class in galaxy.tools.cache) ToolShedTestDriver (class in tool_shed.test.functional_tests) ToolShedUtilityContainerManager (class in tool_shed.utility_containers) ToolSource (class in galaxy.tool_util.parser) (class in galaxy.tool_util.parser.interface) ToolStdioExitCode (class in galaxy.tool_util.parser.stdio) ToolStdioRegex (class in galaxy.tool_util.parser.stdio) ToolsTestCase (class in galaxy_test.api.test_tools) ToolsUploadTestCase (class in galaxy_test.api.test_tools_upload) ToolTagAssociation (class in galaxy.model) ToolTestDescription (class in galaxy.tool_util.verify.interactor) ToolValidator (class in galaxy.tool_shed.tools.tool_validator) (class in tool_shed.tools.tool_validator) ToolVersion (class in galaxy.model.tool_shed_install) ToolVersionAssociation (class in galaxy.model.tool_shed_install) ToolVersionListGrid (class in galaxy.webapps.galaxy.controllers.admin) ToolVersionListGrid.ToolIdColumn (class in galaxy.webapps.galaxy.controllers.admin) ToolVersionListGrid.ToolVersionsColumn (class in galaxy.webapps.galaxy.controllers.admin) ToolVersionManager (class in tool_shed.tools.tool_version_manager) ToolView (class in galaxy.model.search) ToolWatcher (class in galaxy.tools.toolbox.watcher) ToolWithRepositoryDependencies (class in tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies) ToolWithToolDependencies (class in tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies) top (galaxy.workflow.refactor.schema.Position attribute) top_level_stored_workflow() (galaxy.model.Workflow property) top_level_workflow() (galaxy.model.Workflow property) topsort() (in module galaxy.util.topsort) topsort_levels() (in module galaxy.util.topsort) Torque (class in galaxy.jobs.runners.util.cli.job.torque) total_disk_usage() (galaxy.model.GalaxySession property) (galaxy.model.User property) (tool_shed.webapp.model.User property) total_size (galaxy.model.Dataset attribute) total_size() (in module galaxy.model.custom_types) Tour (class in galaxy.tours) tour_contents() (galaxy.tours.ToursRegistry method) tour_wait_for_clickable_element() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) tour_wait_for_element_present() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) TourApiTestCase (class in galaxy_test.api.test_tours) TourCore (class in galaxy.tours) TourDetails (class in galaxy.tours) TourList (class in galaxy.tours) ToursController (class in galaxy.webapps.galaxy.api.tours) ToursRegistry (class in galaxy.tours) TourStep (class in galaxy.tours) trace() (galaxy.web.framework.base.WebApplication method) (in module galaxy.util.custom_logging) traceback (galaxy.model.Job attribute) (galaxy.model.Task attribute) TraceLogger (class in galaxy.util.custom_logging) track() (galaxy.job_metrics.collectl.stats.StatisticsTracker method) track_type (galaxy.datatypes.binary.Bam attribute) (galaxy.datatypes.binary.BigWig attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.interval.Bed attribute) (galaxy.datatypes.interval.BedGraph attribute) (galaxy.datatypes.interval.ChromatinInteractions attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Gff3 attribute) (galaxy.datatypes.interval.Gtf attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.interval.Wiggle attribute) (galaxy.datatypes.tabular.BaseVcf attribute) (galaxy.datatypes.tabular.Sam attribute) trackster() (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) TracksterConfig (class in galaxy.tools) TracksterSelectionGrid (class in galaxy.webapps.galaxy.controllers.visualization) TrafoXML (class in galaxy.datatypes.proteomics) TraML (class in galaxy.datatypes.proteomics) transaction_chooser() (galaxy.webapps.base.webapp.WebApplication method) transfer (galaxy.model.GenomeIndexToolData attribute) transfer_job (galaxy.model.TransferJob attribute) transfer_job_id (galaxy.model.GenomeIndexToolData attribute) transfer_part() (in module galaxy.objectstore.s3_multipart_upload) transfer_status() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) TransferJob (class in galaxy.model) TransferJob.states (class in galaxy.model) TransferManager (class in galaxy.jobs.transfer_manager) transform (galaxy.model.DatasetSource attribute) transform_publicname() (in module galaxy.security.validate_user_input) translate() (galaxy.tools.parameters.input_translation.ToolInputTranslator method) TransLogger (class in galaxy.web.framework.middleware.translogger) transport_class (galaxy.web_stack.ApplicationStack attribute) (galaxy.web_stack.UWSGIApplicationStack attribute) Tree (class in galaxy.model.dataset_collections.structure) TrimmedString (class in galaxy.model.custom_types) Triples (class in galaxy.datatypes.triples) Trk (class in galaxy.datatypes.images) Trr (class in galaxy.datatypes.binary) TrsConsumeAPIController (class in galaxy.webapps.galaxy.api.trs_consumer) TrsProxy (class in galaxy.workflow.trs_proxy) TrsSearchAPIController (class in galaxy.webapps.galaxy.api.trs_search) truncate() (galaxy.datatypes.dataproviders.base.DataProvider method) (in module galaxy.web.framework.helpers) truncate_index_name() (in module galaxy.model.migrate.versions.util) trust_hid() (galaxy.model.store.DirectoryImportModelStore1901 method) (galaxy.model.store.DirectoryImportModelStoreLatest method) (galaxy.model.store.ModelImportStore method) try_a_func() (in module galaxy.tool_util.deps.mulled.get_tests) try_get_authz_config() (galaxy.authnz.managers.AuthnzManager static method) ts_repo_cache (galaxy.tools.error_reports.plugins.base_git.BaseGitPlugin attribute) ts_urls (galaxy.tools.error_reports.plugins.base_git.BaseGitPlugin attribute) TSV (class in galaxy.datatypes.tabular) tuples_of_repository_dependencies_needed_for_compiling_td() (galaxy.model.tool_shed_install.ToolShedRepository property) Turtle (class in galaxy.datatypes.triples) TwoBit (class in galaxy.datatypes.binary) TwoBitFastaDataProvider (class in galaxy.datatypes.dataproviders.dataset) type (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter attribute) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter attribute) (galaxy.datatypes.display_applications.parameters.DisplayApplicationTemplateParameter attribute) (galaxy.forms.forms.FormDefinitionAddressFieldFactory attribute) (galaxy.forms.forms.FormDefinitionFieldFactory attribute) (galaxy.forms.forms.FormDefinitionHistoryFieldFactory attribute) (galaxy.forms.forms.FormDefinitionPasswordFieldFactory attribute) (galaxy.forms.forms.FormDefinitionSelectFieldFactory attribute) (galaxy.forms.forms.FormDefinitionTextFieldFactory attribute) (galaxy.forms.forms.FormDefinitionWorkflowFieldFactory attribute) (galaxy.forms.forms.FormDefinitionWorkflowMappingFieldFactory attribute) (galaxy.managers.roles.RoleModel attribute) (galaxy.model.DefaultQuotaAssociation attribute) (galaxy.model.FormDefinition attribute) (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) (galaxy.model.Role attribute) (galaxy.model.Tag attribute) (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.Visualization attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.model.WorkflowStep attribute) (galaxy.tools.parameters.grouping.Conditional attribute) (galaxy.tools.parameters.grouping.Repeat attribute) (galaxy.tools.parameters.grouping.Section attribute) (galaxy.tools.parameters.grouping.UploadDataset attribute) (galaxy.workflow.modules.InputDataCollectionModule attribute) (galaxy.workflow.modules.InputDataModule attribute) (galaxy.workflow.modules.InputParameterModule attribute) (galaxy.workflow.modules.PauseModule attribute) (galaxy.workflow.modules.SubWorkflowModule attribute) (galaxy.workflow.modules.ToolModule attribute) (galaxy.workflow.refactor.schema.AddInputAction attribute) (galaxy.workflow.refactor.schema.AddStepAction attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.Role attribute) (tool_shed.webapp.model.Tag attribute) type() (galaxy.managers.base.ModelValidator method) (galaxy.util.plugin_config.PluginConfigSource property) type_descriptions_for_field_types() (in module galaxy.tool_util.cwl.representation) type_id (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) type_key (galaxy.tools.data.RefgenieToolDataTable attribute) (galaxy.tools.data.TabularToolDataTable attribute) (galaxy.tools.data.ToolDataTable attribute) type_representation_from_name() (in module galaxy.tool_util.cwl.representation) type_to_object_store_class() (in module galaxy.objectstore) TypeRepresentation (class in galaxy.tool_util.cwl.representation) types (tool_shed.webapp.model.Role attribute) types_and_mapping() (galaxy.webapps.galaxy.api.datatypes.DatatypesController method)

U

UCI (class in galaxy.model) ucsc_links() (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.interval.CustomTrack method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.Wiggle method) UCSCLimitException, [1] UCSCOutWrapper (class in galaxy.tools.exception_handling) (class in galaxy.util.ucsc) UCSCTrackHub (class in galaxy.datatypes.tracks) uid (galaxy.model.UserAuthnzToken attribute) umask_fix_perms() (in module galaxy.util) UnamePlugin (class in galaxy.job_metrics.instrumenters.uname) uncompress() (in module tool_shed.util.commit_util) undeletable() (galaxy.model.DatasetInstance method) undelete() (galaxy.managers.deletable.DeletableManagerMixin method) (galaxy.managers.users.UserManager method) (galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController method) (galaxy.webapps.galaxy.api.extended_metadata.BaseExtendedMetadataController method) (galaxy.webapps.galaxy.api.histories.HistoriesController method) (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method) (galaxy.webapps.galaxy.api.users.UserAPIController method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) undelete_async() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) undelete_category() (tool_shed.webapp.controllers.admin.AdminController method) undelete_group() (tool_shed.util.admin_util.Admin method) undelete_operation (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) (tool_shed.util.admin_util.Admin attribute) (tool_shed.webapp.controllers.admin.AdminController attribute) undelete_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) (tool_shed.webapp.controllers.admin.AdminController method) undelete_role() (tool_shed.util.admin_util.Admin method) undelete_user() (tool_shed.util.admin_util.Admin method) UNDERSCORED_OPS (galaxy.managers.base.ModelFilterParser attribute) unhide() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) unhide_datasets() (galaxy.model.History method) unicodify() (in module galaxy.util) UNINITIALIZED_ELEMENT (galaxy.model.DatasetCollectionElement attribute) UninitializedTree (class in galaxy.model.dataset_collections.structure) uninstall() (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method) uninstall_dependencies() (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tools.ToolsController method) uninstall_environments() (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method) uninstall_repository() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method) (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) uninstall_tool_dependencies() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) uninstallable_resolvers() (galaxy.tool_util.deps.views.DependencyResolversView property) UNINSTALLED (galaxy.model.tool_shed_install.ToolDependency.states attribute) uninstalled (galaxy.model.tool_shed_install.ToolShedRepository attribute) UNINSTALLED (galaxy.model.tool_shed_install.ToolShedRepository.installation_status attribute) (galaxy.model.tool_shed_install.ToolShedRepository.states attribute) uninstalled_repository_dependencies() (galaxy.model.tool_shed_install.ToolShedRepository property) uninstalled_tool_dependencies() (galaxy.model.tool_shed_install.ToolShedRepository property) UninstallingAndReinstallingRepositories (class in tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository) (class in tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies) (class in tool_shed.test.functional.test_1220_uninstall_reinstall_repository_with_repository_dependencies) (class in tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions) UniProtXML (class in galaxy.datatypes.proteomics) unique_id() (in module galaxy.util) unique_workflow_outputs() (galaxy.model.WorkflowStep property) UniqueValueFilter (class in galaxy.tools.parameters.dynamic_options) UnivaJobRunner (class in galaxy.jobs.runners.univa) UniverseApplication (class in galaxy.app) (class in galaxy.webapps.reports.app) (class in tool_shed.webapp.app) UNKNOWN (galaxy.model.DatasetInstance.validated_states attribute) (galaxy.model.TransferJob.states attribute) UnknownContentsType UnlinkedToolShedPackageDependencyResolver (class in galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages) unload_certified_level_one_repository_and_suite_tuple() (tool_shed.repository_registry.Registry method) unload_repository_and_suite_tuple() (tool_shed.repository_registry.Registry method) unpack_archive() (in module galaxy.tools.imp_exp.unpack_tar_gz_archive) unpause_dependent_jobs() (galaxy.model.HistoryDatasetAssociation method) unpublish() (galaxy.managers.sharable.SharableModelManager method) UNREGISTERED (galaxy.model.DefaultQuotaAssociation.types attribute) Unrestricted (class in tool_shed.repository_types.unrestricted) unsafe_walk() (in module galaxy.util.path) unset_dataset_matcher_factory() (in module galaxy.tools.parameters.dataset_matcher) unset_filter() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method) (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase method) unset_item_extended_metadata_obj() (galaxy.webapps.base.controller.UsesExtendedMetadataMixin method) unshare_with() (galaxy.managers.sharable.SharableModelManager method) UnspecifiedBuildValidator (class in galaxy.tools.parameters.validation) unstructured_path_rewrite() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) UNSUPPORTED_HANDLER_ASSIGNMENT_METHODS (galaxy.web_stack.handlers.ConfiguresHandlers attribute) (galaxy.workflow.scheduling_manager.WorkflowSchedulingManager attribute) unused_dependency_paths() (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method) (galaxy.tool_util.deps.views.DependencyResolversView property) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) unused_port() (in module galaxy.util.sockets) UnusedMetadataSourceProvider (class in galaxy.model.store.discover) UnusedPermissionProvider (class in galaxy.model.store.discover) unvalidated() (galaxy.datatypes.data.DatatypeValidation static method) unversioned_install() (in module galaxy.tool_util.deps.brew_exts) unwrap() (galaxy.datatypes.metadata.MetadataElementSpec method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.model.metadata.MetadataElementSpec method) (galaxy.model.metadata.MetadataParameter method) UnzipCollectionTool (class in galaxy.tools) up_to_date() (galaxy.model.JobExportHistoryArchive property) update() (galaxy.managers.base.ModelManager method) (galaxy.managers.collections.DatasetCollectionManager method) (galaxy.managers.folders.FolderManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.managers.library_datasets.LibraryDatasetsManager method) (galaxy.model.custom_types.MutationDict method) (galaxy.model.DatasetInstance method) (galaxy.model.WorkflowInvocation method) (galaxy.util.odict.odict method) (galaxy.util.Params method) (galaxy.webapps.galaxy.api.cloudauthz.CloudAuthzController method) (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method) (galaxy.webapps.galaxy.api.folders.FoldersController method) (galaxy.webapps.galaxy.api.group_roles.GroupRolesAPIController method) (galaxy.webapps.galaxy.api.group_users.GroupUsersAPIController method) (galaxy.webapps.galaxy.api.groups.GroupAPIController method) (galaxy.webapps.galaxy.api.histories.HistoriesController method) (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method) (galaxy.webapps.galaxy.api.item_tags.BaseItemTagsController method) (galaxy.webapps.galaxy.api.libraries.LibrariesController method) (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method) (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method) (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method) (galaxy.webapps.galaxy.api.tags.TagsController method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method) (galaxy.webapps.galaxy.api.users.UserAPIController method) (galaxy.webapps.galaxy.api.visualizations.VisualizationsController method) (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) (tool_shed.managers.groups.GroupManager method) (tool_shed.managers.repositories.RepoManager method) (tool_shed.webapp.api.repositories.RepositoriesController method) (tool_shed.webapp.api.repository_revisions.RepositoryRevisionsController method) update_batch() (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method) update_circular_repository_dependencies() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) update_existing_tool_dependency() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) update_files() (galaxy.tools.data.ToolDataPathFiles method) update_from_file() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) update_in_shed_tool_config() (galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) update_installed_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) update_invocation_step() (galaxy.managers.workflows.WorkflowsManager method) (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) update_job_lock() (galaxy.managers.jobs.JobManager method) (galaxy.webapps.galaxy.api.jobs.JobController method) (in module galaxy.webapps.galaxy.api.job_lock) update_object_store_with_datasets() (galaxy.model.store.discover.ModelPersistenceContext method) update_or_append() (galaxy.tools.toolbox.panel.ToolPanelElements method) update_output_states() (galaxy.model.Job method) update_parent_folder_update_times() (galaxy.model.LibraryDatasetDatasetAssociation method) update_permissions() (galaxy.managers.datasets.DatasetAssociationManager method) (galaxy.webapps.galaxy.api.datasets.DatasetsController method) (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method) (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method) update_proxy() (galaxy.web.proxy.ProxyManager method) update_repository() (galaxy.tool_util.verify.test_data.GitDataResolver method) (in module galaxy.tool_shed.util.hg_util) (in module tool_shed.util.hg_util) (in module tool_shed.util.repository_util) update_repository_dependencies_metadata() (galaxy.tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) update_repository_record() (galaxy.tool_shed.galaxy_install.update_repository_manager.UpdateRepositoryManager method) update_requests() (galaxy.web.proxy.JsonFileProxyIpc method) (galaxy.web.proxy.SqliteProxyIpc method) update_sequencer_id_in_request_type() (in module galaxy.model.migrate.versions.0067_populate_sequencer_table) update_shed_config() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) update_stored_workflow_attributes (galaxy.managers.workflows.WorkflowUpdateOptions attribute) update_time (galaxy.model.DataManagerHistoryAssociation attribute) (galaxy.model.DataManagerJobAssociation attribute) (galaxy.model.Dataset attribute) (galaxy.model.DatasetCollection attribute) (galaxy.model.DatasetPermissions attribute) (galaxy.model.DefaultQuotaAssociation attribute) (galaxy.model.DeferredJob attribute) (galaxy.model.DynamicTool attribute) (galaxy.model.Event attribute) (galaxy.model.FormDefinition attribute) (galaxy.model.FormDefinitionCurrent attribute) (galaxy.model.FormValues attribute) (galaxy.model.GalaxySession attribute) (galaxy.model.Group attribute) (galaxy.model.GroupQuotaAssociation attribute) (galaxy.model.GroupRoleAssociation attribute) (galaxy.model.History attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization attribute) (galaxy.model.HistoryDatasetAssociationHistory 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.TransferJob attribute) (galaxy.model.User attribute) (galaxy.model.UserAddress attribute) (galaxy.model.UserGroupAssociation attribute) (galaxy.model.UserQuotaAssociation attribute) (galaxy.model.UserRoleAssociation attribute) (galaxy.model.Visualization attribute) (galaxy.model.VisualizationRevision attribute) (galaxy.model.WorkerProcess attribute) (galaxy.model.Workflow attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowStep attribute) (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) update_to_changeset_revision() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) update_tool_panel_dict() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) update_tool_shed_repository() (galaxy.tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) update_tool_shed_repository_status() (galaxy.tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) update_tool_shed_status() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) update_tour() (galaxy.webapps.galaxy.api.tours.FastAPITours method) (galaxy.webapps.galaxy.api.tours.ToursController method) update_watch_data_table_paths() (galaxy.config_watchers.ConfigWatchers method) update_watcher_designation() (galaxy.model.database_heartbeat.DatabaseHeartbeat method) update_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method) update_workflow_from_raw_description() (galaxy.managers.workflows.WorkflowContentsManager method) UpdateAnnotationAction (class in galaxy.workflow.refactor.schema) UpdateCreatorAction (class in galaxy.workflow.refactor.schema) updated_changeset_revisions() (tool_shed.webapp.controllers.repository.RepositoryController method) UpdateLicenseAction (class in galaxy.workflow.refactor.schema) UpdateNameAction (class in galaxy.workflow.refactor.schema) UpdateOutputLabelAction (class in galaxy.workflow.refactor.schema) UpdateReportAction (class in galaxy.workflow.refactor.schema) UpdateRepositoryManager (class in galaxy.tool_shed.galaxy_install.update_repository_manager) updates() (tool_shed.webapp.api.repositories.RepositoriesController method) UpdateStepLabelAction (class in galaxy.workflow.refactor.schema) UpdateStepPositionAction (class in galaxy.workflow.refactor.schema) upgrade() (in module galaxy.model.migrate.versions.0001_initial_tables) (in module galaxy.model.migrate.versions.0002_metadata_file_table) (in module galaxy.model.migrate.versions.0003_security_and_libraries) (in module galaxy.model.migrate.versions.0004_indexes_and_defaults) (in module galaxy.model.migrate.versions.0005_cleanup_datasets_fix) (in module galaxy.model.migrate.versions.0006_change_qual_datatype) (in module galaxy.model.migrate.versions.0007_sharing_histories) (in module galaxy.model.migrate.versions.0008_galaxy_forms) (in module galaxy.model.migrate.versions.0009_request_table) (in module galaxy.model.migrate.versions.0010_hda_display_at_authz_table) (in module galaxy.model.migrate.versions.0011_v0010_mysql_index_fix) (in module galaxy.model.migrate.versions.0012_user_address) (in module galaxy.model.migrate.versions.0013_change_lib_item_templates_to_forms) (in module galaxy.model.migrate.versions.0014_pages) (in module galaxy.model.migrate.versions.0015_tagging) (in module galaxy.model.migrate.versions.0016_v0015_mysql_index_fix) (in module galaxy.model.migrate.versions.0017_library_item_indexes) (in module galaxy.model.migrate.versions.0018_ordered_tags_and_page_tags) (in module galaxy.model.migrate.versions.0019_request_library_folder) (in module galaxy.model.migrate.versions.0020_library_upload_job) (in module galaxy.model.migrate.versions.0021_user_prefs) (in module galaxy.model.migrate.versions.0022_visualization_tables) (in module galaxy.model.migrate.versions.0023_page_published_and_deleted_columns) (in module galaxy.model.migrate.versions.0024_page_slug_unique_constraint) (in module galaxy.model.migrate.versions.0025_user_info) (in module galaxy.model.migrate.versions.0026_cloud_tables) (in module galaxy.model.migrate.versions.0027_request_events) (in module galaxy.model.migrate.versions.0028_external_metadata_file_override) (in module galaxy.model.migrate.versions.0029_user_actions) (in module galaxy.model.migrate.versions.0030_history_slug_column) (in module galaxy.model.migrate.versions.0031_community_and_workflow_tags) (in module galaxy.model.migrate.versions.0032_stored_workflow_slug_column) (in module galaxy.model.migrate.versions.0033_published_cols_for_histories_and_workflows) (in module galaxy.model.migrate.versions.0034_page_user_share_association) (in module galaxy.model.migrate.versions.0035_item_annotations_and_workflow_step_tags) (in module galaxy.model.migrate.versions.0036_add_deleted_column_to_library_template_assoc_tables) (in module galaxy.model.migrate.versions.0037_samples_library) (in module galaxy.model.migrate.versions.0038_add_inheritable_column_to_library_template_assoc_tables) (in module galaxy.model.migrate.versions.0039_add_synopsis_column_to_library_table) (in module galaxy.model.migrate.versions.0040_page_annotations) (in module galaxy.model.migrate.versions.0041_workflow_invocation) (in module galaxy.model.migrate.versions.0042_workflow_invocation_fix) (in module galaxy.model.migrate.versions.0043_visualization_sharing_tagging_annotating) (in module galaxy.model.migrate.versions.0044_add_notify_column_to_request_table) (in module galaxy.model.migrate.versions.0045_request_type_permissions_table) (in module galaxy.model.migrate.versions.0046_post_job_actions) (in module galaxy.model.migrate.versions.0047_job_table_user_id_column) (in module galaxy.model.migrate.versions.0048_dataset_instance_state_column) (in module galaxy.model.migrate.versions.0049_api_keys_table) (in module galaxy.model.migrate.versions.0050_drop_cloud_tables) (in module galaxy.model.migrate.versions.0051_imported_col_for_jobs_table) (in module galaxy.model.migrate.versions.0052_sample_dataset_table) (in module galaxy.model.migrate.versions.0053_item_ratings) (in module galaxy.model.migrate.versions.0054_visualization_dbkey) (in module galaxy.model.migrate.versions.0055_add_pja_assoc_for_jobs) (in module galaxy.model.migrate.versions.0056_workflow_outputs) (in module galaxy.model.migrate.versions.0057_request_notify) (in module galaxy.model.migrate.versions.0058_history_import_export) (in module galaxy.model.migrate.versions.0059_sample_dataset_file_path) (in module galaxy.model.migrate.versions.0060_history_archive_import) (in module galaxy.model.migrate.versions.0061_tasks) (in module galaxy.model.migrate.versions.0062_user_openid_table) (in module galaxy.model.migrate.versions.0063_sequencer_table) (in module galaxy.model.migrate.versions.0064_add_run_and_sample_run_association_tables) (in module galaxy.model.migrate.versions.0065_add_name_to_form_fields_and_values) (in module galaxy.model.migrate.versions.0066_deferred_job_and_transfer_job_tables) (in module galaxy.model.migrate.versions.0067_populate_sequencer_table) (in module galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services) (in module galaxy.model.migrate.versions.0069_rename_sequencer_form_type) (in module galaxy.model.migrate.versions.0070_add_info_column_to_deferred_job_table) (in module galaxy.model.migrate.versions.0071_add_history_and_workflow_to_sample) (in module galaxy.model.migrate.versions.0072_add_pid_and_socket_columns_to_transfer_job_table) (in module galaxy.model.migrate.versions.0073_add_ldda_to_implicit_conversion_table) (in module galaxy.model.migrate.versions.0074_add_purged_column_to_library_dataset_table) (in module galaxy.model.migrate.versions.0075_add_subindex_column_to_run_table) (in module galaxy.model.migrate.versions.0076_fix_form_values_data_corruption) (in module galaxy.model.migrate.versions.0077_create_tool_tag_association_table) (in module galaxy.model.migrate.versions.0078_add_columns_for_disk_usage_accounting) (in module galaxy.model.migrate.versions.0079_input_library_to_job_table) (in module galaxy.model.migrate.versions.0080_quota_tables) (in module galaxy.model.migrate.versions.0081_add_tool_version_to_hda_ldda) (in module galaxy.model.migrate.versions.0082_add_tool_shed_repository_table) (in module galaxy.model.migrate.versions.0083_add_prepare_files_to_task) (in module galaxy.model.migrate.versions.0084_add_ldda_id_to_implicit_conversion_table) (in module galaxy.model.migrate.versions.0085_add_task_info) (in module galaxy.model.migrate.versions.0086_add_tool_shed_repository_table_columns) (in module galaxy.model.migrate.versions.0087_tool_id_guid_map_table) (in module galaxy.model.migrate.versions.0088_add_installed_changeset_revison_column) (in module galaxy.model.migrate.versions.0089_add_object_store_id_columns) (in module galaxy.model.migrate.versions.0090_add_tool_shed_repository_table_columns) (in module galaxy.model.migrate.versions.0091_add_tool_version_tables) (in module galaxy.model.migrate.versions.0092_add_migrate_tools_table) (in module galaxy.model.migrate.versions.0093_add_job_params_col) (in module galaxy.model.migrate.versions.0094_add_job_handler_col) (in module galaxy.model.migrate.versions.0095_hda_subsets) (in module galaxy.model.migrate.versions.0096_openid_provider) (in module galaxy.model.migrate.versions.0097_add_ctx_rev_column) (in module galaxy.model.migrate.versions.0098_genome_index_tool_data_table) (in module galaxy.model.migrate.versions.0099_add_tool_dependency_table) (in module galaxy.model.migrate.versions.0100_alter_tool_dependency_table_version_column) (in module galaxy.model.migrate.versions.0101_drop_installed_changeset_revision_column) (in module galaxy.model.migrate.versions.0102_add_tool_dependency_status_columns) (in module galaxy.model.migrate.versions.0103_add_tool_shed_repository_status_columns) (in module galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters) (in module galaxy.model.migrate.versions.0105_add_cleanup_event_table) (in module galaxy.model.migrate.versions.0106_add_missing_indexes) (in module galaxy.model.migrate.versions.0107_add_exit_code_to_job_and_task) (in module galaxy.model.migrate.versions.0108_add_extended_metadata) (in module galaxy.model.migrate.versions.0109_add_repository_dependency_tables) (in module galaxy.model.migrate.versions.0110_add_dataset_uuid) (in module galaxy.model.migrate.versions.0111_add_job_destinations) (in module galaxy.model.migrate.versions.0112_add_data_manager_history_association_and_data_manager_job_association_tables) (in module galaxy.model.migrate.versions.0113_update_migrate_tools_table) (in module galaxy.model.migrate.versions.0114_update_migrate_tools_table_again) (in module galaxy.model.migrate.versions.0115_longer_user_password_field) (in module galaxy.model.migrate.versions.0116_drop_update_available_col_add_tool_shed_status_col) (in module galaxy.model.migrate.versions.0117_add_user_activation) (in module galaxy.model.migrate.versions.0118_add_hda_extended_metadata) (in module galaxy.model.migrate.versions.0119_job_metrics) (in module galaxy.model.migrate.versions.0120_dataset_collections) (in module galaxy.model.migrate.versions.0121_workflow_uuids) (in module galaxy.model.migrate.versions.0122_grow_mysql_blobs) (in module galaxy.model.migrate.versions.0123_add_workflow_request_tables) (in module galaxy.model.migrate.versions.0124_job_state_history) (in module galaxy.model.migrate.versions.0125_workflow_step_tracking) (in module galaxy.model.migrate.versions.0126_password_reset) (in module galaxy.model.migrate.versions.0127_output_collection_adjustments) (in module galaxy.model.migrate.versions.0128_session_timeout) (in module galaxy.model.migrate.versions.0129_job_external_output_metadata_validity) (in module galaxy.model.migrate.versions.0130_change_pref_datatype) (in module galaxy.model.migrate.versions.0131_subworkflow_and_input_parameter_modules) (in module galaxy.model.migrate.versions.0132_add_lastpasswordchange_to_user) (in module galaxy.model.migrate.versions.0133_add_dependency_column_to_job) (in module galaxy.model.migrate.versions.0134_hda_set_deleted_if_purged) (in module galaxy.model.migrate.versions.0135_add_library_tags) (in module galaxy.model.migrate.versions.0136_collection_and_workflow_state) (in module galaxy.model.migrate.versions.0137_add_copied_from_job_id_column) (in module galaxy.model.migrate.versions.0138_add_hda_version) (in module galaxy.model.migrate.versions.0139_add_history_dataset_association_history_table) (in module galaxy.model.migrate.versions.0140_add_dataset_version_to_job_to_input_dataset_association_table) (in module galaxy.model.migrate.versions.0141_add_oidc_tables) (in module galaxy.model.migrate.versions.0142_change_numeric_metric_precision) (in module galaxy.model.migrate.versions.0143_add_cloudauthz_tables) (in module galaxy.model.migrate.versions.0144_add_cleanup_event_user_table) (in module galaxy.model.migrate.versions.0145_add_workflow_step_input) (in module galaxy.model.migrate.versions.0146_workflow_paths) (in module galaxy.model.migrate.versions.0147_job_messages) (in module galaxy.model.migrate.versions.0148_add_checksum_table) (in module galaxy.model.migrate.versions.0149_dynamic_tools) (in module galaxy.model.migrate.versions.0150_add_create_time_field_for_cloudauthz) (in module galaxy.model.migrate.versions.0151_add_worker_process) (in module galaxy.model.migrate.versions.0152_add_metadata_file_uuid) (in module galaxy.model.migrate.versions.0153_add_custos_authnz_token_table) (in module galaxy.model.migrate.versions.0154_created_from_basename) (in module galaxy.model.migrate.versions.0155_job_galaxy_version) (in module galaxy.model.migrate.versions.0156_add_interactivetools) (in module galaxy.model.migrate.versions.0157_rework_dataset_validation) (in module galaxy.model.migrate.versions.0158_workflow_reports) (in module galaxy.model.migrate.versions.0159_add_job_external_id_index) (in module galaxy.model.migrate.versions.0160_hda_set_deleted_if_purged_again) (in module galaxy.model.migrate.versions.0161_add_workflow_invocation_output_table) (in module galaxy.model.migrate.versions.0162_job_only_pjas) (in module galaxy.model.migrate.versions.0163_worker_process_pid) (in module galaxy.model.migrate.versions.0164_page_format) (in module galaxy.model.migrate.versions.0165_add_content_update_time) (in module galaxy.model.migrate.versions.0166_job_state_summary_view) (in module galaxy.model.migrate.versions.0167_add_job_to_input_dataset_collection_element_association) (in module galaxy.model.migrate.versions.0168_stored_workflow_hidden_col) (in module galaxy.model.migrate.versions.0169_add_missing_indexes) (in module galaxy.model.migrate.versions.0170_add_more_missing_indexes) (in module galaxy.model.migrate.versions.0171_schemaorg_metadata) (in module galaxy.model.migrate.versions.0172_it_entrypoint_requires_domain) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0001_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0002_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0003_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0004_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0005_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0006_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0007_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0008_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0009_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0010_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0011_tools) (in module galaxy.tool_shed.galaxy_install.migrate.versions.0012_tools) (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)

upgrade_available() (galaxy.model.tool_shed_install.ToolShedRepository property) UpgradeSubworkflowAction (class in galaxy.workflow.refactor.schema) UpgradeToolAction (class in galaxy.workflow.refactor.schema) UPLOAD (galaxy.model.Dataset.states attribute) (galaxy.model.DatasetInstance.states attribute) (galaxy.model.Job.states attribute) upload (galaxy.model.view.HistoryDatasetCollectionJobStateSummary attribute) upload() (tool_shed.webapp.controllers.upload.UploadController method) upload_build() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_collection() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method) upload_directory() (tool_shed.webapp.controllers.upload.UploadController method) upload_file() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) upload_list() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_options (galaxy.model.LibraryDataset attribute) upload_pair() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_paired_list() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_paste_data() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_payload() (galaxy_test.base.populators.BaseDatasetPopulator method) upload_queue_local_file() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_rule_build() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_rule_set_data_type() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_rule_set_dataset() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_rule_set_input_type() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_rule_start() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_set_collection_type() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_set_footer_extension() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_set_footer_genome() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_start() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_start_click() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_tab_click() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) upload_tar() (in module tool_shed.util.repository_content_util) upload_url() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) upload_yaml_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method) (galaxy_test.selenium.framework.SeleniumSessionWorkflowPopulator method) UploadConfig (class in galaxy.tools.data_fetch) UploadController (class in tool_shed.webapp.controllers.upload) UploadDataset (class in galaxy.tools.parameters.grouping) UploadProblemException UploadsAPIController (class in galaxy.webapps.galaxy.api.uploads) UploadsTestCase (class in galaxy_test.selenium.test_uploads) UploadToolAction (class in galaxy.tools.actions.upload) uri() (galaxy.tool_util.cwl.schema.RawProcessReference property) (galaxy.tool_util.cwl.schema.ResolvedProcessDefinition property) uri_from_path() (galaxy.files.sources.BaseFilesSource method) uri_join() (in module galaxy.files.sources) url (galaxy.managers.licenses.LicenseMetadataModel attribute) (galaxy.managers.roles.RoleModel attribute) url() (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper property) url_auth() (galaxy.tool_shed.tool_shed_registry.Registry method) url_download() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.Download method) url_for() (galaxy.managers.base.ModelSerializer static method) (in module galaxy.web) (in module galaxy.webapps.reports) (in module tool_shed.webapp) url_get() (in module galaxy.util) url_template() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) url_to_destination() (galaxy.jobs.handler.DefaultJobDispatcher method) (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) (galaxy.jobs.runners.pbs.PBSJobRunner method) URLDataProvider (class in galaxy.datatypes.dataproviders.external) usage (galaxy.util.pastescript.serve.Command attribute) (galaxy.util.pastescript.serve.ServeCommand attribute) use() (galaxy.model.PSANonce class method) use_async (galaxy.web.legacy_framework.grids.Grid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) use_default_filter (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) use_fetch_api() (galaxy.tool_util.client.staging.InteractorStaging property) (galaxy.tool_util.client.staging.StagingInterace property) use_final (tool_shed.webapp.search.repo_search.RepoWeighting attribute) use_hide_message (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.web.legacy_framework.grids.Grid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) use_messaging() (galaxy.web_stack.handlers.ConfiguresHandlers property) use_metadata_binary() (galaxy.jobs.JobWrapper property) use_mq (galaxy.jobs.runners.pulsar.PulsarMQJobRunner attribute) use_paging (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.page.ItemSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.TracksterSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid 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.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) use_panels (galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageListGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid attribute) use_pbkdf2 (galaxy.model.User attribute) use_tmp_dir() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method) use_virtual_display() (in module galaxy_test.selenium.framework) use_volumes() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest property) User (class in galaxy.model) (class in galaxy.webapps.galaxy.controllers.user) (class in galaxy.webapps.galaxy.controllers.userskeys) (class in tool_shed.webapp.controllers.user) (class in tool_shed.webapp.model) user (galaxy.authnz.psa_authnz.Storage attribute) (galaxy.model.APIKeys attribute) (galaxy.model.CloudAuthz attribute) (galaxy.model.CustosAuthnzToken attribute) (galaxy.model.DataManagerHistoryAssociation attribute) (galaxy.model.DefaultUserPermissions attribute) (galaxy.model.Event attribute) (galaxy.model.GalaxySession attribute) (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.History attribute) (galaxy.model.HistoryAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization attribute) (galaxy.model.HistoryDatasetAssociationRatingAssociation attribute) (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetCollectionRatingAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryRatingAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.HistoryUserShareAssociation attribute) (galaxy.model.Job attribute) (galaxy.model.LibraryDatasetCollectionAnnotationAssociation attribute) (galaxy.model.LibraryDatasetCollectionRatingAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.Page attribute) (galaxy.model.PageAnnotationAssociation attribute) (galaxy.model.PageRatingAssociation attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.PageUserShareAssociation attribute) (galaxy.model.PasswordResetToken attribute) USER (galaxy.model.Role.types attribute) user (galaxy.model.StoredWorkflow attribute) (galaxy.model.StoredWorkflowAnnotationAssociation attribute) (galaxy.model.StoredWorkflowMenuEntry attribute) (galaxy.model.StoredWorkflowRatingAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.StoredWorkflowUserShareAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.UserAction attribute) (galaxy.model.UserAddress attribute) (galaxy.model.UserAuthnzToken attribute) (galaxy.model.UserGroupAssociation attribute) (galaxy.model.UserPreference attribute) (galaxy.model.UserQuotaAssociation attribute) (galaxy.model.UserRoleAssociation attribute) (galaxy.model.UserShareAssociation attribute) (galaxy.model.Visualization attribute) (galaxy.model.VisualizationAnnotationAssociation attribute) (galaxy.model.VisualizationRatingAssociation attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.VisualizationUserShareAssociation attribute) (galaxy.model.WorkflowStepAnnotationAssociation attribute) (galaxy.model.WorkflowStepTagAssociation attribute) (tool_shed.webapp.model.GalaxySession attribute) (tool_shed.webapp.model.PasswordResetToken attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.RepositoryRatingAssociation attribute) (tool_shed.webapp.model.RepositoryReview attribute) (tool_shed.webapp.model.UserGroupAssociation attribute) (tool_shed.webapp.model.UserRoleAssociation attribute) user() (galaxy.job_execution.output_collect.JobContext property) (galaxy.jobs.JobWrapper property) (galaxy.model.store.discover.ModelPersistenceContext property) (galaxy.model.store.discover.SessionlessModelPersistenceContext property) (galaxy.webapps.base.webapp.GalaxyWebTransaction property) (galaxy.work.context.WorkRequestContext property) user_assoc (galaxy.managers.roles.RoleManager attribute) USER_BOOTSTRAP_KEYS (galaxy.webapps.base.controller.JSAppLauncher attribute) user_can_administer_repository() (tool_shed.webapp.security.CommunityRBACAgent method) user_can_browse_component_review() (tool_shed.webapp.security.CommunityRBACAgent method) user_can_do_run_as() (galaxy.managers.context.ProvidesUserContext property) user_can_import_repository_archive() (tool_shed.webapp.security.CommunityRBACAgent method) user_can_purge() (galaxy.model.Dataset property) user_can_review_repositories() (tool_shed.webapp.security.CommunityRBACAgent method) user_checks() (galaxy.webapps.base.webapp.GalaxyWebTransaction method) user_disk_usage() (galaxy.webapps.reports.controllers.users.Users method) user_email() (galaxy_test.base.populators.BaseDatasetPopulator method) (galaxy_test.base.populators.LibraryPopulator method) user_exists() (galaxy.model.UserAuthnzToken class method) user_ftp_dir() (galaxy.managers.context.ProvidesUserContext property) user_get_default_permissions() (galaxy.model.security.GalaxyRBACAgent method) user_id (galaxy.model.APIKeys attribute) (galaxy.model.CloudAuthz attribute) (galaxy.model.CustosAuthnzToken attribute) (galaxy.model.DataManagerHistoryAssociation attribute) (galaxy.model.DefaultUserPermissions attribute) (galaxy.model.Event attribute) (galaxy.model.GalaxySession attribute) (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.History attribute) (galaxy.model.HistoryAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization attribute) (galaxy.model.HistoryDatasetAssociationRatingAssociation attribute) (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetCollectionRatingAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryRatingAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.HistoryUserShareAssociation attribute) (galaxy.model.Job attribute) (galaxy.model.LibraryDatasetCollectionAnnotationAssociation attribute) (galaxy.model.LibraryDatasetCollectionRatingAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.Page attribute) (galaxy.model.PageAnnotationAssociation attribute) (galaxy.model.PageRatingAssociation attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.PageUserShareAssociation attribute) (galaxy.model.PasswordResetToken attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.StoredWorkflowAnnotationAssociation attribute) (galaxy.model.StoredWorkflowMenuEntry attribute) (galaxy.model.StoredWorkflowRatingAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.StoredWorkflowUserShareAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.UserAction attribute) (galaxy.model.UserAddress attribute) (galaxy.model.UserAuthnzToken attribute) (galaxy.model.UserGroupAssociation attribute) (galaxy.model.UserPreference attribute) (galaxy.model.UserQuotaAssociation attribute) (galaxy.model.UserRoleAssociation attribute) (galaxy.model.Visualization attribute) (galaxy.model.VisualizationAnnotationAssociation attribute) (galaxy.model.VisualizationRatingAssociation attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.VisualizationUserShareAssociation attribute) (galaxy.model.WorkflowStepAnnotationAssociation attribute) (galaxy.model.WorkflowStepTagAssociation attribute) (tool_shed.webapp.model.APIKeys attribute) (tool_shed.webapp.model.GalaxySession attribute) (tool_shed.webapp.model.PasswordResetToken attribute) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.RepositoryRatingAssociation attribute) (tool_shed.webapp.model.RepositoryReview attribute) (tool_shed.webapp.model.UserGroupAssociation attribute) (tool_shed.webapp.model.UserRoleAssociation attribute) user_id() (galaxy_test.base.populators.BaseDatasetPopulator method) user_ids (galaxy.managers.roles.RoleDefinitionModel attribute) USER_INFO (galaxy.model.FormDefinition.types attribute) user_is_active() (galaxy.managers.context.ProvidesUserContext property) user_is_admin() (galaxy.managers.context.ProvidesUserContext property) user_list_grid (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) (tool_shed.util.admin_util.Admin attribute) (tool_shed.webapp.controllers.admin.AdminController attribute) user_model() (galaxy.model.UserAuthnzToken class method) user_per_month() (galaxy.webapps.reports.controllers.jobs.Jobs method) (galaxy.webapps.reports.controllers.workflows.Workflows method) user_private_role_id() (galaxy_test.base.populators.BaseDatasetPopulator method) (galaxy_test.base.populators.LibraryPopulator method) user_query() (galaxy.model.UserAuthnzToken class method) user_set_default_permissions() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) user_share_model (galaxy.managers.cloud.CloudManager attribute) (galaxy.managers.cloudauthzs.CloudAuthzManager attribute) (galaxy.managers.histories.HistoryManager attribute) (galaxy.managers.pages.PageManager attribute) (galaxy.managers.sharable.SharableModelManager attribute) (galaxy.managers.visualizations.VisualizationManager attribute) user_system_pwent() (galaxy.jobs.JobWrapper property) user_template_environment() (galaxy.model.User static method) user_tname (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.WorkflowStepTagAssociation attribute) user_value (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.WorkflowStepTagAssociation attribute) UserAction (class in galaxy.model) UserActivationRequiredException UserAddress (class in galaxy.model) UserAPIController (class in galaxy.webapps.galaxy.api.users) UserAuthnzToken (class in galaxy.model) UserDeserializer (class in galaxy.managers.users) UserFtpFilesSource (class in galaxy.files.sources.galaxy) UserGrid (class in tool_shed.grids.admin_grids) UserGrid.EmailColumn (class in tool_shed.grids.admin_grids) UserGrid.ExternalColumn (class in tool_shed.grids.admin_grids) UserGrid.GroupsColumn (class in tool_shed.grids.admin_grids) UserGrid.LastLoginColumn (class in tool_shed.grids.admin_grids) UserGrid.RolesColumn (class in tool_shed.grids.admin_grids) UserGrid.StatusColumn (class in tool_shed.grids.admin_grids) UserGrid.UserLoginColumn (class in tool_shed.grids.admin_grids) UserGrid.UserNameColumn (class in tool_shed.grids.admin_grids) UserGroupAssociation (class in galaxy.model) (class in tool_shed.webapp.model) userless_histories() (galaxy.webapps.reports.controllers.system.System method) UserLibraryImportFilesSource (class in galaxy.files.sources.galaxy) UserListGrid (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.ActivatedColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.DiskUsageColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.EmailColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.ExternalColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.GroupsColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.LastLoginColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.RolesColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.StatusColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.TimeCreatedColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.UserNameColumn (class in galaxy.webapps.galaxy.controllers.admin) UserManager (class in galaxy.managers.users) username (galaxy.model.User attribute) (tool_shed.webapp.model.User attribute) username() (galaxy.files.DictFileSourcesUserContext property) (galaxy.files.ProvidesUserFileSourcesUserContext property) (galaxy.model.Page property) username_max_length() (galaxy.model.UserAuthnzToken class method) UserPreference (class in galaxy.model) UserQuotaAssociation (class in galaxy.model) UserRoleAssociation (class in galaxy.model) (class in tool_shed.webapp.model) Users (class in galaxy.webapps.reports.controllers.users) users (galaxy.model.Group attribute) (galaxy.model.Quota attribute) (galaxy.model.Role attribute) (tool_shed.webapp.model.Group attribute) (tool_shed.webapp.model.Role attribute) users() (tool_shed.util.admin_util.Admin method) users_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) users_shared_with (galaxy.model.History attribute) (galaxy.model.Page attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.Visualization attribute) users_shared_with_count (galaxy.model.History attribute) users_shared_with_dot_users (galaxy.model.History attribute) (galaxy.model.Page attribute) (galaxy.model.StoredWorkflow attribute) (galaxy.model.Visualization attribute) UsersApiTestCase (class in galaxy_test.api.test_users) UsersController (class in tool_shed.webapp.api.users) UserSerializer (class in galaxy.managers.users) UserShareAssociation (class in galaxy.model) uses_param() (galaxy.tool_util.cwl.representation.TypeRepresentation property) uses_test_history() (in module galaxy_test.base.populators) uses_tool_shed_dependencies() (galaxy.tool_util.deps.DependencyManager method) (galaxy.tool_util.deps.NullDependencyManager method) UsesAnnotations (class in galaxy.model.item_attrs) UsesApiTestCaseMixin (class in galaxy_test.base.api) UsesCreateAndUpdateTime (class in galaxy.model) UsesExtendedMetadataMixin (class in galaxy.webapps.base.controller) UsesFormDefinitionsMixin (class in galaxy.webapps.base.controller) UsesHistoryItemAssertions (class in galaxy_test.selenium.framework) UsesHomebrewMixin (class in galaxy.tool_util.deps.resolvers.resolver_mixins) UsesInstalledRepositoriesMixin (class in galaxy.tool_util.deps.resolvers.resolver_mixins) UsesItemRatings (class in galaxy.model.item_attrs) UsesLibraryMixin (class in galaxy.webapps.base.controller) UsesLibraryMixinItems (class in galaxy.webapps.base.controller) UsesQuotaMixin (class in galaxy.webapps.base.controller) UsesStoredWorkflowMixin (class in galaxy.webapps.base.controller) UsesTagsMixin (class in galaxy.webapps.base.controller) UsesToolDependencyDirMixin (class in galaxy.tool_util.deps.resolvers.resolver_mixins) UsesVisualizationMixin (class in galaxy.webapps.base.controller) utf8_text_file_open() (in module galaxy.datatypes.isa) UtilityContainerManager (class in tool_shed.utility_containers.utility_container_manager) uuid (galaxy.model.Dataset attribute) (galaxy.model.DynamicTool attribute) (galaxy.model.MetadataFile attribute) (galaxy.model.Workflow attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowOutput attribute) (galaxy.model.WorkflowStep attribute) UUIDType (class in galaxy.model.custom_types) uwsgi_app() (in module galaxy.webapps.galaxy.buildapp) (in module galaxy.webapps.reports.buildapp) (in module tool_shed.webapp.buildapp) uwsgi_app_factory() (in module galaxy.webapps.galaxy.buildapp) uwsgi_module() (galaxy.config.config_manage.App property) UWSGI_MULE_MESSAGE (galaxy.web_stack.handlers.HANDLER_ASSIGNMENT_METHODS attribute) UWSGIApplicationStack (class in galaxy.web_stack) UWSGIFarmMessageTransport (class in galaxy.web_stack.transport) UWSGILogFilter (class in galaxy.web_stack) UX_POPUP (galaxy.selenium.navigates_galaxy.WAIT_TYPES attribute) UX_RENDER (galaxy.selenium.navigates_galaxy.WAIT_TYPES attribute) UX_TRANSITION (galaxy.selenium.navigates_galaxy.WAIT_TYPES attribute)

V

v1_image_name() (in module galaxy.tool_util.deps.mulled.util) v2_image_name() (in module galaxy.tool_util.deps.mulled.util) valid() (galaxy.tool_util.lint.LintContext method) valid_api_key() (galaxy.managers.users.UserManager method) valid_category_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) valid_chroms() (galaxy.visualization.data_providers.genome.BBIDataProvider method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) VALID_FLAGS (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider attribute) valid_gff3_phase (galaxy.datatypes.interval.Gff3 attribute) valid_gff3_strand (galaxy.datatypes.interval.Gff3 attribute) valid_gff_frame (galaxy.datatypes.interval.Gff attribute) valid_input_states (galaxy.model.Dataset attribute) valid_input_states() (galaxy.tools.DatabaseOperationTool property) (galaxy.tools.Tool property) VALID_METHODS (galaxy.datatypes.dataproviders.external.URLDataProvider attribute) valid_modes (galaxy.containers.ContainerVolume attribute) valid_operations (galaxy.model.Quota attribute) valid_ops (galaxy.managers.taggable.TaggableFilterMixin attribute) VALID_PRESET (galaxy.tools.parameters.sanitize.ToolParameterSanitizer attribute) VALID_RENDER_TARGETS (galaxy.visualization.plugins.config_parser.VisualizationsConfigParser attribute) valid_repository_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) valid_update_keys (galaxy.web.proxy.ProxyManager attribute) validate() (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.datatypes.sequence.BaseFastq method) (galaxy.datatypes.tabular.BaseVcf method) (galaxy.model.DatasetCollection method) (galaxy.model.metadata.MetadataParameter method) (galaxy.schema.fields.EncodedDatabaseIdField class method) (galaxy.tools.parameters.basic.BaseDataToolParameter method) (galaxy.tools.parameters.basic.RulesListToolParameter method) (galaxy.tools.parameters.basic.TextToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.validation.DatasetEmptyValidator method) (galaxy.tools.parameters.validation.DatasetExtraFilesPathEmptyValidator method) (galaxy.tools.parameters.validation.DatasetOkValidator method) (galaxy.tools.parameters.validation.EmptyTextfieldValidator method) (galaxy.tools.parameters.validation.ExpressionValidator method) (galaxy.tools.parameters.validation.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.NoOptionsValidator method) (galaxy.tools.parameters.validation.RegexValidator method) (galaxy.tools.parameters.validation.UnspecifiedBuildValidator method) (galaxy.tools.parameters.validation.Validator method) (galaxy.tools.parameters.validation.ValueInDataTableColumnValidator method) (galaxy.tools.parameters.validation.ValueNotInDataTableColumnValidator method) (galaxy.web_stack.message.ApplicationStackMessage method) (galaxy.web_stack.message.ParamMessage method) (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method) (in module galaxy.datatypes.data) validate_and_load_datatypes_config() (in module galaxy.metadata.set_metadata) validate_and_normalize_target() (in module galaxy.model.store.discover) validate_and_sanitize_basestring() (in module galaxy.util.validation) validate_and_sanitize_basestring_list() (in module galaxy.util.validation) validate_biocompute_object() (galaxy_test.base.populators.BaseWorkflowPopulator method) validate_boolean() (in module galaxy.util.validation) validate_by_group_workflow_parameters_mapper() (in module galaxy.workflow.resources) validate_changeset_revision() (tool_shed.webapp.controllers.repository.RepositoryController method) validate_config() (galaxy.containers.ContainerInterface method) (galaxy.containers.docker.DockerAPIInterface method) (galaxy.containers.docker.DockerCLIInterface method) (galaxy.containers.docker.DockerInterface method) (galaxy.containers.docker_swarm.DockerSwarmInterface method) (in module galaxy.jobs.dynamic_tool_destination) validate_dataset() (galaxy_test.base.populators.BaseDatasetPopulator method) validate_dataset_and_wait() (galaxy_test.base.populators.BaseDatasetPopulator method) validate_datatype_extension() (in module galaxy.tools.actions.upload_common) validate_destination() (in module galaxy.jobs.dynamic_tool_destination) validate_email() (in module galaxy.security.validate_user_input) validate_email_str() (in module galaxy.security.validate_user_input) validate_galaxy_markdown() (in module galaxy.managers.markdown_parse) validate_in_users_and_groups() (galaxy.webapps.base.controller.BaseAPIController method) validate_jsonrpc_request() (in module galaxy.util.json) validate_jsonrpc_response() (in module galaxy.util.json) validate_outputs() (galaxy.jobs.JobWrapper property) validate_password() (in module galaxy.security.validate_user_input) validate_password_str() (in module galaxy.security.validate_user_input) validate_path_resolution_graph() (galaxy.config.schema.AppSchema method) validate_path_upload() (in module galaxy.actions.library) validate_publicname() (in module galaxy.security.validate_user_input) validate_publicname_str() (in module galaxy.security.validate_user_input) validate_repository_name() (in module tool_shed.util.repository_util) validate_rule() (galaxy.jobs.dynamic_tool_destination.RuleValidator class method) (galaxy.util.rules_dsl.AddColumnBasenameRuleDefinition method) (galaxy.util.rules_dsl.AddColumnConcatenateRuleDefinition method) (galaxy.util.rules_dsl.AddColumnGroupTagValueRuleDefinition method) (galaxy.util.rules_dsl.AddColumnMetadataRuleDefinition method) (galaxy.util.rules_dsl.AddColumnRegexRuleDefinition method) (galaxy.util.rules_dsl.AddColumnRownumRuleDefinition method) (galaxy.util.rules_dsl.AddColumnSubstrRuleDefinition method) (galaxy.util.rules_dsl.AddColumnValueRuleDefinition method) (galaxy.util.rules_dsl.AddFilterCompareRuleDefinition method) (galaxy.util.rules_dsl.AddFilterCountRuleDefinition method) (galaxy.util.rules_dsl.AddFilterEmptyRuleDefinition method) (galaxy.util.rules_dsl.AddFilterMatchesRuleDefinition method) (galaxy.util.rules_dsl.AddFilterRegexRuleDefinition method) (galaxy.util.rules_dsl.BaseRuleDefinition method) (galaxy.util.rules_dsl.RemoveColumnsRuleDefinition method) (galaxy.util.rules_dsl.SortRuleDefinition method) (galaxy.util.rules_dsl.SplitColumnsRuleDefinition method) (galaxy.util.rules_dsl.SwapColumnsRuleDefinition method) validate_server_directory_upload() (in module galaxy.actions.library) validate_source() (galaxy.datatypes.dataproviders.base.DataProvider method) (galaxy.datatypes.dataproviders.chunk.ChunkDataProvider method) validate_tabular() (in module galaxy.datatypes.sniff) validate_uri_root() (galaxy.files.ConfiguredFileSources method) validate_url() (in module galaxy.tools.actions.upload_common) validated() (galaxy.datatypes.data.DatatypeValidation static method) validated_state (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) validated_state_message (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) ValidateOutputsAction (class in galaxy.jobs.actions.post) validation_error_to_message_exception() (in module galaxy.web.framework.decorators) ValidationContext (class in galaxy.tools.repositories) Validator (class in galaxy.tools.parameters.validation) ValidCategoryGrid (class in tool_shed.grids.repository_grids) ValidCategoryGrid.RepositoriesColumn (class in tool_shed.grids.repository_grids) ValidRepositoryGrid (class in tool_shed.grids.repository_grids) ValidRepositoryGrid.CategoryColumn (class in tool_shed.grids.repository_grids) ValidRepositoryGrid.InstallableRevisionColumn (class in tool_shed.grids.repository_grids) ValidRepositoryGrid.RepositoryCategoryColumn (class in tool_shed.grids.repository_grids) value (galaxy.model.DynamicTool attribute) (galaxy.model.ExtendedMetadataIndex attribute) (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.JobParameter attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.UserPreference attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.WorkflowInvocationOutputValue attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.model.WorkflowRequestStepState attribute) (galaxy.model.WorkflowStepTagAssociation attribute)

value() (galaxy.config.config_manage.OptionValue property) (galaxy.containers.docker_model.DockerNodeLabel property) (galaxy.containers.docker_model.DockerServiceConstraint property) value_from (galaxy.model.WorkflowStepInput attribute) value_from_basic() (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.grouping.Conditional method) (galaxy.tools.parameters.grouping.Group method) (galaxy.tools.parameters.grouping.Repeat method) (galaxy.tools.parameters.grouping.Section method) (galaxy.tools.parameters.grouping.UploadDataset method) value_from_type (galaxy.model.WorkflowStepInput attribute) value_to_basic() (galaxy.tools.parameters.basic.BaseJsonToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.grouping.Conditional method) (galaxy.tools.parameters.grouping.Group method) (galaxy.tools.parameters.grouping.Repeat method) (galaxy.tools.parameters.grouping.Section method) (galaxy.tools.parameters.grouping.UploadDataset method) value_to_display_text() (galaxy.tools.parameters.basic.ToolParameter method) ValueInDataTableColumnValidator (class in galaxy.tools.parameters.validation) ValueNotInDataTableColumnValidator (class in galaxy.tools.parameters.validation) values (galaxy.model.User attribute) values() (galaxy.model.Dataset.states class method) (galaxy.model.DatasetInstance.states class method) (galaxy.util.bunch.Bunch method) (galaxy.util.odict.odict method) ValueToolOutputActionConditionalWhen (class in galaxy.tool_util.parser.output_actions) Vcf (class in galaxy.datatypes.tabular) VcfDataProvider (class in galaxy.visualization.data_providers.genome) VcfGz (class in galaxy.datatypes.tabular) VcfTabixDataProvider (class in galaxy.visualization.data_providers.genome) Vel (class in galaxy.datatypes.binary) Velvet (class in galaxy.datatypes.assembly) verbose (in module galaxy.jobs.dynamic_tool_destination) verbose_name (galaxy.jobs.actions.post.ChangeDatatypeAction attribute) (galaxy.jobs.actions.post.ColumnSetAction attribute) (galaxy.jobs.actions.post.DefaultJobAction attribute) (galaxy.jobs.actions.post.DeleteDatasetAction attribute) (galaxy.jobs.actions.post.DeleteIntermediatesAction attribute) (galaxy.jobs.actions.post.EmailAction attribute) (galaxy.jobs.actions.post.HideDatasetAction attribute) (galaxy.jobs.actions.post.RemoveTagDatasetAction attribute) (galaxy.jobs.actions.post.RenameDatasetAction attribute) (galaxy.jobs.actions.post.TagDatasetAction attribute) (galaxy.jobs.actions.post.ValidateOutputsAction attribute) verify() (in module galaxy.authnz.psa_authnz) (in module galaxy.tool_util.verify) verify_assertion() (in module galaxy.tool_util.verify.asserts) verify_assertions() (in module galaxy.tool_util.verify.asserts) verify_collection() (in module galaxy.tool_util.verify.interactor) verify_hid() (in module galaxy.tool_util.verify.interactor) verify_installed_repositories() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) verify_installed_repository_data_table_entries() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) verify_installed_repository_metadata_unchanged() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) verify_installed_repository_no_tool_panel_section() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) verify_output() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) verify_output_collection() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) verify_output_dataset() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) verify_repository_reviews() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) verify_tool() (in module galaxy.tool_util.verify.interactor) verify_tool_metadata_for_installed_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) verify_tools() (in module galaxy.tool_shed.galaxy_install.migrate.check) verify_unchanged_repository_metadata() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) version (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetAssociationHistory attribute) (galaxy.model.tool_shed_install.ToolDependency attribute) version() (galaxy.containers.docker_model.DockerNode property) (galaxy.tool_util.deps.mulled.util.Target property) (galaxy.tool_util.deps.resolvers.ContainerDependency property) (galaxy.webapps.galaxy.api.configuration.ConfigurationController method) (tool_shed.webapp.api.configuration.ConfigurationController method) version_object() (galaxy.tools.Tool property) version_path() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) version_sorted() (in module galaxy.tool_util.deps.mulled.util) versioned_install() (in module galaxy.tool_util.deps.brew_exts) versioned_objects() (in module galaxy.model.base) versioned_session() (in module galaxy.model.base) Video (class in galaxy.datatypes.media) View (class in galaxy.model.view.utils) view() (galaxy.webapps.galaxy.controllers.history.HistoryController method) view_changelog() (tool_shed.webapp.controllers.repository.RepositoryController method) view_changeset() (tool_shed.webapp.controllers.repository.RepositoryController method) view_multiple() (galaxy.webapps.galaxy.controllers.history.HistoryController method) VIEW_NAME (galaxy.model.search.LibraryDatasetDatasetView attribute) (galaxy.model.search.LibraryDatasetView attribute) (galaxy.model.search.LibraryFolderView attribute) (galaxy.model.search.LibraryView attribute) (galaxy.model.search.ToolView attribute) (galaxy.model.search.ViewQueryBaseClass attribute) view_or_manage_repository() (tool_shed.webapp.controllers.repository.RepositoryController method) (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method) view_repository() (tool_shed.webapp.controllers.repository.RepositoryController method) view_show_job() (in module galaxy.managers.jobs) view_tool_metadata() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (tool_shed.webapp.controllers.repository.RepositoryController method) ViewField (class in galaxy.model.search) ViewQueryBaseClass (class in galaxy.model.search) virtual_display_if_enabled() (in module galaxy.selenium.driver_factory) visible (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) visible() (galaxy.model.store.discover.JsonCollectedDatasetMatch property) (galaxy.tools.parameters.basic.FTPFileToolParameter property) (galaxy.tools.parameters.basic.ToolParameter property) (galaxy.tools.parameters.grouping.Group property) visible_dataset_collections (galaxy.model.History attribute) visible_datasets (galaxy.model.History attribute) visit_galaxy_url() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) visit_inputs() (galaxy.tools.Tool method) visit_url() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) visualizaiton (galaxy.model.VisualizationRatingAssociation attribute) Visualization (class in galaxy.model) visualization (galaxy.model.VisualizationAnnotationAssociation attribute) (galaxy.model.VisualizationRevision attribute) (galaxy.model.VisualizationUserShareAssociation attribute) visualization_id (galaxy.model.VisualizationAnnotationAssociation attribute) (galaxy.model.VisualizationRatingAssociation attribute) (galaxy.model.VisualizationRevision attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.VisualizationUserShareAssociation attribute) VisualizationAllPublishedGrid (class in galaxy.webapps.galaxy.controllers.visualization) VisualizationAnnotationAssociation (class in galaxy.model) VisualizationController (class in galaxy.webapps.galaxy.controllers.visualization) VisualizationDeserializer (class in galaxy.managers.visualizations) VisualizationListGrid (class in galaxy.webapps.galaxy.controllers.visualization) VisualizationManager (class in galaxy.managers.visualizations) VisualizationPlugin (class in galaxy.visualization.plugins.plugin) VisualizationRatingAssociation (class in galaxy.model) VisualizationRevision (class in galaxy.model) visualizations (galaxy.model.VisualizationAnnotationAssociation attribute) (galaxy.model.VisualizationRatingAssociation attribute) (galaxy.model.VisualizationTagAssociation attribute) visualizations_shared_by_others (galaxy.model.User attribute) VisualizationsApiTestCase (class in galaxy_test.api.test_visualizations) VisualizationsConfigParser (class in galaxy.visualization.plugins.config_parser) VisualizationsController (class in galaxy.webapps.galaxy.api.visualizations) VisualizationSelectionGrid (class in galaxy.webapps.galaxy.controllers.page) VisualizationSerializer (class in galaxy.managers.visualizations) VisualizationsRegistry (class in galaxy.visualization.plugins.registry) VisualizationTagAssociation (class in galaxy.model) VisualizationUserShareAssociation (class in galaxy.model) volume() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) volume_class (galaxy.containers.ContainerInterface attribute) (galaxy.containers.docker.DockerInterface attribute) Vtk (class in galaxy.datatypes.constructive_solid_geometry) VtkAscii (class in galaxy.datatypes.constructive_solid_geometry) VtkBinary (class in galaxy.datatypes.constructive_solid_geometry)

W

wait() (galaxy.selenium.has_driver.HasDriver method) wait_for() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) wait_for_absent() (galaxy.selenium.has_driver.HasDriver method) (galaxy.selenium.smart_components.SmartTarget method) wait_for_absent_or_hidden() (galaxy.selenium.has_driver.HasDriver method) (galaxy.selenium.smart_components.SmartTarget method) wait_for_and_click() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) (galaxy.selenium.smart_components.SmartTarget method) wait_for_and_click_selector() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) wait_for_and_send_keys() (galaxy.selenium.smart_components.SmartTarget method) wait_for_clickable() (galaxy.selenium.has_driver.HasDriver method) (galaxy.selenium.smart_components.SmartTarget method) wait_for_dataset() (galaxy_test.base.populators.DatasetPopulator method) wait_for_dataset_collection() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method) wait_for_fetched_collection() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method) wait_for_history() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) (galaxy_test.base.populators.BaseDatasetPopulator method) wait_for_history_jobs() (galaxy_test.base.populators.BaseDatasetPopulator method) wait_for_history_workflows() (galaxy_test.base.populators.BaseWorkflowPopulator method) wait_for_http_server() (in module galaxy_test.driver.driver_util) wait_for_id() (galaxy.selenium.has_driver.HasDriver method) wait_for_invocation() (galaxy_test.base.populators.BaseWorkflowPopulator method) wait_for_invocation_and_jobs() (galaxy_test.api.test_workflows.BaseWorkflowsApiTestCase method) wait_for_job() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) (galaxy_test.base.populators.BaseDatasetPopulator method) wait_for_jobs() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) wait_for_logged_in() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) wait_for_overlays_cleared() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) wait_for_present() (galaxy.selenium.has_driver.HasDriver method) (galaxy.selenium.smart_components.SmartTarget method) wait_for_repository_installation() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) wait_for_selector() (galaxy.selenium.has_driver.HasDriver method) wait_for_selector_absent() (galaxy.selenium.has_driver.HasDriver method) wait_for_selector_absent_or_hidden() (galaxy.selenium.has_driver.HasDriver method) wait_for_selector_clickable() (galaxy.selenium.has_driver.HasDriver method) wait_for_selector_visible() (galaxy.selenium.has_driver.HasDriver method) wait_for_sizzle_selector_clickable() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) wait_for_text() (galaxy.selenium.smart_components.SmartTarget method) wait_for_tool_run() (galaxy_test.base.populators.BaseDatasetPopulator method) wait_for_toolbox_reload() (galaxy.config.ConfiguresGalaxyMixin method) wait_for_value() (galaxy.selenium.smart_components.SmartTarget method) wait_for_visible() (galaxy.selenium.has_driver.HasDriver method) (galaxy.selenium.smart_components.SmartTarget method) wait_for_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method) wait_for_xpath() (galaxy.selenium.has_driver.HasDriver method) wait_for_xpath_visible() (galaxy.selenium.has_driver.HasDriver method) wait_length() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) wait_on() (in module galaxy.tool_util.verify.wait) (in module galaxy_test.base.populators) wait_on_history_length() (galaxy_test.base.populators.BaseDatasetPopulator method) wait_on_library_dataset() (galaxy_test.base.populators.LibraryPopulator method) wait_on_state() (in module galaxy_test.base.populators) WAIT_TYPES (class in galaxy.selenium.navigates_galaxy) wait_types (galaxy.selenium.navigates_galaxy.NavigatesGalaxy attribute) WAITING (galaxy.model.DeferredJob.states attribute) (galaxy.model.Job.states attribute) (galaxy.model.Task.states attribute) waiting (galaxy.model.view.HistoryDatasetCollectionJobStateSummary attribute) waiting_for_elements() (galaxy.model.DatasetCollection property) (galaxy.model.HistoryDatasetCollectionAssociation property) WaitType (class in galaxy.selenium.navigates_galaxy) wake() (galaxy.tool_shed.galaxy_install.update_repository_manager.Sleeper method) (galaxy.util.sleeper.Sleeper method) walk_collections() (galaxy.model.dataset_collections.structure.Tree method) walk_over_extra_files() (in module galaxy.job_execution.output_collect) walk_over_file_collectors() (in module galaxy.job_execution.output_collect) warn() (galaxy.tool_util.lint.LintContext method) (in module galaxy.tools.util.galaxyops) WARNING (galaxy.model.tool_shed_install.ToolDependency.states attribute) (galaxy.model.tool_shed_install.ToolShedRepository.states attribute) (galaxy.tool_util.parser.stdio.StdioErrorLevel attribute) was_recorded() (galaxy.tool_util.verify.script.TestException property) watch_directory() (galaxy.tools.toolbox.watcher.ToolWatcher method) (galaxy.util.watcher.NullWatcher method) (galaxy.util.watcher.Watcher method) watch_file() (galaxy.tools.toolbox.watcher.ToolConfWatcher method) (galaxy.tools.toolbox.watcher.ToolWatcher method) (galaxy.util.watcher.NullWatcher method) (galaxy.util.watcher.Watcher method) watch_tool() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) Watcher (class in galaxy.util.watcher) watchers() (galaxy.config_watchers.ConfigWatchers property) Wav (class in galaxy.datatypes.media) WebApplication (class in galaxy.web.framework.base) (class in galaxy.webapps.base.webapp) WebDavFilesSource (class in galaxy.files.sources.webdav) Webhook (class in galaxy.webhooks) webhook_data() (galaxy.webapps.galaxy.api.webhooks.WebhooksController method) WebhooksApiTestCase (class in galaxy_test.api.test_webhooks) WebhooksController (class in galaxy.webapps.galaxy.api.webhooks) WebhooksRegistry (class in galaxy.webhooks) WeblessApplicationStack (class in galaxy.web_stack) welcome() (galaxy.webapps.galaxy.controllers.root.RootController method) which() (in module galaxy.tool_util.deps.brew_exts) (in module galaxy.util) (in module galaxy.util.commands) whoami() (galaxy.webapps.galaxy.api.configuration.ConfigurationController method) Wiff (class in galaxy.datatypes.proteomics) WiffTar (class in galaxy.datatypes.binary) Wiggle (class in galaxy.datatypes.interval) wiggle_dataprovider() (galaxy.datatypes.interval.Wiggle method) wiggle_dict_dataprovider() (galaxy.datatypes.interval.Wiggle method) WiggleDataProvider (class in galaxy.datatypes.dataproviders.dataset) with_class() (galaxy.selenium.components.SelectorTemplate method) with_path_for_job() (galaxy.job_execution.datasets.DatasetPath method) work_context() (galaxy.job_execution.output_collect.JobContext property) worker_process() (galaxy.model.database_heartbeat.DatabaseHeartbeat property) WorkerProcess (class in galaxy.model) workers() (galaxy.web_stack.ApplicationStack method) (galaxy.web_stack.UWSGIApplicationStack method) Workflow (class in galaxy.model) (class in tool_shed.utility_containers.utility_container_manager) (class in tool_shed.webapp.model) workflow (galaxy.managers.workflows.RefactorResponse attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowStep attribute) workflow() (galaxy.managers.workflows.CreatedWorkflow property) workflow_click_option() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_create_new() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) workflow_dict() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method) workflow_editor_add_input() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) workflow_editor_click_option() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_editor_click_options() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_editor_click_run() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_editor_click_save() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_editor_connect() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) workflow_editor_destroy_connection() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) workflow_editor_maximize_center_pane() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) workflow_editor_options_menu_element() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_editor_source_sink_terminal_ids() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) workflow_id (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowStep attribute) workflow_id() (galaxy_test.api.test_workflow_extraction.RunJobsSummary property) (galaxy_test.base.populators.RunJobsSummary property) workflow_import_submit_url() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_click_import() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_click_option() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_click_search() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_click_tag_display() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_column_text() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_name() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_open() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_open_with_name() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) workflow_index_rename() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_search_for() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_table_elements() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_table_row() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_tags() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_invocation (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationOutputValue attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.model.WorkflowRequestInputStepParameter attribute) (galaxy.model.WorkflowRequestStepState attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) workflow_invocation_id (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationOutputValue attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.model.WorkflowRequestInputStepParameter attribute) (galaxy.model.WorkflowRequestStepState attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) workflow_invocation_step (galaxy.model.ImplicitCollectionJobs attribute) (galaxy.model.Job attribute) (galaxy.model.WorkflowInvocationOutputValue attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation attribute) workflow_invocation_step_id (galaxy.model.WorkflowInvocationStepOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation attribute) workflow_invocations (galaxy.model.History attribute) workflow_output (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationOutputValue attribute)

workflow_output_drop_forced (galaxy.workflow.refactor.schema.RefactorActionExecutionMessageTypeEnum attribute) workflow_output_for() (galaxy.model.Workflow method) (galaxy.model.WorkflowStep method) workflow_output_id (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationOutputValue attribute) workflow_output_labels() (galaxy.model.Workflow property) workflow_outputs (galaxy.model.WorkflowStep attribute) workflow_outputs() (galaxy.model.Workflow property) workflow_populator() (galaxy_test.selenium.framework.TestWithSeleniumMixin property) workflow_proxy() (in module galaxy.tool_util.cwl) workflow_report_json() (galaxy_test.base.populators.BaseWorkflowPopulator method) workflow_request() (galaxy_test.base.populators.RunJobsSummary property) workflow_request_to_run_config() (in module galaxy.workflow.run_request) workflow_run_config_to_request() (in module galaxy.workflow.run_request) workflow_run_setup_inputs() (galaxy_test.selenium.test_workflow_run.WorkflowRunTestCase method) workflow_run_specify_inputs() (galaxy_test.selenium.test_workflow_run.WorkflowRunTestCase method) workflow_run_submit() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_run_with_name() (galaxy_test.selenium.test_workflow_run.WorkflowRunTestCase method) workflow_sharing_click_publish() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_step (galaxy.model.PostJobAction attribute) (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationOutputValue attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute) (galaxy.model.WorkflowOutput attribute) (galaxy.model.WorkflowRequestInputStepParameter attribute) (galaxy.model.WorkflowRequestStepState attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowStepAnnotationAssociation attribute) (galaxy.model.WorkflowStepInput attribute) workflow_step_id (galaxy.model.PostJobAction attribute) (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationOutputValue attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute) (galaxy.model.WorkflowOutput attribute) (galaxy.model.WorkflowRequestInputStepParameter attribute) (galaxy.model.WorkflowRequestStepState attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowStepAnnotationAssociation attribute) (galaxy.model.WorkflowStepInput attribute) (galaxy.model.WorkflowStepTagAssociation attribute) workflow_steps (galaxy.model.DynamicTool attribute) (galaxy.model.WorkflowStepAnnotationAssociation attribute) (galaxy.model.WorkflowStepTagAssociation attribute) workflow_tag_handler() (in module galaxy.model.search) workflow_to_dict() (galaxy.managers.workflows.WorkflowContentsManager method) workflow_upload_yaml_with_random_name() (galaxy_test.selenium.framework.TestWithSeleniumMixin method) (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method) WorkflowAnnotationsController (class in galaxy.webapps.galaxy.api.annotations) WorkflowCanvas (class in galaxy.workflow.render) WorkflowContentsManager (class in galaxy.managers.workflows) WorkflowController (class in galaxy.webapps.galaxy.controllers.workflow) WorkflowCreateOptions (class in galaxy.managers.workflows) WorkflowEditorTestCase (class in galaxy_test.selenium.test_workflow_editor) WorkflowExtractionApiTestCase (class in galaxy_test.api.test_workflow_extraction) WorkflowField (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) WorkflowInvocation (class in galaxy.model) WorkflowInvocation.states (class in galaxy.model) WorkflowInvocationOutputDatasetAssociation (class in galaxy.model) WorkflowInvocationOutputDatasetCollectionAssociation (class in galaxy.model) WorkflowInvocationOutputValue (class in galaxy.model) WorkflowInvocationStep (class in galaxy.model) WorkflowInvocationStep.states (class in galaxy.model) WorkflowInvocationStepOutputDatasetAssociation (class in galaxy.model) WorkflowInvocationStepOutputDatasetCollectionAssociation (class in galaxy.model) WorkflowInvocationToSubworkflowInvocationAssociation (class in galaxy.model) WorkflowManagementTestCase (class in galaxy_test.selenium.test_workflow_management) WorkflowMappingField (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) WorkflowMarkdownGeneratorPlugin (class in galaxy.workflow.reports.generators) WorkflowModule (class in galaxy.workflow.modules) WorkflowModuleFactory (class in galaxy.workflow.modules) WorkflowModuleInjector (class in galaxy.workflow.modules) WorkflowOutput (class in galaxy.model) WorkflowParameterExpansion (class in galaxy.tools.parameters.meta) WorkflowPopulator (class in galaxy_test.base.populators) WorkflowRefactorExecutor (class in galaxy.workflow.refactor.execute) WorkflowReportGeneratorPlugin (class in galaxy.workflow.reports.generators) WorkflowRequestInputParameter (class in galaxy.model) WorkflowRequestInputParameter.types (class in galaxy.model) WorkflowRequestInputStepParameter (class in galaxy.model) WorkflowRequestMonitor (class in galaxy.workflow.scheduling_manager) WorkflowRequestStepState (class in galaxy.model) WorkflowRequestToInputDatasetAssociation (class in galaxy.model) WorkflowRequestToInputDatasetCollectionAssociation (class in galaxy.model) WorkflowRunConfig (class in galaxy.workflow.run) (class in galaxy.workflow.run_request) WorkflowRunTestCase (class in galaxy_test.selenium.test_workflow_run) Workflows (class in galaxy.webapps.reports.controllers.workflows) workflows (galaxy.model.StoredWorkflow attribute) workflows_shared_by_others (galaxy.model.User attribute) WorkflowsAPIController (class in galaxy.webapps.galaxy.api.workflows) WorkflowsApiTestCase (class in galaxy_test.api.test_workflows) WorkflowSchedulingManager (class in galaxy.workflow.scheduling_manager) WorkflowSchedulingMessage (class in galaxy.web_stack.message) WorkflowSchedulingPlugin (class in galaxy.workflow.schedulers) WorkflowSelectionGrid (class in galaxy.webapps.galaxy.controllers.page) WorkflowsFromYamlApiTestCase (class in galaxy_test.api.test_workflows_from_yaml) WorkflowsManager (class in galaxy.managers.workflows) WorkflowStateResolutionOptions (class in galaxy.managers.workflows) WorkflowStep (class in galaxy.model) (class in tool_shed.webapp.model) WorkflowStepAnnotationAssociation (class in galaxy.model) (class in tool_shed.webapp.model) WorkflowStepConnection (class in galaxy.model) (class in tool_shed.webapp.model) WorkflowStepInput (class in galaxy.model) (class in tool_shed.webapp.model) WorkflowStepTagAssociation (class in galaxy.model) WorkflowTagsController (class in galaxy.webapps.galaxy.api.item_tags) WorkflowUpdateOptions (class in galaxy.managers.workflows) WorkflowView (class in galaxy.model.search) working_directory (galaxy.model.Task attribute) working_directory() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.JobWrapper property) (galaxy.jobs.SharedComputeEnvironment method) working_directory_exists() (galaxy.jobs.JobWrapper method) WorkRequestContext (class in galaxy.work.context) wrap() (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.MetadataElementSpec method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.datatypes.metadata.SelectParameter method) (galaxy.model.metadata.FileParameter method) (galaxy.model.metadata.MetadataElementSpec method) (galaxy.model.metadata.MetadataParameter method) (galaxy.model.metadata.SelectParameter method) wrap_if_allowed() (in module galaxy.webapps.util) wrap_if_allowed_or_fail() (in module galaxy.webapps.util) wrap_in_middleware() (in module galaxy.webapps.galaxy.buildapp) (in module galaxy.webapps.reports.buildapp) (in module tool_shed.webapp.buildapp) wrap_in_static() (in module galaxy.webapps.galaxy.buildapp) (in module galaxy.webapps.reports.buildapp) (in module tool_shed.webapp.buildapp) wrap_values() (galaxy.tools.parameters.wrapped.WrappedParameters method) wrap_with_safe_string() (in module galaxy.util.object_wrapper) WrappedParameters (class in galaxy.tools.parameters.wrapped) writable_files() (galaxy.datatypes.data.Data property) write() (galaxy.datatypes.dataproviders.base.DataProvider method) (galaxy.tool_util.verify.script.Results method) (galaxy.util.pastescript.serve.LazyWriter method) (galaxy.util.zipstream.ZipstreamWrapper method) write_config() (tool_shed.util.hgweb_config.HgWebConfigManager method) write_data_to_file() (galaxy.visualization.data_providers.basic.BaseDataProvider method) (galaxy.visualization.data_providers.genome.BamDataProvider method) (galaxy.visualization.data_providers.genome.BedDataProvider method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) (galaxy.visualization.data_providers.genome.IntervalDataProvider method) (galaxy.visualization.data_providers.genome.IntervalIndexDataProvider method) (galaxy.visualization.data_providers.genome.TabixDataProvider method) (galaxy.visualization.data_providers.genome.VcfDataProvider method) write_evalute_script() (in module galaxy.tools.expressions) (in module galaxy.tools.expressions.script) write_executable_script() (galaxy.jobs.runners.BaseJobRunner method) write_from() (galaxy.files.sources.BaseFilesSource method) (galaxy.files.sources.FilesSource method) write_job_metadata() (in module galaxy.metadata.set_metadata) write_log() (galaxy.web.framework.middleware.translogger.TransLogger method) write_object_store_conf (galaxy.metadata.ExtendedDirectoryMetadataGenerator attribute) (galaxy.metadata.PortableDirectoryMetadataGenerator attribute) write_screenshot_directory_file() (galaxy_test.selenium.framework.TestWithSeleniumMixin method) write_script() (in module galaxy.jobs.runners.util.job_script) write_split_files() (galaxy.datatypes.sequence.Sequence class method) write_temp_file() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) write_to_error_directory() (galaxy_test.selenium.framework.TestSnapshot method) write_to_file() (galaxy.datatypes.dataproviders.external.TempfileDataProvider method) writelines() (galaxy.datatypes.dataproviders.base.DataProvider method) (galaxy.util.pastescript.serve.LazyWriter method) wsgi_headeritems() (galaxy.web.framework.base.Response method) wsgi_status() (galaxy.web.framework.base.Response method) WSGIEnvironmentProperty (class in galaxy.web.framework.base)

X

Xbm (class in galaxy.datatypes.images) XForwardedHostMiddleware (class in galaxy.web.framework.middleware.xforwardedhost) Xgmml (class in galaxy.datatypes.graph) XGMMLGraphDataProvider (class in galaxy.datatypes.graph) XHunterAslFormat (class in galaxy.datatypes.proteomics) Xlsx (class in galaxy.datatypes.binary) xml_dataprovider() (galaxy.datatypes.xml.GenericXml method) xml_element_compare() (in module galaxy.util) xml_element_list_compare() (in module galaxy.util) xml_element_to_dict() (in module galaxy.util) xml_find() (in module galaxy.tool_util.verify.asserts.xml) xml_find_text() (in module galaxy.tool_util.verify.asserts.xml) xml_string() (galaxy.tools.data.TabularToolDataTable property)

xml_text() (in module galaxy.util) xml_to_dict() (galaxy.web_stack.handlers.ConfiguresHandlers static method) xml_to_string() (in module galaxy.util) XMLDataProvider (class in galaxy.datatypes.dataproviders.hierarchy) XmlInputSource (class in galaxy.tool_util.parser.xml) XmlPageSource (class in galaxy.tool_util.parser.xml) XmlPagesSource (class in galaxy.tool_util.parser.xml) XmlToolSource (class in galaxy.tool_util.parser.xml) Xpm (class in galaxy.datatypes.images) XquestSpecXML (class in galaxy.datatypes.proteomics) XquestXML (class in galaxy.datatypes.proteomics) xrefs() (galaxy.webapps.galaxy.api.tools.ToolsController method) Xtc (class in galaxy.datatypes.binary)

Y

YamlInputSource (class in galaxy.tool_util.parser.yaml) YamlPageSource (class in galaxy.tool_util.parser.yaml)

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

Z

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

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