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.IdentityProvider method) (galaxy.authnz.custos_authnz.CustosAuthnz method) (galaxy.authnz.managers.AuthnzManager method) (galaxy.authnz.psa_authnz.PSAAuthnz method) (galaxy.authnz.psa_authnz.Strategy method) (galaxy.config.BaseAppConfiguration method) (galaxy.config.GalaxyAppConfiguration method) (galaxy.config.config_manage.GzipFilter method) (galaxy.config.config_manage.PrefixFilter 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.DMND method) (galaxy.datatypes.binary.Dcd method) (galaxy.datatypes.binary.H5 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.data.Newick method) (galaxy.datatypes.data.Nexus 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.BGzipTabixDataProvider method) (galaxy.datatypes.dataproviders.dataset.BcftoolsDataProvider 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.SQliteDataDictProvider method) (galaxy.datatypes.dataproviders.dataset.SQliteDataProvider method) (galaxy.datatypes.dataproviders.dataset.SQliteDataTableProvider method) (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider 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.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.ldIndep method) (galaxy.datatypes.genetics.rgFeatureList method) (galaxy.datatypes.genetics.rgSampleList method) (galaxy.datatypes.genetics.rgTabList method) (galaxy.datatypes.gis.Shapefile 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.Analyze75 method) (galaxy.datatypes.proteomics.ImzML method) (galaxy.datatypes.proteomics.Kroenik method) (galaxy.datatypes.proteomics.MzTab method) (galaxy.datatypes.proteomics.MzTab2 method) (galaxy.datatypes.proteomics.PSMS method) (galaxy.datatypes.proteomics.PepList method) (galaxy.datatypes.proteomics.PepXmlReport method) (galaxy.datatypes.proteomics.ProtXmlReport 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.tracks.GeneTrack method) (galaxy.datatypes.tracks.UCSCTrackHub 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.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.HandlerAssignmentError method) (galaxy.exceptions.MessageException method) (galaxy.exceptions.ToolExecutionError method) (galaxy.exceptions.ToolMissingException method) (galaxy.exceptions.error_codes.ErrorCode 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.JobInstrumenter method) (galaxy.job_metrics.JobMetrics 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.jobs.JobConfiguration method) (galaxy.jobs.JobDestination method) (galaxy.jobs.JobToolConfiguration method) (galaxy.jobs.JobWrapper method) (galaxy.jobs.SharedComputeEnvironment method) (galaxy.jobs.TaskWrapper 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.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.JobState 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) (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.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.CloudAuthzManager 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.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.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.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.JobExternalOutputMetadataWrapper method) (galaxy.metadata.PortableDirectoryMetadataGenerator method) (galaxy.model.APIKeys method) (galaxy.model.BaseJobMetric method) (galaxy.model.CloudAuthz method) (galaxy.model.ConverterDependencyException method) (galaxy.model.CustosAuthnzToken method) (galaxy.model.DataManagerHistoryAssociation method) (galaxy.model.DataManagerJobAssociation method) (galaxy.model.Dataset 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.MetadataFile method) (galaxy.model.NoConverterException method) (galaxy.model.PSAAssociation method) (galaxy.model.PSACode method) (galaxy.model.PSANonce method) (galaxy.model.PSAPartial 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.Quota method) (galaxy.model.Role method) (galaxy.model.SerializationOptions method) (galaxy.model.StorableObject 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.Task method) (galaxy.model.TaskMetricNumeric method) (galaxy.model.TaskMetricText 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.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.model.base.ModelMapping method) (galaxy.model.database_heartbeat.DatabaseHeartbeat 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.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.migrate.versions.0005_cleanup_datasets_fix.Dataset method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDataset method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation method) (galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters.DeferredJob method) (galaxy.model.none_like.NoneDataset method) (galaxy.model.orm.logging_connection_proxy.TraceLoggerProxy 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.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.ImportOptions method) (galaxy.model.store.ModelImportStore method) (galaxy.model.store.ObjectImportTracker method) (galaxy.model.store.SessionlessContext method) (galaxy.model.store.TarModelExportStore method) (galaxy.model.store.discover.JsonCollectedDatasetMatch method) (galaxy.model.store.discover.RegexCollectedDatasetMatch method) (galaxy.model.store.discover.SessionlessModelPersistenceContext 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.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.objectstore.BaseObjectStore method) (galaxy.objectstore.ConcreteObjectStore method) (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.DistributedObjectStore method) (galaxy.objectstore.HierarchicalObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStorePopulator method) (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.cloud.Cloud method) (galaxy.objectstore.irods.IRODSObjectStore 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.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.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.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.CachedDependencyManager method) (galaxy.tool_util.deps.DependencyManager method) (galaxy.tool_util.deps.NullDependencyManager 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.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.mulled.mulled_search.CondaSearch method) (galaxy.tool_util.deps.mulled.mulled_search.QuaySearch 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.ContainerDependency method) (galaxy.tool_util.deps.resolvers.NullDependency method) (galaxy.tool_util.deps.resolvers.RequirementMapping 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.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.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.ToolOutputCollectionPart 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.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.test_data.FileDataResolver method) (galaxy.tool_util.verify.test_data.GitDataResolver method) (galaxy.tool_util.verify.test_data.TestDataResolver method) (galaxy.tools.BadValue method) (galaxy.tools.DataManagerTool method) (galaxy.tools.DefaultToolState method) (galaxy.tools.InteractiveTool method) (galaxy.tools.SetParamAction method) (galaxy.tools.Tool method) (galaxy.tools.ToolBox method) (galaxy.tools.ToolErrorLog method) (galaxy.tools.TracksterConfig method) (galaxy.tools.actions.OutputCollections method) (galaxy.tools.actions.ToolExecutionCache 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.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.parameters.DataCollectionToolParameter method) (galaxy.tools.parameters.DataToolParameter method) (galaxy.tools.parameters.SelectToolParameter 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.FTPFileToolParameter method) (galaxy.tools.parameters.basic.FileToolParameter method) (galaxy.tools.parameters.basic.FloatToolParameter 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.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.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.test.ParamContext method) (galaxy.tools.test.RootParamContext method) (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.BaseGalaxyToolBox method) (galaxy.tools.toolbox.ToolSection method) (galaxy.tools.toolbox.ToolSectionLabel method) (galaxy.tools.toolbox.base.AbstractToolBox method) (galaxy.tools.toolbox.base.BaseGalaxyToolBox method) (galaxy.tools.toolbox.filters.FilterFactory method) (galaxy.tools.toolbox.lineages.LineageMap method) (galaxy.tools.toolbox.lineages.ToolLineage 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.panel.ToolSection method) (galaxy.tools.toolbox.panel.ToolSectionLabel method) (galaxy.tools.toolbox.tags.PersistentToolTagManager method) (galaxy.tools.toolbox.watcher.ToolConfWatcher method) (galaxy.tools.toolbox.watcher.ToolFileEventHandler method) (galaxy.tools.toolbox.watcher.ToolWatcher 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.tours.ToursRegistry method) (galaxy.util.ExecutionTimer method) (galaxy.util.Params method) (galaxy.util.ParamsWithSpecs method) (galaxy.util.StructuredExecutionTimer 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.TraceLogger method) (galaxy.util.custom_logging.fluent_log.FluentTraceLogger method) (galaxy.util.dbkeys.GenomeBuilds 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.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.streamball.StreamBall method) (galaxy.util.streamball.ZipBall 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.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.PhylovizDataProvider 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.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.WSGIEnvironmentProperty method) (galaxy.web.framework.base.WebApplication method) (galaxy.web.framework.helpers.grids.CommunityTagsColumn method) (galaxy.web.framework.helpers.grids.Grid method) (galaxy.web.framework.helpers.grids.GridAction method) (galaxy.web.framework.helpers.grids.GridColumn method) (galaxy.web.framework.helpers.grids.GridColumnFilter method) (galaxy.web.framework.helpers.grids.GridOperation method) (galaxy.web.framework.helpers.grids.MulticolFilterColumn method) (galaxy.web.framework.helpers.grids.OwnerAnnotationColumn method) (galaxy.web.framework.helpers.grids.SharingStatusColumn method) (galaxy.web.framework.middleware.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.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.MessageApplicationStack method) (galaxy.web_stack.UWSGIApplicationStack method) (galaxy.web_stack.WeblessApplicationStack method) (galaxy.web_stack.message.ApplicationStackMessage method) (galaxy.web_stack.message.ApplicationStackMessageDispatcher method) (galaxy.web_stack.message.ParamMessage method) (galaxy.web_stack.transport.ApplicationStackTransport method) (galaxy.web_stack.transport.UWSGIFarmMessageTransport method) (galaxy.webapps.base.controller.BaseController method) (galaxy.webapps.base.controller.Datatype method) (galaxy.webapps.base.controller.JSAppLauncher method) (galaxy.webapps.galaxy.api.annotations.HistoryAnnotationsController method), [1] (galaxy.webapps.galaxy.api.annotations.HistoryContentAnnotationsController method), [1] (galaxy.webapps.galaxy.api.authenticate.AuthenticationController method), [1] (galaxy.webapps.galaxy.api.cloud.CloudController method), [1] (galaxy.webapps.galaxy.api.cloudauthz.CloudAuthzController method), [1] (galaxy.webapps.galaxy.api.configuration.ConfigurationController method), [1] (galaxy.webapps.galaxy.api.container_resolution.ContainerResolutionAPIController method), [1] (galaxy.webapps.galaxy.api.dataset_collections.DatasetCollectionsController method), [1] (galaxy.webapps.galaxy.api.datasets.DatasetsController method), [1] (galaxy.webapps.galaxy.api.dynamic_tools.DynamicToolsController method), [1] (galaxy.webapps.galaxy.api.extended_metadata.HistoryDatasetExtendMetadataController method), [1] (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method), [1] (galaxy.webapps.galaxy.api.folders.FoldersController method), [1] (galaxy.webapps.galaxy.api.histories.HistoriesController method), [1] (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method), [1] (galaxy.webapps.galaxy.api.job_ports.JobPortsAPIController method), [1] (galaxy.webapps.galaxy.api.jobs.JobController method), [1] (galaxy.webapps.galaxy.api.libraries.LibrariesController method), [1] (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method), [1] (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method), [1] (galaxy.webapps.galaxy.api.metrics.MetricsController method), [1] (galaxy.webapps.galaxy.api.page_revisions.PageRevisionsController method), [1] (galaxy.webapps.galaxy.api.pages.PagesController method), [1] (galaxy.webapps.galaxy.api.plugins.PluginsController method), [1] (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method), [1] (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method), [1] (galaxy.webapps.galaxy.api.tool_entry_points.ToolEntryPointsAPIController method), [1] (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] (galaxy.webapps.galaxy.api.tours.ToursController method), [1] (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] (galaxy.webapps.galaxy.api.visualizations.VisualizationsController method), [1] (galaxy.webapps.galaxy.api.webhooks.WebhooksController method), [1] (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] (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.webapps.reports.framework.grids.CommunityTagsColumn method) (galaxy.webapps.reports.framework.grids.Grid method) (galaxy.webapps.reports.framework.grids.GridAction method) (galaxy.webapps.reports.framework.grids.GridColumn method) (galaxy.webapps.reports.framework.grids.GridColumnFilter method) (galaxy.webapps.reports.framework.grids.GridOperation method) (galaxy.webapps.reports.framework.grids.MulticolFilterColumn method) (galaxy.webapps.reports.framework.grids.OwnerAnnotationColumn method) (galaxy.webhooks.Webhook method) (galaxy.webhooks.WebhooksRegistry 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.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_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), [1] (tool_shed.webapp.api.groups.GroupsController method), [1] (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), [1] 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) acquire_session() (in module galaxy.objectstore.irods) Action (class in galaxy.security) (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) action_arguments (galaxy.model.PostJobAction attribute) action_chains() (galaxy.selenium.has_driver.HasDriver method) ACTION_NAME (galaxy.datatypes.display_applications.parameters.DisplayDataValueWrapper attribute) action_name (galaxy.datatypes.display_applications.parameters.DisplayDataValueWrapper attribute) ACTION_NAME (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper attribute) action_name (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper attribute) (galaxy.managers.rbac_secured.AccessDatasetRBACPermission attribute) (galaxy.managers.rbac_secured.DatasetRBACPermission attribute) (galaxy.managers.rbac_secured.ManageDatasetRBACPermission attribute) action_type (galaxy.model.PostJobAction 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) activatable_datasets (galaxy.model.History attribute) activatable_library_datasets (galaxy.model.LibraryFolder attribute) activate (galaxy.tool_util.deps.conda_util.CondaContext attribute) activate() (galaxy.managers.users.UserManager method) (galaxy.webapps.galaxy.controllers.user.User method) activate_operation (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) activate_repository() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) activation_token (galaxy.model.User attribute) active (galaxy.model.DynamicTool attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.User attribute) (galaxy.model.WorkflowInvocation attribute) active_authenticators() (galaxy.auth.AuthManager method) active_contents (galaxy.model.History attribute) active_counts() (galaxy.managers.history_contents.HistoryContentsManager method) active_dataset_and_roles_query (galaxy.model.History attribute) active_dataset_collections (galaxy.model.History attribute) active_datasets (galaxy.model.History attribute) (galaxy.model.LibraryFolder attribute) active_datasets_and_roles (galaxy.model.History attribute) 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset attribute) active_history_jobs() (galaxy_test.base.populators.BaseDatasetPopulator method) active_library_associations (galaxy.model.Dataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset attribute) active_repositories (tool_shed.webapp.model.User attribute) active_visible_dataset_collections (galaxy.model.History attribute) active_visible_datasets_and_roles (galaxy.model.History attribute) 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) (galaxy.util.streamball.StreamBall method) add_api_controller() (galaxy.web.framework.base.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), [1] 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_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_pending_datasets() (galaxy.model.History method) add_post_job_action() (galaxy.model.Job method) add_repository_registry_entry() (tool_shed.webapp.api.repositories.RepositoriesController method), [1] 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() (in module galaxy.webapps.reports.buildapp) (in module tool_shed.webapp.buildapp) add_validation_error() (galaxy.model.DatasetInstance method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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) AdditionalValueFilter (class in galaxy.tools.parameters.dynamic_options) addMiscToJson() (galaxy.visualization.data_providers.phyloviz.baseparser.Node method) address (galaxy.containers.Container attribute) (galaxy.containers.docker_model.DockerContainer attribute) (galaxy.containers.docker_model.DockerService attribute) (galaxy.model.UserAddress attribute) addresses (galaxy.model.User attribute) AddressField (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) addRoot() (galaxy.visualization.data_providers.phyloviz.baseparser.PhyloTree method) 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_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 attribute) admin_users (galaxy.config.CommonConfigurationMixin attribute) 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 attribute) all_requirements (galaxy.tools.ToolBox attribute) all_requirements() (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] all_roles() (galaxy.model.User 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), [1] 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 attribute) allow_datatype_change (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.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.interval.BedStrict 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.Analyze75 attribute) (galaxy.datatypes.proteomics.ImzML attribute) (galaxy.datatypes.proteomics.Wiff attribute) (galaxy.datatypes.text.SnpSiftDbNSFP attribute)

allow_errored_inputs (galaxy.tools.DatabaseOperationTool attribute) allow_fetching_all_results (galaxy.webapps.reports.framework.grids.Grid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid 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.webapps.reports.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) 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 attribute) Analyze75 (class in galaxy.datatypes.proteomics) 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) 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), [1] anonymous (galaxy.managers.context.ProvidesUserContext attribute) 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_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), [1] 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) 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 attribute) 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_query_filter() (galaxy.web.framework.helpers.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) (galaxy.webapps.reports.framework.grids.Grid 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), [1] archive_dir (galaxy.model.JobImportHistoryArchive attribute) archive_download() (galaxy.webapps.galaxy.api.histories.HistoriesController method), [1] archive_export() (galaxy.webapps.galaxy.api.histories.HistoriesController method), [1] archive_repository_revision() (in module tool_shed.util.hg_util) Arff (class in galaxy.datatypes.text) argv_to_str() (in module galaxy.util.commands) artifact_class() (in module galaxy.managers.executables) as_css_class (galaxy.selenium.components.SelectorTemplate attribute) 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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_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.webapps.reports.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_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) 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.IdentityProvider method) (galaxy.authnz.custos_authnz.CustosAuthnz 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), [1] 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 attribute) 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 attribute) Axes (class in galaxy.datatypes.mothur) Axt (class in galaxy.datatypes.sequence) AzureBlobObjectStore (class in galaxy.objectstore.azure_blob)

B

backend (galaxy.model.PSAPartial attribute) 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) BaseAnnotationsController (class in galaxy.webapps.galaxy.api.annotations), [1] 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), [1] BaseFastq (class in galaxy.datatypes.sequence) BaseField (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) 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), [1] 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), [1] 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) BcftoolsDataProvider (class in galaxy.datatypes.dataproviders.dataset) 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) begin() (galaxy.model.orm.logging_connection_proxy.LoggingProxy method) BGzipTabixDataProvider (class in galaxy.datatypes.dataproviders.dataset) 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.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.TraML attribute) (galaxy.datatypes.proteomics.TrafoXML attribute) (galaxy.datatypes.proteomics.UniProtXML attribute) (galaxy.datatypes.proteomics.XquestSpecXML attribute) (galaxy.datatypes.proteomics.XquestXML attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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_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.webapps.reports.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) 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) 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.tool_util.deps.mulled.util.Target attribute) build() (galaxy.model.dataset_collections.builder.CollectionBuilder method) (galaxy.tools.evaluation.ToolEvaluator method) (galaxy.tools.parameters.basic.ToolParameter class method) (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] 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_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), [1] 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), [1] 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.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) (galaxy.webapps.reports.framework.grids.Grid 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.RepositoriesIOwnGrid method) (tool_shed.grids.repository_grids.RepositoriesInCategoryGrid 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.RepositoriesWithReviewsGrid method) (tool_shed.grids.repository_review_grids.RepositoriesWithoutReviewsGrid 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), [1] build_mulled_singularity_pull_command() (galaxy.tool_util.deps.container_classes.SingularityContainer method) 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), [1] 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_url() (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter method) (galaxy.selenium.cli.DriverWrapper method) (galaxy_test.selenium.framework.TestWithSeleniumMixin method) (in module galaxy.util) 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_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 attribute) 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) 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 attribute) 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 attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) can_install() (galaxy.tool_util.deps.conda_util.CondaContext method) (galaxy.tool_util.deps.installable.InstallableContext method) can_install_conda() (galaxy.tool_util.deps.conda_util.CondaContext method) can_list_containers (galaxy.tool_util.deps.container_resolvers.mulled.MulledDockerContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.MulledSingularityContainerResolver attribute) 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 attribute) can_reset_metadata (galaxy.model.tool_shed_install.ToolShedRepository attribute) can_split() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) can_uninstall (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) can_uninstall_dependencies (galaxy.tool_util.deps.container_resolvers.ContainerResolver attribute) (galaxy.tool_util.deps.resolvers.DependencyResolver attribute) can_update (galaxy.model.tool_shed_install.ToolDependency attribute) 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), [1] cancel_job() (galaxy_test.base.populators.BaseDatasetPopulator method) CancelWorkflowEvaluation categories (tool_shed.webapp.model.Repository attribute) CategoriesController (class in tool_shed.webapp.api.categories), [1] 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_1160_tool_help_images) (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 attribute) 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_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_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), [1] (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_dropboxfs() (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 attribute) 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_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_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_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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation 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), [1] (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] 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), [1] 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.TaskWrapper method) (galaxy.jobs.runners.JobState method) (galaxy.tools.cache.ToolCache method) cleanup_after_job() (galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper method) cleanup_external_metadata() (galaxy.metadata.JobExternalOutputMetadataWrapper method) (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 attribute) 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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_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) 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), [1] 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), [1] 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) 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.DatasetCollection attribute) (galaxy.model.dataset_collections.types.paired.PairedDatasetCollectionType attribute) (galaxy.tool_util.cwl.representation.TypeRepresentation attribute) (galaxy.util.rules_dsl.RuleSet attribute) (galaxy.workflow.modules.InputDataCollectionModule attribute) collection_types (galaxy.tools.parameters.basic.DataCollectionToolParameter attribute) (galaxy.tools.parameters.DataCollectionToolParameter attribute) 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 attribute) (galaxy.model.store.discover.DiscoveredFileError attribute) 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.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) (galaxy.webapps.reports.framework.grids.Grid 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.RepositoriesIOwnGrid attribute) (tool_shed.grids.repository_grids.RepositoriesInCategoryGrid 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.RepositoriesWithReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithoutReviewsGrid 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 attribute) CommandLineException, [1] commands_in_new_shell (galaxy.jobs.JobWrapper attribute) 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() (galaxy.model.orm.logging_connection_proxy.LoggingProxy method) commit_and_push() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) commit_changeset() (in module tool_shed.util.hg_util) commit_for_version() (in module galaxy.tool_util.deps.brew_exts) common_columns (galaxy.managers.history_contents.HistoryContentsManager attribute) common_prefix_dir (galaxy.util.compression_utils.CompressedFile attribute) common_problems() (galaxy.webapps.galaxy.api.jobs.JobController method), [1] CommonConfigurationMixin (class in galaxy.config) CommunityRatingColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.webapps.reports.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.webapps.reports.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) 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 attribute) components_are_associated() (galaxy.security.RBACAgent method) composite_files (galaxy.datatypes.data.Data attribute) composite_type (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.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.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.Analyze75 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 attribute) 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 attribute) 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) 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 attribute) config_options (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.DependencyResolver attribute) config_paths (galaxy.config.config_manage.App attribute) config_to_dict() (in module galaxy.objectstore) 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), [1] (class in tool_shed.webapp.api.configuration), [1] 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 attribute) (galaxy.web_stack.UWSGIApplicationStack attribute) (galaxy.web_stack.WeblessApplicationStack attribute) 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) ConnectedValue (class in galaxy.tools.parameters.basic) connection (galaxy.queue_worker.ControlTask attribute) connection_configuration (galaxy.tool_util.deps.container_classes.DockerContainer attribute) (galaxy.tool_util.deps.container_classes.SingularityContainer 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 attribute) constraint_add() (galaxy.containers.docker_model.DockerService method) constraint_string (galaxy.containers.docker_model.DockerNodeLabel attribute) constraints (galaxy.containers.docker_model.DockerNodeLabels attribute) (galaxy.containers.docker_model.DockerService attribute) 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 attribute) container_from_element() (in module galaxy.tool_util.deps.requirements) container_ids (galaxy.web.proxy.ProxyMapping attribute) container_info (galaxy.model.JobContainerAssociation attribute) container_interface (galaxy.web.proxy.ProxyMapping attribute) container_monitor_command() (galaxy.jobs.JobWrapper method) container_name (galaxy.model.JobContainerAssociation attribute) container_resolver (galaxy.tool_util.deps.containers.ResolvedContainerDescription attribute) 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), [1] ContainerResolutionView (class in galaxy.tool_util.deps.views) ContainerResolver (class in galaxy.tool_util.deps.container_resolvers) ContainerRunError containers_config_file (galaxy.containers.ContainerInterface attribute) 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) content_format (galaxy.model.PageRevision attribute) content_id (galaxy.model.WorkflowStep attribute) 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), [1] contents_count() (galaxy.managers.history_contents.HistoryContentsManager method) contents_iter() (galaxy.model.History 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 attribute) control_queues_from_config() (in module galaxy.queues) controller_name (galaxy.webapps.galaxy.api.annotations.HistoryAnnotationsController attribute), [1] (galaxy.webapps.galaxy.api.annotations.HistoryContentAnnotationsController attribute), [1] (galaxy.webapps.galaxy.api.annotations.WorkflowAnnotationsController attribute), [1] (galaxy.webapps.galaxy.api.extended_metadata.HistoryDatasetExtendMetadataController attribute), [1] (galaxy.webapps.galaxy.api.extended_metadata.LibraryDatasetExtendMetadataController attribute), [1] (galaxy.webapps.galaxy.api.item_tags.HistoryContentTagsController attribute), [1] (galaxy.webapps.galaxy.api.item_tags.HistoryTagsController attribute), [1] (galaxy.webapps.galaxy.api.item_tags.WorkflowTagsController attribute), [1] (galaxy.webapps.galaxy.api.provenance.HDAProvenanceController attribute), [1] (galaxy.webapps.galaxy.api.provenance.LDDAProvenanceController attribute), [1] ControllerUnavailable ControlTask (class in galaxy.queue_worker) conversion_messages (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance attribute) 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), [1] 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), [1] 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation attribute) copied_to_history_dataset_associations (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation 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.ToolSection method) (galaxy.tools.toolbox.panel.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_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 attribute) (galaxy.containers.docker_model.DockerService attribute) (galaxy.containers.docker_model.DockerTask attribute) 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.users.UserManager method) (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController method), [1] (galaxy.webapps.galaxy.api.cloudauthz.CloudAuthzController method), [1] (galaxy.webapps.galaxy.api.dataset_collections.DatasetCollectionsController method), [1] (galaxy.webapps.galaxy.api.dynamic_tools.DynamicToolsController method), [1] (galaxy.webapps.galaxy.api.extended_metadata.BaseExtendedMetadataController method), [1] (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method), [1] (galaxy.webapps.galaxy.api.folders.FoldersController method), [1] (galaxy.webapps.galaxy.api.forms.FormDefinitionAPIController method), [1] (galaxy.webapps.galaxy.api.groups.GroupAPIController method), [1] (galaxy.webapps.galaxy.api.histories.HistoriesController method), [1] (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method), [1] (galaxy.webapps.galaxy.api.item_tags.BaseItemTagsController method), [1] (galaxy.webapps.galaxy.api.job_files.JobFilesAPIController method), [1] (galaxy.webapps.galaxy.api.job_ports.JobPortsAPIController method), [1] (galaxy.webapps.galaxy.api.jobs.JobController method), [1] (galaxy.webapps.galaxy.api.libraries.LibrariesController method), [1] (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method), [1] (galaxy.webapps.galaxy.api.metrics.MetricsController method), [1] (galaxy.webapps.galaxy.api.page_revisions.PageRevisionsController method), [1] (galaxy.webapps.galaxy.api.pages.PagesController method), [1] (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method), [1] (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method), [1] (galaxy.webapps.galaxy.api.roles.RoleAPIController method), [1] (galaxy.webapps.galaxy.api.search.SearchController method), [1] (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] (galaxy.webapps.galaxy.api.uploads.UploadsAPIController method), [1] (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] (galaxy.webapps.galaxy.api.visualizations.VisualizationsController method), [1] (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] (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), [1] (tool_shed.webapp.api.groups.GroupsController method), [1] (tool_shed.webapp.api.repositories.RepositoriesController method), [1] (tool_shed.webapp.api.users.UsersController method), [1] (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), [1] 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_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_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) 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.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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation attribute) (galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters.DeferredJob 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) (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.model.UserAuthnzToken class 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) created_from_basename (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance attribute) (galaxy.model.store.discover.JsonCollectedDatasetMatch attribute) created_time (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.JobContainerAssociation attribute) created_with_galaxy_version (galaxy.jobs.JobWrapper attribute) CreatedWorkflow (class in galaxy.managers.workflows) CreatesApiKeysMixin (class in galaxy.webapps.base.controller) creating_job (galaxy.model.DatasetInstance attribute) creating_job() (galaxy.managers.datasets.DatasetAssociationManager method) creating_job_associations (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation 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.webapps.reports.framework.grids.Grid attribute) cur_sort_key_pref_name (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.reports.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 attribute) current_state_time (galaxy.containers.docker_model.DockerTask attribute) current_user() (galaxy.managers.users.UserManager method) CurrentUserSerializer (class in galaxy.managers.users) cursor_execute() (galaxy.model.orm.logging_connection_proxy.LoggingProxy method) (galaxy.model.orm.logging_connection_proxy.TraceLoggerProxy method) 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) 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.ExtendedMetadata attribute) (galaxy.model.PSAPartial 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 attribute) 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 attribute) data_source_redirect() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) data_sources (galaxy.datatypes.binary.Bam attribute) (galaxy.datatypes.binary.BigBed attribute) (galaxy.datatypes.binary.BigWig attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.interval.Bed attribute) (galaxy.datatypes.interval.BedGraph attribute) (galaxy.datatypes.interval.ChromatinInteractions attribute) (galaxy.datatypes.interval.ENCODEPeak attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.interval.Wiggle attribute) (galaxy.datatypes.tabular.BaseVcf attribute) (galaxy.datatypes.tabular.Pileup attribute) (galaxy.datatypes.tabular.Sam attribute) data_tables_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) 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.TSV attribute) (galaxy.datatypes.tabular.Tabular attribute) (galaxy.datatypes.tabular.TabularData attribute) (galaxy.datatypes.xml.GenericXml attribute) Dataset (class in galaxy.model) (class in galaxy.model.migrate.versions.0005_cleanup_datasets_fix) dataset (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.DatasetHash attribute) (galaxy.model.DatasetPermissions attribute) (galaxy.model.DatasetSource attribute) (galaxy.model.GenomeIndexToolData attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) (galaxy.model.JobExportHistoryArchive attribute) (galaxy.model.JobExternalOutputMetadata 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation attribute) dataset_access_mapping() (galaxy.model.security.GalaxyRBACAgent method) dataset_action_tuples (galaxy.model.DatasetCollection attribute) 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 attribute) 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 attribute) 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 attribute) 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation attribute) dataset_info() (galaxy.webapps.reports.controllers.system.System method) dataset_instance (galaxy.model.DatasetCollectionElement attribute) dataset_instances (galaxy.model.DatasetCollection attribute) (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.DatasetCollectionInstance attribute) 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 attribute) (galaxy.jobs.TaskWrapper attribute) 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 attribute) dataset_source_id (galaxy.model.DatasetSourceHash attribute) dataset_states_and_extensions_summary (galaxy.model.DatasetCollection attribute) 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.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) 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), [1] 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) (class in galaxy.model.migrate.versions.0005_cleanup_datasets_fix) 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), [1] 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 attribute) 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), [1] 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.webapps.reports.framework.grids) db_builds (galaxy.managers.context.ProvidesHistoryContext attribute) db_dataset_for() (galaxy.managers.context.ProvidesHistoryContext method) db_next_hid() (in module galaxy.model.mapping) dbkey (galaxy.model.DatasetInstance attribute) (galaxy.model.Visualization attribute) (galaxy.model.VisualizationRevision attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance attribute) (galaxy.model.store.discover.JsonCollectedDatasetMatch attribute) 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.tool_util.deps.conda_util.CondaContext attribute) deactivate() (galaxy.managers.tools.DynamicToolManager method) deactivate_dynamic_tool() (galaxy_test.base.populators.BaseDatasetPopulator method) deactivate_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) debug_handler() (in module tool_shed.util.shed_index) debugging (galaxy.webapps.galaxy.api.metrics.MetricsController attribute), [1] declare_queues (galaxy.queue_worker.ControlTask attribute) (galaxy.queue_worker.GalaxyQueueWorker attribute) 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), [1] (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) 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.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.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) (galaxy.webapps.reports.framework.grids.Grid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.grids.admin_grids.AdminRepositoryGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoriesByUserGrid 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) 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 attribute) default_length (galaxy.selenium.navigates_galaxy.WaitType attribute) default_loader() (in module galaxy.tool_util.cwl.cwltool_deps) DEFAULT_MAX_OPEN_FILES (galaxy.datatypes.util.maf_utilities.TempFileHandler attribute) (galaxy.tools.util.maf_utilities.TempFileHandler attribute) default_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 attribute) default_permissions (galaxy.model.History attribute) (galaxy.model.User attribute) default_permissions() (galaxy.managers.users.UserManager method) default_port (galaxy.config.config_manage.App attribute) default_printer() (in module galaxy.tools.util.galaxyops) default_quota (galaxy.quota.NoQuotaAgent attribute) default_registered_quota (galaxy.quota.QuotaAgent attribute) 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.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) (galaxy.webapps.reports.framework.grids.Grid 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 attribute) default_tool_action (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.Tool attribute) default_unregistered_quota (galaxy.quota.QuotaAgent attribute) 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) defaults (galaxy.config.schema.AppSchema attribute) defaults() (galaxy.util.properties.NicerConfigParser method) DefaultToolAction (class in galaxy.tools.actions) DefaultToolState (class in galaxy.tools) DefaultUserPermissions (class in galaxy.model) DefaultWebTransaction (class in galaxy.web.framework.base) deferred (galaxy.model.GenomeIndexToolData attribute) deferred_job (galaxy.model.DeferredJob attribute) deferred_job_id (galaxy.model.GenomeIndexToolData attribute) DeferredJob (class in galaxy.model) (class in galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters) 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), [1] (galaxy.webapps.galaxy.api.cloudauthz.CloudAuthzController method), [1] (galaxy.webapps.galaxy.api.dynamic_tools.DynamicToolsController method), [1] (galaxy.webapps.galaxy.api.extended_metadata.BaseExtendedMetadataController method), [1] (galaxy.webapps.galaxy.api.folders.FoldersController method), [1] (galaxy.webapps.galaxy.api.group_roles.GroupRolesAPIController method), [1] (galaxy.webapps.galaxy.api.group_users.GroupUsersAPIController method), [1] (galaxy.webapps.galaxy.api.histories.HistoriesController method), [1] (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method), [1] (galaxy.webapps.galaxy.api.item_tags.BaseItemTagsController method), [1] (galaxy.webapps.galaxy.api.jobs.JobController method), [1] (galaxy.webapps.galaxy.api.libraries.LibrariesController method), [1] (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method), [1] (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method), [1] (galaxy.webapps.galaxy.api.pages.PagesController method), [1] (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method), [1] (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method), [1] (galaxy.webapps.galaxy.api.tool_data.ToolData method), [1] (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController 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), [1] 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) 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), [1] 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) (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) (galaxy.model.User attribute) (galaxy.model.UserAddress attribute) (galaxy.model.Visualization attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation attribute) (galaxy.model.tool_shed_install.ToolShedRepository 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) DeleteDatasetAction (class in galaxy.jobs.actions.post) DeletedColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.webapps.reports.framework.grids) DeleteIntermediatesAction (class in galaxy.jobs.actions.post) 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 attribute) dependency_shell_commands() (galaxy.tool_util.deps.CachedDependencyManager method) (galaxy.tool_util.deps.DependencyManager method) (galaxy.tool_util.deps.NullDependencyManager method) dependency_type (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependency attribute) (galaxy.tool_util.deps.resolvers.NullDependency attribute) (galaxy.tool_util.deps.resolvers.galaxy_packages.ToolShedDependency 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.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.selenium.components.Label attribute) (galaxy.selenium.components.SelectorTemplate attribute) (galaxy.selenium.components.Target attribute) (galaxy.selenium.components.Text 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_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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation attribute) (galaxy.model.store.discover.JsonCollectedDatasetMatch attribute) desired_state (galaxy.containers.docker_model.DockerTask attribute) destination (galaxy.config.config_manage.App attribute) destination_defaults (galaxy.jobs.runners.pulsar.PulsarEmbeddedJobRunner attribute) (galaxy.jobs.runners.pulsar.PulsarLegacyJobRunner attribute) (galaxy.jobs.runners.pulsar.PulsarMQJobRunner attribute) (galaxy.jobs.runners.pulsar.PulsarRESTJobRunner attribute) destination_id (galaxy.model.Job attribute) destination_list (in module galaxy.jobs.dynamic_tool_destination) destination_params (galaxy.model.Job attribute) destination_params() (galaxy.webapps.galaxy.api.jobs.JobController method), [1] DESTINATION_PARAMS_SPEC (galaxy.jobs.runners.chronos.ChronosJobRunner attribute) destroy() (galaxy.model.PSAPartial class method) destroyable() (galaxy.containers.docker_model.DockerNode method) detect_datatype() (galaxy.managers.datasets.DatasetAssociationManager method) determine_output_format() (in module galaxy.tools.actions) deterministic_handler_assignment (galaxy.web_stack.handlers.ConfiguresHandlers attribute) diagnostics() (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] 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.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.model.tool_shed_install.ToolShedRepository attribute) (galaxy.tool_util.deps.container_resolvers.ContainerResolver 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.conda.CondaDependencyResolver 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.Tool 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.toolbox.ToolSection attribute) (galaxy.tools.toolbox.ToolSectionLabel attribute) (galaxy.tools.toolbox.panel.ToolSection attribute) (galaxy.tools.toolbox.panel.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.User attribute) (galaxy.model.UserQuotaAssociation attribute) (galaxy.model.Workflow attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.model.tool_shed_install.ToolVersion 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) 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 attribute) 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.model.migrate.versions.0005_cleanup_datasets_fix) (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) 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) 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 attribute) 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 attribute) display() (galaxy.webapps.galaxy.api.datasets.DatasetsController method), [1] (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 attribute) 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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.SQlite method) (galaxy.datatypes.binary.Scf method) (galaxy.datatypes.binary.SearchGuiArchive method) (galaxy.datatypes.binary.Sff 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.PSMS method) (galaxy.datatypes.proteomics.PepList method) (galaxy.datatypes.proteomics.PepXmlReport method) (galaxy.datatypes.proteomics.ProtXmlReport 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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), [1] DisplayApplicationTemplateParameter (class in galaxy.datatypes.display_applications.parameters) DisplayByUsernameAndSlugGridOperation (class in galaxy.web.framework.helpers.grids) (class in galaxy.webapps.reports.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_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 attribute) 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) 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.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), [1] (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] (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), [1] download_dataset_from_library() (galaxy_test.selenium.test_library_contents.LibraryContentsTestCase method) download_field_file() (galaxy.webapps.galaxy.api.tool_data.ToolData method), [1] download_invocation_bco() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] 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) 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) 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 attribute) dynamic_tool (galaxy.model.WorkflowStep attribute) dynamic_tool_confs() (galaxy.webapps.galaxy.api.configuration.ConfigurationController method), [1] 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), [1]

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.CRAM attribute) (galaxy.datatypes.binary.Cel 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.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.ProtXmlReport attribute) (galaxy.datatypes.proteomics.ProteomicsXml attribute) (galaxy.datatypes.proteomics.ThermoRAW attribute) (galaxy.datatypes.proteomics.Wiff attribute) (galaxy.datatypes.qualityscore.QualityScore attribute) (galaxy.datatypes.registry.Registry 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.webapps.galaxy.api.datatypes.DatatypesController method), [1] 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.CRAM attribute) (galaxy.datatypes.binary.Cel 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.SQlite 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.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.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.QualityScoreSOLiD attribute) (galaxy.datatypes.qualityscore.QualityScoreSolexa attribute) (galaxy.datatypes.sequence.Axt attribute) (galaxy.datatypes.sequence.BaseFastq 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.sequence.csFasta 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 attribute) edam_formats() (galaxy.webapps.galaxy.api.datatypes.DatatypesController method), [1] 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 attribute) (galaxy.tool_util.parser.ToolOutputCollectionPart attribute) 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 attribute) (galaxy.util.StructuredExecutionTimer attribute) elem() (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.xml.XmlInputSource method) element_as_dict() (galaxy.datatypes.dataproviders.hierarchy.XMLDataProvider method) element_count (galaxy.model.DatasetCollection attribute) element_identifier (galaxy.model.DatasetCollectionElement attribute) (galaxy.tools.wrappers.DatasetCollectionWrapper attribute) (galaxy.tools.wrappers.DatasetFilenameWrapper attribute) element_identifiers (galaxy.model.store.discover.JsonCollectedDatasetMatch attribute) 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 attribute) (galaxy.selenium.components.SelectorTemplate attribute) (galaxy.selenium.components.Target attribute) (galaxy.selenium.components.Text attribute) element_object (galaxy.model.DatasetCollectionElement attribute) element_type (galaxy.model.DatasetCollectionElement attribute) 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) (tool_shed.webapp.model.User attribute) email_alerts (tool_shed.webapp.model.Repository attribute) email_alerts_repository_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) 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.History attribute) empty() (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ObjectStore method) EmptyTextfieldValidator (class in galaxy.tools.parameters.validation) enable_email_alerts() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) enabled_container_types (galaxy.tool_util.deps.DependencyManager attribute) 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), [1] 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 attribute) (galaxy.tools.util.maf_utilities.SplicedAlignment attribute) endpoint_spec_option_map (galaxy.containers.docker_swarm.DockerSwarmAPIInterface attribute) engine (galaxy.model.Dataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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_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 attribute) env_path() (galaxy.tool_util.deps.conda_util.CondaContext method) env_to_statement() (in module galaxy.jobs.runners.util.env) EnvAction (class in galaxy.tool_util.deps.brew_exts) 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 attribute) 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.tool_util.lint.LintContext method) (galaxy.web.framework.middleware.remoteuser.RemoteUser method) (galaxy.webapps.galaxy.api.jobs.JobController method), [1] (in module galaxy.web) (in module galaxy.web.framework.decorators) (tool_shed.webapp.framework.middleware.remoteuser.RemoteUser method) error_if_anonymous() (galaxy.managers.users.UserManager method) error_if_uploading() (galaxy.managers.hdas.HDAManager method) error_message (galaxy.model.store.discover.DiscoveredFileError attribute) (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) error_on_exit_code() (in module galaxy.tool_util.parser.stdio) error_stack() (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] 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.ContainerDependency attribute) (galaxy.tool_util.deps.resolvers.Dependency attribute) (galaxy.tool_util.deps.resolvers.NullDependency attribute) (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependency attribute) (galaxy.tool_util.deps.resolvers.resolver_mixins.HomebrewDependency attribute) example_datatype_registry_for_sample() (in module galaxy.datatypes.registry) ExcelXls (class in galaxy.datatypes.binary) 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 attribute) exec_after_process() (galaxy.tools.DataManagerTool 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.Tool method) (galaxy.tools.actions.DefaultToolAction method) (galaxy.tools.actions.ToolAction method) (galaxy.tools.actions.data_manager.DataManagerToolAction 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.upload.BaseUploadToolAction 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), [1] (galaxy.webapps.galaxy.api.extended_metadata.LibraryDatasetExtendMetadataController attribute), [1] expand_here_template() (in module galaxy.tools.data) expand_incoming() (galaxy.tools.Tool method) 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 attribute) 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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), [1] export_library() (galaxy.model.store.DirectoryModelExportStore method) export_list() (galaxy.tool_util.deps.conda_util.CondaContext method) export_name (galaxy.model.JobExportHistoryArchive attribute) 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) (galaxy.model.DatasetInstance attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance attribute) (galaxy.model.store.discover.JsonCollectedDatasetMatch attribute) extend() (galaxy.model.custom_types.MutationList method) extend_data_with() (galaxy.tools.data.TabularToolDataTable method) extend_validation_errors() (galaxy.model.DatasetInstance method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation attribute) external (galaxy.model.User attribute) (tool_shed.webapp.model.User attribute) external_filename (galaxy.model.Dataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset attribute) external_metadata_set_successfully() (galaxy.metadata.JobExternalOutputMetadataWrapper method) (galaxy.metadata.MetadataCollectionStrategy method) (galaxy.metadata.PortableDirectoryMetadataGenerator method) external_output_metadata (galaxy.jobs.JobWrapper attribute) (galaxy.model.Job attribute) external_runjob() (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) external_user_id (galaxy.model.CustosAuthnzToken attribute) extra_data (galaxy.model.UserAuthnzToken attribute) extra_files (galaxy.model.store.discover.JsonCollectedDatasetMatch attribute) extra_files() (galaxy.managers.datasets.DatasetAssociationManager method) (galaxy.webapps.galaxy.api.datasets.DatasetsController method), [1] extra_files_path (galaxy.model.Dataset attribute) (galaxy.model.DatasetHash attribute) (galaxy.model.DatasetInstance attribute) (galaxy.model.DatasetSource attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance attribute) extra_files_path_exists() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) extra_files_path_name (galaxy.model.Dataset attribute) extra_files_path_name_from() (galaxy.model.Dataset method) extra_preferences (galaxy.model.User attribute) extract() (galaxy.util.compression_utils.CompressedFile method) extract_components_from_tuple() (in module galaxy.tool_shed.util.repository_util) (in module tool_shed.util.repository_util) extract_domain() (in module galaxy.security.validate_user_input) extract_options_from_dict() (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider class method) extract_value() (galaxy.tools.test.ParamContext method) extract_workflow() (in module galaxy.workflow.extract) ExtractDatasetCollectionTool (class in galaxy.tools)

F

Facts (class in galaxy.util.facts) facts (galaxy.web_stack.ApplicationStack attribute) (galaxy.web_stack.UWSGIApplicationStack attribute) 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.tool_util.lint.LintContext method) FailedTest (class in tool_shed.utility_containers) FAILURE (galaxy.openid.openid_manager.OpenIDManager attribute) failure() (in module galaxy.jobs.runners.state_handlers.resubmit) 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) 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 attribute) 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), [1] (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) 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.CRAM 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.CuffDiffSQlite attribute) (galaxy.datatypes.binary.DAA attribute) (galaxy.datatypes.binary.DMND attribute) (galaxy.datatypes.binary.Dcd attribute) (galaxy.datatypes.binary.DlibSQlite 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.MCool attribute) (galaxy.datatypes.binary.MashSketch attribute) (galaxy.datatypes.binary.MassHunterTar attribute) (galaxy.datatypes.binary.MassLynxTar 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.PQP attribute) (galaxy.datatypes.binary.PostgresqlArchive attribute) (galaxy.datatypes.binary.ProBam attribute) (galaxy.datatypes.binary.RData attribute) (galaxy.datatypes.binary.RMA6 attribute) (galaxy.datatypes.binary.SQlite attribute) (galaxy.datatypes.binary.SQmass attribute) (galaxy.datatypes.binary.Scf attribute) (galaxy.datatypes.binary.SearchGuiArchive attribute) (galaxy.datatypes.binary.Sff 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.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.SNPMatrix attribute) (galaxy.datatypes.genetics.Snptest attribute) (galaxy.datatypes.genetics.ldIndep attribute) (galaxy.datatypes.genetics.rgFeatureList attribute) (galaxy.datatypes.genetics.rgSampleList attribute) (galaxy.datatypes.genetics.rgTabList attribute) (galaxy.datatypes.gis.Shapefile attribute) (galaxy.datatypes.graph.Sif attribute) (galaxy.datatypes.graph.Xgmml attribute) (galaxy.datatypes.images.Bmp attribute) (galaxy.datatypes.images.Eps attribute) (galaxy.datatypes.images.Gif 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.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.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.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.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.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.molecules.grd attribute) (galaxy.datatypes.molecules.grdtgz 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.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.Analyze75 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.PEFF attribute) (galaxy.datatypes.proteomics.PSMS attribute) (galaxy.datatypes.proteomics.ParamXml 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.QCML attribute) (galaxy.datatypes.proteomics.SPLib attribute) (galaxy.datatypes.proteomics.SPLibNoIndex attribute) (galaxy.datatypes.proteomics.Sf3 attribute) (galaxy.datatypes.proteomics.TandemXML attribute) (galaxy.datatypes.proteomics.ThermoRAW attribute) (galaxy.datatypes.proteomics.TraML attribute) (galaxy.datatypes.proteomics.TrafoXML 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.QualityScoreSOLiD attribute) (galaxy.datatypes.qualityscore.QualityScoreSolexa attribute) (galaxy.datatypes.sequence.Axt attribute) (galaxy.datatypes.sequence.BaseFastq 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.sequence.csFasta attribute) (galaxy.datatypes.spaln.SpalnNuclDb attribute) (galaxy.datatypes.spaln.SpalnProtDb attribute) (galaxy.datatypes.tabular.CSV attribute) (galaxy.datatypes.tabular.ConnectivityTable 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.Html attribute) (galaxy.datatypes.text.IQTree attribute) (galaxy.datatypes.text.ImgtJson attribute) (galaxy.datatypes.text.Ipynb 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.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 attribute) (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance attribute) (galaxy.model.MetadataFile attribute) (galaxy.model.metadata.MetadataTempFile attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance attribute)

file_path (galaxy.model.Dataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset attribute) file_reader() (in module galaxy.util) file_ready() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.cloud.Cloud method) (galaxy.objectstore.irods.IRODSObjectStore method) (galaxy.objectstore.pulsar.PulsarObjectStore method) (galaxy.objectstore.s3.S3ObjectStore method) file_size (galaxy.datatypes.sniff.FilePrefix attribute) (galaxy.model.Dataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset attribute) file_states (tool_shed.webapp.model.Repository attribute) FileDataResolver (class in galaxy.tool_util.verify.test_data) 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) FileToolParameter (class in galaxy.tools.parameters.basic) FileUploadTarget (class in galaxy.tool_util.cwl.util) fill() (galaxy.selenium.has_driver.HasDriver method) 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() (in module galaxy.util.template) 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_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) (galaxy.webapps.reports.framework.grids.CommunityTagsColumn method) (galaxy.webapps.reports.framework.grids.DeletedColumn method) (galaxy.webapps.reports.framework.grids.GridColumn method) (galaxy.webapps.reports.framework.grids.MulticolFilterColumn method) (galaxy.webapps.reports.framework.grids.SharingStatusColumn method) (galaxy.webapps.reports.framework.grids.StateColumn method) (galaxy.webapps.reports.framework.grids.TextColumn 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 attribute) 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 attribute) first_changeset_hash (in module tool_shed.test.functional.test_0420_citable_urls_for_repositories) first_dataset_element (galaxy.model.DatasetCollection attribute) 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_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.SessionlessContext method) (galaxy.model.store.discover.ModelPersistenceContext method) (galaxy.model.store.discover.SessionlessModelPersistenceContext 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) 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), [1] FolderManager (class in galaxy.managers.folders) folders (galaxy.model.LibraryFolder attribute) FoldersController (class in galaxy.webapps.galaxy.api.folders), [1] 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.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 attribute) formatted() (galaxy.webapps.reports.controllers.tools.Tools method) formatter (galaxy.job_metrics.instrumenters.cgroup.CgroupPlugin attribute) (galaxy.job_metrics.instrumenters.InstrumentPlugin 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) FormatToolOutputAction (class in galaxy.tool_util.parser.output_actions) FormDefinition (class in galaxy.model) FormDefinitionAddressFieldFactory (class in galaxy.forms.forms) FormDefinitionAPIController (class in galaxy.webapps.galaxy.api.forms), [1] 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_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.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.DataCollectionToolParameter method) (galaxy.tools.parameters.DataToolParameter method) (galaxy.tools.parameters.SelectToolParameter 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.FileToolParameter method) (galaxy.tools.parameters.basic.FloatToolParameter 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) 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_parameter() (galaxy.tools.parameters.history_query.HistoryQuery static method) from_path (galaxy.model.StoredWorkflow 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_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) FTPFileToolParameter (class in galaxy.tools.parameters.basic) full_delete() (galaxy.model.Dataset method) func_std_string() (in module galaxy.web.framework.middleware.profile) 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 (galaxy.web.framework.middleware.batch.BatchMiddleware attribute) (module) 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.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.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.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.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.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.util (module) galaxy.model.none_like (module) galaxy.model.orm (module) galaxy.model.orm.engine_factory (module) galaxy.model.orm.logging_connection_proxy (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.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.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.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.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.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.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.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.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.simplegraph (module) galaxy.util.sleeper (module) galaxy.util.sockets (module) galaxy.util.specs (module) galaxy.util.sqlite (module) galaxy.util.streamball (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.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.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.galaxy (module) galaxy.webapps.galaxy.api (module) galaxy.webapps.galaxy.api.annotations (module), [1] galaxy.webapps.galaxy.api.authenticate (module), [1] galaxy.webapps.galaxy.api.cloud (module), [1] galaxy.webapps.galaxy.api.cloudauthz (module), [1] galaxy.webapps.galaxy.api.configuration (module), [1] galaxy.webapps.galaxy.api.container_resolution (module), [1] galaxy.webapps.galaxy.api.dataset_collections (module), [1] galaxy.webapps.galaxy.api.datasets (module), [1] galaxy.webapps.galaxy.api.datatypes (module), [1] galaxy.webapps.galaxy.api.display_applications (module), [1] galaxy.webapps.galaxy.api.dynamic_tools (module), [1] galaxy.webapps.galaxy.api.extended_metadata (module), [1] galaxy.webapps.galaxy.api.folder_contents (module), [1] galaxy.webapps.galaxy.api.folders (module), [1] galaxy.webapps.galaxy.api.forms (module), [1] galaxy.webapps.galaxy.api.genomes (module), [1] galaxy.webapps.galaxy.api.group_roles (module), [1] galaxy.webapps.galaxy.api.group_users (module), [1] galaxy.webapps.galaxy.api.groups (module), [1] galaxy.webapps.galaxy.api.histories (module), [1] galaxy.webapps.galaxy.api.history_contents (module), [1] galaxy.webapps.galaxy.api.item_tags (module), [1] galaxy.webapps.galaxy.api.job_files (module), [1] galaxy.webapps.galaxy.api.job_ports (module), [1] galaxy.webapps.galaxy.api.jobs (module), [1] galaxy.webapps.galaxy.api.libraries (module), [1] galaxy.webapps.galaxy.api.library_contents (module), [1] galaxy.webapps.galaxy.api.library_datasets (module), [1] galaxy.webapps.galaxy.api.metrics (module), [1] galaxy.webapps.galaxy.api.page_revisions (module), [1] galaxy.webapps.galaxy.api.pages (module), [1] galaxy.webapps.galaxy.api.plugins (module), [1] galaxy.webapps.galaxy.api.provenance (module), [1] galaxy.webapps.galaxy.api.quotas (module), [1] galaxy.webapps.galaxy.api.remote_files (module), [1] galaxy.webapps.galaxy.api.roles (module), [1] galaxy.webapps.galaxy.api.search (module), [1] galaxy.webapps.galaxy.api.tags (module), [1] galaxy.webapps.galaxy.api.tool_data (module), [1] galaxy.webapps.galaxy.api.tool_dependencies (module), [1] galaxy.webapps.galaxy.api.tool_entry_points (module), [1] galaxy.webapps.galaxy.api.tool_shed_repositories (module), [1] galaxy.webapps.galaxy.api.tools (module), [1] galaxy.webapps.galaxy.api.toolshed (module), [1] galaxy.webapps.galaxy.api.tours (module), [1] galaxy.webapps.galaxy.api.uploads (module), [1] galaxy.webapps.galaxy.api.users (module), [1] galaxy.webapps.galaxy.api.visualizations (module), [1] galaxy.webapps.galaxy.api.webhooks (module), [1] galaxy.webapps.galaxy.api.workflows (module), [1] 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.interactivetool (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.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.reports.framework (module) galaxy.webapps.reports.framework.grids (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.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_directory() (in module galaxy.util) galaxy_driver_class (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 attribute) 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 attribute) 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 attribute) 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_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_asserts (module) galaxy_test.base.api_util (module) galaxy_test.base.constants (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.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_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 attribute) 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) GalaxySession (class in galaxy.model) (class in tool_shed.webapp.model) 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) 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.neo4j.Neo4j method) (galaxy.datatypes.ngsindex.BowtieIndex method) (galaxy.datatypes.proteomics.Analyze75 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), [1] 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.MetadataCollection 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.roles.RoleManager method) (galaxy.model.PSAAssociation class method) (galaxy.model.dataset_collections.registry.DatasetCollectionTypesRegistry method) (galaxy.model.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataElementSpec 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.LineageMap method) (galaxy.tools.toolbox.lineages.factory.LineageMap method) (galaxy.tools.wrappers.DatasetFilenameWrapper.MetadataWrapper method) (galaxy.util.Params method) (galaxy.util.bunch.Bunch method) (galaxy.webapps.galaxy.api.cloud.CloudController method), [1] (galaxy.webapps.reports.config.Configuration 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.webapps.reports.framework.grids.DeletedColumn method) (galaxy.webapps.reports.framework.grids.GridColumn method) (galaxy.webapps.reports.framework.grids.SharingStatusColumn method) (galaxy.webapps.reports.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_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), [1] (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] 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_child_by_designation() (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance 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_communication() (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] 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_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), [1] 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_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_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), [1] 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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_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.webapps.galaxy.controllers.admin.UserListGrid method) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid method) (galaxy.webapps.reports.framework.grids.Grid 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), [1] (galaxy_test.selenium.test_custom_builds.CustomBuildsTestcase method) get_custom_builds_metadata() (galaxy.webapps.galaxy.api.histories.HistoriesController method), [1] 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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_dbkey() (galaxy.model.DatasetInstance method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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.DataToolParameter method) (galaxy.tools.parameters.SelectToolParameter 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) 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_driver() (in module galaxy_test.selenium.framework) 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_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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance method) get_file_peek() (galaxy.datatypes.genetics.RexpBase method) (in module galaxy.datatypes.data) get_file_size() (in module galaxy.util) get_file_sources() (in module galaxy.tools.data_fetch) 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) (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.webapps.reports.framework.grids.CommunityTagsColumn method) (galaxy.webapps.reports.framework.grids.IndividualTagsColumn method) (galaxy.webapps.reports.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) 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_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() (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.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_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() (in module galaxy.webapps.galaxy.api.genomes), [1] 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.webapps.reports.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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDataset method) get_information() (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] get_inital_values() (galaxy.datatypes.display_applications.application.DisplayApplicationLink method) get_initial_value() (galaxy.tools.parameters.basic.BaseDataToolParameter method) (galaxy.tools.parameters.SelectToolParameter 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.FTPFileToolParameter method) (galaxy.tools.parameters.basic.FloatToolParameter 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) 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), [1] 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_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_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_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_values() (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.SelectToolParameter 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) 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_library_item_info_templates() (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDataset method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation method) get_link() (galaxy.datatypes.display_applications.application.DisplayApplication method) (galaxy.web.framework.helpers.grids.GridColumn method) (galaxy.web.framework.helpers.grids.PublicURLColumn method) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid.HistoryListNameColumn method) (galaxy.webapps.reports.framework.grids.GridColumn method) (galaxy.webapps.reports.framework.grids.PublicURLColumn method) (galaxy.webapps.reports.framework.grids.SharingStatusColumn 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) (in module galaxy_test.selenium.framework) 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_for_no_shed_tool_config() (in module galaxy.webapps.galaxy.api.tool_shed_repositories), [1] get_metadata() (galaxy.model.DatasetInstance method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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), [1] (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.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_mutable_output_fnames() (galaxy.jobs.JobWrapper method) get_name() (galaxy.model.LibraryDataset method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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.SelectToolParameter 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) 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) get_or_create_index() (in module galaxy.tools.search) 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), [1] 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_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), [1] get_path_key() (in module galaxy.managers.jobs) get_peek() (galaxy.datatypes.genetics.RexpBase method) get_percent() (galaxy.quota.NoQuotaAgent method) (galaxy.quota.QuotaAgent method) get_permissions() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) (galaxy.webapps.galaxy.api.folders.FoldersController method), [1] (galaxy.webapps.galaxy.api.libraries.LibrariesController method), [1] (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] get_permitted_actions() (in module galaxy.model.migrate.versions.0005_cleanup_datasets_fix) (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_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_purged() (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDataset 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.quota.QuotaAgent method) (galaxy.webapps.base.controller.UsesQuotaMixin method) (in module galaxy.webapps.galaxy.controllers.admin) get_quota_params() (galaxy.web.params.QuotaParamParser method) get_random_name() (galaxy_test.base.populators.BaseDatasetPopulator method) get_raw_data() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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_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) (in module galaxy_test.selenium.framework) 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), [1] 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), [1] 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_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_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_session() (galaxy.openid.openid_manager.OpenIDManager method) get_session_id() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.model.Job method) (galaxy.model.Task method) 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.webapps.reports.framework.grids.BooleanColumn method) (galaxy.webapps.reports.framework.grids.IntegerColumn method) (galaxy.webapps.reports.framework.grids.OwnerAnnotationColumn method) (galaxy.webapps.reports.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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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) 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), [1] 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), [1] 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.ToolLocationResolver method) (galaxy.tool_util.locations.file.HttpToolResolver method) (galaxy.tool_util.locations.http.HttpToolResolver 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), [1] get_toolbox_parser() (in module galaxy.tools.toolbox.parser) 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_track_resolution() (galaxy.datatypes.coverage.LastzCoverage method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.Wiggle method) 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_url_args() (galaxy.web.framework.helpers.grids.DisplayByUsernameAndSlugGridOperation method) (galaxy.web.framework.helpers.grids.GridColumnFilter method) (galaxy.web.framework.helpers.grids.GridOperation method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationListGrid method) (galaxy.webapps.reports.framework.grids.DisplayByUsernameAndSlugGridOperation method) (galaxy.webapps.reports.framework.grids.GridColumnFilter method) (galaxy.webapps.reports.framework.grids.GridOperation method) get_usage() (galaxy.quota.NoQuotaAgent method) get_user() (galaxy.model.Job method) (galaxy.model.UserAuthnzToken class method) (galaxy.webapps.base.controller.BaseController method) (galaxy.work.context.WorkRequestContext method) (in module galaxy.tool_shed.util.shed_util_common) (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_quotas() (galaxy.quota.NoQuotaAgent method) (galaxy.quota.QuotaAgent method) 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.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.APIKeyColumn method) (galaxy.webapps.galaxy.controllers.admin.UserListGrid.ActivatedColumn 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) (galaxy.webapps.reports.framework.grids.CommunityRatingColumn method) (galaxy.webapps.reports.framework.grids.CommunityTagsColumn method) (galaxy.webapps.reports.framework.grids.GridColumn method) (galaxy.webapps.reports.framework.grids.IndividualTagsColumn method) (galaxy.webapps.reports.framework.grids.OwnerAnnotationColumn method) (galaxy.webapps.reports.framework.grids.OwnerColumn method) (galaxy.webapps.reports.framework.grids.SharingStatusColumn method) (galaxy.webapps.reports.framework.grids.StateColumn 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.WithReviewsRevisionColumn method) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn 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.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule 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) 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.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), [1] get_workflow_parameter_list() (in module galaxy.workflow.resources) get_workflows_list() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] get_working_directory() (galaxy.model.Task 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) 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) Gif (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.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.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.page.PageListGrid attribute) (galaxy.webapps.reports.framework.grids.Grid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid 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.CategoryGrid attribute) (tool_shed.grids.repository_grids.EmailAlertsRepositoryGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid 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.webapps.reports.framework.grids) grid_fields() (galaxy.model.FormDefinition method) GridAction (class in galaxy.web.framework.helpers.grids) (class in galaxy.webapps.reports.framework.grids) GridColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.webapps.reports.framework.grids) GridColumnFilter (class in galaxy.web.framework.helpers.grids) (class in galaxy.webapps.reports.framework.grids) GridOperation (class in galaxy.web.framework.helpers.grids) (class in galaxy.webapps.reports.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_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), [1] 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), [1] 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), [1] GroupUsersAPIController (class in galaxy.webapps.galaxy.api.group_users), [1] 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 attribute) 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) 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.webapps.reports.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_uwsgi_cli_command() (galaxy_test.driver.integration_util.IntegrationInstance class method) handler (galaxy.model.Job attribute) (galaxy.model.WorkflowInvocation attribute) handler_count (galaxy.web_stack.message.ApplicationStackMessageDispatcher attribute) handler_tags (galaxy.web_stack.handlers.ConfiguresHandlers attribute) 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.model.migrate.versions.0005_cleanup_datasets_fix.Dataset method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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) (galaxy.util.rules_dsl.RuleSet attribute) 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 attribute) 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 attribute) has_reference_data() (galaxy.visualization.genomes.Genomes method) has_reloaded() (galaxy.tools.ToolBox method) has_repository_dependencies (galaxy.model.tool_shed_install.ToolShedRepository attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) has_repository_dependencies_only_if_compiling_contained_td (galaxy.model.tool_shed_install.ToolShedRepository attribute) has_resolution (galaxy.datatypes.data.Data attribute) has_subcollections (galaxy.model.DatasetCollection attribute) has_subcollections() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) has_subcollections_of_type() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method) has_tool() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) has_tool_with_id() (galaxy.tools.toolbox.panel.ToolPanelElements 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.tools.cache.ToolHash attribute) hash() (galaxy.containers.docker_model.DockerAttributeContainer method) 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) (galaxy.model.store.discover.JsonCollectedDatasetMatch attribute) 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_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), [1] hdas (galaxy.model.HistoryDatasetAssociationAnnotationAssociation attribute) (galaxy.model.HistoryDatasetAssociationRatingAssociation attribute) HDASerializer (class in galaxy.managers.hdas) HDCAManager (class in galaxy.managers.hdcas) HDCASerializer (class in galaxy.managers.hdcas) HDT (class in galaxy.datatypes.triples) 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 attribute) help() (tool_shed.webapp.controllers.repository.RepositoryController method) help_by_page (galaxy.tools.Tool attribute) hg_repo (tool_shed.webapp.model.Repository attribute) HgController (class in tool_shed.webapp.controllers.hg) hgweb_config (tool_shed.util.hgweb_config.HgWebConfigManager attribute) HgWebConfigManager (class in tool_shed.util.hgweb_config) hid (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation 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_shared_by_others (galaxy.model.User attribute) HistoriesApiTestCase (class in galaxy_test.api.test_histories) HistoriesController (class in galaxy.webapps.galaxy.api.histories), [1] 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) (galaxy.work.context.WorkRequestContext attribute) 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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 attribute) history_content_type (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) (galaxy.tool_util.cwl.util.GalaxyOutput attribute) history_contents() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) history_data() (galaxy.webapps.galaxy.controllers.history.HistoryController method) history_dataset (galaxy.model.MetadataFile attribute) history_dataset_association (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization attribute) (galaxy.model.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) (galaxy.tool_util.cwl.util.GalaxyOutput attribute) (galaxy_test.api.test_workflow_extraction.RunJobsSummary attribute) (galaxy_test.base.populators.RunJobsSummary attribute) 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 attribute) 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), [1] HistoryContentAnnotationsController (class in galaxy.webapps.galaxy.api.annotations), [1] HistoryContentsApiTestCase (class in galaxy_test.api.test_history_contents) HistoryContentsController (class in galaxy.webapps.galaxy.api.history_contents), [1] 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), [1] HistoryController (class in galaxy.webapps.galaxy.controllers.history) HistoryCopyElementsTestCase (class in galaxy_test.selenium.test_history_copy_elements) HistoryDatasetAssociation (class in galaxy.model) (class in galaxy.model.migrate.versions.0005_cleanup_datasets_fix) HistoryDatasetAssociationAnnotationAssociation (class in galaxy.model) HistoryDatasetAssociationDisplayAtAuthorization (class in galaxy.model) HistoryDatasetAssociationHistory (class in galaxy.model) 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) HistoryDatasetCollectionRatingAssociation (class in galaxy.model) HistoryDatasetCollectionTagAssociation (class in galaxy.model) HistoryDatasetExtendMetadataController (class in galaxy.webapps.galaxy.api.extended_metadata), [1] 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) 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) HistoryTagAssociation (class in galaxy.model) HistoryTagsController (class in galaxy.webapps.galaxy.api.item_tags), [1] 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 attribute) 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.containers.docker.DockerInterface attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.web.proxy.ProxyMapping attribute) host_config_option_map (galaxy.containers.docker.DockerAPIInterface attribute) host_iter (galaxy.containers.docker.DockerInterface attribute) HostAgent (class in galaxy.model.security) hostname (galaxy.model.WorkerProcess attribute) HostnamePlugin (class in galaxy.job_metrics.instrumenters.hostname) 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.containers.Container attribute) (galaxy.containers.docker_model.DockerNode attribute) (galaxy.containers.docker_model.DockerTask 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.PSAAssociation attribute) (galaxy.model.PSACode attribute) (galaxy.model.PSANonce attribute) (galaxy.model.PSAPartial 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.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.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.model.migrate.versions.0005_cleanup_datasets_fix.Dataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation attribute) (galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters.DeferredJob 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.tools.data_manager.manager.DataManager attribute) (galaxy.util.jstree.Path 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_based (galaxy.tools.toolbox.lineages.interface.ToolLineageVersion attribute) 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 attribute) 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 attribute) 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) 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), [1] import_shared_workflow_deprecated() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] import_submodules() (in module galaxy.util.submodules) import_tool() (galaxy_test.base.populators.WorkflowPopulator method) 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.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 attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) 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 attribute) includes_datatypes (galaxy.model.tool_shed_install.ToolShedRepository attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) includes_tool_dependencies (galaxy.model.tool_shed_install.ToolShedRepository attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) includes_tools (galaxy.model.tool_shed_install.ToolShedRepository attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) includes_tools_for_display_in_tool_panel (galaxy.model.tool_shed_install.ToolShedRepository attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) includes_workflows (galaxy.model.tool_shed_install.ToolShedRepository attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) InconsistentDatabase incr() (galaxy.web.statsd_client.GalaxyStatsdClient method) increase_running_job_count() (galaxy.jobs.handler.JobHandlerQueue method) index() (galaxy.tool_util.deps.views.ContainerResolutionView method) (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController method), [1] (galaxy.webapps.galaxy.api.cloud.CloudController method), [1] (galaxy.webapps.galaxy.api.cloudauthz.CloudAuthzController method), [1] (galaxy.webapps.galaxy.api.configuration.ConfigurationController method), [1] (galaxy.webapps.galaxy.api.container_resolution.ContainerResolutionAPIController method), [1] (galaxy.webapps.galaxy.api.dataset_collections.DatasetCollectionsController method), [1] (galaxy.webapps.galaxy.api.datasets.DatasetsController method), [1] (galaxy.webapps.galaxy.api.datatypes.DatatypesController method), [1] (galaxy.webapps.galaxy.api.display_applications.DisplayApplicationsController method), [1] (galaxy.webapps.galaxy.api.dynamic_tools.DynamicToolsController method), [1] (galaxy.webapps.galaxy.api.extended_metadata.BaseExtendedMetadataController method), [1] (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method), [1] (galaxy.webapps.galaxy.api.folders.FoldersController method), [1] (galaxy.webapps.galaxy.api.forms.FormDefinitionAPIController method), [1] (galaxy.webapps.galaxy.api.genomes.GenomesController method), [1] (galaxy.webapps.galaxy.api.group_roles.GroupRolesAPIController method), [1] (galaxy.webapps.galaxy.api.group_users.GroupUsersAPIController method), [1] (galaxy.webapps.galaxy.api.groups.GroupAPIController method), [1] (galaxy.webapps.galaxy.api.histories.HistoriesController method), [1] (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method), [1] (galaxy.webapps.galaxy.api.item_tags.BaseItemTagsController method), [1] (galaxy.webapps.galaxy.api.job_files.JobFilesAPIController method), [1] (galaxy.webapps.galaxy.api.jobs.JobController method), [1] (galaxy.webapps.galaxy.api.libraries.LibrariesController method), [1] (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method), [1] (galaxy.webapps.galaxy.api.page_revisions.PageRevisionsController method), [1] (galaxy.webapps.galaxy.api.pages.PagesController method), [1] (galaxy.webapps.galaxy.api.plugins.PluginsController method), [1] (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method), [1] (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method), [1] (galaxy.webapps.galaxy.api.remote_files.RemoteFilesAPIController method), [1] (galaxy.webapps.galaxy.api.roles.RoleAPIController method), [1] (galaxy.webapps.galaxy.api.tool_data.ToolData method), [1] (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method), [1] (galaxy.webapps.galaxy.api.tool_entry_points.ToolEntryPointsAPIController method), [1] (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method), [1] (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] (galaxy.webapps.galaxy.api.toolshed.ToolShedController method), [1] (galaxy.webapps.galaxy.api.tours.ToursController method), [1] (galaxy.webapps.galaxy.api.uploads.UploadsAPIController method), [1] (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] (galaxy.webapps.galaxy.api.visualizations.VisualizationsController method), [1] (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] (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), [1] (tool_shed.webapp.api.groups.GroupsController method), [1] (tool_shed.webapp.api.repositories.RepositoriesController method), [1] (tool_shed.webapp.api.repository_revisions.RepositoryRevisionsController method), [1] (tool_shed.webapp.api.tools.ToolsController method), [1] (tool_shed.webapp.api.users.UsersController method), [1] (tool_shed.webapp.controllers.groups.Group method) (tool_shed.webapp.controllers.repository.RepositoryController method) (tool_shed.webapp.controllers.user.User method) index_invocations() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] index_jobs_summary() (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method), [1] index_of_tool_id() (galaxy.tools.toolbox.panel.ToolPanelElements method) indexer (galaxy.model.GenomeIndexToolData attribute) indexes() (galaxy.webapps.galaxy.api.genomes.GenomesController method), [1] IndividualTagsColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.webapps.reports.framework.grids) InfernalCM (class in galaxy.datatypes.msa) Inflector (class in galaxy.util.inflection) InfluxDBPlugin (class in galaxy.tools.error_reports.plugins.influxdb) info (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.Job attribute) (galaxy.model.JobStateHistory attribute) (galaxy.model.LibraryDataset 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation attribute) info() (galaxy.tool_util.lint.LintContext method) info_association (galaxy.model.Library attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryFolder attribute) info_text (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (galaxy.webapps.reports.framework.grids.Grid attribute) inheritable (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryInfoAssociation attribute) 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.data.Newick method) (galaxy.datatypes.data.Nexus 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.datatypes.text.SnpSiftDbNSFP method) (galaxy.model.DatasetInstance method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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) 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_associations (galaxy.model.WorkflowInvocation attribute) input_combinations (galaxy.tools.parameters.meta.WorkflowParameterExpansion attribute) input_connections (galaxy.model.WorkflowStep attribute) (tool_shed.webapp.model.WorkflowStep attribute) input_connections_by_name (galaxy.model.WorkflowStep attribute) input_dataset_collection (galaxy.model.ImplicitlyCreatedDatasetCollectionInput attribute) input_dataset_collection_elements (galaxy.model.Job attribute) input_dataset_collection_id (galaxy.model.ImplicitlyCreatedDatasetCollectionInput attribute) input_dataset_collections (galaxy.model.Job attribute) (galaxy.model.WorkflowInvocation attribute) input_datasets (galaxy.model.Job attribute) (galaxy.model.WorkflowInvocation attribute) input_default_value (galaxy.model.WorkflowStep attribute) 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.model.WorkflowStepConnection attribute) input_parameters (galaxy.model.WorkflowInvocation attribute) input_path_rewrite() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) input_step (galaxy.model.WorkflowStepConnection attribute) input_step_id (galaxy.model.WorkflowStepConnection attribute) 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 attribute) input_subworkflow_step (galaxy.model.WorkflowStepConnection attribute) input_subworkflow_step_id (galaxy.model.WorkflowStepConnection attribute) 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) inputs (galaxy.model.WorkflowStep attribute) (galaxy_test.api.test_workflow_extraction.RunJobsSummary attribute) (galaxy_test.base.populators.RunJobsSummary attribute) inputs() (galaxy.webapps.galaxy.api.jobs.JobController method), [1] inputs_defined (galaxy.tool_util.parser.interface.PagesSource attribute) (galaxy.tool_util.parser.xml.XmlPagesSource attribute) 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_model.DockerContainer attribute) (galaxy.containers.docker_model.DockerNode attribute) (galaxy.containers.docker_model.DockerService attribute) (galaxy.containers.docker_model.DockerTask attribute) inspect() (galaxy.containers.docker.DockerAPIInterface method) (galaxy.containers.docker.DockerCLIInterface method) 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), [1] install_dependency() (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method) (galaxy.tool_util.deps.resolvers.InstallableDependencyResolver method) (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method), [1] install_environment (galaxy.tool_util.deps.conda_util.CondaTarget attribute) 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 attribute) 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_revision() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method), [1] install_repository_revisions() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method), [1] 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_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_virtualenv() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupVirtualEnv method) installable_description (galaxy.tool_util.deps.conda_util.CondaContext attribute) (galaxy.tool_util.deps.installable.InstallableContext attribute) installable_resolvers (galaxy.tool_util.deps.views.DependencyResolversView attribute) installable_revisions() (tool_shed.webapp.model.Repository method) InstallableContext (class in galaxy.tool_util.deps.installable) InstallableDependencyResolver (class in galaxy.tool_util.deps.resolvers) 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) (galaxy.model.tool_shed_install.ToolShedRepository 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 attribute) installed_repository_grid (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed attribute) installed_tool_dependencies (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.tools.Tool attribute) 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) 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 attribute) 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) IntegerColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.webapps.reports.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) (class in galaxy.webapps.galaxy.controllers.interactivetool) interactivetool_entry_points (galaxy.model.Job attribute) InteractiveToolEntryPoint (class in galaxy.model) InteractiveToolManager (class in galaxy.managers.interactivetool) InteractiveToolSqlite (class in galaxy.managers.interactivetool) 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.datatypes.data.DatatypeValidation static method) invalidate_external_metadata() (galaxy.jobs.JobWrapper method) (galaxy.metadata.JobExternalOutputMetadataWrapper 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 attribute) invocation_id (galaxy_test.base.populators.RunJobsSummary attribute) invocation_job_source_iter() (in module galaxy.managers.jobs) invocation_jobs_summary() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] invocation_step() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] invocation_step_jobs_summary() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] invocation_to_output() (in module galaxy.tool_util.cwl.util) invoke() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] (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) 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 attribute) 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 attribute) (galaxy.tools.wrappers.DatasetCollectionWrapper attribute) (galaxy.tools.wrappers.DatasetFilenameWrapper attribute) 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 attribute) is_current_version() (galaxy.tools.data.ToolDataTable method) is_data_index_sample_file() (in module galaxy.tool_shed.util.tool_util) is_datatype_converter (galaxy.tools.Tool attribute) is_deactivated_or_installed (galaxy.model.tool_shed_install.ToolShedRepository attribute) is_deprecated_in_tool_shed (galaxy.model.tool_shed_install.ToolShedRepository attribute) is_dict() (in module galaxy.tool_util.parser.util) is_displayed (galaxy.selenium.smart_components.SmartTarget attribute) is_displayed() (galaxy.selenium.has_driver.HasDriver method) is_downloadable() (in module tool_shed.util.metadata_util) is_extension_unsniffable_binary() (galaxy.datatypes.registry.Registry method) is_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 attribute) is_hashable() (in module galaxy.util.hash_util) is_hda() (in module galaxy.model) is_id() (galaxy.jobs.JobConfiguration method) 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 attribute) is_installed (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) is_installed() (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 attribute) 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 attribute) is_latest_version (galaxy.tools.Tool attribute) is_leaf (galaxy.model.dataset_collections.structure.Leaf attribute) (galaxy.model.dataset_collections.structure.Tree attribute) (galaxy.model.dataset_collections.structure.UninitializedTree attribute) 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 attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) is_new() (tool_shed.webapp.model.Repository method) is_new_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method) is_object_applicable() (galaxy.visualization.plugins.registry.VisualizationsRegistry method) is_of_type() (galaxy.tools.wrappers.DatasetFilenameWrapper method) is_ok (galaxy.model.DatasetInstance attribute) is_ok() (galaxy.containers.docker_model.DockerNode method) is_outside_grace_period() (galaxy.webapps.galaxy.controllers.user.User 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 attribute) 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 attribute) 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_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_virtual_display_available() (in module galaxy.selenium.driver_factory) is_workflow_compatible (galaxy.tools.Tool attribute) is_zip() (in module galaxy.util.checkers) IsaJson (class in galaxy.datatypes.isa) IsaTab (class in galaxy.datatypes.isa) 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) 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.datatypes.metadata.MetadataCollection method) (galaxy.model.dataset_collections.matching.CollectionsToMatch method) (galaxy.model.metadata.MetadataCollection 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_config_xml_to_dict() (in module galaxy.jobs) job_count() (galaxy.jobs.rule_helper.RuleHelper method) job_destination (galaxy.jobs.JobWrapper attribute) 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 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.InstrumentPlugin 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) JOB_RESOURCE_CONDITIONAL_XML (galaxy.jobs.JobConfiguration attribute) job_rule_modules() (in module galaxy.queue_worker) job_rules_paths (galaxy.config_watchers.ConfigWatchers attribute) 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_source_id (galaxy.model.HistoryDatasetCollectionAssociation attribute) job_source_type (galaxy.model.HistoryDatasetCollectionAssociation attribute) job_state_summary (galaxy.model.HistoryDatasetCollectionAssociation attribute) 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), [1] JobDestination (class in galaxy.jobs) JobExportHistoryArchive (class in galaxy.model) JobExportHistoryArchiveWrapper (class in galaxy.tools.imp_exp) JobExternalOutputMetadata (class in galaxy.model) JobExternalOutputMetadataWrapper (class in galaxy.metadata) JobFilesAPIController (class in galaxy.webapps.galaxy.api.job_files), [1] 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) 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), [1] JobPortsView (class in galaxy.job_execution.ports) (class in galaxy.job_execution.ports.view) JobRunnerMapper (class in galaxy.jobs.mapper) Jobs (class in galaxy.webapps.reports.controllers.jobs) jobs (galaxy.model.History attribute) (galaxy.model.ImplicitCollectionJobs attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy_test.api.test_workflow_extraction.RunJobsSummary attribute) (galaxy_test.base.populators.RunJobsSummary attribute) 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() (in module galaxy.web.framework.helpers) 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), [1] 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.containers.ContainerInterface attribute) (galaxy.model.APIKeys attribute) (tool_shed.webapp.model.APIKeys attribute) 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.containers.docker_model.DockerServiceConstraint attribute) (galaxy.model.WorkflowOutput attribute) (galaxy.model.WorkflowStep attribute) (galaxy.tool_util.cwl.representation.TypeRepresentation attribute) (galaxy.tools.parameters.grouping.Conditional attribute) (galaxy.workflow.modules.InputProxy attribute) label() (galaxy.tools.parameters.grouping.Repeat method) (galaxy.tools.parameters.grouping.Section method) 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 attribute) (galaxy.containers.docker_model.DockerServiceConstraints attribute) labels_as_constraints (galaxy.containers.docker_model.DockerNode attribute) 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 attribute) 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 attribute) 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 attribute) 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), [1] ldIndep (class in galaxy.datatypes.genetics) Leaf (class in galaxy.model.dataset_collections.structure) 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 attribute) legend (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.reports.framework.grids.Grid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) 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), [1] 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset attribute) library_dataset (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryDatasetPermissions attribute) (galaxy.model.MetadataFile attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDataset 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDataset attribute) library_dataset_id (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryDatasetPermissions attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation 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 attribute) 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), [1] LibraryContentsTestCase (class in galaxy_test.selenium.test_library_contents) LibraryDataset (class in galaxy.model) (class in galaxy.model.migrate.versions.0005_cleanup_datasets_fix) 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) (class in galaxy.model.migrate.versions.0005_cleanup_datasets_fix) 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), [1] LibraryDatasetPermissions (class in galaxy.model) LibraryDatasetsController (class in galaxy.webapps.galaxy.api.library_datasets), [1] 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) 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) LibraryView (class in galaxy.model.search) 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 attribute) 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 attribute) 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.managers.base.ModelManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.interactivetool.InteractiveTool 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.ListableDependencyResolver method) (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependencyResolver 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 (tool_shed.utility_containers.utility_container_manager.RepositoryDependency attribute) (tool_shed.utility_containers.utility_container_manager.ToolDependency attribute) listify() (in module galaxy.util) 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), [1] (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.JobExternalOutputMetadataWrapper 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_tours() (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 attribute) (galaxy.tool_util.cwl.schema.ResolvedProcessDefinition attribute) loading_context() (galaxy.tool_util.cwl.schema.SchemaLoader method) 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) LoggingProxy (class in galaxy.model.orm.logging_connection_proxy) 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) 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 attribute) (galaxy.tool_util.parser.ToolSource attribute) (galaxy.tool_util.parser.xml.XmlToolSource attribute) 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_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_backup() (tool_shed.util.hgweb_config.HgWebConfigManager method) make_body_iterable() (galaxy.web.framework.base.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) managed_session() (in module galaxy.objectstore.irods) ManageDatasetRBACPermission (class in galaxy.managers.rbac_secured) ManageInformationTestCase (class in galaxy_test.selenium.test_personal_information) manager (galaxy.managers.base.HasAModelManager attribute) (galaxy.webapps.base.controller.SharableMixin attribute) manager_dependency() (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method), [1] manager_requirements() (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method), [1] ManagesIntegratedToolPanelMixin (class in galaxy.tools.toolbox.integrated_panel) 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), [1] mapping_as_dict (galaxy.util.rules_dsl.RuleSet attribute) 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance 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_tool_dependency_installed() (galaxy.tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) mark_undeleted() (galaxy.model.DatasetInstance method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance method) mark_unhidden() (galaxy.model.DatasetInstance method) mark_user_deleted() (tool_shed.util.admin_util.Admin method) MarkdownWorkflowMarkdownReportGeneratorPlugin (class in galaxy.workflow.reports.generators.markdown) MarkerMap (class in galaxy.datatypes.genetics) marshal() (galaxy.datatypes.metadata.FileParameter class method) (galaxy.datatypes.metadata.MetadataParameter class method) (galaxy.datatypes.metadata.PythonObjectParameter class method) (galaxy.datatypes.metadata.RangeParameter class method) (galaxy.datatypes.metadata.SelectParameter class method) (galaxy.model.metadata.FileParameter class method) (galaxy.model.metadata.MetadataParameter class method) (galaxy.model.metadata.PythonObjectParameter class method) (galaxy.model.metadata.RangeParameter class method) (galaxy.model.metadata.SelectParameter class method) MascotDat (class in galaxy.datatypes.proteomics) MascotXML (class in galaxy.datatypes.proteomics) MashSketch (class in galaxy.datatypes.binary) mask_password_from_url() (in module galaxy.util) MassHunterTar (class in galaxy.datatypes.binary) MassLynxTar (class in galaxy.datatypes.binary) match (galaxy.model.store.discover.DiscoveredFile attribute) (galaxy.model.store.discover.DiscoveredFileError attribute) match() (galaxy.job_execution.output_collect.DatasetCollector method) match_collections() (galaxy.managers.collections.DatasetCollectionManager method) (galaxy.tools.parameters.DataCollectionToolParameter method) (galaxy.tools.parameters.basic.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 attribute) 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) member_class (galaxy.containers.docker_model.DockerNodeLabels attribute) (galaxy.containers.docker_model.DockerServiceConstraints attribute) members (galaxy.containers.docker_model.DockerAttributeContainer attribute) (galaxy.model.Group attribute) 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) message (galaxy.model.Event attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation attribute) (galaxy.util.pastescript.serve.BadCommand attribute) (galaxy.util.pastescript.serve.Command.BadCommand attribute) message_exception() (galaxy.webapps.base.controller.BaseUIController method) MessageApplicationStack (class in galaxy.web_stack) MessageException Metadata (class in tool_shed.repository_types.metadata) metadata (galaxy.model.DatasetInstance attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.tool_util.cwl.util.GalaxyOutput 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() (tool_shed.webapp.api.repositories.RepositoriesController method), [1] metadata_file_types (galaxy.model.DatasetInstance attribute) 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.CRAM 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.CuffDiffSQlite attribute) (galaxy.datatypes.binary.DAA attribute) (galaxy.datatypes.binary.DMND attribute) (galaxy.datatypes.binary.Dcd attribute) (galaxy.datatypes.binary.DlibSQlite 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.MCool attribute) (galaxy.datatypes.binary.MashSketch attribute) (galaxy.datatypes.binary.MassHunterTar attribute) (galaxy.datatypes.binary.MassLynxTar 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.PQP attribute) (galaxy.datatypes.binary.PostgresqlArchive attribute) (galaxy.datatypes.binary.ProBam attribute) (galaxy.datatypes.binary.RData attribute) (galaxy.datatypes.binary.RMA6 attribute) (galaxy.datatypes.binary.SQlite attribute) (galaxy.datatypes.binary.SQmass attribute) (galaxy.datatypes.binary.Scf attribute) (galaxy.datatypes.binary.SearchGuiArchive attribute) (galaxy.datatypes.binary.Sff 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.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.SNPMatrix attribute) (galaxy.datatypes.genetics.Snptest attribute) (galaxy.datatypes.genetics.ldIndep attribute) (galaxy.datatypes.genetics.rgFeatureList attribute) (galaxy.datatypes.genetics.rgSampleList attribute) (galaxy.datatypes.genetics.rgTabList attribute) (galaxy.datatypes.gis.Shapefile attribute) (galaxy.datatypes.graph.Sif attribute) (galaxy.datatypes.graph.Xgmml attribute) (galaxy.datatypes.images.Bmp attribute) (galaxy.datatypes.images.Eps attribute) (galaxy.datatypes.images.Gif 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.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.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.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.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.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.molecules.grd attribute) (galaxy.datatypes.molecules.grdtgz 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.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.Analyze75 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.PEFF attribute) (galaxy.datatypes.proteomics.PSMS attribute) (galaxy.datatypes.proteomics.ParamXml 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.ProteomicsXml attribute) (galaxy.datatypes.proteomics.QCML attribute) (galaxy.datatypes.proteomics.SPLib attribute) (galaxy.datatypes.proteomics.SPLibNoIndex attribute) (galaxy.datatypes.proteomics.Sf3 attribute) (galaxy.datatypes.proteomics.TandemXML attribute) (galaxy.datatypes.proteomics.ThermoRAW attribute) (galaxy.datatypes.proteomics.TraML attribute) (galaxy.datatypes.proteomics.TrafoXML 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.QualityScoreSOLiD attribute) (galaxy.datatypes.qualityscore.QualityScoreSolexa attribute) (galaxy.datatypes.sequence.Alignment attribute) (galaxy.datatypes.sequence.Axt attribute) (galaxy.datatypes.sequence.BaseFastq 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.sequence.csFasta attribute) (galaxy.datatypes.spaln.SpalnNuclDb attribute) (galaxy.datatypes.spaln.SpalnProtDb attribute) (galaxy.datatypes.tabular.BaseCSV attribute) (galaxy.datatypes.tabular.BaseVcf attribute) (galaxy.datatypes.tabular.CSV attribute) (galaxy.datatypes.tabular.ConnectivityTable 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.TSV attribute) (galaxy.datatypes.tabular.Tabular attribute) (galaxy.datatypes.tabular.TabularData attribute) (galaxy.datatypes.tabular.Taxonomy 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.Html attribute) (galaxy.datatypes.text.IQTree attribute) (galaxy.datatypes.text.ImgtJson attribute) (galaxy.datatypes.text.Ipynb 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.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 attribute) metrics() (galaxy.webapps.galaxy.api.jobs.JobController method), [1] MetricsController (class in galaxy.webapps.galaxy.api.metrics), [1] 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.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance method) (galaxy.model.none_like.NoneDataset method) missing_repository_dependencies (galaxy.model.tool_shed_install.ToolShedRepository attribute) missing_test_components (tool_shed.webapp.model.RepositoryMetadata attribute) missing_tool_data_table_name (galaxy.tools.parameters.dynamic_options.DynamicOptions attribute) missing_tool_dependencies (galaxy.model.tool_shed_install.ToolShedRepository attribute) missing_tools (galaxy.managers.workflows.CreatedWorkflow attribute) MissingTestComponent (class in tool_shed.utility_containers) MissingToolsException mkdtemp() (galaxy_test.driver.driver_util.TestDriver method) mkstemp_ln() (in module galaxy.util) modal_body_selector() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) mode_is_valid (galaxy.containers.ContainerVolume attribute) model (galaxy.managers.context.ProvidesAppContext attribute) model_class (galaxy.managers.base.ModelFilterParser attribute) (galaxy.managers.base.ModelManager attribute) (galaxy.managers.cloud.CloudManager attribute) (galaxy.managers.cloudauthzs.CloudAuthzManager attribute) (galaxy.managers.datasets.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.tools.DynamicToolManager attribute) (galaxy.managers.users.AdminUserFilterParser attribute) (galaxy.managers.visualizations.VisualizationManager attribute) (galaxy.web.framework.helpers.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) (galaxy.webapps.reports.framework.grids.Grid 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.cloudauthzs.CloudAuthzsDeserializer attribute) (galaxy.managers.cloudauthzs.CloudAuthzsSerializer attribute) (galaxy.managers.datasets.DatasetSerializer attribute) (galaxy.managers.hdas.HDADeserializer attribute) (galaxy.managers.hdas.HDAFilterParser attribute) (galaxy.managers.hdas.HDASerializer 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.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_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) mp_from_ids() (in module galaxy.objectstore.s3_multipart_upload) Ms2 (class in galaxy.datatypes.proteomics) 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.webapps.reports.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.config.config_manage.OptionValue attribute) (galaxy.containers.Container attribute) (galaxy.containers.docker_model.DockerNode attribute) (galaxy.containers.docker_model.DockerNodeLabel attribute) (galaxy.containers.docker_model.DockerServiceConstraint attribute) (galaxy.containers.docker_model.DockerTask attribute) (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.model.FormDefinition attribute) (galaxy.model.Group attribute) (galaxy.model.History attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetAssociationHistory attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.ImplicitlyCreatedDatasetCollectionInput attribute) (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.model.JobParameter attribute) (galaxy.model.JobToImplicitOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetAssociation attribute) (galaxy.model.JobToInputDatasetCollectionAssociation attribute) (galaxy.model.JobToInputDatasetCollectionElementAssociation attribute) (galaxy.model.JobToInputLibraryDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetAssociation attribute) (galaxy.model.JobToOutputDatasetCollectionAssociation attribute) (galaxy.model.JobToOutputLibraryDatasetAssociation attribute) (galaxy.model.Library attribute) (galaxy.model.LibraryDataset 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.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.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation attribute) (galaxy.model.store.discover.JsonCollectedDatasetMatch attribute) (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.selenium.navigates_galaxy.WaitType attribute) (galaxy.tool_util.cwl.representation.TypeRepresentation attribute) (galaxy.tool_util.deps.resolvers.ContainerDependency 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.InputProxy attribute) (galaxy.workflow.modules.PauseModule attribute) (galaxy.workflow.modules.SubWorkflowModule attribute) (galaxy.workflow.modules.ToolModule 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.datatypes.util.gff_util.GFFFeature method) 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_test.selenium.test_histories_list.SavedHistoriesTestCase 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 attribute) 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.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_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_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 attribute) (tool_shed.webapp.model.User attribute) NicerConfigParser (class in galaxy.util.properties) NicerConfigParser.InterpolateWrapper (class in galaxy.util.properties) NmrML (class in galaxy.datatypes.proteomics) NO_ERROR (galaxy.tool_util.parser.stdio.StdioErrorLevel attribute) NO_PROVIDER_ID (galaxy.openid.providers.OpenIDProviders attribute) NoConverterException

Node (class in galaxy.util.jstree) (class in galaxy.visualization.data_providers.phyloviz.baseparser) node (galaxy.containers.docker_model.DockerService attribute) (galaxy.containers.docker_model.DockerTask attribute) node() (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 attribute) 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 attribute) non_terminal_states (galaxy.model.WorkflowInvocation attribute) non_terminal_tasks (galaxy.containers.docker_model.DockerNode attribute) 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_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.0005_cleanup_datasets_fix) (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.0104_update_genome_downloader_job_parameters) (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.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.webapps.reports.framework.grids.Grid attribute) num_rows_per_page (galaxy.web.framework.helpers.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) (galaxy.webapps.reports.framework.grids.Grid 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 attribute) object_key (galaxy.model.store.DirectoryImportModelStore1901 attribute) (galaxy.model.store.DirectoryImportModelStoreLatest attribute) (galaxy.model.store.ModelImportStore attribute) object_store (galaxy.jobs.JobWrapper attribute) (galaxy.model.Dataset attribute) 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_to_display() (galaxy.model.security.GalaxyRBACAgent method) ok_to_edit_metadata() (galaxy.managers.datasets.DatasetAssociationManager 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 attribute) 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.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.PageListGrid 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.framework.grids.Grid 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.CategoryGrid 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_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.RepositoriesIOwnGrid attribute) (tool_shed.grids.repository_grids.RepositoriesInCategoryGrid attribute) (tool_shed.grids.repository_grids.RepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithInvalidToolsGrid 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_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.RepositoriesWithReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithoutReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) (tool_shed.grids.repository_review_grids.ReviewedRepositoriesIOwnGrid attribute)

option (galaxy.config.config_manage.OptionValue attribute) 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) optional() (in module galaxy.dependencies) optional_param() (in module galaxy.workflow.modules) options (galaxy.auth.util.Authenticator attribute) (galaxy.util.jstree.Path attribute) options() (galaxy.webapps.galaxy.api.authenticate.AuthenticationController method), [1] (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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDataset attribute) order_index (galaxy.model.ImplicitCollectionJobsJobAssociation attribute) (galaxy.model.StoredWorkflowMenuEntry attribute) (galaxy.model.WorkflowStep 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.managers.pages.PageContentProcessor method) output_associations (galaxy.model.WorkflowInvocation attribute) 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_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) 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) outputs() (galaxy.webapps.galaxy.api.jobs.JobController method), [1] outputs_directory (galaxy.jobs.JobWrapper attribute) 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.webapps.reports.framework.grids) OwnerColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.webapps.reports.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 attribute) 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 attribute) package_specifier (galaxy.tool_util.deps.conda_util.CondaTarget attribute) package_tool() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) packages (galaxy.tool_util.deps.requirements.ToolRequirements attribute) 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), [1] 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), [1] 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.ToolSection method) (galaxy.tools.toolbox.panel.ToolPanelElements method) (galaxy.tools.toolbox.panel.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 attribute) param_filename (galaxy.model.Job attribute) (galaxy.model.Task attribute) param_keys (galaxy.tools.parameters.meta.WorkflowParameterExpansion attribute) param_names() (galaxy.tools.test.ParamContext method) (galaxy.tools.test.RootParamContext method) ParamContext (class in galaxy.tools.test) parameter_type (galaxy.workflow.modules.InputParameterModule attribute) parameter_value (galaxy.model.WorkflowRequestInputStepParameter attribute) parameters (galaxy.model.Job attribute) parameters_display() (galaxy.webapps.galaxy.api.jobs.JobController method), [1] 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) (galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters.DeferredJob attribute) (galaxy.tools.parameters.wrapped.WrappedParameters attribute) (galaxy.web_stack.message.ParamMessage attribute) params_from_strings() (galaxy.tools.Tool method) params_to_strings() (galaxy.tools.Tool method) params_with_missing_data_table_entry (galaxy.tools.Tool attribute) params_with_missing_index_file (galaxy.tools.Tool attribute) ParamsWithSpecs (class in galaxy.util) ParamValueFilter (class in galaxy.tools.parameters.dynamic_options) ParamValueToolOutputActionOptionFilter (class in galaxy.tool_util.parser.output_actions) ParamXml (class in galaxy.datatypes.proteomics) parent (galaxy.datatypes.metadata.MetadataCollection attribute) (galaxy.model.ExtendedMetadataIndex attribute) (galaxy.model.LibraryFolder attribute) (galaxy.model.Tag attribute) (galaxy.model.metadata.MetadataCollection attribute) parent_hda (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) parent_id (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.LibraryFolder attribute) (galaxy.model.Tag attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation 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 attribute) parent_path (galaxy.tool_util.deps.conda_util.CondaContext attribute) (galaxy.tool_util.deps.installable.InstallableContext attribute) 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) 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.ToolSource method) (galaxy.tool_util.parser.interface.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_date() (galaxy.managers.base.ModelFilterParser method) parse_description() (galaxy.tool_util.parser.cwl.CwlToolSource method) (galaxy.tool_util.parser.ToolSource method) (galaxy.tool_util.parser.interface.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.ToolSource method) (galaxy.tool_util.parser.interface.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) 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.ToolSource method) (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.interface.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.ToolSource method) (galaxy.tool_util.parser.interface.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.ToolSource method) (galaxy.tool_util.parser.interface.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.ToolSource method) (galaxy.tool_util.parser.interface.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.ToolSource method) (galaxy.tool_util.parser.interface.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_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.ToolSource method) (galaxy.tool_util.parser.interface.InputSource method) (galaxy.tool_util.parser.interface.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.ToolSource method) (galaxy.tool_util.parser.interface.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.ToolSource method) (galaxy.tool_util.parser.interface.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.ToolSource method) (galaxy.tool_util.parser.interface.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.ToolSource method) (galaxy.tool_util.parser.interface.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.ToolSource method) (galaxy.tool_util.parser.interface.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_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.ToolSource method) (galaxy.tool_util.parser.interface.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.ToolSource method) (galaxy.tool_util.parser.interface.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.ToolSource method) (galaxy.tool_util.parser.interface.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.ToolSource method) (galaxy.tool_util.parser.interface.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.DiskObjectStore class method) (galaxy.objectstore.DistributedObjectStore class method) (galaxy.objectstore.HierarchicalObjectStore class method) (galaxy.objectstore.cloud.Cloud 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) Path (class in galaxy.util.jstree) path (galaxy.model.ExtendedMetadataIndex attribute) (galaxy.model.TransferJob attribute) (galaxy.model.store.discover.DiscoveredFile attribute) (galaxy.model.store.discover.DiscoveredFileError attribute) (galaxy.util.jstree.Path attribute) (galaxy.web.framework.base.Request attribute) path() (galaxy.tool_util.verify.test_data.FileDataResolver method) 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 attribute) pause() (galaxy.jobs.JobWrapper method) paused_jobs (galaxy.model.History attribute) 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 attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation attribute) peek_size (galaxy.datatypes.tabular.BaseCSV attribute) PEFF (class in galaxy.datatypes.proteomics) 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) 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 attribute) (galaxy.model.store.discover.PermissionProvider attribute) permissions() (galaxy.webapps.galaxy.controllers.history.HistoryController method) permissions_class (galaxy.managers.rbac_secured.DatasetRBACPermission attribute) (galaxy.managers.rbac_secured.RBACPermission attribute) permitted_actions (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance attribute) (galaxy.model.Library attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance 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_option_map (galaxy.containers.docker_swarm.DockerSwarmAPIInterface attribute) PlantTribesKsComponents (class in galaxy.datatypes.plant_tribes) plugin (galaxy.auth.util.Authenticator attribute) (galaxy.model.DeferredJob attribute) (galaxy.model.JobMetricNumeric attribute) (galaxy.model.JobMetricText attribute) (galaxy.model.TaskMetricNumeric attribute) (galaxy.model.TaskMetricText attribute) (galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters.DeferredJob attribute) plugin_source_from_dict() (in module galaxy.util.plugin_config) plugin_source_from_path() (in module galaxy.util.plugin_config) plugin_type (galaxy.auth.providers.alwaysreject.AlwaysReject attribute) (galaxy.auth.providers.AuthProvider 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.job_metrics.instrumenters.InstrumentPlugin 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.ErrorPlugin 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.WorkflowReportGeneratorPlugin attribute) (galaxy.workflow.reports.generators.markdown.MarkdownWorkflowMarkdownReportGeneratorPlugin attribute) (galaxy.workflow.schedulers.WorkflowSchedulingPlugin attribute) (galaxy.workflow.schedulers.core.CoreWorkflowSchedulingPlugin attribute) PluginConfigSource (class in galaxy.util.plugin_config) plugins() (galaxy.webapps.galaxy.api.remote_files.RemoteFilesAPIController method), [1] plugins_dict() (in module galaxy.util.plugin_config) PluginsController (class in galaxy.webapps.galaxy.api.plugins), [1] 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 attribute) pop() (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 attribute) (galaxy.model.DatasetCollectionInstance attribute) populated_optimized (galaxy.model.DatasetCollection attribute) populated_state (galaxy.model.DatasetCollection attribute) (galaxy.model.ImplicitCollectionJobs attribute) populated_state_message (galaxy.model.DatasetCollection attribute) populated_states (galaxy.model.DatasetCollection attribute) (galaxy.model.ImplicitCollectionJobs attribute) PopulatedDisplayApplicationLink (class in galaxy.datatypes.display_applications.application) port (galaxy.model.InteractiveToolEntryPoint attribute) (galaxy.web.proxy.ProxyMapping attribute) portable (galaxy.metadata.JobExternalOutputMetadataWrapper attribute) (galaxy.metadata.PortableDirectoryMetadataGenerator attribute) PortableDirectoryMetadataGenerator (class in galaxy.metadata) ports (galaxy.containers.Container attribute) (galaxy.containers.docker_model.DockerContainer attribute) (galaxy.containers.docker_model.DockerService attribute) position (galaxy.model.WorkflowStep attribute) possible_subcommands (galaxy.util.pastescript.serve.ServeCommand attribute) 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.InstrumentPlugin method) (galaxy.job_metrics.instrumenters.collectl.CollectlPlugin method) (galaxy.job_metrics.instrumenters.core.CorePlugin method) (galaxy.job_metrics.instrumenters.env.EnvPlugin 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) 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.InstrumentPlugin 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) precache (galaxy.tool_util.deps.DependencyManager 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) preferences() (galaxy.managers.users.UserManager method) prefix (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver attribute) 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_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 attribute) preparing_display() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) prepend_anaconda_url() (in module galaxy.tool_util.deps.mulled.get_tests) prepend_timeout_message() (galaxy.selenium.has_driver.HasDriver method) preprocess_volumes() (in module galaxy.tool_util.deps.container_classes) 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.logging_connection_proxy) 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_folders() (in module galaxy.tool_shed.util.container_util) (in module tool_shed.util.container_util) 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 (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 attribute) process_package_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_repository_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_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 attribute) produces_entry_points (galaxy.tools.InteractiveTool attribute) (galaxy.tools.Tool attribute) produces_real_jobs (galaxy.tools.actions.DefaultToolAction attribute) (galaxy.tools.actions.history_imp_exp.ExportHistoryToolAction attribute) (galaxy.tools.actions.history_imp_exp.ImportHistoryToolAction attribute) (galaxy.tools.actions.metadata.SetMetadataToolAction attribute) (galaxy.tools.actions.model_operations.ModelOperationToolAction attribute) (galaxy.tools.actions.upload.BaseUploadToolAction attribute) ProfileMiddleware (class in galaxy.web.framework.middleware.profile) prohibited_middleware (galaxy.web_stack.ApplicationStack attribute) (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) 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), [1] (galaxy.webapps.galaxy.api.provenance.LDDAProvenanceController attribute), [1] provenance_item_id (galaxy.webapps.galaxy.api.provenance.HDAProvenanceController attribute), [1] (galaxy.webapps.galaxy.api.provenance.LDDAProvenanceController attribute), [1] 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) 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.webapps.reports.framework.grids) publish() (galaxy.managers.sharable.SharableModelManager method) publish_current_history() (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase 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), [1] 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDataset 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.NoopQueue method) (galaxy.jobs.handler.JobHandlerQueue method) (galaxy.jobs.handler.JobHandlerStopQueue method) (galaxy.jobs.runners.BaseJobRunner 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 attribute) (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper attribute) 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)

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) QuotaAgent (class in galaxy.quota) QuotaAPIController (class in galaxy.webapps.galaxy.api.quotas), [1] 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 attribute) raw_element_identifiers (galaxy.model.store.discover.JsonCollectedDatasetMatch attribute) raw_help (galaxy.tools.Tool attribute) raw_library_contents_create() (galaxy_test.base.populators.LibraryPopulator method) raw_metadata() (in module galaxy.tool_util.deps.conda_compat) raw_param_dict() (galaxy.model.Job method) raw_process_reference (galaxy.tool_util.cwl.schema.ResolvedProcessDefinition attribute) raw_process_reference() (galaxy.tool_util.cwl.schema.SchemaLoader method) raw_process_reference_for_object() (galaxy.tool_util.cwl.schema.SchemaLoader method) raw_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), [1] read_config() (tool_shed.util.hgweb_config.HgWebConfigManager method) read_dbnames() (in module galaxy.util) 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_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.JobExportHistoryArchive attribute) ready() (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter method) (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) 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) 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) reference() (galaxy.visualization.genomes.Genomes method) 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.LineageMap method) (galaxy.tools.toolbox.lineages.factory.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_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_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_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) 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) release_session() (in module galaxy.objectstore.irods) 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), [1] (galaxy.webapps.galaxy.api.tool_data.ToolData method), [1] (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] 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), [1] (in module galaxy.queue_worker) reload_tour() (galaxy.tours.ToursRegistry method) (in module galaxy.queue_worker) reloadable_options (galaxy.config.schema.AppSchema attribute) 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), [1] 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.PSAAssociation class method) (galaxy.model.custom_types.MutationList 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), [1] 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), [1] 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) 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) repo_files_directory() (galaxy.model.tool_shed_install.ToolShedRepository method) 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) 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), [1] 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 attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) repository_dependencies() (tool_shed.webapp.api.repository_revisions.RepositoryRevisionsController method), [1] repository_dependencies_being_installed (galaxy.model.tool_shed_install.ToolShedRepository attribute) repository_dependencies_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) repository_dependencies_missing_or_being_installed (galaxy.model.tool_shed_install.ToolShedRepository attribute) repository_dependencies_with_installation_errors (galaxy.model.tool_shed_install.ToolShedRepository attribute) 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), [1] 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), [1] 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), [1] 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_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_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), [1] 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) requires_config_file (galaxy.util.pastescript.serve.ServeCommand attribute) requires_containerization (galaxy.jobs.JobWrapper attribute) requires_dataset_id (galaxy.datatypes.metadata.MetadataCollection attribute) (galaxy.model.metadata.MetadataCollection attribute) 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_galaxy_python_environment (galaxy.tools.Tool attribute) requires_js_runtime (galaxy.tools.ExpressionTool attribute) requires_prior_installation_of (galaxy.model.tool_shed_install.ToolShedRepository attribute) requires_setting_metadata (galaxy.jobs.JobWrapper attribute) (galaxy.tools.SetMetadataTool attribute) (galaxy.tools.Tool attribute) 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), [1] 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), [1] reset_metadata_on_repository() (tool_shed.webapp.api.repositories.RepositoriesController method), [1] reset_metadata_on_selected_installed_repositories() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method), [1] (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 attribute) 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.DependencyResolver 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.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), [1] 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 attribute) 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), [1] resolve_toolbox_with_install() (galaxy.webapps.galaxy.api.container_resolution.ContainerResolutionAPIController method), [1] resolve_with_install() (galaxy.webapps.galaxy.api.container_resolution.ContainerResolutionAPIController method), [1] 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), [1] resolver_msg (galaxy.tool_util.deps.resolvers.Dependency attribute) (galaxy.tool_util.deps.resolvers.NullDependency attribute) resolver_requirements() (galaxy.tool_util.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method), [1] resolver_type (galaxy.tool_util.deps.container_resolvers.ContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.ExplicitContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.ExplicitSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.FallbackContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.FallbackNoRequirementsContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.FallbackNoRequirementsSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.FallbackSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.MappingContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.RequiresGalaxyEnvironmentContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.explicit.RequiresGalaxyEnvironmentSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledDockerContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.CachedMulledDockerContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.CachedMulledSingularityContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.MulledDockerContainerResolver attribute) (galaxy.tool_util.deps.container_resolvers.mulled.MulledSingularityContainerResolver attribute) (galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages.HomebrewToolShedDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.homebrew.HomebrewDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.lmod.LmodDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.modules.ModuleDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.tool_shed_packages.ToolShedPackageDependencyResolver attribute) (galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages.UnlinkedToolShedPackageDependencyResolver attribute) resolves_simple_dependencies (galaxy.tool_util.deps.resolvers.DependencyResolver attribute) (galaxy.tool_util.deps.resolvers.tool_shed_packages.ToolShedPackageDependencyResolver attribute) resource_parameters (galaxy.model.WorkflowInvocation attribute) ResourceParser (class in galaxy.visualization.plugins.resource_parser) resources_option_map (galaxy.containers.docker_swarm.DockerSwarmAPIInterface attribute) Response (class in galaxy.web.framework.base) 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) result_processor() (galaxy.model.custom_types.GalaxyLargeBinary method) resume() (galaxy.model.Job method) (galaxy.webapps.galaxy.api.jobs.JobController method), [1] 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_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.webapps.reports.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 attribute) revisions (galaxy.model.Page attribute) (galaxy.model.Visualization attribute) revoke() (galaxy.managers.rbac_secured.AccessDatasetRBACPermission method) (galaxy.managers.rbac_secured.ManageDatasetRBACPermission method) (galaxy.managers.rbac_secured.RBACPermission method) revoke_write_access() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method) rewrite() (galaxy.tool_util.provided_metadata.BaseToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.LegacyToolProvidedMetadata method) (galaxy.tool_util.provided_metadata.ToolProvidedMetadata method) rewrite_content_for_export() (galaxy.managers.pages.PageManager method) rewrite_content_for_import() (galaxy.managers.pages.PageManager method) rewrite_dataset_path() (galaxy.job_execution.datasets.DatasetPathRewriter method) (galaxy.job_execution.datasets.NullDatasetPathRewriter method) (galaxy.job_execution.datasets.OutputsToWorkingDirectoryPathRewriter method) (galaxy.job_execution.datasets.TaskPathRewriter method) RexpBase (class in galaxy.datatypes.genetics) 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_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_search_option (galaxy.auth.providers.ldap_ad.LDAP attribute) RoleAPIController (class in galaxy.webapps.galaxy.api.roles), [1] 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) RoleManager (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) rollback() (galaxy.model.orm.logging_connection_proxy.LoggingProxy method) 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.TraML attribute) (galaxy.datatypes.proteomics.TrafoXML 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.BaseRuleDefinition 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) RuleHelper (class in galaxy.jobs.rule_helper) rules (galaxy.util.rules_dsl.RuleSet attribute) RuleSet (class in galaxy.util.rules_dsl) RulesListToolParameter (class in galaxy.tools.parameters.basic) RuleValidator (class in galaxy.jobs.dynamic_tool_destination) run() (galaxy.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_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.jobs.runners.AsynchronousJobState attribute) (galaxy.model.Job attribute) (galaxy.util.lazy_process.LazyProcess attribute) (galaxy.util.lazy_process.NoOpLazyProcess attribute) 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

S3ObjectStore (class in galaxy.objectstore.s3) sa_session (galaxy.managers.context.ProvidesAppContext attribute) (galaxy.model.PSAAssociation attribute) (galaxy.model.PSACode attribute) (galaxy.model.PSANonce attribute) (galaxy.model.PSAPartial attribute) (galaxy.model.UserAuthnzToken attribute) (galaxy.model.database_heartbeat.DatabaseHeartbeat attribute) (galaxy.model.security.GalaxyRBACAgent attribute) (galaxy.model.security.HostAgent attribute) (galaxy.tool_shed.galaxy_install.migrate.common.MigrateToolsApplication attribute) (galaxy.tools.Tool attribute) (galaxy.tools.toolbox.BaseGalaxyToolBox attribute) (galaxy.tools.toolbox.base.BaseGalaxyToolBox attribute) (tool_shed.repository_registry.Registry attribute) (tool_shed.webapp.security.CommunityRBACAgent attribute) (tool_shed.webapp.util.shed_statistics.ShedCounter attribute) 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 attribute) 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) scheduler (galaxy.model.WorkflowInvocation attribute) Schema (class in galaxy.config.schema) schema (galaxy.config.config_manage.App attribute) schema_path (galaxy.config.config_manage.App attribute) SchemaLoader (class in galaxy.tool_util.cwl.schema) scheme (galaxy.tool_util.locations.dockstore.DockStoreResolver attribute) (galaxy.tool_util.locations.ToolLocationResolver attribute) (galaxy.tool_util.locations.file.HttpToolResolver attribute) (galaxy.tool_util.locations.http.HttpToolResolver attribute) (galaxy.tool_util.locations.http.HttpsToolResolver attribute) ScIdx (class in galaxy.datatypes.interval) screenshot() (galaxy_test.selenium.framework.TestWithSeleniumMixin 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), [1] (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), [1] SearchGuiArchive (class in galaxy.datatypes.binary) SearchQuery (class in galaxy.model.search) SecondaryStructureMap (class in galaxy.datatypes.mothur) seconds_since_created (galaxy.model.UsesCreateAndUpdateTime attribute) seconds_since_updated (galaxy.model.UsesCreateAndUpdateTime attribute) 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) 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 attribute) (galaxy.selenium.components.SelectorTemplate attribute) 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 attribute) send() (galaxy.managers.cloud.CloudManager method) (galaxy.webapps.galaxy.api.cloud.CloudController method), [1] 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 attribute) (galaxy.webapps.reports.config.Configuration attribute) 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), [1] 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.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.database_heartbeat.DatabaseHeartbeat attribute) (galaxy.model.WorkerProcess attribute) 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 attribute) service() (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.model.base.ModelMapping attribute) session (galaxy.web.framework.base.DefaultWebTransaction attribute) session() (galaxy.managers.base.ModelManager method) (galaxy.managers.rbac_secured.RBACPermission method) 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) 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), [1] 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_communication() (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] set_compute_environment() (galaxy.tools.evaluation.ToolEvaluator method) set_container() (galaxy.jobs.JobWrapper method) set_content_type() (galaxy.web.framework.base.Response method) set_copied_from_job_id() (galaxy.model.Job 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance method) set_default_hda_permissions() (galaxy.job_execution.output_collect.PermissionProvider method) (galaxy.model.store.discover.PermissionProvider method) set_default_quota() (galaxy.quota.QuotaAgent 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_quota_associations() (galaxy.quota.QuotaAgent 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), [1] set_file_name() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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.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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDataset method) set_information() (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] 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.JobExternalOutputMetadataWrapper method) (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_dataset_dataset_association() (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDataset method) set_library_item_permission() (galaxy.model.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) set_malicious() (tool_shed.webapp.controllers.repository.RepositoryController method) set_max_optional_metadata_filesize() (galaxy.datatypes.data.Data 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.CRAM method) (galaxy.datatypes.binary.Cel method) (galaxy.datatypes.binary.ChiraSQLite 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.PQP method) (galaxy.datatypes.binary.PostgresqlArchive method) (galaxy.datatypes.binary.SQlite method) (galaxy.datatypes.binary.SQmass method) (galaxy.datatypes.binary.SearchGuiArchive 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.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.DotBracket method) (galaxy.datatypes.sequence.Fastg method) (galaxy.datatypes.sequence.Maf method) (galaxy.datatypes.sequence.MafCustomTrack method) (galaxy.datatypes.sequence.Sequence method) (galaxy.datatypes.sequence.csFasta method) (galaxy.datatypes.tabular.BaseCSV method) (galaxy.datatypes.tabular.BaseVcf 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.model.DatasetInstance method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance method) set_meta_with_tool_provided() (in module galaxy.metadata.set_metadata) set_metadata() (galaxy.managers.datasets.DatasetAssociationManager method) (galaxy.model.DatasetInstance method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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_legacy() (in module galaxy.metadata.set_metadata) set_metadata_portable() (in module galaxy.metadata.set_metadata) set_metadata_requires_flush (galaxy.model.DatasetInstance attribute) set_name() (galaxy.model.LibraryDataset method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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.web_stack.message.ParamMessage attribute) 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), [1] 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.CRAM method) (galaxy.datatypes.binary.Cel 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.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.SQlite method) (galaxy.datatypes.binary.Scf method) (galaxy.datatypes.binary.SearchGuiArchive method) (galaxy.datatypes.binary.Sff 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.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.molecules.grd method) (galaxy.datatypes.molecules.grdtgz 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.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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance method) set_permission_roles() (galaxy.managers.libraries.LibraryManager method) set_permissions() (galaxy.webapps.galaxy.api.folders.FoldersController method), [1] (galaxy.webapps.galaxy.api.libraries.LibrariesController method), [1] (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] (galaxy_test.base.populators.LibraryPopulator method) set_permissions_old() (galaxy.webapps.galaxy.api.libraries.LibrariesController method), [1] 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_purged() (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDataset 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance method) set_skip_tool_tsts_flag() (tool_shed.test.base.twilltestcase.ShedTwillTestCase 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 attribute) set_task_runner_external_id() (galaxy.model.Task method) set_task_runner_name() (galaxy.model.Task 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), [1] set_total_size() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) set_transaction_factory() (galaxy.web.framework.base.WebApplication method) set_user() (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), [1] 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) 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.BGzipTabixDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.BcftoolsDataProvider 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.SQliteDataDictProvider attribute) (galaxy.datatypes.dataproviders.dataset.SQliteDataProvider attribute) (galaxy.datatypes.dataproviders.dataset.SQliteDataTableProvider attribute) (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider 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) 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.JobExternalOutputMetadataWrapper 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_input_connections_by_name() (galaxy.model.WorkflowStep method) setup_job() (galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper method) (galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper method) 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.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), [1] 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.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.webapps.reports.framework.grids) shed_config_filename (galaxy.model.tool_shed_install.ToolShedRepository attribute) shed_tool_data_path (tool_shed.webapp.config.ToolShedAppConfiguration attribute) 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.jobs.JobWrapper attribute) (galaxy.tool_util.deps.container_classes.Container 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) shell() (in module galaxy.util.commands) shell_commands (galaxy.tool_util.deps.resolvers.ContainerDependency attribute) shell_commands() (galaxy.tool_util.deps.resolvers.Dependency method) (galaxy.tool_util.deps.resolvers.NullDependency method) (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependency 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 attribute) 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), [1] (galaxy.webapps.galaxy.api.dataset_collections.DatasetCollectionsController method), [1] (galaxy.webapps.galaxy.api.datasets.DatasetsController method), [1] (galaxy.webapps.galaxy.api.dynamic_tools.DynamicToolsController method), [1] (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method), [1] (galaxy.webapps.galaxy.api.folders.FoldersController method), [1] (galaxy.webapps.galaxy.api.forms.FormDefinitionAPIController method), [1] (galaxy.webapps.galaxy.api.genomes.GenomesController method), [1] (galaxy.webapps.galaxy.api.group_roles.GroupRolesAPIController method), [1] (galaxy.webapps.galaxy.api.group_users.GroupUsersAPIController method), [1] (galaxy.webapps.galaxy.api.groups.GroupAPIController method), [1] (galaxy.webapps.galaxy.api.histories.HistoriesController method), [1] (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method), [1] (galaxy.webapps.galaxy.api.item_tags.BaseItemTagsController method), [1] (galaxy.webapps.galaxy.api.jobs.JobController method), [1] (galaxy.webapps.galaxy.api.libraries.LibrariesController method), [1] (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method), [1] (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method), [1] (galaxy.webapps.galaxy.api.pages.PagesController method), [1] (galaxy.webapps.galaxy.api.plugins.PluginsController method), [1] (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method), [1] (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method), [1] (galaxy.webapps.galaxy.api.roles.RoleAPIController method), [1] (galaxy.webapps.galaxy.api.tool_data.ToolData method), [1] (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method), [1] (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method), [1] (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] (galaxy.webapps.galaxy.api.tours.ToursController method), [1] (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] (galaxy.webapps.galaxy.api.visualizations.VisualizationsController method), [1] (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] (tool_shed.webapp.api.categories.CategoriesController method), [1] (tool_shed.webapp.api.groups.GroupsController method), [1] (tool_shed.webapp.api.repositories.RepositoriesController method), [1] (tool_shed.webapp.api.repository_revisions.RepositoryRevisionsController method), [1] (tool_shed.webapp.api.users.UsersController method), [1]

show_dependencies() (galaxy.tool_util.deps.views.DependencyResolversView method) show_dynamic_tool() (galaxy_test.base.populators.BaseDatasetPopulator method) show_field() (galaxy.webapps.galaxy.api.tool_data.ToolData method), [1] show_in_tool_panel() (galaxy.model.StoredWorkflow method) show_invocation() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] show_invocation_report() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] show_invocation_report_pdf() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] show_item_checkboxes (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.TracksterSelectionGrid attribute) (galaxy.webapps.reports.framework.grids.Grid attribute) (tool_shed.grids.repository_grids.DockerImageGrid attribute) show_job_lock() (galaxy.webapps.galaxy.api.jobs.JobController method), [1] show_jobs_summary() (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method), [1] show_ldda() (galaxy_test.base.populators.LibraryPopulator method) show_library_item() (galaxy.model.security.GalaxyRBACAgent method) show_params() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) show_pdf() (galaxy.webapps.galaxy.api.pages.PagesController method), [1] show_roles() (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method), [1] (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method), [1] show_status() (galaxy.util.pastescript.serve.ServeCommand method) show_tools() (tool_shed.webapp.api.repositories.RepositoriesController method), [1] show_version() (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method), [1] show_versions() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] 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.NoopQueue 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.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.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.UWSGIApplicationStack method) (galaxy.web_stack.transport.ApplicationStackTransport method) (galaxy.web_stack.transport.UWSGIFarmMessageTransport method) (galaxy.webapps.reports.app.UniverseApplication method) (galaxy.workflow.schedulers.WorkflowSchedulingPlugin method) (galaxy.workflow.schedulers.core.CoreWorkflowSchedulingPlugin 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_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) 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 attribute) 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.CRAM method) (galaxy.datatypes.binary.Cel method) (galaxy.datatypes.binary.ChiraSQLite method) (galaxy.datatypes.binary.CompressedZipArchive method) (galaxy.datatypes.binary.Cool method) (galaxy.datatypes.binary.CuffDiffSQlite method) (galaxy.datatypes.binary.DAA method) (galaxy.datatypes.binary.DMND method) (galaxy.datatypes.binary.Dcd method) (galaxy.datatypes.binary.DlibSQlite 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.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.PQP method) (galaxy.datatypes.binary.PostgresqlArchive method) (galaxy.datatypes.binary.RData method) (galaxy.datatypes.binary.RMA6 method) (galaxy.datatypes.binary.SQlite method) (galaxy.datatypes.binary.SQmass method) (galaxy.datatypes.binary.SearchGuiArchive method) (galaxy.datatypes.binary.Sff 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.Gmaj method) (galaxy.datatypes.images.Image method) (galaxy.datatypes.images.Pdf 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.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.PSMS method) (galaxy.datatypes.proteomics.PepList 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.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.sequence.csFasta method) (galaxy.datatypes.tabular.BaseCSV method) (galaxy.datatypes.tabular.BaseVcf 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.Html method) (galaxy.datatypes.text.IQTree method) (galaxy.datatypes.text.ImgtJson method) (galaxy.datatypes.text.Ipynb 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.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.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.PSMS method) (galaxy.datatypes.proteomics.PepList method) (galaxy.datatypes.proteomics.ProteomicsXml 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.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.sequence.csFasta 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.Html method) (galaxy.datatypes.text.IQTree method) (galaxy.datatypes.text.ImgtJson method) (galaxy.datatypes.text.Ipynb 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.GenericXml method) (galaxy.datatypes.xml.MEMEXml method) (galaxy.datatypes.xml.Owl method) (galaxy.datatypes.xml.Phyloxml method) (galaxy.datatypes.xml.Sbml 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), [1] 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.webapps.galaxy.controllers.history.HistoryListGrid.DeletedColumn method) (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid.HistoryColumn method) (galaxy.webapps.reports.framework.grids.BooleanColumn method) (galaxy.webapps.reports.framework.grids.CommunityRatingColumn method) (galaxy.webapps.reports.framework.grids.DateTimeColumn method) (galaxy.webapps.reports.framework.grids.GridColumn method) (galaxy.webapps.reports.framework.grids.IntegerColumn method) (galaxy.webapps.reports.framework.grids.OwnerColumn method) (galaxy.webapps.reports.framework.grids.ReverseSortColumn method) (galaxy.webapps.reports.framework.grids.TextColumn 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) (galaxy.util.plugin_config.PluginConfigSource attribute) source_dataset_chain (galaxy.model.DatasetInstance attribute) source_environment (galaxy.tool_util.deps.container_classes.Container attribute) source_library_dataset (galaxy.model.DatasetInstance attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance attribute) source_path (galaxy.tool_util.parser.cwl.CwlToolSource attribute) (galaxy.tool_util.parser.ToolSource attribute) (galaxy.tool_util.parser.interface.ToolSource attribute) (galaxy.tool_util.parser.xml.XmlToolSource attribute) (galaxy.tool_util.parser.yaml.YamlToolSource attribute) source_uri (galaxy.model.DatasetSource attribute) sources (galaxy.model.Dataset attribute) (galaxy.model.store.discover.JsonCollectedDatasetMatch attribute) SpalnNuclDb (class in galaxy.datatypes.spaln) SpalnProtDb (class in galaxy.datatypes.spaln) spec (galaxy.datatypes.metadata.MetadataCollection attribute) (galaxy.model.metadata.MetadataCollection attribute) 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 attribute) 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_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) standard_filters (galaxy.web.framework.helpers.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.history.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.framework.grids.Grid 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.CategoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoriesByUserGrid 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) standard_parser() (galaxy.util.pastescript.serve.Command class method) start (galaxy.datatypes.util.maf_utilities.SplicedAlignment attribute) (galaxy.tools.util.maf_utilities.SplicedAlignment attribute) start() (galaxy.authnz.psa_authnz.Strategy method) (galaxy.config_watchers.ConfigWatchers 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.model.database_heartbeat.DatabaseHeartbeat method) (galaxy.tools.toolbox.watcher.ToolConfWatcher method) (galaxy.util.watcher.BaseWatcher method) (galaxy.util.watcher.NullWatcher method) (galaxy.web_stack.ApplicationStack method) (galaxy.web_stack.MessageApplicationStack method) (galaxy.web_stack.UWSGIApplicationStack method) (galaxy.web_stack.transport.ApplicationStackTransport method) (galaxy.web_stack.transport.UWSGIFarmMessageTransport 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) startup() (galaxy.workflow.schedulers.core.CoreWorkflowSchedulingPlugin method) (galaxy.workflow.schedulers.WorkflowSchedulingPlugin method) state (galaxy.containers.docker_model.DockerNode attribute) (galaxy.containers.docker_model.DockerService attribute) (galaxy.containers.docker_model.DockerTask attribute) (galaxy.model.Dataset attribute) (galaxy.model.DatasetCollection attribute) (galaxy.model.DatasetCollectionInstance attribute) (galaxy.model.DatasetInstance 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance attribute) (galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters.DeferredJob attribute) 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.webapps.reports.framework.grids) Statement (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) states (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance attribute) (galaxy.model.DeferredJob attribute) (galaxy.model.Job attribute) (galaxy.model.Task attribute) (galaxy.model.TransferJob attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowInvocationStep attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance attribute) (galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters.DeferredJob attribute) (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) 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.ToolMetaParameterException attribute) (galaxy.exceptions.ToolMissingException attribute) (galaxy.exceptions.UnknownContentsType attribute) (galaxy.exceptions.UserActivationRequiredException attribute) stderr (galaxy.model.JobLike attribute) stderr() (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 attribute) stdout() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) step_by_index() (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_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) StepManager (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager) steps (galaxy.model.Workflow attribute) (galaxy.model.WorkflowInvocation attribute) steps_by_id (galaxy.model.Workflow attribute) 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_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) StorableObject (class in galaxy.model) Storage (class in galaxy.authnz.psa_authnz) store() (galaxy.model.PSAAssociation class method) store_by (galaxy.model.Dataset attribute) store_jobtemplate() (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) store_type (galaxy.objectstore.azure_blob.AzureBlobObjectStore attribute) (galaxy.objectstore.DiskObjectStore attribute) (galaxy.objectstore.DistributedObjectStore attribute) (galaxy.objectstore.HierarchicalObjectStore attribute) (galaxy.objectstore.cloud.Cloud 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.managers.workflows.CreatedWorkflow attribute) (galaxy.model.StoredWorkflowAnnotationAssociation attribute) (galaxy.model.StoredWorkflowMenuEntry attribute) (galaxy.model.StoredWorkflowRatingAssociation attribute) (galaxy.model.StoredWorkflowUserShareAssociation attribute) (galaxy.model.Workflow attribute) stored_workflow_id (galaxy.model.StoredWorkflowAnnotationAssociation attribute) (galaxy.model.StoredWorkflowMenuEntry attribute) (galaxy.model.StoredWorkflowRatingAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.StoredWorkflowUserShareAssociation attribute) (galaxy.model.Workflow attribute) stored_workflow_menu_entries (galaxy.model.User attribute) stored_workflows (galaxy.model.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() (galaxy.util.streamball.StreamBall method) (galaxy.util.streamball.ZipBall method) stream_archive() (in module galaxy.util.streamball) 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) StreamBall (class in galaxy.util.streamball) strict_shell (galaxy.jobs.JobWrapper attribute) 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_control_characters_nested() (in module galaxy.util) strip_path() (in module galaxy.tool_shed.util.basic_util) stripwd() (in module galaxy.model.orm.logging_connection_proxy) structure (galaxy.model.dataset_collections.matching.MatchingCollections attribute) 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) 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) subcontainer_model_class (galaxy.managers.base.ModelFilterParser attribute) (galaxy.managers.history_contents.HistoryContentsFilters 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.ErrorPlugin 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) 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) sudo_popen() (in module galaxy.jobs.runners.util.sudo) 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), [1] 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 attribute) 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_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.PSAAssociation attribute) (galaxy.model.PSACode attribute) (galaxy.model.PSANonce attribute) (galaxy.model.PSAPartial 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.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.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.model.migrate.versions.0005_cleanup_datasets_fix.Dataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation attribute) (galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters.DeferredJob 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) (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 attribute) (galaxy.model.store.discover.ModelPersistenceContext attribute) (galaxy.model.store.discover.SessionlessModelPersistenceContext attribute) tag_id (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.WorkflowStepTagAssociation attribute) tag_list (galaxy.model.store.discover.JsonCollectedDatasetMatch attribute) tag_mapping() (in module galaxy.model.mapping) tag_outputs() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) 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), [1] (galaxy.webapps.galaxy.api.item_tags.HistoryTagsController attribute), [1] (galaxy.webapps.galaxy.api.item_tags.WorkflowTagsController attribute), [1] tagged_item_id (galaxy.webapps.galaxy.api.annotations.HistoryAnnotationsController attribute), [1] (galaxy.webapps.galaxy.api.annotations.HistoryContentAnnotationsController attribute), [1] (galaxy.webapps.galaxy.api.annotations.WorkflowAnnotationsController attribute), [1] (galaxy.webapps.galaxy.api.item_tags.HistoryContentTagsController attribute), [1] (galaxy.webapps.galaxy.api.item_tags.HistoryTagsController attribute), [1] (galaxy.webapps.galaxy.api.item_tags.WorkflowTagsController attribute), [1] 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) tags_used() (galaxy.managers.users.UserManager method) TagsController (class in galaxy.webapps.galaxy.api.tags), [1] (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 attribute) 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.ApplicationStackMessage attribute) (galaxy.web_stack.message.JobHandlerMessage attribute) (galaxy.web_stack.message.WorkflowSchedulingMessage attribute) target_galaxy_version (galaxy.tool_util.verify.interactor.GalaxyInteractorApi attribute) target_history() (galaxy.model.store.ModelImportStore method) target_if_active() (galaxy.managers.interactivetool.InteractiveToolManager method) TarModelExportStore (class in galaxy.model.store) Task (class in galaxy.model) task (galaxy.model.TaskMetricNumeric attribute) (galaxy.model.TaskMetricText attribute) (galaxy.web_stack.message.TaskMessage attribute) task_add() (galaxy.containers.docker_model.DockerNode method) (galaxy.containers.docker_model.DockerService method) task_count (galaxy.containers.docker_model.DockerNode attribute) (galaxy.containers.docker_model.DockerService attribute) 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.containers.docker_model.DockerNode attribute) (galaxy.containers.docker_model.DockerService attribute) (galaxy.model.Job attribute) TaskWrapper (class in galaxy.jobs) Taxonomy (class in galaxy.datatypes.tabular) TaxonomySummary (class in galaxy.datatypes.mothur) 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.selenium.framework.SeleniumTestCase method) tearDownClass() (galaxy_test.driver.integration_util.IntegrationInstance class method) temp_config_dir() (galaxy_test.driver.integration_util.IntegrationInstance class method) temp_directory (galaxy.model.JobExportHistoryArchive attribute) TempfileDataProvider (class in galaxy.datatypes.dataproviders.external) TempFileHandler (class in galaxy.datatypes.util.maf_utilities) (class in galaxy.tools.util.maf_utilities) template (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) (galaxy.model.LibraryFolderInfoAssociation attribute) (galaxy.model.LibraryInfoAssociation attribute) (galaxy.webapps.reports.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_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) templates() (in module galaxy.web.framework.helpers) terminal (galaxy.containers.docker_model.DockerService attribute) (galaxy.containers.docker_model.DockerTask attribute) 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_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_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_hide_items() (galaxy_test.selenium.test_collection_builders.CollectionBuildersTestCase method) test_build_list_simple() (galaxy_test.selenium.test_collection_builders.CollectionBuildersTestCase method) test_build_pair_simple() (galaxy_test.selenium.test_collection_builders.CollectionBuildersTestCase method) test_build_paired_list_hide_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() (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_common_problems() (galaxy_test.api.test_jobs.JobsApiTestCase method) test_communication() (galaxy_test.api.test_users.UsersApiTestCase 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_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_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), [1] test_data_download() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method) (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] 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), [1] 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_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_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_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_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_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_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_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_test.api.test_datasets.DatasetsApiTestCase method) (galaxy_test.api.test_datatypes.DatatypesApiTestCase method) (galaxy_test.api.test_jobs.JobsApiTestCase 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_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_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_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_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_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_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_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_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_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_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_yaml_tools() (galaxy_test.api.test_tools.ToolsTestCase method) test_tool_deactivate() (galaxy_test.api.test_tools.ToolsTestCase method) 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_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_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_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_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_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_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) 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) 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 attribute) tests_summary() (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] 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_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.webapps.reports.framework.grids) TextField (class in galaxy.util.form_builder) (class in galaxy.web.form_builder) 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 attribute) 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.tools.parameters.grouping.Repeat attribute) (galaxy.web.framework.helpers.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) (galaxy.webapps.reports.framework.grids.Grid 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.RepositoriesIOwnGrid attribute) (tool_shed.grids.repository_grids.RepositoriesInCategoryGrid 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.RepositoriesWithReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithoutReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) (tool_shed.grids.repository_review_grids.ReviewedRepositoriesIOwnGrid attribute) title_by_index() (galaxy.tools.parameters.grouping.UploadDataset method) 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 attribute) (galaxy.tools.parameters.grouping.Section attribute) (galaxy.tools.parameters.grouping.UploadDataset attribute) tmp_dir (galaxy.datatypes.metadata.MetadataTempFile attribute) (galaxy.model.metadata.MetadataTempFile attribute) tmp_dir_creation_statement (galaxy.jobs.JobWrapper attribute) tmp_directory() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.JobWrapper method) (galaxy.jobs.SharedComputeEnvironment method) tmp_target (galaxy.jobs.JobWrapper attribute) 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.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.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.UserAddress method) (galaxy.model.Workflow method) (galaxy.model.WorkflowInvocation method) (galaxy.model.WorkflowInvocationStep method) (galaxy.model.tool_shed_install.ToolShedRepository method) (galaxy.model.tool_shed_install.ToolVersion method) (galaxy.objectstore.BaseObjectStore method) (galaxy.objectstore.ConcreteObjectStore method) (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.DistributedObjectStore method) (galaxy.objectstore.HierarchicalObjectStore method) (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.cloud.Cloud method) (galaxy.objectstore.irods.IRODSObjectStore method) (galaxy.objectstore.pithos.PithosObjectStore method) (galaxy.objectstore.s3.S3ObjectStore method) (galaxy.tool_util.deps.DependencyManager method) (galaxy.tool_util.deps.NullDependencyManager method) (galaxy.tool_util.deps.dependencies.DependenciesDescription 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.Tool method) (galaxy.tools.data.TabularToolDataField method) (galaxy.tools.data.TabularToolDataTable method) (galaxy.tools.parameters.DataCollectionToolParameter method) (galaxy.tools.parameters.DataToolParameter method) (galaxy.tools.parameters.SelectToolParameter 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.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.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.ToolSection method) (galaxy.tools.toolbox.ToolSectionLabel method) (galaxy.tools.toolbox.base.AbstractToolBox method) (galaxy.tools.toolbox.lineages.ToolLineage method) (galaxy.tools.toolbox.lineages.interface.ToolLineage method) (galaxy.tools.toolbox.lineages.interface.ToolLineageVersion method) (galaxy.tools.toolbox.panel.ToolSection method) (galaxy.tools.toolbox.panel.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) (tool_shed.webapp.model.Repository 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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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.Tool method) (galaxy.tools.parameters.SelectToolParameter method) (galaxy.tools.parameters.basic.BaseJsonToolParameter method) (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.FileToolParameter 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) to_JSON_dict() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataCollection method) to_library_dataset_dataset_association() (galaxy.model.HistoryDatasetAssociation method) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.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.DataToolParameter method) (galaxy.tools.parameters.SelectToolParameter 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) to_python() (galaxy.tools.parameters.basic.BaseDataToolParameter method) (galaxy.tools.parameters.basic.BaseJsonToolParameter method) (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.FileToolParameter method) (galaxy.tools.parameters.basic.FloatToolParameter 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.DataCollectionToolParameter method) (galaxy.tools.parameters.DataToolParameter method) (galaxy.tools.parameters.SelectToolParameter 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) 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.PSAPartial attribute) (galaxy.model.PasswordResetToken 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.parser.output_actions.ToolOutputAction attribute) (galaxy.tool_util.parser.output_actions.ToolOutputActionConditional 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) tool() (galaxy.tool_util.cwl.schema.SchemaLoader method) tool_class (in module galaxy.tools) tool_config_paths (galaxy.config_watchers.ConfigWatchers attribute) tool_data_path_files (galaxy.tools.data.ToolDataPathFiles attribute) tool_data_paths (galaxy.config_watchers.ConfigWatchers attribute) tool_data_table (galaxy.tools.parameters.dynamic_options.DynamicOptions attribute) tool_data_table_info() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) tool_data_table_info_1() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) tool_data_table_items() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) tool_dependencies (galaxy.model.tool_shed_install.ToolShedRepository attribute) tool_dependencies_being_installed (galaxy.model.tool_shed_install.ToolShedRepository attribute) tool_dependencies_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute) tool_dependencies_installed_or_in_error (galaxy.model.tool_shed_install.ToolShedRepository attribute) tool_dependencies_missing_or_being_installed (galaxy.model.tool_shed_install.ToolShedRepository attribute) tool_dependencies_with_installation_errors (galaxy.model.tool_shed_install.ToolShedRepository attribute) tool_dependency_dir (galaxy.config.ConfiguresGalaxyMixin attribute) 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.ToolTagAssociation attribute) (galaxy.model.WorkflowStep attribute) (galaxy.model.tool_shed_install.ToolVersion attribute) (galaxy.model.tool_shed_install.ToolVersionAssociation attribute) tool_ids (galaxy.tools.toolbox.lineages.interface.ToolLineage attribute) (galaxy.tools.toolbox.lineages.ToolLineage attribute) tool_ids_by_requirements (galaxy.tool_util.deps.views.DependencyResolversView attribute) tool_inputs (galaxy.model.WorkflowStep attribute) tool_lineages() (galaxy.webapps.galaxy.api.configuration.ConfigurationController method), [1] 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_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 attribute) 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 attribute) tool_proxy() (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 attribute) tool_requirements_status (galaxy.tools.Tool attribute) 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 (galaxy.model.tool_shed_install.ToolShedRepository attribute) (module) 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), [1] tool_shed.webapp.api.categories (module), [1] tool_shed.webapp.api.configuration (module), [1] tool_shed.webapp.api.groups (module), [1] tool_shed.webapp.api.repositories (module), [1] tool_shed.webapp.api.repository_revisions (module), [1] tool_shed.webapp.api.tools (module), [1] tool_shed.webapp.api.users (module), [1] 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 attribute) tool_shed_repository (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolVersion attribute) (galaxy.tools.Tool attribute) tool_shed_repository_id (galaxy.model.tool_shed_install.RepositoryDependency attribute) (galaxy.model.tool_shed_install.RepositoryRepositoryDependencyAssociation attribute) (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.model.tool_shed_install.ToolVersion attribute) tool_shed_status (galaxy.model.tool_shed_install.ToolShedRepository attribute) 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 attribute) tool_version (galaxy.model.DynamicTool attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.Job attribute) (galaxy.model.LibraryDatasetDatasetAssociation attribute) (galaxy.model.WorkflowStep attribute) tool_version_list_grid (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) tool_versions (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.tools.Tool attribute) (tool_shed.webapp.model.RepositoryMetadata attribute) tool_versions_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) tool_working_directory (galaxy.jobs.JobWrapper attribute) ToolAction (class in galaxy.tools.actions) ToolBox (class in galaxy.tools) toolbox_install() (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method), [1] toolbox_requirements_status (galaxy.tool_util.deps.views.DependencyResolversView attribute) toolbox_uninstall() (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method), [1] 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), [1] 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), [1] 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) 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), [1] 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.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 attribute) 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), [1] (class in tool_shed.webapp.api.tools), [1] 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), [1] ToolShedController (class in galaxy.webapps.galaxy.api.toolshed), [1] 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), [1] ToolShedRepository (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_level_stored_workflow (galaxy.model.Workflow attribute) top_level_workflow (galaxy.model.Workflow attribute) topsort() (in module galaxy.util.topsort) topsort_levels() (in module galaxy.util.topsort) Torque (class in galaxy.jobs.runners.util.cli.job.torque) total_disk_usage (galaxy.model.GalaxySession attribute) (galaxy.model.User attribute) (tool_shed.webapp.model.User attribute) total_size (galaxy.model.Dataset attribute) total_size() (in module galaxy.model.custom_types) tour_contents() (galaxy.tours.ToursRegistry method) tour_loader() (in module galaxy.tours) 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) tours_by_id_with_description() (galaxy.tours.ToursRegistry method) ToursController (class in galaxy.webapps.galaxy.api.tours), [1] ToursRegistry (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) TraceLoggerProxy (class in galaxy.model.orm.logging_connection_proxy) 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) 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) 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) Trr (class in galaxy.datatypes.binary) 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.ModelImportStore attribute) trust_hid() (galaxy.model.store.DirectoryImportModelStore1901 method) (galaxy.model.store.DirectoryImportModelStoreLatest 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 attribute) 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.model.DefaultQuotaAssociation attribute) (galaxy.model.FormDefinition attribute) (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute) (galaxy.model.Role attribute) (galaxy.model.Tag attribute) (galaxy.model.Visualization attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.model.WorkflowStep attribute) (galaxy.model.tool_shed_install.ToolDependency 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.util.plugin_config.PluginConfigSource 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) (tool_shed.webapp.model.Repository attribute) (tool_shed.webapp.model.Role attribute) (tool_shed.webapp.model.Tag attribute) type() (galaxy.managers.base.ModelValidator method) 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) type_representation_from_name() (in module galaxy.tool_util.cwl.representation) type_to_object_store_class() (in module galaxy.objectstore) TypeRepresentation (class in galaxy.tool_util.cwl.representation) types (galaxy.model.DefaultQuotaAssociation attribute) (galaxy.model.FormDefinition attribute) (galaxy.model.Role attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (tool_shed.webapp.model.Role attribute) types_and_mapping() (galaxy.webapps.galaxy.api.datatypes.DatatypesController method), [1]

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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance method) undelete() (galaxy.managers.deletable.DeletableManagerMixin method) (galaxy.managers.users.UserManager method) (galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController method), [1] (galaxy.webapps.galaxy.api.extended_metadata.BaseExtendedMetadataController method), [1] (galaxy.webapps.galaxy.api.histories.HistoriesController method), [1] (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method), [1] (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] (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), [1] 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), [1] (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 attribute) uninstalled (galaxy.model.tool_shed_install.ToolShedRepository attribute) uninstalled_repository_dependencies (galaxy.model.tool_shed_install.ToolShedRepository attribute) uninstalled_tool_dependencies (galaxy.model.tool_shed_install.ToolShedRepository attribute) 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 attribute) 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) 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) 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.views.DependencyResolversView attribute) unused_dependency_paths() (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method), [1] 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 attribute) 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.DatasetInstance method) (galaxy.model.WorkflowInvocation method) (galaxy.util.Params method) (galaxy.util.odict.odict method) (galaxy.webapps.galaxy.api.cloudauthz.CloudAuthzController method), [1] (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method), [1] (galaxy.webapps.galaxy.api.folders.FoldersController method), [1] (galaxy.webapps.galaxy.api.group_roles.GroupRolesAPIController method), [1] (galaxy.webapps.galaxy.api.group_users.GroupUsersAPIController method), [1] (galaxy.webapps.galaxy.api.groups.GroupAPIController method), [1] (galaxy.webapps.galaxy.api.histories.HistoriesController method), [1] (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method), [1] (galaxy.webapps.galaxy.api.item_tags.BaseItemTagsController method), [1] (galaxy.webapps.galaxy.api.libraries.LibrariesController method), [1] (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method), [1] (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method), [1] (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method), [1] (galaxy.webapps.galaxy.api.tags.TagsController method), [1] (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method), [1] (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] (galaxy.webapps.galaxy.api.visualizations.VisualizationsController method), [1] (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] (tool_shed.managers.groups.GroupManager method) (tool_shed.managers.repositories.RepoManager method) (tool_shed.webapp.api.repositories.RepositoriesController method), [1] (tool_shed.webapp.api.repository_revisions.RepositoryRevisionsController method), [1] update_batch() (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method), [1] 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), [1] update_job_lock() (galaxy.webapps.galaxy.api.jobs.JobController method), [1] 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), [1] (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method), [1] (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method), [1] 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_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.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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDataset attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation attribute) (galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters.DeferredJob 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) (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.ToursController method), [1] 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) updated_changeset_revisions() (tool_shed.webapp.controllers.repository.RepositoryController method) UpdateRepositoryManager (class in galaxy.tool_shed.galaxy_install.update_repository_manager) updates() (tool_shed.webapp.api.repositories.RepositoriesController method), [1] 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.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 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_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), [1] UploadsTestCase (class in galaxy_test.selenium.test_uploads) UploadToolAction (class in galaxy.tools.actions.upload) uri (galaxy.tool_util.cwl.schema.RawProcessReference attribute) (galaxy.tool_util.cwl.schema.ResolvedProcessDefinition attribute) url (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper attribute) 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) url_to_file() (in module galaxy.tools.imp_exp.unpack_tar_gz_archive) 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.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.framework.grids.Grid attribute) use_default_filter (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute) use_final (tool_shed.webapp.search.repo_search.RepoWeighting attribute) use_hide_message (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.reports.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 attribute) use_metadata_binary (galaxy.jobs.JobWrapper attribute) use_mq (galaxy.jobs.runners.pulsar.PulsarMQJobRunner attribute) use_paging (galaxy.web.framework.helpers.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) (galaxy.webapps.reports.framework.grids.Grid 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.RepositoriesInCategoryGrid 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) 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 attribute) 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.job_execution.output_collect.JobContext attribute) (galaxy.jobs.JobWrapper 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) (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) (galaxy.model.store.discover.ModelPersistenceContext attribute) (galaxy.model.store.discover.SessionlessModelPersistenceContext attribute) (galaxy.work.context.WorkRequestContext 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_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 attribute) user_can_import_repository_archive() (tool_shed.webapp.security.CommunityRBACAgent method) user_can_purge (galaxy.model.Dataset attribute) user_can_review_repositories() (tool_shed.webapp.security.CommunityRBACAgent 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 attribute) 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_is_active (galaxy.managers.context.ProvidesUserContext attribute) user_is_admin (galaxy.managers.context.ProvidesUserContext attribute) user_list_grid (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) (tool_shed.util.admin_util.Admin attribute) (tool_shed.webapp.controllers.admin.AdminController attribute) user_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.histories.HistoryManager attribute) (galaxy.managers.pages.PageManager attribute) (galaxy.managers.sharable.SharableModelManager attribute) (galaxy.managers.visualizations.VisualizationManager attribute) user_system_pwent (galaxy.jobs.JobWrapper attribute) user_template_environment() (galaxy.model.User static method) user_tname (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.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), [1] UserAuthnzToken (class in galaxy.model) UserDeserializer (class in galaxy.managers.users) 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) UserListGrid (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.ActivatedColumn (class in galaxy.webapps.galaxy.controllers.admin) UserListGrid.APIKeyColumn (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.Page attribute) (galaxy.model.User attribute) (tool_shed.webapp.model.User attribute) 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), [1] UserSerializer (class in galaxy.managers.users) uses_param() (galaxy.tool_util.cwl.representation.TypeRepresentation method) 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) 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 attribute) UWSGIApplicationStack (class in galaxy.web_stack) UWSGIFarmMessageTransport (class in galaxy.web_stack.transport) UWSGILogFilter (class in galaxy.web_stack)

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) (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.Tool attribute) 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.tools.parameters.DataCollectionToolParameter method) (galaxy.tools.parameters.DataToolParameter method) (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.basic.DataToolParameter 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), [1] (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 attribute) 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_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) validated_states (galaxy.model.DatasetInstance attribute) ValidateOutputsAction (class in galaxy.jobs.actions.post) 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.config.config_manage.OptionValue attribute) (galaxy.containers.docker_model.DockerNodeLabel attribute) (galaxy.containers.docker_model.DockerServiceConstraint attribute) (galaxy.model.DynamicTool attribute) (galaxy.model.ExtendedMetadataIndex attribute) (galaxy.model.HistoryDatasetAssociationTagAssociation attribute) (galaxy.model.HistoryDatasetCollectionTagAssociation attribute) (galaxy.model.HistoryTagAssociation attribute) (galaxy.model.JobParameter attribute) (galaxy.model.LibraryDatasetCollectionTagAssociation attribute) (galaxy.model.LibraryDatasetDatasetAssociationTagAssociation attribute) (galaxy.model.PageTagAssociation attribute) (galaxy.model.StoredWorkflowTagAssociation attribute) (galaxy.model.ToolTagAssociation attribute) (galaxy.model.UserPreference attribute) (galaxy.model.VisualizationTagAssociation attribute) (galaxy.model.WorkflowInvocationOutputValue attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.model.WorkflowRequestStepState attribute) (galaxy.model.WorkflowStepTagAssociation attribute)

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.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.containers.docker_model.DockerNode attribute) (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetAssociationHistory attribute) (galaxy.model.tool_shed_install.ToolDependency attribute) (galaxy.tool_util.deps.mulled.util.Target attribute) (galaxy.tool_util.deps.resolvers.ContainerDependency attribute) version() (galaxy.webapps.galaxy.api.configuration.ConfigurationController method), [1] (tool_shed.webapp.api.configuration.ConfigurationController method), [1] version_object (galaxy.tools.Tool attribute) 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) 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_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) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation attribute) (galaxy.model.store.discover.JsonCollectedDatasetMatch attribute) (galaxy.tools.parameters.basic.FTPFileToolParameter attribute) (galaxy.tools.parameters.basic.ToolParameter attribute) (galaxy.tools.parameters.grouping.Group attribute) visible_children (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation attribute) (galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation attribute) 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), [1] 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_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 (galaxy.selenium.navigates_galaxy.NavigatesGalaxy attribute) waiting_for_elements (galaxy.model.DatasetCollection attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) 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.tool_util.parser.stdio.StdioErrorLevel attribute) 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 attribute) WebApplication (class in galaxy.web.framework.base) Webhook (class in galaxy.webhooks) webhook_data() (galaxy.webapps.galaxy.api.webhooks.WebhooksController method), [1] WebhooksApiTestCase (class in galaxy_test.api.test_webhooks) WebhooksController (class in galaxy.webapps.galaxy.api.webhooks), [1] 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), [1] 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 attribute) worker_process (galaxy.model.database_heartbeat.DatabaseHeartbeat attribute) 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.CreatedWorkflow attribute) (galaxy.model.WorkflowInvocation attribute) (galaxy.model.WorkflowStep attribute) 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), [1] 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) (galaxy_test.api.test_workflow_extraction.RunJobsSummary attribute) (galaxy_test.base.populators.RunJobsSummary attribute) workflow_import_submit_url() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method) workflow_index_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_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 attribute) workflow_outputs (galaxy.model.Workflow attribute) (galaxy.model.WorkflowStep attribute) workflow_populator (galaxy_test.selenium.framework.TestWithSeleniumMixin attribute) workflow_proxy() (in module galaxy.tool_util.cwl) workflow_report_json() (galaxy_test.base.populators.BaseWorkflowPopulator method) workflow_request (galaxy_test.base.populators.RunJobsSummary attribute) workflow_request_to_run_config() (in module galaxy.workflow.run_request) workflow_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), [1] WorkflowCanvas (class in galaxy.workflow.render) WorkflowContentsManager (class in galaxy.managers.workflows) WorkflowController (class in galaxy.webapps.galaxy.controllers.workflow) 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) WorkflowInvocationOutputDatasetAssociation (class in galaxy.model) WorkflowInvocationOutputDatasetCollectionAssociation (class in galaxy.model) WorkflowInvocationOutputValue (class in galaxy.model) WorkflowInvocationStep (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) WorkflowReportGeneratorPlugin (class in galaxy.workflow.reports.generators) WorkflowRequestInputParameter (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), [1] 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) 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), [1] WorkflowView (class in galaxy.model.search) working_directory (galaxy.jobs.JobWrapper attribute) (galaxy.model.Task attribute) working_directory() (galaxy.jobs.ComputeEnvironment method) (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 attribute) write() (galaxy.datatypes.dataproviders.base.DataProvider method) (galaxy.util.pastescript.serve.LazyWriter 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_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 attribute)

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), [1] 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) ZipBall (class in galaxy.util.streamball)

ZipCollectionTool (class in galaxy.tools) zipfile_ok() (galaxy.util.compression_utils.CompressedFile method)