Index

_

__init__() (galaxy.app.UniverseApplication method) (galaxy.auth.AuthManager method) (galaxy.auth.providers.ldap_ad.LDAP method) (galaxy.config.Configuration method) (galaxy.containers.Container method) (galaxy.containers.ContainerInterface 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.containers.docker_swarm_manager.SwarmManager method) (galaxy.containers.docker_swarm_manager.SwarmState method) (galaxy.dataset_collections.builder.BoundCollectionBuilder method) (galaxy.dataset_collections.builder.CollectionBuilder method) (galaxy.dataset_collections.matching.CollectionsToMatch method) (galaxy.dataset_collections.matching.MatchingCollections method) (galaxy.dataset_collections.registry.DatasetCollectionTypesRegistry method) (galaxy.dataset_collections.structure.BaseTree method) (galaxy.dataset_collections.structure.Tree method) (galaxy.dataset_collections.type_description.CollectionTypeDescription method) (galaxy.dataset_collections.type_description.CollectionTypeDescriptionFactory method) (galaxy.dataset_collections.types.list.ListDatasetCollectionType method) (galaxy.dataset_collections.types.paired.PairedDatasetCollectionType method) (galaxy.datatypes.assembly.Velvet method) (galaxy.datatypes.binary.BigBed method) (galaxy.datatypes.binary.BigWig method) (galaxy.datatypes.binary.DMND method) (galaxy.datatypes.binary.H5 method) (galaxy.datatypes.blast.BlastDomainDb method) (galaxy.datatypes.blast.BlastNucDb method) (galaxy.datatypes.blast.BlastProtDb 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.converters.bedgraph_to_array_tree_converter.BedGraphReader method) (galaxy.datatypes.converters.interval_to_coverage.CoverageWriter method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.data.DataMeta 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.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.metadata.JobExternalOutputMetadataWrapper 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.PepXmlReport method) (galaxy.datatypes.proteomics.ProtXmlReport method) (galaxy.datatypes.proteomics.SPLib method) (galaxy.datatypes.proteomics.Wiff method) (galaxy.datatypes.registry.Registry method) (galaxy.datatypes.tabular.ConnectivityTable method) (galaxy.datatypes.tabular.Eland 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.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.MessageException method) (galaxy.exceptions.error_codes.ErrorCode method) (galaxy.forms.forms.FormDefinitionFactory method) (galaxy.jobs.JobConfiguration method) (galaxy.jobs.JobDestination method) (galaxy.jobs.JobToolConfiguration method) (galaxy.jobs.JobWrapper method) (galaxy.jobs.ParallelismInfo method) (galaxy.jobs.SharedComputeEnvironment method) (galaxy.jobs.TaskWrapper method) (galaxy.jobs.datasets.DatasetPath method) (galaxy.jobs.datasets.OutputsToWorkingDirectoryPathRewriter method) (galaxy.jobs.datasets.TaskPathRewriter 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.MessageJobHandler method) (galaxy.jobs.manager.MessageJobQueue method) (galaxy.jobs.manager.NoopHandler method) (galaxy.jobs.mapper.JobMappingException method) (galaxy.jobs.mapper.JobNotReadyException method) (galaxy.jobs.mapper.JobRunnerMapper method) (galaxy.jobs.metrics.JobInstrumenter method) (galaxy.jobs.metrics.JobMetrics method) (galaxy.jobs.metrics.collectl.cli.CollectlCli method) (galaxy.jobs.metrics.collectl.stats.StatisticsTracker method) (galaxy.jobs.metrics.instrumenters.collectl.CollectlPlugin method) (galaxy.jobs.metrics.instrumenters.core.CorePlugin method) (galaxy.jobs.metrics.instrumenters.cpuinfo.CpuInfoPlugin method) (galaxy.jobs.metrics.instrumenters.env.EnvPlugin method) (galaxy.jobs.metrics.instrumenters.meminfo.MemInfoPlugin method) (galaxy.jobs.metrics.instrumenters.uname.UnamePlugin 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.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.Bunch method) (galaxy.jobs.runners.util.cli.CliInterface method) (galaxy.jobs.runners.util.cli.job.BaseJobExec 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.runners.util.drmaa.DrmaaSessionFactory method) (galaxy.jobs.runners.util.retry.RetryActionExecutor 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.collections.DatasetCollectionManager method) (galaxy.managers.configuration.ConfigSerializer method) (galaxy.managers.datasets.DatasetAssociationManager method) (galaxy.managers.datasets.DatasetDeserializer 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.lddas.LDDAManager method) (galaxy.managers.libraries.LibraryManager 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.tags.CommunityTagManager method) (galaxy.managers.tags.GalaxyTagManager method) (galaxy.managers.tags.ItemTagAssocInfo method) (galaxy.managers.tags.TagManager 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.WorkflowContentsManager method) (galaxy.managers.workflows.WorkflowsManager method) (galaxy.model.APIKeys method) (galaxy.model.BaseJobMetric method) (galaxy.model.ConverterDependencyException 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.DatasetInstance method) (galaxy.model.DatasetPermissions method) (galaxy.model.DatasetToValidationErrorAssociation method) (galaxy.model.DefaultHistoryPermissions method) (galaxy.model.DefaultQuotaAssociation method) (galaxy.model.DefaultUserPermissions method) (galaxy.model.DeferredJob method) (galaxy.model.Event method) (galaxy.model.ExtendedMetadata method) (galaxy.model.ExtendedMetadataIndex 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.HistoryDatasetAssociation method) (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization method) (galaxy.model.HistoryDatasetAssociationHistory method) (galaxy.model.HistoryDatasetAssociationSubset method) (galaxy.model.HistoryDatasetCollectionAssociation method) (galaxy.model.HistoryUserShareAssociation method) (galaxy.model.ImplicitCollectionJobs method) (galaxy.model.ImplicitCollectionJobsJobAssociation method) (galaxy.model.ImplicitlyConvertedDatasetAssociation method) (galaxy.model.ImplicitlyCreatedDatasetCollectionInput method) (galaxy.model.ItemRatingAssociation method) (galaxy.model.ItemTagAssociation method) (galaxy.model.Job method) (galaxy.model.JobExportHistoryArchive method) (galaxy.model.JobExternalOutputMetadata method) (galaxy.model.JobImportHistoryArchive method) (galaxy.model.JobParameter method) (galaxy.model.JobStateHistory method) (galaxy.model.JobToImplicitOutputDatasetCollectionAssociation method) (galaxy.model.JobToInputDatasetAssociation method) (galaxy.model.JobToInputDatasetCollectionAssociation 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.LibraryDatasetCollectionAssociation method) (galaxy.model.LibraryDatasetDatasetAssociation method) (galaxy.model.LibraryDatasetDatasetAssociationPermissions 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.Page method) (galaxy.model.PageRevision 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.StorableObject method) (galaxy.model.StoredWorkflow method) (galaxy.model.StoredWorkflowMenuEntry method) (galaxy.model.StoredWorkflowUserShareAssociation method) (galaxy.model.Tag method) (galaxy.model.Task 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.UserGroupAssociation method) (galaxy.model.UserOpenID method) (galaxy.model.UserPreference method) (galaxy.model.UserQuotaAssociation method) (galaxy.model.UserRoleAssociation method) (galaxy.model.ValidationError method) (galaxy.model.Visualization method) (galaxy.model.VisualizationRevision method) (galaxy.model.VisualizationUserShareAssociation method) (galaxy.model.WorkRequestTagAssociation method) (galaxy.model.Workflow method) (galaxy.model.WorkflowInvocation method) (galaxy.model.WorkflowOutput method) (galaxy.model.WorkflowRequestInputParameter method) (galaxy.model.WorkflowRequestStepState method) (galaxy.model.WorkflowStep method) (galaxy.model.WorkflowStepConnection method) (galaxy.model.base.ModelMapping method) (galaxy.model.metadata.JobExternalOutputMetadataWrapper 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.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.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.DiskObjectStore method) (galaxy.objectstore.DistributedObjectStore method) (galaxy.objectstore.HierarchicalObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.pulsar.PulsarObjectStore method) (galaxy.objectstore.rods.IRODSObjectStore method) (galaxy.objectstore.s3.S3ObjectStore method) (galaxy.openid.providers.OpenIDProvider method) (galaxy.openid.providers.OpenIDProviders method) (galaxy.queue_worker.GalaxyQueueWorker method) (galaxy.quota.NoQuotaAgent method) (galaxy.security.Action method) (galaxy.security.GalaxyRBACAgent method) (galaxy.security.HostAgent method) (galaxy.tools.BadValue method) (galaxy.tools.DataManagerTool method) (galaxy.tools.DefaultToolState method) (galaxy.tools.SetParamAction method) (galaxy.tools.Tool method) (galaxy.tools.ToolBox method) (galaxy.tools.ToolErrorLog method) (galaxy.tools.TracksterConfig method) (galaxy.tools.actions.ObjectStorePopulator method) (galaxy.tools.actions.OutputCollections method) (galaxy.tools.actions.ToolExecutionCache method) (galaxy.tools.cwl.schema.SchemaLoader 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_manager.manager.DataManager method) (galaxy.tools.data_manager.manager.DataManagers method) (galaxy.tools.deps.CachedDependencyManager method) (galaxy.tools.deps.DependencyManager method) (galaxy.tools.deps.brew_exts.BrewContext method) (galaxy.tools.deps.brew_exts.CommandLineException method) (galaxy.tools.deps.brew_exts.EnvAction method) (galaxy.tools.deps.brew_exts.RecipeContext method) (galaxy.tools.deps.brew_util.HomebrewRecipe method) (galaxy.tools.deps.commands.CommandLineException method) (galaxy.tools.deps.conda_util.CondaContext method) (galaxy.tools.deps.conda_util.CondaTarget method) (galaxy.tools.deps.container_resolvers.ContainerResolver method) (galaxy.tools.deps.container_resolvers.mulled.BuildMulledDockerContainerResolver method) (galaxy.tools.deps.container_resolvers.mulled.BuildMulledSingularityContainerResolver method) (galaxy.tools.deps.container_resolvers.mulled.CachedMulledDockerContainerResolver method) (galaxy.tools.deps.container_resolvers.mulled.CachedMulledSingularityContainerResolver method) (galaxy.tools.deps.container_resolvers.mulled.MulledDockerContainerResolver method) (galaxy.tools.deps.containers.AppInfo method) (galaxy.tools.deps.containers.Container method) (galaxy.tools.deps.containers.ContainerFinder method) (galaxy.tools.deps.containers.ContainerRegistry method) (galaxy.tools.deps.containers.JobInfo method) (galaxy.tools.deps.containers.NullContainer method) (galaxy.tools.deps.containers.ToolInfo method) (galaxy.tools.deps.dependencies.DependenciesDescription method) (galaxy.tools.deps.docker_util.DockerVolume method) (galaxy.tools.deps.mulled.mulled_search.QuaySearch method) (galaxy.tools.deps.requirements.ContainerDescription method) (galaxy.tools.deps.requirements.RequirementSpecification method) (galaxy.tools.deps.requirements.ToolRequirement method) (galaxy.tools.deps.requirements.ToolRequirements method) (galaxy.tools.deps.resolvers.NullDependency method) (galaxy.tools.deps.resolvers.RequirementMapping method) (galaxy.tools.deps.resolvers.brewed_tool_shed_packages.HomebrewToolShedDependencyResolver method) (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method) (galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency method) (galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependencyResolver method) (galaxy.tools.deps.resolvers.homebrew.HomebrewDependencyResolver method) (galaxy.tools.deps.resolvers.modules.ModuleDependencyResolver method) (galaxy.tools.deps.resolvers.resolver_mixins.HomebrewDependency method) (galaxy.tools.deps.resolvers.tool_shed_packages.ToolShedPackageDependencyResolver method) (galaxy.tools.deps.resolvers.unlinked_tool_shed_packages.UnlinkedToolShedPackageDependencyResolver method) (galaxy.tools.deps.views.DependencyResolversView method) (galaxy.tools.errors.ErrorReporter method) (galaxy.tools.evaluation.ToolEvaluator method) (galaxy.tools.exception_handling.UCSCOutWrapper method) (galaxy.tools.fetcher.ToolLocationFetcher method) (galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper method) (galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper method) (galaxy.tools.lint.LintContext method) (galaxy.tools.locations.http.HttpToolResolver 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.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.GenomespaceFileToolParameter 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.SelectToolParameter method) (galaxy.tools.parameters.basic.TextToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.dataset_matcher.DatasetCollectionMatcher method) (galaxy.tools.parameters.dataset_matcher.DatasetMatcher 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.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.output_collect.DatasetCollector method) (galaxy.tools.parameters.output_collect.JobContext method) (galaxy.tools.parameters.output_collect.JsonCollectedDatasetMatch method) (galaxy.tools.parameters.output_collect.LegacyToolProvidedMetadata method) (galaxy.tools.parameters.output_collect.RegexCollectedDatasetMatch method) (galaxy.tools.parameters.output_collect.ToolMetadataDatasetCollector method) (galaxy.tools.parameters.output_collect.ToolProvidedMetadata 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.MetadataValidator method) (galaxy.tools.parameters.validation.NoOptionsValidator method) (galaxy.tools.parameters.validation.RegexValidator method) (galaxy.tools.parameters.validation.UnspecifiedBuildValidator method) (galaxy.tools.parameters.wrapped.WrappedParameters method) (galaxy.tools.parser.ToolOutputCollectionPart method) (galaxy.tools.parser.cwl.CwlPageSource method) (galaxy.tools.parser.cwl.CwlToolSource method) (galaxy.tools.parser.interface.PagesSource method) (galaxy.tools.parser.interface.TestCollectionDef method) (galaxy.tools.parser.interface.TestCollectionOutputDef method) (galaxy.tools.parser.interface.ToolStdioExitCode method) (galaxy.tools.parser.interface.ToolStdioRegex method) (galaxy.tools.parser.output_actions.BooleanFilter method) (galaxy.tools.parser.output_actions.ColumnReplaceFilter method) (galaxy.tools.parser.output_actions.ColumnStripFilter method) (galaxy.tools.parser.output_actions.DatatypeIsInstanceToolOutputActionConditionalWhen method) (galaxy.tools.parser.output_actions.FormatToolOutputAction method) (galaxy.tools.parser.output_actions.FromDataTableOutputActionOption method) (galaxy.tools.parser.output_actions.FromFileToolOutputActionOption method) (galaxy.tools.parser.output_actions.FromParamToolOutputActionOption method) (galaxy.tools.parser.output_actions.InsertColumnToolOutputActionOptionFilter method) (galaxy.tools.parser.output_actions.MetadataToolOutputAction method) (galaxy.tools.parser.output_actions.MetadataValueFilter method) (galaxy.tools.parser.output_actions.MultipleSplitterFilter method) (galaxy.tools.parser.output_actions.ParamValueToolOutputActionOptionFilter method) (galaxy.tools.parser.output_actions.StringFunctionFilter method) (galaxy.tools.parser.output_actions.ToolOutputAction method) (galaxy.tools.parser.output_actions.ToolOutputActionConditional method) (galaxy.tools.parser.output_actions.ToolOutputActionConditionalWhen method) (galaxy.tools.parser.output_actions.ToolOutputActionGroup method) (galaxy.tools.parser.output_actions.ToolOutputActionOption method) (galaxy.tools.parser.output_actions.ToolOutputActionOptionFilter method) (galaxy.tools.parser.output_collection_def.DatasetCollectionDescription method) (galaxy.tools.parser.output_collection_def.FilePatternDatasetCollectionDescription method) (galaxy.tools.parser.output_objects.ToolOutput method) (galaxy.tools.parser.output_objects.ToolOutputBase method) (galaxy.tools.parser.output_objects.ToolOutputCollection method) (galaxy.tools.parser.output_objects.ToolOutputCollectionPart method) (galaxy.tools.parser.output_objects.ToolOutputCollectionStructure method) (galaxy.tools.parser.xml.StdioParser method) (galaxy.tools.parser.xml.XmlInputSource method) (galaxy.tools.parser.xml.XmlPageSource method) (galaxy.tools.parser.xml.XmlPagesSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlInputSource method) (galaxy.tools.parser.yaml.YamlPageSource method) (galaxy.tools.parser.yaml.YamlToolSource method) (galaxy.tools.search.ToolBoxSearch method) (galaxy.tools.test.ParamContext method) (galaxy.tools.test.RootParamContext method) (galaxy.tools.test.ToolTestBuilder 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.LocFileEventHandler method) (galaxy.tools.toolbox.watcher.ToolConfWatcher method) (galaxy.tools.toolbox.watcher.ToolDataWatcher 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.verify.test_data.FileDataResolver method) (galaxy.tools.verify.test_data.GitDataResolver method) (galaxy.tools.verify.test_data.TestDataResolver 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.aliaspickler.AliasPickleModule method) (galaxy.util.aliaspickler.AliasUnpickler method) (galaxy.util.bunch.Bunch method) (galaxy.util.dbkeys.GenomeBuilds method) (galaxy.util.expressions.ExpressionContext method) (galaxy.util.filelock.FileLock method) (galaxy.util.heartbeat.Heartbeat method) (galaxy.util.inflection.Inflector method) (galaxy.util.jstree.JSTree method) (galaxy.util.jstree.Node method) (galaxy.util.lazy_process.LazyProcess method) (galaxy.util.none_like.NoneDataset 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.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.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.VisualizationsConfigParser 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.base.controller.BaseController method) (galaxy.web.base.controller.Datatype method) (galaxy.web.base.controller.JSAppLauncher 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.graphite.GraphiteMiddleware 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.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.framework.openid_manager.OpenIDManager method) (galaxy.web.framework.webapp.GalaxyWebTransaction method) (galaxy.web.framework.webapp.WebApplication 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.security.SecurityHelper method) (galaxy.web.stack.ApplicationStack method) (galaxy.web.stack.MessageApplicationStack method) (galaxy.web.stack.UWSGIApplicationStack 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.configuration.ConfigurationController method), [1] (galaxy.webapps.galaxy.api.dataset_collections.DatasetCollectionsController method), [1] (galaxy.webapps.galaxy.api.datasets.DatasetsController 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.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.provenance.BaseProvenanceController method), [1] (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController 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.webhooks.WebhooksController method), [1] (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] (galaxy.webapps.galaxy.config_watchers.ConfigWatchers method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.root.RootController method) (galaxy.webapps.galaxy.controllers.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.tool_shed.api.configuration.ConfigurationController method), [1] (galaxy.webapps.tool_shed.api.groups.GroupsController method), [1] (galaxy.webapps.tool_shed.app.UniverseApplication method) (galaxy.webapps.tool_shed.config.Configuration method) (galaxy.webapps.tool_shed.framework.middleware.remoteuser.RemoteUser method) (galaxy.webapps.tool_shed.model.APIKeys method) (galaxy.webapps.tool_shed.model.Category method) (galaxy.webapps.tool_shed.model.Component method) (galaxy.webapps.tool_shed.model.ComponentReview method) (galaxy.webapps.tool_shed.model.GalaxySession method) (galaxy.webapps.tool_shed.model.Group method) (galaxy.webapps.tool_shed.model.GroupRoleAssociation method) (galaxy.webapps.tool_shed.model.ItemRatingAssociation method) (galaxy.webapps.tool_shed.model.ItemTagAssociation method) (galaxy.webapps.tool_shed.model.PasswordResetToken method) (galaxy.webapps.tool_shed.model.PostJobAction method) (galaxy.webapps.tool_shed.model.Repository method) (galaxy.webapps.tool_shed.model.RepositoryCategoryAssociation method) (galaxy.webapps.tool_shed.model.RepositoryMetadata method) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation method) (galaxy.webapps.tool_shed.model.RepositoryReview method) (galaxy.webapps.tool_shed.model.RepositoryRoleAssociation method) (galaxy.webapps.tool_shed.model.Role method) (galaxy.webapps.tool_shed.model.Tag method) (galaxy.webapps.tool_shed.model.User method) (galaxy.webapps.tool_shed.model.UserGroupAssociation method) (galaxy.webapps.tool_shed.model.UserRoleAssociation method) (galaxy.webapps.tool_shed.model.Workflow method) (galaxy.webapps.tool_shed.model.WorkflowStep method) (galaxy.webapps.tool_shed.model.WorkflowStepConnection method) (galaxy.webapps.tool_shed.security.Action method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) (galaxy.webapps.tool_shed.util.hgweb_config.HgWebConfigManager method) (galaxy.webapps.tool_shed.util.shed_statistics.ShedCounter method) (galaxy.webhooks.Webhook method) (galaxy.webhooks.WebhooksRegistry method) (galaxy.work.context.WorkRequestContext method) (galaxy.workflow.modules.DelayedWorkflowEvaluation 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) (log_tempfile.TempFile method) (tool_shed.capsule.capsule_manager.ExportRepositoryManager method) (tool_shed.capsule.capsule_manager.ExportedRepositoryRegistry method) (tool_shed.capsule.capsule_manager.ImportRepositoryManager 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.datatypes.custom_datatype_manager.CustomDatatypeLoader method) (tool_shed.galaxy_install.dependency_display.DependencyDisplayer method) (tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) (tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) (tool_shed.galaxy_install.install_manager.RepositoriesInstalledException method) (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) (tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) (tool_shed.galaxy_install.migrate.common.MigrateToolsApplication method) (tool_shed.galaxy_install.repair_repository_manager.RepairRepositoryManager method) (tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) (tool_shed.galaxy_install.tool_dependencies.env_manager.EnvManager method) (tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader.AsynchronousReader method) (tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder.EnvFileBuilder method) (tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method) (tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager.StepManager method) (tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager.TagManager method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertDirectoryExecutable method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertDirectoryExists method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertFileExecutable method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertFileExists method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.Autoconf method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.ChangeDirectory method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.Chmod method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.CompressedFile method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadBinary method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadByUrl method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadFile method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MakeDirectory method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MakeInstall method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MoveDirectoryFiles method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MoveFile method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.RegexReplace method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetEnvironment method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetEnvironmentForInstall method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupPerlEnvironment method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupPythonEnvironment method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupREnvironment method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupRubyEnvironment method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupVirtualEnv method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.ShellCommand method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.TemplateCommand method) (tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Install method) (tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Package method) (tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.ReadMe method) (tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Repository method) (tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.SetEnvironment method) (tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager method) (tool_shed.galaxy_install.tools.data_manager.DataManagerHandler method) (tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) (tool_shed.galaxy_install.update_repository_manager.Sleeper method) (tool_shed.galaxy_install.update_repository_manager.UpdateRepositoryManager 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.tool_shed_registry.Registry method) (tool_shed.tools.data_table_manager.ShedToolDataTableManager method) (tool_shed.tools.tool_validator.ToolValidator method) (tool_shed.tools.tool_version_manager.ToolVersionManager method) (tool_shed.util.workflow_util.RepoToolModule method) (tool_shed.util.workflow_util.RepoWorkflowModuleFactory method) (tool_shed.util.xml_util.Py26CommentedTreeBuilder 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)

A

Ab1 (class in galaxy.datatypes.binary) 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) AccessDatasetRBACPermission (class in galaxy.managers.rbac_secured) AccessibleManagerMixin (class in galaxy.managers.secured) AccNos (class in galaxy.datatypes.mothur) accumulate_tool_dependencies() (in module tool_shed.util.common_util) acquire() (galaxy.util.filelock.FileLock method) Action (class in galaxy.security) (class in galaxy.webapps.tool_shed.security) action (galaxy.jobs.actions.post.RemoveTagDatasetAction attribute) (galaxy.jobs.actions.post.TagDatasetAction attribute) 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 (in module galaxy.tools.parser.output_actions) ActionBox (class in galaxy.jobs.actions.post) ActionInputError actions (galaxy.jobs.actions.post.ActionBox attribute) activatable_datasets (galaxy.model.History attribute) activatable_library_datasets (galaxy.model.LibraryFolder attribute) activate (galaxy.tools.deps.conda_util.CondaContext attribute) activate() (galaxy.webapps.galaxy.controllers.user.User method) activate_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) active (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_datasets_and_roles (galaxy.model.History attribute) active_folders() (in module galaxy.tools.actions.upload_common) active_repositories (galaxy.webapps.tool_shed.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.dataset_collections.matching.CollectionsToMatch method) (galaxy.managers.citations.CitationCollection method) (galaxy.util.oset.OrderedSet method) (galaxy.util.streamball.StreamBall method) add_api_controller() (galaxy.web.framework.base.WebApplication method) add_api_controllers() (galaxy.web.framework.webapp.WebApplication method) add_boxes() (galaxy.workflow.render.WorkflowCanvas method) add_category_entry() (tool_shed.repository_registry.Registry method) add_changeset() (in module tool_shed.util.hg_util) add_client_route() (galaxy.web.framework.base.WebApplication method) add_composite_file() (galaxy.datatypes.data.Data method) add_connection() (galaxy.workflow.render.WorkflowCanvas 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.dataset_collections.builder.CollectionBuilder method) (galaxy.model.History method) add_dataset_collection() (galaxy.model.History method) add_datasets() (galaxy.model.History method) add_deserializers() (galaxy.managers.annotatable.AnnotatableDeserializerMixin method) (galaxy.managers.base.ModelDeserializer method) (galaxy.managers.datasets.DatasetAssociationDeserializer method) (galaxy.managers.datasets.DatasetDeserializer 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) (galaxy.webapps.tool_shed.util.hgweb_config.HgWebConfigManager method) (tool_shed.repository_registry.Registry method) add_entry_to_installed_repository_dependencies_of_installed_repositories() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) add_entry_to_installed_tool_dependencies_of_installed_repositories() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) add_entry_to_repository_dependencies_of_installed_repositories() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) add_entry_to_tool_dependencies_of_installed_repositories() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) add_env_shell_file_paths() (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_history() (galaxy.model.GalaxySession method) add_implicit_input_collection() (galaxy.model.HistoryDatasetCollectionAssociation method) add_implicit_output_dataset_collection() (galaxy.model.Job method) add_input() (galaxy.model.WorkflowInvocation method) add_input_dataset() (galaxy.model.Job method) add_input_dataset_collection() (galaxy.model.Job method) add_input_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_library_dataset() (galaxy.model.LibraryFolder method) add_line_to_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider 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.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_collection() (galaxy.model.Job method) add_output_library_dataset() (galaxy.model.Job method) add_parameter() (galaxy.model.Job method) add_post_job_action() (galaxy.model.Job method) add_repository_registry_entry() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method), [1] add_route() (galaxy.web.framework.base.WebApplication method) add_serializers() (galaxy.managers.annotatable.AnnotatableSerializerMixin method) (galaxy.managers.base.ModelSerializer 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.tools.util.maf_utilities.RegionAlignment method) add_sreg() (galaxy.web.framework.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.managers.tags.TagManager method) add_text() (galaxy.workflow.render.WorkflowCanvas method) add_to_shed_tool_config() (tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) add_to_tool_panel() (tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) add_tool_to_cache() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) add_tool_versions() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) add_ui_controller() (galaxy.web.framework.base.WebApplication method) add_ui_controllers() (galaxy.web.framework.webapp.WebApplication method) (in module galaxy.webapps.reports.buildapp) (in module galaxy.webapps.tool_shed.buildapp) add_validation_error() (galaxy.model.DatasetInstance method) add_view() (galaxy.managers.base.ModelSerializer method) add_visualization_revision() (galaxy.web.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) 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) AddressField (class in galaxy.web.form_builder) addRoot() (galaxy.visualization.data_providers.phyloviz.baseparser.PhyloTree method) adjust_hidden() (galaxy.webapps.galaxy.controllers.history.HistoryController method) adjust_total_disk_usage() (galaxy.model.User method) admin_api_keys() (galaxy.webapps.galaxy.controllers.userskeys.User method) admin_job_lock() (in module galaxy.queue_worker) admin_role (galaxy.webapps.tool_shed.model.Repository attribute) AdminActions (class in galaxy.actions.admin) AdminConfigSerializer (class in galaxy.managers.configuration) AdminController (class in galaxy.webapps.tool_shed.controllers.admin) AdminGalaxy (class in galaxy.webapps.galaxy.controllers.admin) AdminRepositoryGrid (class in tool_shed.grids.admin_grids) AdminRepositoryGrid.DeletedColumn (class in tool_shed.grids.admin_grids) AdminRequiredException admins() (galaxy.managers.users.UserManager method) AdminToolshed (class in galaxy.webapps.galaxy.controllers.admin_toolshed) AdminUserFilterParser (class in galaxy.managers.users) Affybatch (class in galaxy.datatypes.genetics) after_setting_metadata() (galaxy.datatypes.data.Data method) aggressive_error_checks() (in module galaxy.tools.parser.util) 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_control_queues_for_declare() (in module galaxy.queues) all_requirements (galaxy.tools.ToolBox attribute) all_requirements() (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] all_roles() (galaxy.model.User method) (galaxy.webapps.tool_shed.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.security.GalaxyRBACAgent method) (galaxy.security.HostAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method)

allow_action_on_libitems() (galaxy.security.GalaxyRBACAgent method) allow_datatype_change (galaxy.datatypes.assembly.Velvet attribute) (galaxy.datatypes.blast.BlastDomainDb attribute) (galaxy.datatypes.blast.BlastNucDb attribute) (galaxy.datatypes.blast.BlastProtDb attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.genetics.IdeasPre attribute) (galaxy.datatypes.genetics.RexpBase attribute) (galaxy.datatypes.genetics.Rgenetics 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_push() (galaxy.webapps.tool_shed.model.Repository method) allow_user_access() (galaxy.tools.DataManagerTool method) (galaxy.tools.Tool method) allowed() (galaxy.web.framework.helpers.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) alter_config_and_load_prorietary_datatypes() (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) 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.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) anon_user_api_value() (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] anonymous (galaxy.managers.context.ProvidesUserContext attribute) api_key() (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] api_keys (galaxy.webapps.tool_shed.model.User attribute) api_keys() (galaxy.webapps.tool_shed.controllers.user.User method) api_payload_to_create_params() (in module galaxy.managers.collections_util) ApiKeyManager (class in galaxy.managers.api_keys) APIKeys (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) app_factory() (in module galaxy.web.buildapp) (in module galaxy.webapps.galaxy.buildapp) (in module galaxy.webapps.reports.buildapp) (in module galaxy.webapps.tool_shed.buildapp) app_kwds() (galaxy.main.GalaxyConfigBuilder method) app_loop() (in module galaxy.main) 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.tools.deps.requirements.ToolRequirements method) append_line() (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.tools.deps.containers) application (galaxy.web.framework.middleware.batch.BatchMiddleware 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) apply() (galaxy.tools.deps.resolvers.RequirementMapping method) apply_action() (galaxy.tools.parser.output_actions.FormatToolOutputAction method) (galaxy.tools.parser.output_actions.MetadataToolOutputAction method) (galaxy.tools.parser.output_actions.ToolOutputAction method) (galaxy.tools.parser.output_actions.ToolOutputActionConditional method) (galaxy.tools.parser.output_actions.ToolOutputActionConditionalWhen method) (galaxy.tools.parser.output_actions.ToolOutputActionGroup method) apply_item_tag() (galaxy.managers.tags.TagManager method) apply_item_tags() (galaxy.managers.tags.TagManager 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) (tool_shed.grids.admin_grids.RoleGrid method) approve_repository_review() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) approved (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) approved_states (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) archive() (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method), [1] 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.tools.deps.commands) as_dict() (galaxy.model.tool_shed_install.ToolShedRepository method) (galaxy.util.simplegraph.SimpleGraph method) as_display_type() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) as_gbrowse_display_file() (galaxy.datatypes.tabular.Tabular method) as_ucsc_display_file() (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.interval.Bed method) (galaxy.datatypes.interval.BedGraph method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.tabular.Tabular method) as_xml() (galaxy.webapps.galaxy.controllers.history.HistoryController method) asbool() (in module galaxy.util) assemble_current_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method) assert_attribute_is() (in module galaxy.tools.verify.asserts.xml) assert_attribute_matches() (in module galaxy.tools.verify.asserts.xml) assert_directory_executable() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertDirectoryExecutable method) assert_directory_exists() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertDirectoryExists method) assert_element_text() (in module galaxy.tools.verify.asserts.xml) assert_element_text_is() (in module galaxy.tools.verify.asserts.xml) assert_element_text_matches() (in module galaxy.tools.verify.asserts.xml) assert_file_executable() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertFileExecutable method) assert_file_exists() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertFileExists method) assert_has_element_with_path() (in module galaxy.tools.verify.asserts.xml) assert_has_line() (in module galaxy.tools.verify.asserts.text) assert_has_line_matching() (in module galaxy.tools.verify.asserts.text) assert_has_n_columns() (in module galaxy.tools.verify.asserts.tabular) assert_has_n_elements_with_path() (in module galaxy.tools.verify.asserts.xml) assert_has_text() (in module galaxy.tools.verify.asserts.text) assert_has_text_matching() (in module galaxy.tools.verify.asserts.text) assert_is_valid_xml() (in module galaxy.tools.verify.asserts.xml) assert_not_has_text() (in module galaxy.tools.verify.asserts.text) AssertDirectoryExecutable (class in tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) AssertDirectoryExists (class in tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) AssertFileExecutable (class in tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) AssertFileExists (class in tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) associate() (galaxy.managers.base.ModelManager method) associate_action_dataset_role() (galaxy.security.GalaxyRBACAgent method) associate_components() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) (galaxy.webapps.tool_shed.security.RBACAgent method) associate_group_role() (galaxy.security.GalaxyRBACAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) associate_repository_category() (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) associate_user_group() (galaxy.security.GalaxyRBACAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) associate_user_role() (galaxy.security.GalaxyRBACAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) (galaxy.webapps.tool_shed.security.RBACAgent method) ASync (class in galaxy.webapps.galaxy.controllers.async) AsyncDataSourceTool (class in galaxy.tools) AsynchronousJobRunner (class in galaxy.jobs.runners) AsynchronousJobState (class in galaxy.jobs.runners) AsynchronousReader (class in tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader) attach_ordered_steps() (in module galaxy.workflow.steps) attach_subworkflow_invocation_for_step() (galaxy.model.WorkflowInvocation method) attempt_unlink() (in module galaxy.tools.deps.brew_exts) attempt_unlink_all() (in module galaxy.tools.deps.brew_exts) ATTRIBUTE_SPLIT_CHAR (galaxy.visualization.plugins.config_parser.DataSourceParser attribute) AttributeValueSplitterFilter (class in galaxy.tools.parameters.dynamic_options) 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) 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) AuthenticationController (class in galaxy.webapps.galaxy.api.authenticate), [1] AuthenticationFailed AuthenticationRequired AuthenticationToken (class in galaxy.web.proxy) AuthManager (class in galaxy.auth) AuthProvider (class in galaxy.auth.providers) Autoconf (class in 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) avg (galaxy.jobs.metrics.collectl.stats.StatisticsTracker attribute) avsc_names (galaxy.tools.cwl.schema.ProcessDefinition attribute) Axes (class in galaxy.datatypes.mothur) Axt (class in galaxy.datatypes.sequence) AzureBlobObjectStore (class in galaxy.objectstore.azure_blob)

B

BadCommand BadValue (class in galaxy.tools) 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) Base (class in galaxy.util.inflection) base (galaxy.web.framework.base.Request attribute) Base64ChunkDataProvider (class in galaxy.datatypes.dataproviders.chunk) base_dataprovider() (galaxy.datatypes.data.Data method) Base_Parser (class in galaxy.visualization.data_providers.phyloviz.baseparser) BASE_URL (galaxy.visualization.plugins.registry.VisualizationsRegistry attribute) BaseAnnotationsController (class in galaxy.webapps.galaxy.api.annotations), [1] BaseAPIController (class in galaxy.web.base.controller) BaseBcf (class in galaxy.datatypes.binary) BaseCitation (class in galaxy.managers.citations) BaseController (class in galaxy.web.base.controller) BaseCSV (class in galaxy.datatypes.tabular) BaseDataProvider (class in galaxy.visualization.data_providers.basic) BaseDatasetCollectionType (class in galaxy.dataset_collections.types) BaseDataToolParameter (class in galaxy.tools.parameters.basic) BaseExtendedMetadataController (class in galaxy.webapps.galaxy.api.extended_metadata), [1] BaseFastq (class in galaxy.datatypes.sequence) BaseField (class in galaxy.web.form_builder) BaseGalaxyToolBox (class in galaxy.tools.toolbox) (class in galaxy.tools.toolbox.base) BaseItemTagsController (class in galaxy.webapps.galaxy.api.item_tags), [1] BaseJobExec (class in galaxy.jobs.runners.util.cli.job) BaseJobMetric (class in galaxy.model) BaseJobRunner (class in galaxy.jobs.runners) BaseParamParser (class in galaxy.web.params) BaseProvenanceController (class in galaxy.webapps.galaxy.api.provenance), [1] BaseShellExec (class in galaxy.jobs.runners.util.cli.shell) basestring() (galaxy.managers.base.ModelValidator method) basestring_list() (galaxy.managers.base.ModelValidator method) BaseTree (class in galaxy.dataset_collections.structure) BaseUIController (class in galaxy.web.base.controller) BaseURLToolParameter (class in galaxy.tools.parameters.basic) BaseVcf (class in galaxy.datatypes.tabular) 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) BedGraphReader (class in galaxy.datatypes.converters.bedgraph_to_array_tree_converter) 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) best_match() (in module mimeparse) 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) Biom1 (class in galaxy.datatypes.text) Biom2 (class in galaxy.datatypes.binary) biomart() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) biostar_enabled() (in module galaxy.util.biostar) biostar_logged_in() (in module galaxy.util.biostar) biostar_logout() (galaxy.webapps.galaxy.controllers.biostar.BiostarController method) (in module galaxy.util.biostar) biostar_question_redirect() (galaxy.webapps.galaxy.controllers.biostar.BiostarController method) biostar_redirect() (galaxy.webapps.galaxy.controllers.biostar.BiostarController method) biostar_tool_bug_report() (galaxy.webapps.galaxy.controllers.biostar.BiostarController method) biostar_tool_question_redirect() (galaxy.webapps.galaxy.controllers.biostar.BiostarController method) biostar_tool_tag_redirect() (galaxy.webapps.galaxy.controllers.biostar.BiostarController method) BiostarController (class in galaxy.webapps.galaxy.controllers.biostar) BiostarErrorReporter (class in galaxy.util.biostar) BlastDomainDb (class in galaxy.datatypes.blast) BlastNucDb (class in galaxy.datatypes.blast) BlastProtDb (class in galaxy.datatypes.blast) BlastXml (class in galaxy.datatypes.blast) 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.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.ProtXML attribute) (galaxy.datatypes.proteomics.TandemXML attribute) (galaxy.datatypes.proteomics.TraML attribute) (galaxy.datatypes.proteomics.UniProtXML 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) BooleanColumn (class in galaxy.web.framework.helpers.grids) BooleanFilter (class in galaxy.tools.parser.output_actions) BooleanToolParameter (class in galaxy.tools.parameters.basic) BoolOptionParser (class in galaxy.util.pastescript.serve) BoundCollectionBuilder (class in galaxy.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.tools.deps.brew_exts) brew_execute() (in module galaxy.tools.deps.brew_exts) brew_head_at_commit() (in module galaxy.tools.deps.brew_exts) brew_head_at_version() (in module galaxy.tools.deps.brew_exts) brew_info() (in module galaxy.tools.deps.brew_exts) brew_versions_info() (in module galaxy.tools.deps.brew_exts) BrewContext (class in galaxy.tools.deps.brew_exts) browse_categories() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_components() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) browse_datatypes() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_deprecated_repositories_i_own() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_my_writable_repositories() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_my_writable_repositories_missing_tool_test_components() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_my_writable_repositories_with_invalid_tools() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repositories() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.admin.AdminController method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repositories_by_user() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repositories_i_can_administer() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repositories_i_own() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repositories_in_category() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repositories_missing_tool_test_components() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repositories_with_invalid_tools() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repository_dependencies() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_repository_metadata() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) browse_review() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) browse_tool_dependencies() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_tool_dependency() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) browse_tool_shed() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) browse_tool_sheds() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) browse_tools() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_toolsheds() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method)

browse_valid_categories() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browse_valid_repositories() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) browser_url (galaxy.web.framework.base.Request attribute) bucket_proxy() (galaxy.webapps.galaxy.controllers.root.RootController method) build (galaxy.tools.deps.mulled.util.Target attribute) build() (galaxy.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_approved_select_field() (in module tool_shed.grids.util) build_cache() (galaxy.tools.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.dataset_collections.builder) build_command() (in module galaxy.jobs.command_factory) (in module galaxy.tools.deps.docker_util) (tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method) build_command_line() (galaxy.jobs.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.tools.deps) build_dependency_shell_commands() (galaxy.tools.Tool method) build_docker_cache_command() (in module galaxy.tools.deps.docker_util) build_docker_images_command() (in module galaxy.tools.deps.docker_util) build_docker_load_command() (in module galaxy.tools.deps.docker_util) build_docker_run_command() (in module galaxy.tools.deps.docker_util) build_elements() (galaxy.dataset_collections.builder.CollectionBuilder method) build_engine() (in module galaxy.model.orm.engine_factory) build_env() (galaxy.tools.deps.brew_exts.EnvAction static method) build_env_actions() (in module galaxy.tools.deps.brew_exts) build_env_statements() (in module galaxy.tools.deps.brew_exts) build_env_statements_from_recipe_context() (in module galaxy.tools.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.tools.deps.mulled.mulled_search.QuaySearch method) (galaxy.tools.search.ToolBoxSearch method) build_initial_query() (galaxy.web.framework.helpers.grids.Grid method) (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid method) (galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid 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.user.UserOpenIDGrid method) (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid method) (galaxy.webapps.galaxy.controllers.visualization.LibraryDatasetsSelectionGrid method) (galaxy.webapps.galaxy.controllers.visualization.TracksterSelectionGrid method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationAllPublishedGrid method) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid method) (tool_shed.grids.admin_grids.AdminRepositoryGrid method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid method) (tool_shed.grids.repository_grids.DatatypesGrid method) (tool_shed.grids.repository_grids.DeprecatedRepositoriesIOwnGrid method) (tool_shed.grids.repository_grids.MatchedRepositoryGrid method) (tool_shed.grids.repository_grids.MyWritableRepositoriesGrid method) (tool_shed.grids.repository_grids.MyWritableRepositoriesMissingToolTestComponentsGrid method) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithInvalidToolsGrid method) (tool_shed.grids.repository_grids.RepositoriesByUserGrid method) (tool_shed.grids.repository_grids.RepositoriesICanAdministerGrid method) (tool_shed.grids.repository_grids.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_maf_index() (in module galaxy.tools.util.maf_utilities) build_maf_index_species_chromosomes() (in module galaxy.tools.util.maf_utilities) build_module() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] build_native_uwsgi_app() (in module galaxy.web.framework.webapp) build_object_store_from_config() (in module galaxy.objectstore) build_param_dict() (galaxy.tools.evaluation.ToolEvaluator method) build_parameter_dict() (galaxy.datatypes.display_applications.application.DisplayApplicationLink method) build_path() (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method), [1] build_pull_command() (in module galaxy.tools.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() (tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) build_repository_ids_select_field() (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.tools.verify.test_data) build_save_image_command() (in module galaxy.tools.deps.docker_util) build_select_input() (in module galaxy.webapps.galaxy.controllers.admin) build_shed_tool_conf_select_field() (in module tool_shed.util.tool_util) 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.tools.deps.mulled.util) build_template_error_formatters() (in module galaxy.webapps.util) build_tool_dependencies_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) build_tool_dependencies_select_field() (in module tool_shed.util.tool_dependency_util) build_tool_panel_section_select_field() (in module 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) (in module galaxy.util) build_url_map() (in module galaxy.web.framework.webapp) build_workflow_from_dict() (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) BuildMulledDockerContainerResolver (class in galaxy.tools.deps.container_resolvers.mulled) BuildMulledSingularityContainerResolver (class in galaxy.tools.deps.container_resolvers.mulled) BUILT_IN_VISUALIZATIONS (galaxy.visualization.plugins.registry.VisualizationsRegistry attribute) Bunch (class in galaxy.jobs.runners.util) (class in galaxy.util.bunch) bundle_to_json() (in module tool_shed.util.hg_util) burst() (in module galaxy.jobs.stock_rules) 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_user() (galaxy.managers.datasets.DatasetAssociationManager method) (galaxy.managers.histories.HistoryManager method) (galaxy.managers.sharable.SharableModelManager method) bytes_to_str() (in module galaxy.jobs.dynamic_tool_destination)

C

cache_job_destination() (galaxy.jobs.mapper.JobRunnerMapper method) cacheable (galaxy.tools.deps.resolvers.Dependency attribute) CacheableStaticURLParser (class in galaxy.web.framework.middleware.static) CachedDependencyManager (class in galaxy.tools.deps) CachedMulledDockerContainerResolver (class in galaxy.tools.deps.container_resolvers.mulled) CachedMulledSingularityContainerResolver (class in galaxy.tools.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) camelize() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) can_access_dataset() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_access_library() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_access_library_item() (galaxy.security.GalaxyRBACAgent method) can_add_item() (galaxy.managers.folders.FolderManager method) can_add_library_item() (galaxy.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() (galaxy.webapps.tool_shed.model.Repository method) can_change_type_to() (galaxy.webapps.tool_shed.model.Repository method) can_convert_to() (galaxy.model.DatasetInstance method) can_current_user_add_to_library_item() (galaxy.web.base.controller.UsesLibraryMixinItems method) can_deactivate (galaxy.model.tool_shed_install.ToolShedRepository attribute) can_eliminate_repository_dependency() (in module tool_shed.util.shed_util_common) can_eliminate_tool_dependency() (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.tools.deps.conda_util.CondaContext method) (galaxy.tools.deps.installable.InstallableContext method) can_install_conda() (galaxy.tools.deps.conda_util.CondaContext method) can_manage_dataset() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_manage_library_item() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_map_over() (galaxy.tools.parameters.history_query.HistoryQuery method) can_match() (galaxy.dataset_collections.structure.Tree method) can_match_type() (galaxy.dataset_collections.type_description.CollectionTypeDescription method) can_modify_library_item() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_push() (galaxy.webapps.tool_shed.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.tools.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) CANCEL (galaxy.web.framework.openid_manager.OpenIDManager attribute) cancel() (galaxy.model.WorkflowInvocation method) cancel_invocation() (galaxy.managers.workflows.WorkflowsManager method) (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] CancelWorkflowEvaluation categories (galaxy.webapps.tool_shed.model.Repository attribute) CategoriesController (class in galaxy.webapps.tool_shed.api.categories), [1] Category (class in galaxy.webapps.tool_shed.model) category (galaxy.webapps.tool_shed.model.RepositoryCategoryAssociation attribute) category() (galaxy.webapps.galaxy.api.toolshed.ToolShedController method), [1] category_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) category_id (galaxy.webapps.tool_shed.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.tools.deps.brew_exts.RecipeContext attribute) center() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) change_datatype() (galaxy.datatypes.registry.Registry method) (galaxy.model.DatasetInstance method) change_entry() (galaxy.webapps.tool_shed.util.hgweb_config.HgWebConfigManager method) change_ownership_for_run() (galaxy.jobs.JobWrapper method) change_password() (galaxy.webapps.galaxy.controllers.user.User method) (galaxy.webapps.tool_shed.controllers.user.User method) change_repository_name_in_hgrc_file() (in module tool_shed.util.repository_util) change_state() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) change_user_group() (galaxy.util.pastescript.serve.ServeCommand method) ChangeDatatypeAction (class in galaxy.jobs.actions.post) ChangeDirectory (class in tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) changeset_revision (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) changeset_revision_reviewed_by_user() (in module tool_shed.util.review_util) check() (galaxy.config.Configuration method) (galaxy.dependencies.ConditionalDependencies method) (galaxy.tools.toolbox.watcher.ToolConfWatcher method) (galaxy.webapps.reports.config.Configuration method) (galaxy.webapps.tool_shed.config.Configuration method) check_accessible() (galaxy.managers.folders.FolderManager method) (galaxy.managers.libraries.LibraryManager 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_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_cloudbridge() (galaxy.dependencies.ConditionalDependencies method) check_config() (galaxy.auth.providers.ldap_ad.LDAP method) check_csrf_token() (galaxy.web.framework.webapp.GalaxyWebTransaction method) check_drmaa() (galaxy.dependencies.ConditionalDependencies 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_fluent_logger() (galaxy.dependencies.ConditionalDependencies method) check_folder_contents() (galaxy.security.GalaxyRBACAgent method) check_for_missing_tools() (in module tool_shed.util.common_util) check_for_tool_dependencies() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) check_for_updates() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method), [1] (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) (in module tool_shed.util.repository_util) check_graphite() (galaxy.dependencies.ConditionalDependencies method) check_gzip() (in module galaxy.datatypes.checkers) (in module galaxy.util.checkers) check_html() (in module galaxy.datatypes.checkers) (in module galaxy.util.checkers) check_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_inputs_ready() (galaxy.tools.actions.model_operations.ModelOperationToolAction method) (galaxy.tools.DatabaseOperationTool method) check_interval (galaxy.model.DeferredJob attribute) check_kamaki() (galaxy.dependencies.ConditionalDependencies method) check_limits() (galaxy.jobs.JobWrapper method) (galaxy.jobs.runners.AsynchronousJobState method) check_manageable() (galaxy.managers.folders.FolderManager method) check_mysql_python() (galaxy.dependencies.ConditionalDependencies method) check_newlines() (in module galaxy.datatypes.sniff) check_or_update_tool_shed_status_for_installed_repository() (in module tool_shed.util.repository_util) check_output() (in module galaxy.jobs.output_checker) check_password() (galaxy.auth.AuthManager method) (galaxy.model.User method) (galaxy.webapps.tool_shed.model.User method) (in module galaxy.security.passwords) check_password_PBKDF2() (in module galaxy.security.passwords) check_pbs_python() (galaxy.dependencies.ConditionalDependencies method) check_psycopg2() (galaxy.dependencies.ConditionalDependencies method) check_pygments() (galaxy.dependencies.ConditionalDependencies method) check_python_ldap() (galaxy.dependencies.ConditionalDependencies method) check_python_openid() (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_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_status_and_reset_downloadable() (tool_shed.capsule.capsule_manager.ImportRepositoryManager method) check_tag_attributes() (tool_shed.dependencies.attribute_handlers.RepositoryDependencyAttributeHandler method) check_tool_input_params() (tool_shed.tools.tool_validator.ToolValidator method) check_tool_output() (galaxy.jobs.JobWrapper method) check_tool_tag_set() (in module tool_shed.util.common_util) check_user_can_add_to_library_item() (galaxy.web.base.controller.UsesLibraryMixinItems method) check_user_library_import_dir() (galaxy.web.framework.webapp.GalaxyWebTransaction method) check_watchdog() (galaxy.dependencies.ConditionalDependencies method) check_watched_item() (galaxy.jobs.runners.AsynchronousJobRunner method) (galaxy.jobs.runners.godocker.GodockerJobRunner method) (galaxy.jobs.runners.kubernetes.KubernetesJobRunner 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_weberror() (galaxy.dependencies.ConditionalDependencies method) check_workflow_compatible() (galaxy.tools.Tool method) check_zip() (in module galaxy.datatypes.checkers) (in module galaxy.util.checkers) CheckboxField (class in galaxy.web.form_builder) checkComments() (galaxy.visualization.data_providers.phyloviz.nexusparser.Nexus_Parser method) children (galaxy.webapps.tool_shed.model.Tag attribute) children_known (galaxy.dataset_collections.structure.Leaf attribute) (galaxy.dataset_collections.structure.Tree attribute) (galaxy.dataset_collections.structure.UnitializedTree attribute) Chmod (class in 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.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) 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) classify() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) clean() (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method) (galaxy.tools.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 tool_shed.util.shed_util_common) clean_repository_metadata() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) clean_services() (galaxy.containers.docker_swarm_manager.SwarmState 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) cleanup_after_job() (galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper method) (galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper method) cleanup_before_exit() (in module galaxy.datatypes.converters.sam_to_bam) cleanup_external_metadata() (galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper method) (galaxy.model.metadata.JobExternalOutputMetadataWrapper method) cleanup_from_JSON_dict_filename() (galaxy.datatypes.metadata.MetadataTempFile class method) (galaxy.model.metadata.MetadataTempFile class method) cleanup_job (galaxy.jobs.JobWrapper attribute) cleanup_unused_precreated_datasets() (in module galaxy.tools.actions.upload_common) clear() (galaxy.managers.rbac_secured.DatasetRBACPermission method) (galaxy.model.ImplicitlyConvertedDatasetAssociation method) (galaxy.util.odict.odict method) clear_associated_files() (galaxy.model.DatasetInstance method) (galaxy.model.HistoryDatasetAssociation method) (galaxy.model.LibraryDatasetDatasetAssociation method) clear_display_apps() (galaxy.datatypes.data.Data method) clear_history() (galaxy.webapps.galaxy.controllers.root.RootController method) clear_node_idle() (galaxy.containers.docker_swarm_manager.SwarmState method) clear_working_directory() (galaxy.jobs.JobWrapper method) client() (galaxy.web.base.controller.JSAppLauncher method) CliInterface (class in galaxy.jobs.runners.util.cli) clone() (galaxy.dataset_collections.structure.Leaf method) (galaxy.dataset_collections.structure.Tree method) (galaxy.dataset_collections.structure.UnitializedTree method) clone_repository() (in module tool_shed.util.hg_util) close() (galaxy.datatypes.converters.interval_to_coverage.CoverageWriter method) (galaxy.tools.util.maf_utilities.TempFileHandler method) close_file_descriptor() (tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method) close_logs() (galaxy.util.heartbeat.Heartbeat method) cls (in module galaxy.tools.data) cmd_exists() (in module galaxy.datatypes.converters.sam_to_bam) CML (class in galaxy.datatypes.molecules) cmp() (in module galaxy.util.object_wrapper) coerce() (galaxy.model.custom_types.MutationDict class method) (galaxy.model.custom_types.MutationList class method) (galaxy.model.custom_types.MutationObj class method) col (tool_shed.grids.admin_grids.ManageCategoryGrid attribute) (tool_shed.grids.repository_grids.InstallMatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithInvalidToolsGrid attribute) 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_collections() (galaxy.tools.Tool method) (in module galaxy.tools.parameters.output_collect) collect_input_dataset_collections() (galaxy.tools.actions.DefaultToolAction method) collect_inputs() (galaxy.tools.parser.interface.TestCollectionDef method) collect_primary_datasets() (galaxy.tools.Tool method) (in module galaxy.tools.parameters.output_collect) collect_properties() (galaxy.jobs.metrics.JobInstrumenter method) (galaxy.jobs.metrics.JobMetrics method) (galaxy.jobs.metrics.NullJobInstrumenter method) collection_builder_for() (galaxy.managers.collections.DatasetCollectionManager method) collection_prototype() (galaxy.tools.parser.output_objects.ToolOutputCollectionStructure method) collection_type (galaxy.dataset_collections.types.list.ListDatasetCollectionType attribute) (galaxy.dataset_collections.types.paired.PairedDatasetCollectionType attribute) (galaxy.workflow.modules.InputDataCollectionModule attribute) collection_types (galaxy.tools.parameters.basic.DataCollectionToolParameter attribute) (galaxy.tools.parameters.DataCollectionToolParameter attribute) CollectionBuilder (class in galaxy.dataset_collections.builder) CollectionsToMatch (class in galaxy.dataset_collections.matching) CollectionTypeDescription (class in galaxy.dataset_collections.type_description) CollectionTypeDescriptionFactory (class in galaxy.dataset_collections.type_description) CollectlCli (class in galaxy.jobs.metrics.collectl.cli) CollectlPlugin (class in galaxy.jobs.metrics.instrumenters.collectl) collector (galaxy.tools.parameters.output_collect.DiscoveredFile 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.molecules.InChI attribute) (galaxy.datatypes.molecules.SMILES attribute) (galaxy.datatypes.tabular.BaseVcf attribute) 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.tools.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.dataset.HistoryDatasetAssociationListGrid 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.user.UserOpenIDGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.LibraryDatasetsSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.TracksterSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationListGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.grids.admin_grids.AdminRepositoryGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.ManageCategoryGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.DatatypesGrid attribute) (tool_shed.grids.repository_grids.DeprecatedRepositoriesIOwnGrid attribute) (tool_shed.grids.repository_grids.DockerImageGrid attribute) (tool_shed.grids.repository_grids.EmailAlertsRepositoryGrid attribute) (tool_shed.grids.repository_grids.InstallMatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithInvalidToolsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesByUserGrid attribute) (tool_shed.grids.repository_grids.RepositoriesICanAdministerGrid attribute) (tool_shed.grids.repository_grids.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.tools.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_list() (in module galaxy.tools.deps.docker_util) command_shell() (in module galaxy.tools.deps.docker_util) CommandLineException, [1] commands_in_new_shell (galaxy.jobs.JobWrapper attribute) comment (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation attribute) comment() (tool_shed.util.xml_util.Py27CommentedTreeBuilder method) comment_lines (galaxy.datatypes.proteomics.ProtXmlReport attribute) commit() (galaxy.model.orm.logging_connection_proxy.LoggingProxy method) commit_changeset() (in module tool_shed.util.hg_util) commit_for_version() (in module galaxy.tools.deps.brew_exts) common_columns (galaxy.managers.history_contents.HistoryContentsManager attribute) CommunityRatingColumn (class in galaxy.web.framework.helpers.grids) CommunityRBACAgent (class in galaxy.webapps.tool_shed.security) CommunityTagManager (class in galaxy.managers.tags) CommunityTagsColumn (class in galaxy.web.framework.helpers.grids) CommunityWebApplication (class in galaxy.webapps.tool_shed.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.tools.parser.output_actions) compare_eq() (in module galaxy.tools.parser.output_actions) compare_gt() (in module galaxy.tools.parser.output_actions) compare_gte() (in module galaxy.tools.parser.output_actions) compare_in() (in module galaxy.tools.parser.output_actions) compare_lt() (in module galaxy.tools.parser.output_actions) compare_lte() (in module galaxy.tools.parser.output_actions) compare_neq() (in module galaxy.tools.parser.output_actions) compare_re_search() (in module galaxy.tools.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.tools.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) Component (class in galaxy.webapps.tool_shed.model) component (galaxy.webapps.tool_shed.model.ComponentReview attribute) component_grid (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController attribute) component_id (galaxy.webapps.tool_shed.model.ComponentReview attribute) component_overlaps_region() (in module galaxy.tools.util.maf_utilities) component_reviews (galaxy.webapps.tool_shed.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 galaxy.webapps.tool_shed.model) components_are_associated() (galaxy.security.RBACAgent method) composite_files (galaxy.datatypes.data.Data attribute) composite_type (galaxy.datatypes.assembly.Velvet attribute) (galaxy.datatypes.blast.BlastDomainDb attribute) (galaxy.datatypes.blast.BlastNucDb attribute) (galaxy.datatypes.blast.BlastProtDb attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.genetics.IdeasPre attribute) (galaxy.datatypes.genetics.RexpBase attribute) (galaxy.datatypes.genetics.Rgenetics 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.binary.CompressedArchive attribute) (galaxy.datatypes.sequence.FastaGz attribute) (galaxy.datatypes.sequence.FastqBz2 attribute) (galaxy.datatypes.sequence.FastqGz attribute) (galaxy.datatypes.tabular.VcfGz attribute) CompressedArchive (class in galaxy.datatypes.binary) CompressedFile (class in tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) CompressedZipArchive (class in galaxy.datatypes.binary) 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) cond_plural() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) conda_build_available (galaxy.tools.deps.conda_util.CondaContext attribute) conda_build_target_str() (in module galaxy.tools.deps.mulled.util) conda_info() (galaxy.tools.deps.conda_util.CondaContext method) conda_version (galaxy.tools.deps.conda_util.CondaContext attribute) CondaContext (class in galaxy.tools.deps.conda_util) CondaDependencyResolver (class in galaxy.tools.deps.resolvers.conda) CondaTarget (class in galaxy.tools.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) config_directories_from_setting() (in module galaxy.util) config_directory() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SimpleComputeEnvironment method) config_elems_to_xml_file() (tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) config_exception() (in module galaxy.jobs) config_is_ini (galaxy.main.GalaxyConfigBuilder attribute) config_options (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver attribute) (galaxy.tools.deps.resolvers.DependencyResolver attribute) ConfigDoesNotAllowException ConfigSerializer (class in galaxy.managers.configuration) Configuration (class in galaxy.config) (class in galaxy.webapps.reports.config) (class in galaxy.webapps.tool_shed.config) ConfigurationController (class in galaxy.webapps.galaxy.api.configuration), [1] (class in galaxy.webapps.tool_shed.api.configuration), [1] ConfigurationError, [1], [2], [3] configure_and_load() (galaxy.tools.data.TabularToolDataTable method) configure_fluent_log() (galaxy.app.UniverseApplication method) configure_logging() (in module galaxy.config) (in module galaxy.webapps.reports.config) ConfiguresGalaxyMixin (class in galaxy.config) ConfiguresHandlers (class in galaxy.util.handlers) ConfigWatchers (class in galaxy.webapps.galaxy.config_watchers) Conflict connect() (galaxy.jobs.runners.util.cli.shell.rsh.ParamikoShell method) (in module galaxy.util.sqlite) connection_from_config() (in module galaxy.queues) 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() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) ContainableModelMixin (class in galaxy.managers.containers) 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.tools.deps.containers) container_class (galaxy.containers.ContainerInterface attribute) (galaxy.containers.docker.DockerInterface attribute) (galaxy.containers.docker_swarm.DockerSwarmInterface attribute) container_from_element() (in module galaxy.tools.deps.requirements) container_ids (galaxy.web.proxy.ProxyMapping attribute) container_interface (galaxy.web.proxy.ProxyMapping attribute) 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.tools.deps.container_resolvers.mulled.BuildMulledDockerContainerResolver attribute) (galaxy.tools.deps.container_resolvers.mulled.BuildMulledSingularityContainerResolver attribute) (galaxy.tools.deps.container_resolvers.mulled.CachedMulledDockerContainerResolver attribute) (galaxy.tools.deps.container_resolvers.mulled.CachedMulledSingularityContainerResolver attribute) (galaxy.tools.deps.container_resolvers.mulled.MulledDockerContainerResolver attribute) (galaxy.tools.deps.containers.DockerContainer attribute) (galaxy.tools.deps.containers.SingularityContainer attribute) ContainerCLIError ContainerDescription (class in galaxy.tools.deps.requirements) ContainerFinder (class in galaxy.tools.deps.containers) ContainerImageNotFound ContainerInterface (class in galaxy.containers) ContainerInterfaceConfig (class in galaxy.containers) containerize_command() (galaxy.tools.deps.containers.Container method) (galaxy.tools.deps.containers.DockerContainer method) (galaxy.tools.deps.containers.SingularityContainer method) ContainerManagerMixin (class in galaxy.managers.containers) ContainerNotFound ContainerPort (class in galaxy.containers) ContainerRegistry (class in galaxy.tools.deps.containers) ContainerResolver (class in galaxy.tools.deps.container_resolvers) ContainerRunError containers_config_file (galaxy.containers.ContainerInterface attribute) contains_folder() (tool_shed.utility_containers.utility_container_manager.Folder method) contains_repository_dependency() (tool_shed.utility_containers.utility_container_manager.Folder method) contains_workflow_parameter() (in module galaxy.tools.parameters.basic) 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) contents_count() (galaxy.managers.history_contents.HistoryContentsManager method) contents_iter() (galaxy.model.History method) contents_query() (galaxy.managers.history_contents.HistoryContentsManager method) control_queue_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 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) (galaxy.webapps.tool_shed.security.RBACAgent method) convert_statjob_to_bunches() (galaxy.jobs.runners.pbs.PBSJobRunner method) 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) 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.tools.DefaultToolState method) (galaxy.tools.deps.requirements.ToolRequirement 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_dataset_permissions() (galaxy.security.GalaxyRBACAgent 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 tool_shed.util.hg_util) copy_hda_to_library_folder() (galaxy.web.base.controller.UsesLibraryMixinItems method) copy_item_annotation() (galaxy.model.item_attrs.UsesAnnotations method) copy_ldda() (galaxy.managers.hdas.HDAManager method) copy_library_permissions() (galaxy.security.GalaxyRBACAgent method) copy_list() (in module galaxy.model) copy_review() (galaxy.webapps.tool_shed.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 tool_shed.util.tool_util) copy_sample_files() (in module tool_shed.util.tool_util) copy_tags_from() (galaxy.model.HasTags method) (galaxy.model.StoredWorkflow method) copy_tags_to() (galaxy.model.HistoryDatasetAssociation method) copy_to() (galaxy.model.WorkflowStep method) copy_to_collection() (galaxy.model.DatasetCollectionElement method) copy_value() (galaxy.model.custom_types.JSONType method) CorePlugin (class in galaxy.jobs.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_special_lines() (in module galaxy.datatypes.molecules) (in module galaxy.datatypes.util.generic_util) CountTable (class in galaxy.datatypes.mothur) CoverageWriter (class in galaxy.datatypes.converters.interval_to_coverage) CpuInfoPlugin (class in galaxy.jobs.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.users.UserManager method) (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.DistributedObjectStore method) (galaxy.objectstore.HierarchicalObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.pulsar.PulsarObjectStore method) (galaxy.objectstore.rods.IRODSObjectStore method) (galaxy.objectstore.s3.S3ObjectStore method) (galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController method), [1] (galaxy.webapps.galaxy.api.dataset_collections.DatasetCollectionsController 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.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.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) (galaxy.webapps.tool_shed.api.categories.CategoriesController method), [1] (galaxy.webapps.tool_shed.api.groups.GroupsController method), [1] (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method), [1] (galaxy.webapps.tool_shed.api.users.UsersController method), [1] (tool_shed.managers.groups.GroupManager method) (tool_shed.managers.repositories.RepoManager method) create_and_write_tmp_file() (in module tool_shed.util.xml_util) create_api_key() (galaxy.managers.api_keys.ApiKeyManager method) (galaxy.managers.users.UserManager method) (galaxy.web.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() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) create_changeset_revision() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method), [1] create_collection() (galaxy.tools.actions.OutputCollections method) create_component() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) create_cookie() (in module galaxy.util.biostar) create_dataset() (galaxy.tools.parameters.output_collect.JobContext method) create_dataset_collection() (galaxy.managers.collections.DatasetCollectionManager method) create_element() (in module tool_shed.util.xml_util) create_env_var_dict() (tool_shed.galaxy_install.tool_dependencies.env_manager.EnvManager method) create_extended_metadata() (galaxy.web.base.controller.UsesExtendedMetadataMixin method) create_file() (galaxy.datatypes.dataproviders.external.TempfileDataProvider method) create_form() (galaxy.webapps.galaxy.controllers.forms.Forms method) create_galaxy_docker_image() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) create_group() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) create_hgrc_file() (in module tool_shed.util.hg_util) create_item_slug() (galaxy.web.base.controller.SharableMixin method) create_job() (in module galaxy.tools.actions.upload_common) create_list_filter() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) create_log_file() (galaxy.jobs.runners.godocker.GodockerJobRunner method) create_mako_template_lookup() (galaxy.web.framework.webapp.WebApplication method) create_new_current() (galaxy.webapps.galaxy.controllers.history.HistoryController method) create_new_user() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) create_numeric_filter() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) create_openid() (galaxy.webapps.galaxy.controllers.user.User method) create_or_update_env_shell_file() (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 tool_shed.util.tool_dependency_util) create_or_update_tool_shed_repository() (in module tool_shed.util.repository_util) create_or_update_tool_shed_repository_record() (tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager method) create_or_update_tool_shed_repository_records() (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 galaxy.webapps.tool_shed.model.migrate.check) create_panel_section() (in module galaxy.queue_worker) create_paramfile() (in module galaxy.tools.actions.upload_common) create_private_user_role() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) (galaxy.webapps.tool_shed.security.RBACAgent method) create_quota() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) create_repo_info_dict() (in module tool_shed.util.repository_util) create_report() (galaxy.tools.errors.ErrorReporter method) create_repository() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) (in module tool_shed.util.repository_util) create_repository_admin_role() (in module tool_shed.util.repository_util) create_repository_and_import_archive() (tool_shed.capsule.capsule_manager.ImportRepositoryManager method) create_repository_dependency_objects() (tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) create_repository_dict_for_proprietary_datatypes() (tool_shed.galaxy_install.datatypes.custom_datatype_manager.CustomDatatypeLoader method) create_review() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) create_role() (galaxy.security.GalaxyRBACAgent method) (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) create_section() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) create_string_filter() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) create_subworkflow_invocation_for_step() (galaxy.model.WorkflowInvocation method) create_temporary_tool_dependencies_config() (tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Repository method) create_time (galaxy.webapps.tool_shed.model.APIKeys attribute) (galaxy.webapps.tool_shed.model.Category attribute) (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.GalaxySession attribute) (galaxy.webapps.tool_shed.model.Group attribute) (galaxy.webapps.tool_shed.model.GroupRoleAssociation attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.RepositoryRoleAssociation attribute) (galaxy.webapps.tool_shed.model.Role attribute) (galaxy.webapps.tool_shed.model.User attribute) (galaxy.webapps.tool_shed.model.UserGroupAssociation attribute) (galaxy.webapps.tool_shed.model.UserRoleAssociation attribute) create_tool() (galaxy.tools.ToolBox method) (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) create_tool_dependency_objects() (in module tool_shed.util.tool_dependency_util) create_tool_dependency_with_initialized_env_sh_file() (tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Repository method) create_tool_from_source() (in module galaxy.tools) create_unique_slug() (galaxy.managers.sharable.SharableModelManager method) create_user() (galaxy.web.base.controller.CreatesUsersMixin method) create_visualization() (galaxy.web.base.controller.UsesVisualizationMixin method) CreatedWorkflow (class in galaxy.managers.workflows) CreatesApiKeysMixin (class in galaxy.web.base.controller) CreatesUsersMixin (class in galaxy.web.base.controller) creating_job (galaxy.model.DatasetInstance attribute) creating_job() (galaxy.managers.datasets.DatasetAssociationManager method) csFasta (class in galaxy.datatypes.sequence) css() (in module galaxy.web.framework.helpers) CSV (class in galaxy.datatypes.tabular) cur_filter_pref_name (galaxy.web.framework.helpers.grids.Grid attribute) cur_sort_key_pref_name (galaxy.web.framework.helpers.grids.Grid attribute) current_history_json() (galaxy.webapps.galaxy.controllers.history.HistoryController method) 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) CustomDatatypeLoader (class in tool_shed.galaxy_install.datatypes.custom_datatype_manager) CustomTrack (class in galaxy.datatypes.interval) cut_and_decode() (galaxy.managers.folders.FolderManager method) cut_the_prefix() (galaxy.managers.folders.FolderManager method) CwlPageSource (class in galaxy.tools.parser.cwl) CwlToolSource (class in galaxy.tools.parser.cwl) CycleError

D

daemonize() (galaxy.util.pastescript.serve.ServeCommand method) DaemonizeException Data (class in galaxy.datatypes.data) data_conversion_status() (galaxy.managers.hdas.HDAManager method) data_manager_config_elems_to_xml_file() (tool_shed.galaxy_install.tools.data_manager.DataManagerHandler method) data_manager_configs (galaxy.webapps.galaxy.config_watchers.ConfigWatchers attribute) data_managers_path (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) 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 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) dataset (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.JobExternalOutputMetadata attribute) dataset_access_mapping() (galaxy.security.GalaxyRBACAgent method) dataset_collection_description() (in module galaxy.tools.parser.output_collection_def) dataset_collection_match() (galaxy.tools.parameters.dataset_matcher.DatasetCollectionMatcher method) dataset_collector() (in module galaxy.tools.parameters.output_collect) dataset_collector_descriptions (galaxy.tools.parser.output_objects.ToolOutputCollection attribute) dataset_collector_descriptions_from_elem() (in module galaxy.tools.parser.output_collection_def) dataset_collector_descriptions_from_list() (in module galaxy.tools.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_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.security.GalaxyRBACAgent method) dataset_is_public() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) dataset_is_unrestricted() (galaxy.security.GalaxyRBACAgent method) dataset_make_primary() (galaxy.webapps.galaxy.controllers.root.RootController method) dataset_path_rewrites() (in module galaxy.jobs.datasets) dataset_permission_map_for_access() (galaxy.security.GalaxyRBACAgent method) dataset_states_and_extensions_summary (galaxy.model.DatasetCollection attribute) 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) 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) DatasetCollectionAsContainerManagerMixin (class in galaxy.managers.containers) DatasetCollectionDescription (class in galaxy.tools.parser.output_collection_def) DatasetCollectionElement (class in galaxy.model) DatasetCollectionInstance (class in galaxy.model) DatasetCollectionManager (class in galaxy.managers.collections) DatasetCollectionMatcher (class in galaxy.tools.parameters.dataset_matcher) DatasetCollectionsController (class in galaxy.webapps.galaxy.api.dataset_collections), [1] DatasetCollectionType (class in galaxy.dataset_collections.types) DatasetCollectionTypesRegistry (class in galaxy.dataset_collections.registry) DatasetCollectionWrapper (class in galaxy.tools.wrappers) DatasetCollector (class in galaxy.tools.parameters.output_collect) DatasetColumnarDataProvider (class in galaxy.datatypes.dataproviders.dataset) DatasetDataProvider (class in galaxy.datatypes.dataproviders.dataset) DatasetDeserializer (class in galaxy.managers.datasets) 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) DatasetInstance (class in galaxy.model) DatasetInterface (class in galaxy.webapps.galaxy.controllers.dataset) DatasetListWrapper (class in galaxy.tools.wrappers) DatasetManagePermissionFailedException DatasetManager (class in galaxy.managers.datasets) DatasetMatcher (class in galaxy.tools.parameters.dataset_matcher) DatasetOkValidator (class in galaxy.tools.parameters.validation) DatasetPath (class in galaxy.jobs.datasets) DatasetPathRewriter (class in galaxy.jobs.datasets) DatasetPermissions (class in galaxy.model) DatasetRBACPermission (class in galaxy.managers.rbac_secured) DatasetRBACPermissions (class in galaxy.managers.datasets) datasets_are_public() (galaxy.security.GalaxyRBACAgent method) DatasetsController (class in galaxy.webapps.galaxy.api.datasets), [1] DatasetSerializer (class in galaxy.managers.datasets) DatasetSubprocessDataProvider (class in galaxy.datatypes.dataproviders.dataset) DatasetTagAssociation (class in galaxy.model) DatasetToValidationErrorAssociation (class in galaxy.model) 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.web.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.tools.parser.output_actions) datatypes_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) 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) date_string_re (galaxy.managers.base.ModelFilterParser attribute) DateTimeColumn (class in galaxy.web.framework.helpers.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.tools.parameters.output_collect.JsonCollectedDatasetMatch attribute) DBKeyParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) DCASerializer (class in galaxy.managers.hdcas) DCESerializer (class in galaxy.managers.hdcas) DCSerializer (class in galaxy.managers.hdcas) deactivate (galaxy.tools.deps.conda_util.CondaContext attribute) deactivate_or_uninstall_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) debugging (galaxy.webapps.galaxy.api.metrics.MetricsController attribute), [1] decode() (galaxy.tools.DefaultToolState method) 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.web.security.SecurityHelper method) decode_id() (galaxy.web.base.controller.BaseController method) (galaxy.web.security.SecurityHelper 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) default() (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_build_pulsar_app (galaxy.jobs.runners.pulsar.PulsarEmbeddedJobRunner 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_deserializer() (galaxy.managers.base.ModelDeserializer method) DEFAULT_ENTRY_FN (galaxy.web.base.controller.JSAppLauncher attribute) default_exit_code_file() (galaxy.jobs.runners.JobState static method) default_filter (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid attribute) (galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid 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.user.UserOpenIDGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.LibraryDatasetsSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationListGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.grids.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_interactive (galaxy.util.pastescript.serve.Command attribute) DEFAULT_INVALID_CHAR (galaxy.tools.parameters.sanitize.ToolParameterSanitizer attribute) default_is_multi_byte (galaxy.tools.parser.interface.ToolSource attribute) (galaxy.tools.parser.ToolSource attribute) default_job_file() (galaxy.jobs.runners.JobState static method) default_job_tool_configuration (galaxy.jobs.JobConfiguration attribute) DEFAULT_MAX_OPEN_FILES (galaxy.tools.util.maf_utilities.TempFileHandler attribute) default_name (galaxy.model.History attribute) (galaxy.util.dbkeys.GenomeBuilds attribute) DEFAULT_NWORKERS (galaxy.jobs.JobConfiguration attribute) default_optional (galaxy.tools.parser.interface.InputSource 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_PATH_REWRITER() (in module galaxy.tools.wrappers) default_pbs_server (galaxy.jobs.runners.pbs.PBSJobRunner attribute) default_permissions() (galaxy.managers.users.UserManager method) default_printer() (in module galaxy.tools.util.galaxyops) default_quota (galaxy.quota.NoQuotaAgent attribute) default_registered_quota (galaxy.quota.QuotaAgent attribute) default_serializer() (galaxy.managers.base.ModelSerializer method) (galaxy.managers.configuration.ConfigSerializer 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.dataset.HistoryDatasetAssociationListGrid 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.user.UserOpenIDGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.LibraryDatasetsSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.TracksterSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationListGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.DatatypesGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryDependenciesGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ToolDependenciesGrid attribute) (tool_shed.grids.repository_grids.ToolsGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) DEFAULT_SPECS (galaxy.jobs.runners.BaseJobRunner attribute) DEFAULT_TEMPLATE_COLLECTION_SIZE (galaxy.visualization.plugins.plugin.ServesTemplatesPluginMixin attribute) DEFAULT_TEMPLATE_ENCODING (galaxy.visualization.plugins.plugin.ServesTemplatesPluginMixin 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.util.dbkeys.GenomeBuilds attribute) default_verbosity (galaxy.util.pastescript.serve.Command attribute) (galaxy.util.pastescript.serve.ServeCommand attribute) DEFAULT_VERSION (galaxy.tools.data_manager.manager.DataManager attribute) 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.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) DeferredJob (class in galaxy.model) 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.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.DiskObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.pulsar.PulsarObjectStore method) (galaxy.objectstore.rods.IRODSObjectStore method) (galaxy.objectstore.s3.S3ObjectStore method) (galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController 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.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.history.HistoryController 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_cookie() (in module galaxy.util.biostar) delete_custom_builds() (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] delete_extended_metadata() (galaxy.web.base.controller.UsesExtendedMetadataMixin method) delete_item_annotation() (galaxy.model.item_attrs.UsesAnnotations method) delete_item_tags() (galaxy.managers.tags.TagManager method) delete_operation (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) delete_repository() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) delete_repository_metadata() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) delete_task() (galaxy.jobs.runners.godocker.GodockerJobRunner method) deleted (galaxy.webapps.tool_shed.model.Category attribute) (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.Group attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.Role attribute) (galaxy.webapps.tool_shed.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) DeleteIntermediatesAction (class in galaxy.jobs.actions.post) delimiter (galaxy.datatypes.tabular.BaseCSV attribute) demodulize() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) DependenciesDescription (class in galaxy.tools.deps.dependencies) Dependency (class in galaxy.tools.deps.resolvers) dependency_resolvers (galaxy.tools.deps.NullDependencyManager attribute) dependency_shell_commands() (galaxy.tools.deps.CachedDependencyManager method) (galaxy.tools.deps.DependencyManager method) (galaxy.tools.deps.NullDependencyManager method) dependency_type (galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency attribute) (galaxy.tools.deps.resolvers.NullDependency attribute) (galaxy.tools.deps.resolvers.galaxy_packages.ToolShedDependency attribute) (galaxy.tools.deps.resolvers.tool_shed_packages.ToolShedPackageDependencyResolver attribute) DependencyDisplayer (class in tool_shed.galaxy_install.dependency_display) DependencyException DependencyManager (class in galaxy.tools.deps) DependencyResolver (class in galaxy.tools.deps.resolvers) DependencyResolversView (class in galaxy.tools.deps.views) deprecate() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) deprecated (galaxy.webapps.tool_shed.model.Repository attribute) deprecated_options (galaxy.config.Configuration attribute) deprecated_repositories_i_own_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) DeprecatedMethod DeprecatedRepositoriesIOwnGrid (class in tool_shed.grids.repository_grids) deregister_message_handler() (galaxy.web.stack.ApplicationStack method) (galaxy.web.stack.MessageApplicationStack method) derive_roles_from_access() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) desc() (galaxy.jobs.error_level.StdioErrorLevel static method) description (galaxy.util.pastescript.serve.Command attribute) (galaxy.util.pastescript.serve.ServeCommand attribute) (galaxy.webapps.tool_shed.model.Category attribute) (galaxy.webapps.tool_shed.model.Component attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.Role attribute) descs (galaxy.jobs.error_level.StdioErrorLevel attribute) deserialize() (galaxy.managers.base.ModelDeserializer method) deserialize_annotation() (galaxy.managers.annotatable.AnnotatableDeserializerMixin method) deserialize_basestring() (galaxy.managers.base.ModelDeserializer method) deserialize_bool() (galaxy.managers.base.ModelDeserializer 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_permissions() (galaxy.managers.datasets.DatasetDeserializer 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.tools.parameters.output_collect.JsonCollectedDatasetMatch 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) destroyable() (galaxy.containers.docker_model.DockerNode method) determine_cookie_domain() (in module galaxy.util.biostar) determine_output_format() (in module galaxy.tools.actions) diagnostics() (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] dialect (galaxy.datatypes.tabular.CSV attribute) (galaxy.datatypes.tabular.TSV attribute) dict() (galaxy.jobs.runners.util.Bunch method) (galaxy.util.bunch.Bunch method) dict_collection_visible_keys (galaxy.model.DatasetCollection attribute) (galaxy.model.DatasetCollectionElement attribute) (galaxy.model.FormDefinition attribute) (galaxy.model.Group attribute) (galaxy.model.HasTags attribute) (galaxy.model.History 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.WorkflowInvocationStep attribute) (galaxy.model.WorkflowInvocationStepJobAssociation attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetAssociation attribute) (galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation attribute) (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute) (galaxy.model.WorkflowRequest attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.model.WorkflowRequestInputStepParmeter attribute) (galaxy.model.WorkflowRequestStepState attribute) (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute) (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.tools.Tool attribute) (galaxy.tools.data.TabularToolDataField attribute) (galaxy.tools.data.TabularToolDataTable attribute) (galaxy.tools.deps.container_resolvers.ContainerResolver attribute) (galaxy.tools.deps.resolvers.Dependency attribute) (galaxy.tools.deps.resolvers.DependencyResolver attribute) (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver attribute) (galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency attribute) (galaxy.tools.deps.resolvers.modules.ModuleDependencyResolver attribute) (galaxy.tools.deps.resolvers.unlinked_tool_shed_packages.UnlinkedToolShedPackageDependencyResolver 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.parser.output_objects.ToolOutput attribute) (galaxy.tools.parser.output_objects.ToolOutputCollection attribute) (galaxy.tools.toolbox.ToolSection attribute) (galaxy.tools.toolbox.ToolSectionLabel attribute) (galaxy.tools.toolbox.panel.ToolSection attribute) (galaxy.tools.toolbox.panel.ToolSectionLabel attribute) (galaxy.webapps.tool_shed.model.Category attribute) (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.Group attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.Role attribute) (galaxy.webapps.tool_shed.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.FormDefinition attribute) (galaxy.model.Group attribute) (galaxy.model.GroupQuotaAssociation attribute) (galaxy.model.HasTags attribute) (galaxy.model.History 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.WorkflowInvocationStepJobAssociation attribute) (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute) (galaxy.model.WorkflowRequest attribute) (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.model.tool_shed_install.ToolVersion attribute) (galaxy.webapps.tool_shed.model.Category attribute) (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.Group attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.Role attribute) (galaxy.webapps.tool_shed.model.User attribute) dict_map() (in module galaxy.dataset_collections.structure) 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) different_revision_defines_tip_only_repository_dependency() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) difflib (in module galaxy.util.pastescript.serve) dimension (galaxy.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_hash_id() (in module galaxy.util) disable_commands_in_new_shell() (galaxy.jobs.JobWrapper method) disabled (galaxy.tools.deps.resolvers.DependencyResolver attribute) discard() (galaxy.util.oset.OrderedSet method) discover_files() (in module galaxy.tools.parameters.output_collect) discover_target_directory() (in module galaxy.tools.parameters.output_collect) discover_via (galaxy.tools.parser.output_collection_def.FilePatternDatasetCollectionDescription attribute) (galaxy.tools.parser.output_collection_def.ToolProvidedMetadataDatasetCollection attribute) DiscoveredFile (class in galaxy.tools.parameters.output_collect) disk_nice_size (galaxy.model.History attribute) disk_size (galaxy.model.History attribute) disk_usage() (galaxy.webapps.reports.controllers.system.System method) DiskObjectStore (class in galaxy.objectstore) 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_applications() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) display_as() (galaxy.webapps.galaxy.controllers.root.RootController 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.web.base.controller.SharableMixin method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) display_data() (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.binary.Binary method) (galaxy.datatypes.data.Data method) (galaxy.datatypes.molecules.OBFS method) (galaxy.datatypes.neo4j.Neo4j method) (galaxy.datatypes.sequence.BaseFastq method) (galaxy.datatypes.tabular.TabularData method) (galaxy.datatypes.text.Ipynb method) display_image_in_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) display_info() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) display_name() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetCollectionInstance method) (galaxy.model.DatasetInstance method) (galaxy.model.LibraryDataset method) display_peek() (galaxy.datatypes.binary.Ab1 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.ExcelXls method) (galaxy.datatypes.binary.Fast5Archive method) (galaxy.datatypes.binary.GeminiSQLite method) (galaxy.datatypes.binary.H5 method) (galaxy.datatypes.binary.IdpDB 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.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.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.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) display_ready() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) display_structured() (galaxy.webapps.galaxy.controllers.history.HistoryController method) display_tool() (galaxy.webapps.tool_shed.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) DisplayApplicationTemplateParameter (class in galaxy.datatypes.display_applications.parameters) DisplayByUsernameAndSlugGridOperation (class in galaxy.web.framework.helpers.grids) DisplayDataValueWrapper (class in galaxy.datatypes.display_applications.parameters) DisplayParameterValueWrapper (class in galaxy.datatypes.display_applications.parameters) DistanceMatrix (class in galaxy.datatypes.mothur) DistributedObjectStore (class in galaxy.objectstore) DMND (class in galaxy.datatypes.binary) DNA_COMPLEMENT (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_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.tools.deps.containers) docker_columns() (in module galaxy.containers.docker_decorators) docker_dispatch() (in module galaxy.jobs.stock_rules) docker_host_args() (in module galaxy.tools.deps.dockerfiles) docker_image_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) docker_json() (in module galaxy.containers.docker_decorators) 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.tools.deps.containers) dockerfile_build() (in module galaxy.tools.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.tools.deps.docker_util) DockStoreResolver (class in galaxy.tools.locations.dockstore) docstring_trim() (in module galaxy.util) document_loader (galaxy.tools.cwl.schema.ProcessDefinition attribute) doi() (galaxy.managers.citations.DoiCitation method) DoiCache (class in galaxy.managers.citations) DoiCitation (class in galaxy.managers.citations) DOMAIN (galaxy.model.search.HistoryDatasetView attribute) (galaxy.model.search.HistoryView attribute) (galaxy.model.search.JobView attribute) (galaxy.model.search.PageRevisionView attribute) (galaxy.model.search.PageView attribute) (galaxy.model.search.WorkflowView attribute) DotBracket (class in galaxy.datatypes.sequence) Download (class in tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) download() (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) download_binary() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadBinary method) download_command() (in module galaxy.tools.deps.commands) download_dataset_collection() (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method), [1] download_field_file() (galaxy.webapps.galaxy.api.tool_data.ToolData method), [1] download_to_file() (in module galaxy.util) downloadable (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) downloadable_revisions (galaxy.webapps.tool_shed.model.Repository attribute) DownloadBinary (class in tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) DownloadByUrl (class in tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) DownloadFile (class in 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) DRMAAJobRunner (class in galaxy.jobs.runners.drmaa) DrmaaSessionFactory (class in galaxy.jobs.runners.util.drmaa) dump() (galaxy.util.aliaspickler.AliasPickleModule method) (galaxy.util.heartbeat.Heartbeat method) dump_signal_handler() (galaxy.util.heartbeat.Heartbeat method) dumps() (galaxy.util.aliaspickler.AliasPickleModule method) 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.tools.parser.output_objects.ToolOutputCollection attribute) dynamic_tool_confs() (galaxy.webapps.galaxy.api.configuration.ConfigurationController method), [1] DynamicDisplayApplicationBuilder (class in galaxy.datatypes.display_applications.application) DynamicOptions (class in galaxy.tools.parameters.dynamic_options)

E

echo() (galaxy.webapps.galaxy.controllers.root.RootController method) echo_json() (galaxy.webapps.galaxy.controllers.root.RootController method) edam_data (galaxy.datatypes.assembly.Amos attribute) (galaxy.datatypes.assembly.Sequences attribute) (galaxy.datatypes.binary.Ab1 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.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.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.msa.Hmmer attribute) (galaxy.datatypes.msa.Stockholm_1_0 attribute) (galaxy.datatypes.proteomics.MascotDat attribute) (galaxy.datatypes.proteomics.Mgf 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) 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.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.DMND 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.NetCDF 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.Wiggle 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.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.FastaGz attribute) (galaxy.datatypes.sequence.Fastq attribute) (galaxy.datatypes.sequence.FastqBz2 attribute) (galaxy.datatypes.sequence.FastqGz attribute) (galaxy.datatypes.sequence.FastqIllumina attribute) (galaxy.datatypes.sequence.FastqIlluminaBz2 attribute) (galaxy.datatypes.sequence.FastqIlluminaGz attribute) (galaxy.datatypes.sequence.FastqSanger attribute) (galaxy.datatypes.sequence.FastqSangerBz2 attribute) (galaxy.datatypes.sequence.FastqSangerGz attribute) (galaxy.datatypes.sequence.FastqSolexa attribute) (galaxy.datatypes.sequence.FastqSolexaBz2 attribute) (galaxy.datatypes.sequence.FastqSolexaGz 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) 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() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) edit_category_entry() (tool_shed.repository_registry.Registry method) edit_component() (galaxy.webapps.tool_shed.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() (galaxy.webapps.galaxy.controllers.user.User method) (galaxy.webapps.tool_shed.controllers.user.User method) edit_quota() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) edit_review() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) edit_username() (galaxy.webapps.tool_shed.controllers.user.User method) editable_keys (galaxy.model.HistoryDatasetCollectionAssociation attribute) (galaxy.model.LibraryDatasetCollectionAssociation attribute) editor() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) effective_collection_type() (galaxy.dataset_collections.type_description.CollectionTypeDescription method) effective_collection_type_description() (galaxy.dataset_collections.type_description.CollectionTypeDescription method) effective_output_name (galaxy.tools.parser.output_objects.ToolOutputCollectionPart attribute) (galaxy.tools.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) elem() (galaxy.tools.parser.interface.InputSource method) (galaxy.tools.parser.xml.XmlInputSource method) element_as_dict() (galaxy.datatypes.dataproviders.hierarchy.XMLDataProvider method) element_identifier (galaxy.tools.wrappers.DatasetCollectionWrapper attribute) (galaxy.tools.wrappers.DatasetFilenameWrapper attribute) element_identifiers (galaxy.tools.parameters.output_collect.JsonCollectedDatasetMatch attribute) element_identifiers_for_outputs() (galaxy.dataset_collections.structure.Tree method) element_is_set() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataCollection method) element_object (galaxy.model.DatasetCollectionElement attribute) element_type (galaxy.model.DatasetCollectionElement attribute) ElementIdentifierMapper (class in galaxy.tools.wrappers) ELEMENTS_UNINITIALIZED (galaxy.managers.collections.DatasetCollectionManager attribute) email (galaxy.webapps.tool_shed.model.User attribute) email_alerts (galaxy.webapps.tool_shed.model.Repository attribute) email_alerts_repository_grid (galaxy.webapps.tool_shed.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) empty (galaxy.model.History attribute) empty() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.objectstore.pulsar.PulsarObjectStore method) (galaxy.objectstore.rods.IRODSObjectStore method) (galaxy.objectstore.s3.S3ObjectStore method) EmptyTextfieldValidator (class in galaxy.tools.parameters.validation) encode() (galaxy.datatypes.dataproviders.chunk.Base64ChunkDataProvider method) (galaxy.datatypes.dataproviders.chunk.ChunkDataProvider method) (galaxy.tools.DefaultToolState method) encode_all_ids() (galaxy.web.base.controller.BaseController method) (galaxy.web.security.SecurityHelper method) encode_dataset_user() (in module galaxy.datatypes.display_applications.util) encode_dict_ids() (galaxy.web.security.SecurityHelper method) encode_guid() (galaxy.web.security.SecurityHelper method)

encode_id() (galaxy.web.security.SecurityHelper 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) end (galaxy.tools.util.maf_utilities.SplicedAlignment attribute) engine (galaxy.model.Dataset attribute) English (class in galaxy.util.inflection) enqueue_output() (tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method) ensure_brew_on_path() (in module galaxy.tools.deps.brew_exts) ensure_conda_build_installed_if_needed() (galaxy.tools.deps.conda_util.CondaContext method) ensure_cwltool_available() (in module galaxy.tools.cwl.cwltool_deps) ensure_installed() (in module galaxy.tools.deps.installable) ensure_port_cleanup() (in module galaxy.util.pastescript.serve) ensure_tempdir() (galaxy.config.Configuration method) ensure_tool_conf_item() (in module galaxy.tools.toolbox.parser) env_path() (galaxy.tools.deps.conda_util.CondaContext method) env_to_statement() (in module galaxy.jobs.runners.util.env) EnvAction (class in galaxy.tools.deps.brew_exts) EnvFileBuilder (class in tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder) environment_commands() (tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method) environment_dict() (tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method) EnvManager (class in tool_shed.galaxy_install.tool_dependencies.env_manager) EnvPlugin (class in galaxy.jobs.metrics.instrumenters.env) envs_path (galaxy.tools.deps.conda_util.CondaContext attribute) eof_function() (galaxy.datatypes.genetics.DataIn method) Eps (class in galaxy.datatypes.images) eq_datatype() (galaxy.managers.datasets.DatasetAssociationFilterParser method) equals() (galaxy.managers.citations.BaseCitation 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.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.ToolMetaParameterException attribute) (galaxy.exceptions.ToolMissingException attribute) (galaxy.exceptions.UnknownContentsType attribute) Error (class in galaxy.webapps.galaxy.controllers.error) error() (galaxy.tools.lint.LintContext method) (galaxy.web.framework.middleware.remoteuser.RemoteUser method) (galaxy.webapps.galaxy.api.jobs.JobController method), [1] (galaxy.webapps.tool_shed.framework.middleware.remoteuser.RemoteUser method) (in module galaxy.web) (in module galaxy.web.framework.decorators) error_if_anonymous() (galaxy.managers.users.UserManager method) error_if_uploading() (galaxy.managers.hdas.HDAManager method) error_on_exit_code() (in module galaxy.tools.parser.util) 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) ErrorReporter (class in galaxy.tools.errors) 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) Eset (class in galaxy.datatypes.genetics) estimate_file_lines() (galaxy.datatypes.data.Text method) evaluate_template() (in module tool_shed.util.basic_util) Event (class in galaxy.model) exact (galaxy.tools.deps.resolvers.Dependency attribute) (galaxy.tools.deps.resolvers.NullDependency attribute) (galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency attribute) (galaxy.tools.deps.resolvers.resolver_mixins.HomebrewDependency attribute) ExcelXls (class in galaxy.datatypes.binary) exception_handler() (galaxy.web.framework.middleware.error.ErrorMiddleware method) exec_after_process() (galaxy.tools.DataManagerTool method) (galaxy.tools.SetMetadataTool method) (galaxy.tools.Tool method) exec_before_job() (galaxy.tools.DataSourceTool method) (galaxy.tools.OutputParameterJSONTool method) (galaxy.tools.Tool method) exec_clean() (galaxy.tools.deps.conda_util.CondaContext method) exec_command() (galaxy.tools.deps.conda_util.CondaContext method) exec_create() (galaxy.tools.deps.conda_util.CondaContext method) exec_install() (galaxy.tools.deps.conda_util.CondaContext method) exec_remove() (galaxy.tools.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.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.jobs.runners.util.retry.RetryActionExecutor 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.UploadToolAction method) (galaxy.tools.verify.test_data.GitDataResolver 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.tools.deps.brew_exts) (in module galaxy.tools.deps.commands) (in module galaxy.tools.execute) 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_step() (tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager.StepManager method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertDirectoryExecutable method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertDirectoryExists method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertFileExecutable method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertFileExists method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.Autoconf method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.ChangeDirectory method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.Chmod method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadBinary method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadByUrl method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadFile method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MakeDirectory method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MakeInstall method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MoveDirectoryFiles method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MoveFile method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.RecipeStep method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.RegexReplace method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetEnvironment method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetEnvironmentForInstall method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupPerlEnvironment method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupPythonEnvironment method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupREnvironment method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupRubyEnvironment method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupVirtualEnv method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.ShellCommand method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.TemplateCommand method) execute_via_app() (galaxy.tools.actions.metadata.SetMetadataToolAction method) ExecutionTimer (class in galaxy.util) exists() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.HierarchicalObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.objectstore.pulsar.PulsarObjectStore method) (galaxy.objectstore.rods.IRODSObjectStore method) (galaxy.objectstore.s3.S3ObjectStore method) (galaxy.tools.data.ToolDataPathFiles method) (galaxy.tools.verify.test_data.FileDataResolver method) (galaxy.tools.verify.test_data.GitDataResolver method) 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) expiration_time (galaxy.webapps.tool_shed.model.PasswordResetToken attribute) ExplicitContainerResolver (class in galaxy.tools.deps.container_resolvers.explicit) export() (galaxy.webapps.tool_shed.api.repository_revisions.RepositoryRevisionsController method), [1] (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) export_archive() (galaxy.webapps.galaxy.controllers.history.HistoryController method) export_list() (galaxy.tools.deps.conda_util.CondaContext method) export_name (galaxy.model.JobExportHistoryArchive attribute) export_repository() (tool_shed.capsule.capsule_manager.ExportRepositoryManager method) export_to_file() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) export_to_myexp() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) export_via_api() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) exported_workflows() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method), [1] ExportedRepositoryRegistry (class in tool_shed.capsule.capsule_manager) ExportHistoryTool (class in galaxy.tools) ExportHistoryToolAction (class in galaxy.tools.actions.history_imp_exp) ExportRepositoryManager (class in tool_shed.capsule.capsule_manager) ExportsHistoryMixin (class in galaxy.web.base.controller) expose() (in module galaxy.web) (in module galaxy.web.framework.decorators) (in module galaxy.webapps.reports) (in module galaxy.webapps.tool_shed) 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_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) ExpressionContext (class in galaxy.util.expressions) ExpressionValidator (class in galaxy.tools.parameters.validation) expunge_all() (galaxy.managers.context.ProvidesAppContext method) ext (galaxy.model.DatasetInstance attribute) (galaxy.tools.parameters.output_collect.JsonCollectedDatasetMatch attribute) extend() (galaxy.model.custom_types.MutationList method) extend_data_with() (galaxy.tools.data.TabularToolDataTable method) extend_validation_errors() (galaxy.model.DatasetInstance method) extended_brew_info() (in module galaxy.tools.deps.brew_exts) ExtendedMetadata (class in galaxy.model) ExtendedMetadataIndex (class in galaxy.model) external (galaxy.webapps.tool_shed.model.User attribute) external_metadata_set_successfully() (galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper method) (galaxy.model.metadata.JobExternalOutputMetadataWrapper method) external_runjob() (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) extra_files() (galaxy.managers.datasets.DatasetAssociationManager method) extra_files_path (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance attribute) extra_preferences (galaxy.model.User attribute) extract() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.CompressedFile method) extract_capsule_files() (tool_shed.capsule.capsule_manager.ImportRepositoryManager method) extract_components_from_tuple() (in module tool_shed.util.repository_util) 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)

F

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.kubernetes.KubernetesJobRunner method) (galaxy.jobs.runners.pbs.PBSJobRunner method) failed() (galaxy.tools.lint.LintContext method) FailedTest (class in tool_shed.utility_containers) FAILURE (galaxy.web.framework.openid_manager.OpenIDManager attribute) failure() (in module galaxy.jobs.runners.state_handlers.resubmit) FakeConsumer (class in galaxy.web.framework.openid_manager) Fast5Archive (class in galaxy.datatypes.binary) Fast5ArchiveBz2 (class in galaxy.datatypes.binary) Fast5ArchiveGz (class in galaxy.datatypes.binary) Fasta (class in galaxy.datatypes.sequence) FastaDataProvider (class in galaxy.datatypes.dataproviders.dataset) FastaGz (class in galaxy.datatypes.sequence) Fastq (class in galaxy.datatypes.sequence) FastqBz2 (class in galaxy.datatypes.sequence) FastqCSSanger (class in galaxy.datatypes.sequence) FastqCSSangerBz2 (class in galaxy.datatypes.sequence) FastqCSSangerGz (class in galaxy.datatypes.sequence) FastqGz (class in galaxy.datatypes.sequence) FastqIllumina (class in galaxy.datatypes.sequence) FastqIlluminaBz2 (class in galaxy.datatypes.sequence) FastqIlluminaGz (class in galaxy.datatypes.sequence) FastqSanger (class in galaxy.datatypes.sequence) FastqSangerBz2 (class in galaxy.datatypes.sequence) FastqSangerGz (class in galaxy.datatypes.sequence) FastqSolexa (class in galaxy.datatypes.sequence) FastqSolexaBz2 (class in galaxy.datatypes.sequence) FastqSolexaGz (class in galaxy.datatypes.sequence) FATAL (galaxy.jobs.error_level.StdioErrorLevel attribute) FATAL_OOM (galaxy.jobs.error_level.StdioErrorLevel attribute) FeatureLocationIndex (class in galaxy.datatypes.tabular) FeatureLocationIndexDataProvider (class in galaxy.visualization.data_providers.genome) FeatureXML (class in galaxy.datatypes.proteomics) fetch_requests() (galaxy.web.proxy.JsonFileProxyIpc method) (galaxy.web.proxy.ProxyIpc method) (galaxy.web.proxy.SqliteProxyIpc method) field (in module galaxy.forms.forms) 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.web.form_builder.AddressField static method) FieldStorage (class in galaxy.web.framework.base) file_append() (tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder.EnvFileBuilder method) file_ext (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.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.CRAM attribute) (galaxy.datatypes.binary.Cel attribute) (galaxy.datatypes.binary.CompressedArchive attribute) (galaxy.datatypes.binary.CompressedZipArchive attribute) (galaxy.datatypes.binary.Cool attribute) (galaxy.datatypes.binary.DMND attribute) (galaxy.datatypes.binary.ExcelXls attribute) (galaxy.datatypes.binary.Fast5Archive attribute) (galaxy.datatypes.binary.Fast5ArchiveBz2 attribute) (galaxy.datatypes.binary.Fast5ArchiveGz attribute) (galaxy.datatypes.binary.GeminiSQLite attribute) (galaxy.datatypes.binary.GenericAsn1Binary attribute) (galaxy.datatypes.binary.H5 attribute) (galaxy.datatypes.binary.ICM attribute) (galaxy.datatypes.binary.Idat attribute) (galaxy.datatypes.binary.IdpDB attribute) (galaxy.datatypes.binary.MzSQlite attribute) (galaxy.datatypes.binary.NetCDF 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.PostgresqlArchive attribute) (galaxy.datatypes.binary.RData attribute) (galaxy.datatypes.binary.SQlite attribute) (galaxy.datatypes.binary.Scf attribute) (galaxy.datatypes.binary.SearchGuiArchive attribute) (galaxy.datatypes.binary.Sff attribute) (galaxy.datatypes.binary.Sra attribute) (galaxy.datatypes.binary.TwoBit attribute) (galaxy.datatypes.binary.Xlsx attribute) (galaxy.datatypes.blast.BlastDomainDb attribute) (galaxy.datatypes.blast.BlastNucDb attribute) (galaxy.datatypes.blast.BlastProtDb attribute) (galaxy.datatypes.blast.BlastXml 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.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.ScIdx attribute) (galaxy.datatypes.interval.Wiggle 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.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.proteomics.Analyze75 attribute) (galaxy.datatypes.proteomics.ConsensusXML attribute) (galaxy.datatypes.proteomics.FeatureXML attribute) (galaxy.datatypes.proteomics.IdXML attribute) (galaxy.datatypes.proteomics.ImzML attribute) (galaxy.datatypes.proteomics.MascotDat 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.MzXML attribute) (galaxy.datatypes.proteomics.PepXml attribute) (galaxy.datatypes.proteomics.PepXmlReport attribute) (galaxy.datatypes.proteomics.ProtXML attribute) (galaxy.datatypes.proteomics.ProtXmlReport 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.UniProtXML attribute) (galaxy.datatypes.proteomics.Wiff attribute) (galaxy.datatypes.proteomics.XHunterAslFormat 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.FastaGz attribute) (galaxy.datatypes.sequence.Fastq attribute) (galaxy.datatypes.sequence.FastqBz2 attribute) (galaxy.datatypes.sequence.FastqCSSanger attribute) (galaxy.datatypes.sequence.FastqCSSangerBz2 attribute) (galaxy.datatypes.sequence.FastqCSSangerGz attribute) (galaxy.datatypes.sequence.FastqGz attribute) (galaxy.datatypes.sequence.FastqIllumina attribute) (galaxy.datatypes.sequence.FastqIlluminaBz2 attribute) (galaxy.datatypes.sequence.FastqIlluminaGz attribute) (galaxy.datatypes.sequence.FastqSanger attribute) (galaxy.datatypes.sequence.FastqSangerBz2 attribute) (galaxy.datatypes.sequence.FastqSangerGz attribute) (galaxy.datatypes.sequence.FastqSolexa attribute) (galaxy.datatypes.sequence.FastqSolexaBz2 attribute) (galaxy.datatypes.sequence.FastqSolexaGz 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.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.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.Html attribute) (galaxy.datatypes.text.IQTree attribute) (galaxy.datatypes.text.Ipynb attribute) (galaxy.datatypes.text.Json attribute) (galaxy.datatypes.text.Obo 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)

file_iter() (in module galaxy.util) file_name (galaxy.datatypes.metadata.MetadataTempFile attribute) (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance attribute) (galaxy.model.MetadataFile attribute) (galaxy.model.metadata.MetadataTempFile attribute) file_path (galaxy.model.Dataset attribute) file_reader() (in module galaxy.util) file_ready() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.objectstore.pulsar.PulsarObjectStore method) (galaxy.objectstore.s3.S3ObjectStore method) file_states (galaxy.webapps.tool_shed.model.Repository attribute) FileDataResolver (class in galaxy.tools.verify.test_data) FileLock (class in galaxy.util.filelock) FileLockException FileParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) FilePatternDatasetCollectionDescription (class in galaxy.tools.parser.output_collection_def) files_contains() (in module galaxy.tools.verify) files_diff() (in module galaxy.tools.verify) files_re_match() (in module galaxy.tools.verify) files_re_match_multiline() (in module galaxy.tools.verify) FileToolParameter (class in galaxy.tools.parameters.basic) fill_region_alignment() (in module galaxy.tools.util.maf_utilities) fill_template() (galaxy.web.framework.webapp.GalaxyWebTransaction method) (in module galaxy.util.template) fill_template_mako() (galaxy.web.framework.webapp.GalaxyWebTransaction method) fill_template_string() (galaxy.web.framework.webapp.GalaxyWebTransaction method) 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.tools.parameters.dataset_matcher.DatasetMatcher 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.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) (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() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadBinary method) filter_and_persist_proprietary_tool_panel_configs() (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_has_partial_tag() (galaxy.managers.taggable.TaggableFilterMixin method) filter_has_tag() (galaxy.managers.taggable.TaggableFilterMixin method) filter_only_if_compiling_contained_td() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) filter_options() (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.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.parser.output_actions.BooleanFilter method) (galaxy.tools.parser.output_actions.ColumnReplaceFilter method) (galaxy.tools.parser.output_actions.ColumnStripFilter method) (galaxy.tools.parser.output_actions.InsertColumnToolOutputActionOptionFilter method) (galaxy.tools.parser.output_actions.MetadataValueFilter method) (galaxy.tools.parser.output_actions.MultipleSplitterFilter method) (galaxy.tools.parser.output_actions.ParamValueToolOutputActionOptionFilter method) (galaxy.tools.parser.output_actions.StringFunctionFilter method) (galaxy.tools.parser.output_actions.ToolOutputActionOptionFilter method) filter_output() (in module galaxy.tools.actions) filter_owned() (galaxy.managers.secured.OwnableManagerMixin method) filter_type (in module galaxy.tools.parser.output_actions) FilterableMixin (class in galaxy.visualization.data_providers.genome) FilteredDataProvider (class in galaxy.datatypes.dataproviders.base) FilteredLineDataProvider (class in galaxy.datatypes.dataproviders.line) 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() (galaxy.webapps.tool_shed.search.repo_search.RepoWeighting method) finalize() (galaxy.model.DatasetCollection method) finalize_config() (galaxy.web.framework.base.WebApplication method) find_best_container_description() (galaxy.tools.deps.containers.ContainerFinder method) (galaxy.tools.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.tools.deps.containers.ContainerFinder method) (galaxy.tools.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.tools.deps.DependencyManager method) (galaxy.tools.deps.NullDependencyManager method) find_fieldstorage() (galaxy.tools.Tool method) find_files() (galaxy.tools.parameters.output_collect.JobContext method) find_implicit_input_collection() (galaxy.model.HistoryDatasetCollectionAssociation method) find_output_def() (galaxy.tools.Tool method) find_path() (in module galaxy.config) find_possible_tools_from_path() (in module galaxy.tools.loader_directory) find_root() (in module galaxy.config) find_section_id() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) find_tools() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) find_tools_in_tool_shed() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) find_workflows() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) find_workflows_in_tool_shed() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) finish() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.workflow.render.WorkflowCanvas method) finish_job() (galaxy.jobs.runners.AsynchronousJobRunner method) finished (galaxy.model.Job attribute) first_dataset_instance() (galaxy.model.DatasetCollectionElement method) fitness_and_quality_parsed() (in module mimeparse) FLAGS_W_ARGS (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider attribute) FLAGS_WO_ARGS (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider attribute) 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) flush() (galaxy.tools.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.TempFileHandler method) (galaxy.util.pastescript.serve.LazyWriter method) fn_filter_parsers (galaxy.managers.base.ModelFilterParser attribute) Folder (class in tool_shed.utility_containers.utility_container_manager) folder_is_public() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) folder_is_unrestricted() (galaxy.security.GalaxyRBACAgent method) FolderContentsController (class in galaxy.webapps.galaxy.api.folder_contents), [1] FolderManager (class in galaxy.managers.folders) FoldersController (class in galaxy.webapps.galaxy.api.folders), [1] for_collection_type() (galaxy.dataset_collections.type_description.CollectionTypeDescriptionFactory method) for_collections() (galaxy.dataset_collections.matching.MatchingCollections static method) for_dataset_collection() (galaxy.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.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) foreignKey() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) format (galaxy.web.framework.middleware.translogger.TransLogger attribute) format() (galaxy.jobs.metrics.formatting.JobMetricFormatter method) (galaxy.jobs.metrics.JobMetrics method) format_bool() (in module galaxy.webapps.galaxy.controllers.page) format_traceback() (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.jobs.metrics.instrumenters.collectl.CollectlPlugin attribute) (galaxy.jobs.metrics.instrumenters.InstrumentPlugin attribute) (galaxy.jobs.metrics.instrumenters.core.CorePlugin attribute) (galaxy.jobs.metrics.instrumenters.cpuinfo.CpuInfoPlugin attribute) (galaxy.jobs.metrics.instrumenters.env.EnvPlugin attribute) (galaxy.jobs.metrics.instrumenters.meminfo.MemInfoPlugin attribute) (galaxy.jobs.metrics.instrumenters.uname.UnamePlugin attribute) FormatToolOutputAction (class in galaxy.tools.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_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) Frequency (class in galaxy.datatypes.mothur) from_args() (galaxy.tools.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_constraint_string_list() (galaxy.containers.docker_model.DockerServiceConstraints class method) from_dict() (galaxy.tools.deps.dependencies.DependenciesDescription static method) (galaxy.tools.deps.requirements.ContainerDescription static method) (galaxy.tools.deps.requirements.RequirementSpecification static method) (galaxy.tools.deps.requirements.ToolRequirement static method) (galaxy.tools.deps.resolvers.RequirementMapping 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) (tool_shed.util.workflow_util.RepoToolModule class method) (tool_shed.util.workflow_util.RepoWorkflowModuleFactory 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.tools.data.ToolDataTable class method) (galaxy.tools.parser.output_actions.ToolOutputAction class method) (galaxy.tools.parser.output_actions.ToolOutputActionConditionalWhen class method) (galaxy.tools.parser.output_actions.ToolOutputActionOption class method) (galaxy.tools.parser.output_actions.ToolOutputActionOptionFilter class method) from_element() (galaxy.tools.parameters.dynamic_options.Filter class method) (galaxy.tools.parameters.input_translation.ToolInputTranslator class method) (galaxy.tools.parameters.sanitize.ToolParameterSanitizer class method) (galaxy.tools.parameters.validation.DatasetEmptyValidator class method) (galaxy.tools.parameters.validation.DatasetExtraFilesPathEmptyValidator class method) (galaxy.tools.parameters.validation.DatasetOkValidator class method) (galaxy.tools.parameters.validation.EmptyTextfieldValidator class method) (galaxy.tools.parameters.validation.ExpressionValidator class method) (galaxy.tools.parameters.validation.InRangeValidator class method) (galaxy.tools.parameters.validation.LengthValidator class method) (galaxy.tools.parameters.validation.MetadataInDataTableColumnValidator class method) (galaxy.tools.parameters.validation.MetadataInFileColumnValidator 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) 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.jobs.metrics.JobInstrumenter static method) (galaxy.openid.providers.OpenIDProvider class method) (galaxy.openid.providers.OpenIDProviders class method) from_id() (galaxy.containers.Container method) (galaxy.containers.docker_model.DockerContainer 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.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.tools.deps.requirements.ToolRequirements static method) from_parameter() (galaxy.tools.parameters.history_query.HistoryQuery static method) from_str() (galaxy.containers.docker_model.DockerServiceConstraint 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) (tool_shed.util.workflow_util.RepoToolModule class method) (tool_shed.util.workflow_util.RepoWorkflowModuleFactory method) FromDataTableOutputActionOption (class in galaxy.tools.parser.output_actions) FromFileToolOutputActionOption (class in galaxy.tools.parser.output_actions) FromParamToolOutputActionOption (class in galaxy.tools.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)

G

galaxy (galaxy.web.framework.middleware.batch.BatchMiddleware attribute) (module) galaxy.actions (module) galaxy.actions.admin (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.config (module) galaxy.containers (module) galaxy.containers.docker (module) galaxy.containers.docker_decorators (module) galaxy.containers.docker_model (module) galaxy.containers.docker_swarm (module) galaxy.containers.docker_swarm_manager (module) galaxy.dataset_collections (module) galaxy.dataset_collections.builder (module) galaxy.dataset_collections.matching (module) galaxy.dataset_collections.registry (module) galaxy.dataset_collections.structure (module) galaxy.dataset_collections.subcollections (module) galaxy.dataset_collections.type_description (module) galaxy.dataset_collections.types (module) galaxy.dataset_collections.types.list (module) galaxy.dataset_collections.types.paired (module) galaxy.datatypes (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.bedgraph_to_array_tree_converter (module) galaxy.datatypes.converters.bgzip (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_coverage (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.sam_to_bam (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_array_tree_converter (module) galaxy.datatypes.converters.wiggle_to_simple_converter (module) galaxy.datatypes.coverage (module) galaxy.datatypes.data (module) galaxy.datatypes.dataproviders (module) galaxy.datatypes.dataproviders.base (module) galaxy.datatypes.dataproviders.chunk (module) galaxy.datatypes.dataproviders.column (module) galaxy.datatypes.dataproviders.dataset (module) galaxy.datatypes.dataproviders.decorators (module) galaxy.datatypes.dataproviders.exceptions (module) galaxy.datatypes.dataproviders.external (module) galaxy.datatypes.dataproviders.hierarchy (module) galaxy.datatypes.dataproviders.line (module) galaxy.datatypes.display_applications (module) galaxy.datatypes.display_applications.application (module) galaxy.datatypes.display_applications.parameters (module) galaxy.datatypes.display_applications.util (module) galaxy.datatypes.genetics (module) galaxy.datatypes.graph (module) galaxy.datatypes.images (module) galaxy.datatypes.interval (module) galaxy.datatypes.metadata (module) galaxy.datatypes.molecules (module) galaxy.datatypes.mothur (module) galaxy.datatypes.msa (module) galaxy.datatypes.neo4j (module) galaxy.datatypes.ngsindex (module) galaxy.datatypes.proteomics (module) galaxy.datatypes.qualityscore (module) galaxy.datatypes.registry (module) galaxy.datatypes.sequence (module) galaxy.datatypes.sniff (module) galaxy.datatypes.tabular (module) galaxy.datatypes.text (module) galaxy.datatypes.tracks (module) galaxy.datatypes.triples (module) galaxy.datatypes.util (module) galaxy.datatypes.util.generic_util (module) galaxy.datatypes.util.gff_util (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.jobs (module) galaxy.jobs.actions (module) galaxy.jobs.actions.post (module) galaxy.jobs.command_factory (module) galaxy.jobs.datasets (module) galaxy.jobs.dynamic_tool_destination (module) galaxy.jobs.error_level (module) galaxy.jobs.handler (module) galaxy.jobs.manager (module) galaxy.jobs.mapper (module) galaxy.jobs.metrics (module) galaxy.jobs.metrics.collectl (module) galaxy.jobs.metrics.collectl.cli (module) galaxy.jobs.metrics.collectl.processes (module) galaxy.jobs.metrics.collectl.stats (module) galaxy.jobs.metrics.collectl.subsystems (module) galaxy.jobs.metrics.formatting (module) galaxy.jobs.metrics.instrumenters (module) galaxy.jobs.metrics.instrumenters.collectl (module) galaxy.jobs.metrics.instrumenters.core (module) galaxy.jobs.metrics.instrumenters.cpuinfo (module) galaxy.jobs.metrics.instrumenters.env (module) galaxy.jobs.metrics.instrumenters.meminfo (module) galaxy.jobs.metrics.instrumenters.uname (module) galaxy.jobs.output_checker (module) galaxy.jobs.rule_helper (module) galaxy.jobs.runners (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.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.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.drmaa (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.retry (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.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.folders (module) galaxy.managers.hdas (module) galaxy.managers.hdcas (module) galaxy.managers.histories (module) galaxy.managers.history_contents (module) galaxy.managers.lddas (module) galaxy.managers.libraries (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.tags (module) galaxy.managers.users (module) galaxy.managers.visualizations (module) galaxy.managers.workflows (module) galaxy.model (module) galaxy.model.base (module) galaxy.model.custom_types (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.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.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.util (module) galaxy.objectstore (module) galaxy.objectstore.azure_blob (module) galaxy.objectstore.pulsar (module) galaxy.objectstore.rods (module) galaxy.objectstore.s3 (module) galaxy.objectstore.s3_multipart_upload (module) galaxy.openid (module) galaxy.openid.providers (module) galaxy.queue_worker (module) galaxy.queues (module) galaxy.quota (module) galaxy.security (module) galaxy.security.passwords (module) galaxy.security.validate_user_input (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.cwl (module) galaxy.tools.cwl.cwltool_deps (module) galaxy.tools.cwl.parser (module) galaxy.tools.cwl.representation (module) galaxy.tools.cwl.runtime_actions (module) galaxy.tools.cwl.schema (module) galaxy.tools.data (module) galaxy.tools.data_manager (module) galaxy.tools.data_manager.manager (module) galaxy.tools.deps (module) galaxy.tools.deps.brew_exts (module) galaxy.tools.deps.brew_util (module) galaxy.tools.deps.commands (module) galaxy.tools.deps.conda_compat (module) galaxy.tools.deps.conda_util (module) galaxy.tools.deps.container_resolvers (module) galaxy.tools.deps.container_resolvers.explicit (module) galaxy.tools.deps.container_resolvers.mulled (module) galaxy.tools.deps.containers (module) galaxy.tools.deps.dependencies (module) galaxy.tools.deps.docker_util (module) galaxy.tools.deps.dockerfiles (module) galaxy.tools.deps.installable (module) galaxy.tools.deps.mulled (module) galaxy.tools.deps.mulled.mulled_build (module) galaxy.tools.deps.mulled.mulled_build_channel (module) galaxy.tools.deps.mulled.mulled_build_files (module) galaxy.tools.deps.mulled.mulled_build_tool (module) galaxy.tools.deps.mulled.mulled_search (module) galaxy.tools.deps.mulled.util (module) galaxy.tools.deps.requirements (module) galaxy.tools.deps.resolvers (module) galaxy.tools.deps.resolvers.brewed_tool_shed_packages (module) galaxy.tools.deps.resolvers.conda (module) galaxy.tools.deps.resolvers.galaxy_packages (module) galaxy.tools.deps.resolvers.homebrew (module) galaxy.tools.deps.resolvers.modules (module) galaxy.tools.deps.resolvers.resolver_mixins (module) galaxy.tools.deps.resolvers.tool_shed_packages (module) galaxy.tools.deps.resolvers.unlinked_tool_shed_packages (module) galaxy.tools.deps.views (module) galaxy.tools.errors (module) galaxy.tools.evaluation (module) galaxy.tools.exception_handling (module) galaxy.tools.execute (module) galaxy.tools.fetcher (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.lint (module) galaxy.tools.lint_util (module) galaxy.tools.linters (module) galaxy.tools.linters.citations (module) galaxy.tools.linters.command (module) galaxy.tools.linters.general (module) galaxy.tools.linters.help (module) galaxy.tools.linters.inputs (module) galaxy.tools.linters.outputs (module) galaxy.tools.linters.stdio (module) galaxy.tools.linters.tests (module) galaxy.tools.linters.xml_order (module) galaxy.tools.loader (module) galaxy.tools.loader_directory (module) galaxy.tools.locations (module) galaxy.tools.locations.dockstore (module) galaxy.tools.locations.file (module) galaxy.tools.locations.http (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.output_collect (module) galaxy.tools.parameters.sanitize (module) galaxy.tools.parameters.validation (module) galaxy.tools.parameters.wrapped (module) galaxy.tools.parameters.wrapped_json (module) galaxy.tools.parser (module) galaxy.tools.parser.cwl (module) galaxy.tools.parser.factory (module) galaxy.tools.parser.interface (module) galaxy.tools.parser.output_actions (module) galaxy.tools.parser.output_collection_def (module) galaxy.tools.parser.output_objects (module) galaxy.tools.parser.util (module) galaxy.tools.parser.xml (module) galaxy.tools.parser.yaml (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.verify (module) galaxy.tools.verify.asserts (module) galaxy.tools.verify.asserts.tabular (module) galaxy.tools.verify.asserts.text (module) galaxy.tools.verify.asserts.xml (module) galaxy.tools.verify.test_data (module) galaxy.tools.wrappers (module) galaxy.tours (module) galaxy.util (module) galaxy.util.aliaspickler (module) galaxy.util.biostar (module) galaxy.util.bunch (module) galaxy.util.checkers (module) galaxy.util.compression_utils (module) galaxy.util.dbkeys (module) galaxy.util.dictifiable (module) galaxy.util.expressions (module) galaxy.util.filelock (module) galaxy.util.handlers (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.none_like (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.permutations (module) galaxy.util.plugin_config (module) galaxy.util.properties (module) galaxy.util.sanitize_html (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.topsort (module) galaxy.util.ucsc (module) galaxy.util.validation (module) galaxy.util.xml_macros (module) galaxy.version (module) galaxy.visualization (module) galaxy.visualization.data_providers (module) galaxy.visualization.data_providers.basic (module) galaxy.visualization.data_providers.cigar (module) galaxy.visualization.data_providers.genome (module) galaxy.visualization.data_providers.phyloviz (module) galaxy.visualization.data_providers.phyloviz.baseparser (module) galaxy.visualization.data_providers.phyloviz.newickparser (module) galaxy.visualization.data_providers.phyloviz.nexusparser (module) galaxy.visualization.data_providers.phyloviz.phyloxmlparser (module) galaxy.visualization.data_providers.registry (module) galaxy.visualization.genome (module) galaxy.visualization.genomes (module) galaxy.visualization.plugins (module) galaxy.visualization.plugins.config_parser (module) galaxy.visualization.plugins.plugin (module) galaxy.visualization.plugins.registry (module) galaxy.visualization.plugins.resource_parser (module) galaxy.visualization.plugins.utils (module) galaxy.visualization.tracks (module) galaxy.web (module) galaxy.web.base (module) galaxy.web.base.controller (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.middleware (module) galaxy.web.framework.middleware.batch (module) galaxy.web.framework.middleware.error (module) galaxy.web.framework.middleware.graphite (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.static (module) galaxy.web.framework.middleware.statsd (module) galaxy.web.framework.middleware.translogger (module) galaxy.web.framework.middleware.xforwardedhost (module) galaxy.web.framework.openid_manager (module) galaxy.web.framework.webapp (module) galaxy.web.params (module) galaxy.web.proxy (module) galaxy.web.security (module) galaxy.web.stack (module) galaxy.webapps (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.configuration (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.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.jobs (module), [1] galaxy.webapps.galaxy.api.libraries (module), [1] galaxy.webapps.galaxy.api.library_contents (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.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.tool_data (module), [1] galaxy.webapps.galaxy.api.tool_dependencies (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.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.config_watchers (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.biostar (module) galaxy.webapps.galaxy.controllers.data_manager (module) galaxy.webapps.galaxy.controllers.dataset (module) galaxy.webapps.galaxy.controllers.error (module) galaxy.webapps.galaxy.controllers.forms (module) galaxy.webapps.galaxy.controllers.history (module) galaxy.webapps.galaxy.controllers.interactive_environments (module) galaxy.webapps.galaxy.controllers.library (module) galaxy.webapps.galaxy.controllers.page (module) galaxy.webapps.galaxy.controllers.root (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.tool_shed (module) galaxy.webapps.tool_shed.api (module) galaxy.webapps.tool_shed.api.authenticate (module), [1] galaxy.webapps.tool_shed.api.categories (module), [1] galaxy.webapps.tool_shed.api.configuration (module), [1] galaxy.webapps.tool_shed.api.groups (module), [1] galaxy.webapps.tool_shed.api.repositories (module), [1] galaxy.webapps.tool_shed.api.repository_revisions (module), [1] galaxy.webapps.tool_shed.api.tools (module), [1] galaxy.webapps.tool_shed.api.users (module), [1] galaxy.webapps.tool_shed.app (module) galaxy.webapps.tool_shed.buildapp (module) galaxy.webapps.tool_shed.config (module) galaxy.webapps.tool_shed.controllers (module) galaxy.webapps.tool_shed.controllers.admin (module) galaxy.webapps.tool_shed.controllers.groups (module) galaxy.webapps.tool_shed.controllers.hg (module) galaxy.webapps.tool_shed.controllers.repository (module) galaxy.webapps.tool_shed.controllers.repository_review (module) galaxy.webapps.tool_shed.controllers.upload (module) galaxy.webapps.tool_shed.controllers.user (module) galaxy.webapps.tool_shed.framework (module) galaxy.webapps.tool_shed.framework.middleware (module) galaxy.webapps.tool_shed.framework.middleware.remoteuser (module) galaxy.webapps.tool_shed.model (module) galaxy.webapps.tool_shed.model.mapping (module) galaxy.webapps.tool_shed.model.migrate (module) galaxy.webapps.tool_shed.model.migrate.check (module) galaxy.webapps.tool_shed.search (module) galaxy.webapps.tool_shed.search.repo_search (module) galaxy.webapps.tool_shed.search.tool_search (module) galaxy.webapps.tool_shed.security (module) galaxy.webapps.tool_shed.util (module) galaxy.webapps.tool_shed.util.hgweb_config (module) galaxy.webapps.tool_shed.util.ratings_util (module) galaxy.webapps.tool_shed.util.shed_statistics (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.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_ext (module) galaxy_ext.metadata (module) galaxy_ext.metadata.set_metadata (module) galaxy_lib_dir (galaxy.jobs.JobWrapper attribute) galaxy_sessions (galaxy.webapps.tool_shed.model.User attribute) galaxy_system_pwent (galaxy.jobs.JobWrapper attribute) galaxy_virtual_env (galaxy.jobs.JobWrapper attribute) GalaxyConfigBuilder (class in galaxy.main) GalaxyPackageDependency (class in galaxy.tools.deps.resolvers.galaxy_packages) GalaxyPackageDependencyResolver (class in galaxy.tools.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.security) GalaxySearchEngine (class in galaxy.model.search) GalaxySession (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) GalaxySessionToHistoryAssociation (class in galaxy.model) GalaxyTagManager (class in galaxy.managers.tags) GalaxyUtilityContainerManager (class in tool_shed.galaxy_install.utility_containers) GalaxyWebApplication (class in galaxy.webapps.galaxy.buildapp) GalaxyWebTransaction (class in galaxy.web.framework.webapp) gbrowse_links() (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Wiggle method) GeminiSQLite (class in galaxy.datatypes.binary) gen_edge_dicts() (galaxy.util.simplegraph.SimpleGraph method) gen_image() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) gen_node_dicts() (galaxy.util.simplegraph.SimpleGraph method) Genbank (class in galaxy.datatypes.sequence) generate_clone_url_for_installed_repository() (in module tool_shed.util.common_util) generate_clone_url_for_repository_in_tool_shed() (in module tool_shed.util.common_util) generate_clone_url_from_repo_info_tup() (in module tool_shed.util.common_util) generate_data_manager_metadata() (tool_shed.metadata.metadata_generator.MetadataGenerator method) generate_datatypes_metadata() (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.dataset_collections.types.DatasetCollectionType method) (galaxy.dataset_collections.types.list.ListDatasetCollectionType method) (galaxy.dataset_collections.types.paired.PairedDatasetCollectionType method) generate_environment_dependency_metadata() (tool_shed.metadata.metadata_generator.MetadataGenerator method) generate_error() (galaxy.webapps.galaxy.controllers.root.RootController method) generate_export_elem() (tool_shed.capsule.capsule_manager.ExportRepositoryManager method) generate_guid_for_object() (tool_shed.metadata.metadata_generator.MetadataGenerator 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 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() (tool_shed.metadata.metadata_generator.MetadataGenerator method) generate_package_dependency_metadata() (tool_shed.metadata.metadata_generator.MetadataGenerator method) generate_primary_file() (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.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.jobs.metrics.collectl.processes) generate_repository_archive() (tool_shed.capsule.capsule_manager.ExportRepositoryManager method) generate_repository_archive_filename() (tool_shed.capsule.capsule_manager.ExportRepositoryManager 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 tool_shed.util.container_util) generate_repository_dependency_metadata() (tool_shed.metadata.metadata_generator.MetadataGenerator method) generate_repository_info_elem() (tool_shed.tools.data_table_manager.ShedToolDataTableManager method) generate_repository_info_elem_from_repository() (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_statistics() (galaxy.webapps.tool_shed.util.shed_statistics.ShedCounter method) generate_tool_dependencies_key() (tool_shed.utility_containers.ToolShedUtilityContainerManager method) generate_tool_dependency_metadata() (tool_shed.metadata.metadata_generator.MetadataGenerator method) generate_tool_elem() (tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_guid() (in module tool_shed.util.shed_util_common) generate_tool_metadata() (tool_shed.metadata.metadata_generator.MetadataGenerator method) generate_tool_panel_dict_for_new_install() (tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_panel_dict_for_tool_config() (tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_panel_dict_from_shed_tool_conf_entries() (tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_panel_elem_list() (tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_section_dicts() (tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_section_element_from_dict() (tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) generate_tool_shed_repository_install_dir() (in module tool_shed.util.repository_util) generate_unknown_img_str() (in module tool_shed.galaxy_install.grids.admin_toolshed_grids) generate_workflow_image() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) (in module tool_shed.util.workflow_util) generate_workflow_metadata() (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) 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.managers.base.ModelValidator method) 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] GenomespaceFileToolParameter (class in galaxy.tools.parameters.basic) 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.tools.util.maf_utilities) GenomicRegionDataProvider (class in galaxy.datatypes.dataproviders.dataset) GenotypeMatrix (class in galaxy.datatypes.genetics) get() (galaxy.config.Configuration method) (galaxy.containers.ContainerInterfaceConfig method) (galaxy.containers.docker_model.DockerAttributeContainer method) (galaxy.dataset_collections.registry.DatasetCollectionTypesRegistry method) (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.datatypes.metadata.MetadataElementSpec method) (galaxy.jobs.runners.util.Bunch method) (galaxy.jobs.runners.util.drmaa.DrmaaSessionFactory method) (galaxy.managers.datasets.DatasetRBACPermissions method) (galaxy.managers.folders.FolderManager method) (galaxy.managers.lddas.LDDAManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.managers.roles.RoleManager method) (galaxy.model.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataElementSpec method) (galaxy.openid.providers.OpenIDProviders method) (galaxy.tools.data.ToolDataTableManager method) (galaxy.tools.parser.interface.InputSource method) (galaxy.tools.parser.xml.XmlInputSource method) (galaxy.tools.parser.yaml.YamlInputSource 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.reports.config.Configuration method) (galaxy.webapps.tool_shed.config.Configuration method) (tool_shed.managers.groups.GroupManager method) (tool_shed.managers.repositories.RepoManager method) get_absolute_path_to_file_in_repository() (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.SharingStatusColumn method) (galaxy.web.framework.helpers.grids.StateColumn method) (galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid.StatusColumn 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_libraries() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) get_action() (galaxy.security.RBACAgent method) (galaxy.webapps.tool_shed.security.RBACAgent method) get_actions() (galaxy.security.RBACAgent method) (galaxy.webapps.tool_shed.security.RBACAgent method) get_actions_for_items() (galaxy.security.GalaxyRBACAgent method) get_activation_token() (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] (galaxy.webapps.galaxy.controllers.user.User method) get_active_folders() (galaxy.model.Library method) get_add_roles() (galaxy.managers.libraries.LibraryManager method) get_additional_repository_information() (galaxy.tools.deps.mulled.mulled_search.QuaySearch method) get_all_dependencies() (in module tool_shed.util.metadata_util) get_all_forms() (galaxy.web.base.controller.UsesFormDefinitionsMixin method) get_all_roles() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) get_all_users() (galaxy.webapps.galaxy.controllers.userskeys.User method) get_amount() (galaxy.model.Quota method) get_annotation_async() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) get_api_key() (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.tools.deps.DependencyManager method) get_archives_from_manifest() (tool_shed.capsule.capsule_manager.ImportRepositoryManager method) get_attributes_from_fasta_header() (in module galaxy.tools.util.maf_utilities) 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_biostar_url() (in module galaxy.util.biostar) get_blurb() (galaxy.datatypes.constructive_solid_geometry.Vtk method) get_bool() (galaxy.config.Configuration method) (galaxy.tools.parser.interface.InputSource method) (galaxy.tools.parser.xml.XmlInputSource method) (galaxy.tools.parser.yaml.YamlInputSource method) (galaxy.webapps.tool_shed.config.Configuration method) get_bounds() (in module galaxy.visualization.data_providers.genome) get_build() (galaxy.visualization.genomes.Genomes method) get_categories() (in module tool_shed.util.shed_util_common) get_category() (in module tool_shed.util.shed_util_common) get_category_by_name() (in module tool_shed.util.shed_util_common) get_certified_level_one_clause_list() (tool_shed.repository_registry.Registry method) get_certified_level_one_tuple() (tool_shed.repository_registry.Registry method) get_change_lines_in_file_for_tag() (in module tool_shed.util.commit_util) get_changectx_for_changeset() (in module tool_shed.util.hg_util) get_changeset_revision_and_ctx_rev() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) get_changesets_for_setting_metadata() (galaxy.webapps.tool_shed.model.Repository method) (tool_shed.repository_types.metadata.Metadata method) (tool_shed.repository_types.metadata.TipOnly method) get_charset_from_http_headers() (in module galaxy.util) get_check_interval() (galaxy.model.DeferredJob method) get_children() (galaxy.datatypes.dataproviders.hierarchy.XMLDataProvider method) get_chopped_blocks_for_region() (in module galaxy.tools.util.maf_utilities) get_chopped_blocks_with_index_offset_for_region() (in module galaxy.tools.util.maf_utilities) get_chrom_info() (galaxy.util.dbkeys.GenomeBuilds method) get_chunk() (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.tabular.ConnectivityTable method) (galaxy.datatypes.tabular.TabularData method) get_class() (galaxy.web.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_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_type() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) get_command() (in module galaxy.tools.linters.command) get_command_line() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.model.Job method) (galaxy.model.Task method) get_communication() (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] get_community_tags() (galaxy.managers.tags.TagManager method) get_component() (in module tool_shed.util.review_util) get_component_associations() (galaxy.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.tools.util.maf_utilities) get_components_by_src_start() (in module galaxy.tools.util.maf_utilities) get_components_from_key() (in module tool_shed.util.container_util) get_components_from_repo_info_dict() (tool_shed.capsule.capsule_manager.ExportRepositoryManager method) 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_conditional_requirements() (galaxy.dependencies.ConditionalDependencies method) get_config() (in module galaxy.model.orm.scripts) (in module tool_shed.util.hg_util) 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 tool_shed.util.hg_util) get_configured_ui() (in module tool_shed.util.hg_util) get_consumer() (galaxy.web.framework.openid_manager.OpenIDManager method) get_consumers() (galaxy.queue_worker.GalaxyQueueWorker method) get_container() (galaxy.containers.ContainerInterface method) get_containing_repository_for_tool_dependency() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_containing_tool_sections() (tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager method) get_content_id() (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_content_type() (galaxy.web.framework.base.Response method) get_converted_dataset() (galaxy.model.DatasetInstance method) get_converted_dataset_deps() (galaxy.model.DatasetInstance method) get_converted_files_by_type() (galaxy.model.DatasetInstance method) get_converter_and_display_paths() (tool_shed.galaxy_install.datatypes.custom_datatype_manager.CustomDatatypeLoader method) get_converter_by_target_type() (galaxy.datatypes.registry.Registry method) get_converter_types() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) get_converters_by_datatype() (galaxy.datatypes.registry.Registry method) get_cookie() (galaxy.web.framework.webapp.GalaxyWebTransaction method) get_copied_from_job_id() (galaxy.model.Job method) get_cram_version() (galaxy.datatypes.binary.CRAM method) get_ctx_file_path_from_manifest() (in module tool_shed.util.hg_util) get_ctx_rev() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) (in module tool_shed.util.shed_util_common) 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) (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] get_custom_builds_metadata() (galaxy.webapps.galaxy.api.histories.HistoriesController method), [1] get_data() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.objectstore.pulsar.PulsarObjectStore method) (galaxy.objectstore.rods.IRODSObjectStore method) (galaxy.objectstore.s3.S3ObjectStore 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_inputs() (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) (tool_shed.util.workflow_util.RepoToolModule method) get_data_outputs() (galaxy.workflow.modules.InputDataCollectionModule method) (galaxy.workflow.modules.InputDataModule method) (galaxy.workflow.modules.PauseModule method) (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) (tool_shed.util.workflow_util.RepoToolModule 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) (in module galaxy.webapps.tool_shed.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_filename() (in module galaxy.tools.imp_exp.export_history) get_dataset_finish_context() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) get_dataset_metadata_key() (galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper method) (galaxy.model.metadata.JobExternalOutputMetadataWrapper method) get_dataset_state() (galaxy.model.DatasetInstance 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_dbkey() (galaxy.model.DatasetInstance method) (galaxy.tools.parameters.grouping.UploadDataset method) get_dbkeys() (galaxy.visualization.genomes.Genomes method) get_default_history_by_trans() (galaxy.tools.DataManagerTool method) (galaxy.tools.Tool method) get_default_max_vals() (galaxy.visualization.data_providers.genome.ChromatinInteractionsDataProvider method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) get_default_parsers() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) get_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.SelectToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) get_dependencies_for_metadata_revision() (in module tool_shed.util.metadata_util) get_dependencies_for_repository() (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_dependent_downloadable_revisions() (tool_shed.capsule.capsule_manager.ImportRepositoryManager method) get_destination() (galaxy.jobs.JobConfiguration method) get_destination_configuration() (galaxy.jobs.JobWrapper method) (galaxy.model.Job method) get_destinations() (galaxy.jobs.JobConfiguration method) get_dict_checksums() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.Download method) get_disk_usage() (galaxy.model.GalaxySession method) (galaxy.model.User method) (galaxy.webapps.reports.controllers.system.System method) (galaxy.webapps.tool_shed.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_url_for_platform() (in module tool_shed.util.tool_dependency_util) get_edit() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) get_editor_iframe() (galaxy.webapps.galaxy.controllers.page.PageController method) get_elem_checksums() (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) (galaxy.webapps.tool_shed.util.hgweb_config.HgWebConfigManager method) get_env_setup_clause() (galaxy.jobs.JobWrapper method) get_env_shell_file_path() (galaxy.model.tool_shed_install.ToolDependency method) (tool_shed.galaxy_install.tool_dependencies.env_manager.EnvManager method) get_env_shell_file_paths() (tool_shed.galaxy_install.tool_dependencies.env_manager.EnvManager method) get_env_shell_file_paths_from_setup_environment_elem() (tool_shed.galaxy_install.tool_dependencies.env_manager.EnvManager method) get_env_var_values() (in module tool_shed.util.basic_util) get_errors() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_estimated_display_viewport() (galaxy.datatypes.interval.BedGraph method) (galaxy.datatypes.interval.CustomTrack method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.Wiggle method) get_exit_code() (galaxy.jobs.TaskWrapper method) get_export_info_dict() (tool_shed.capsule.capsule_manager.ImportRepositoryManager method) 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_fasta_header() (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) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) get_file_context_from_ctx() (in module tool_shed.util.hg_util) get_file_count() (galaxy.tools.parameters.grouping.UploadDataset method) get_file_name() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) get_file_peek() (galaxy.datatypes.genetics.RexpBase method) (in module galaxy.datatypes.data) get_file_size() (in module galaxy.util) get_file_type() (galaxy.tools.parameters.grouping.UploadDataset method) get_file_type_str() (in module tool_shed.util.basic_util) get_filename() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.objectstore.pulsar.PulsarObjectStore method) (galaxy.objectstore.rods.IRODSObjectStore method) (galaxy.objectstore.s3.S3ObjectStore method) (galaxy.tools.verify.test_data.TestDataResolver method) get_filename_for_source() (galaxy.tools.data.TabularToolDataTable method) get_fileobj() (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) (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.tools.verify.asserts.tabular) get_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) get_folder_dict() (galaxy.managers.folders.FolderManager method) get_form() (in module galaxy.webapps.galaxy.controllers.forms) get_form_values() (galaxy.web.base.controller.UsesFormDefinitionsMixin method) get_func_list() (in module galaxy.web.framework.middleware.profile) get_galaxy_session() (galaxy.web.framework.webapp.GalaxyWebTransaction method) 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_grid_title() (tool_shed.grids.repository_grid_filter_manager.RepositoryGridFilterManager method) get_group() (galaxy.web.base.controller.BaseController method) (in module galaxy.webapps.galaxy.controllers.admin) get_guid() (tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager method) get_handler() (galaxy.model.Job method) (galaxy.util.handlers.ConfiguresHandlers method) get_hashed_dependencies_path() (galaxy.tools.deps.CachedDependencyManager method) get_hda() (galaxy.web.base.controller.UsesVisualizationMixin method) get_hda_or_ldda() (galaxy.web.base.controller.UsesVisualizationMixin method) get_headers() (in module galaxy.datatypes.sniff) get_history() (galaxy.web.framework.webapp.GalaxyWebTransaction method) (galaxy.work.context.WorkRequestContext method) get_history_datasets() (galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper method) get_hook() (galaxy.tools.Tool method) get_id() (galaxy.model.Job method) (galaxy.model.Task method) (in module galaxy.webapps.galaxy.api.genomes), [1] get_id_col_in_item_tag_assoc_table() (galaxy.managers.tags.TagManager method) get_id_tag() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.model.Job method) (galaxy.model.Task method) get_ids() (galaxy.web.framework.helpers.grids.Grid method) get_ids_of_tool_shed_repositories_being_installed() (in module tool_shed.util.repository_util) 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_info() (galaxy.model.Job method) (galaxy.model.LibraryDataset method) (galaxy.model.Task 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.GenomespaceFileToolParameter method) (galaxy.tools.parameters.basic.HiddenToolParameter method) (galaxy.tools.parameters.basic.IntegerToolParameter 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.Group method) (galaxy.tools.parameters.grouping.Repeat method) (galaxy.tools.parameters.grouping.Section method) (galaxy.tools.parameters.grouping.UploadDataset 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_paths() (galaxy.jobs.JobWrapper method) get_input_source() (in module galaxy.tools.parser) (in module galaxy.tools.parser.factory) get_inputs() (galaxy.workflow.modules.InputDataCollectionModule method) (galaxy.workflow.modules.InputParameterModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_installable_revisions() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method), [1] get_installed_and_missing_repository_dependencies() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_installed_and_missing_repository_dependencies_for_new_or_updated_install() (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() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_installed_repositories_from_repository_dependencies() (tool_shed.galaxy_install.repair_repository_manager.RepairRepositoryManager method) get_installed_repository() (in module tool_shed.util.repository_util) get_installed_tool_shed_repository() (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_invalid_file_tups() (tool_shed.metadata.metadata_generator.MetadataGenerator method) get_invocation() (galaxy.managers.workflows.WorkflowsManager method) get_invocation_step() (galaxy.managers.workflows.WorkflowsManager method) get_item() (galaxy.web.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.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) (galaxy.webapps.tool_shed.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.web.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.web.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_file() (galaxy.jobs.runners.BaseJobRunner method) get_job_handler() (galaxy.tools.Tool 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_tool_configurations() (galaxy.jobs.JobConfiguration 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.parameters.basic.HiddenToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) get_last_check() (galaxy.model.DeferredJob method) get_latest_changeset_revision() (in module tool_shed.util.metadata_util) get_latest_downloadable_changeset_revision() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) (in module tool_shed.util.metadata_util) 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_installable_revision() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method), [1] 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.SelectToolParameter method) get_legitimate_roles() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) get_level() (galaxy.dataset_collections.builder.CollectionBuilder method) get_library() (galaxy.web.base.controller.UsesLibraryMixin method) get_library_dataset() (galaxy.web.base.controller.UsesLibraryMixinItems method) get_library_dataset_dataset_association() (galaxy.web.base.controller.UsesLibraryMixinItems method) get_library_dict() (galaxy.managers.libraries.LibraryManager method) get_library_folder() (galaxy.web.base.controller.UsesLibraryMixinItems method) get_limit() (galaxy.containers.docker_swarm_manager.SwarmState 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.web.framework.helpers.grids.SharingStatusColumn method) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid.HistoryListNameColumn method) 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_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_max_optional_metadata_filesize() (galaxy.datatypes.data.Data method) get_mercurial_default_options_dict() (in module tool_shed.util.hg_util) get_message() (galaxy.web.framework.webapp.GalaxyWebTransaction method) get_message_for_no_shed_tool_config() (in module galaxy.webapps.galaxy.api.tool_shed_repositories), [1] get_meta_by_dataset_id() (galaxy.tools.parameters.output_collect.LegacyToolProvidedMetadata method) get_meta_by_name() (galaxy.tools.parameters.output_collect.ToolProvidedMetadata method) get_metadata() (galaxy.model.DatasetInstance method) get_metadata_by_id() (in module tool_shed.util.metadata_util) get_metadata_changeset_revisions() (in module tool_shed.util.metadata_util) get_metadata_column_index_by_name() (galaxy.datatypes.dataproviders.dataset.DatasetDataProvider method) get_metadata_column_names() (galaxy.datatypes.dataproviders.dataset.DatasetDataProvider method) get_metadata_column_types() (galaxy.datatypes.dataproviders.dataset.DatasetDataProvider method) get_metadata_dataset() (galaxy.model.DatasetInstance method) get_metadata_dict() (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_mime() (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.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_modify_roles() (galaxy.managers.libraries.LibraryManager method) get_monitor_id() (in module galaxy.webapps.reports.controllers.jobs) get_most_recent_history() (galaxy.web.framework.webapp.GalaxyWebTransaction method) get_most_recently_used_tool_async() (galaxy.webapps.galaxy.controllers.user.User method) get_mutable_output_fnames() (galaxy.jobs.JobWrapper method) get_name() (galaxy.model.LibraryDataset method) (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_name_and_link_async() (galaxy.web.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.tools.parameters.output_collect.LegacyToolProvidedMetadata method) (galaxy.tools.parameters.output_collect.NullToolProvidedMetadata method) (galaxy.tools.parameters.output_collect.ToolProvidedMetadata method) get_new_datasets() (galaxy.tools.parameters.output_collect.LegacyToolProvidedMetadata method) (galaxy.tools.parameters.output_collect.NullToolProvidedMetadata method) (galaxy.tools.parameters.output_collect.ToolProvidedMetadata method) get_new_guid() (galaxy.web.security.SecurityHelper method) get_new_track_config() (galaxy.web.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 tool_shed.util.shed_util_common) get_non_shed_tool_panel_configs() (in module tool_shed.util.common_util) get_object() (galaxy.web.base.controller.BaseAPIController method) (galaxy.web.base.controller.BaseController method) (galaxy.web.base.controller.BaseUIController method) (in module galaxy.managers.base) get_object_url() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.objectstore.pulsar.PulsarObjectStore method) (galaxy.objectstore.rods.IRODSObjectStore method) (galaxy.objectstore.s3.S3ObjectStore method) get_observer_class() (in module galaxy.tools.toolbox.watcher) get_open_tempfile() (galaxy.tools.util.maf_utilities.TempFileHandler 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.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_create_api_key() (galaxy.managers.api_keys.ApiKeyManager method) get_or_create_default_history() (galaxy.web.framework.webapp.GalaxyWebTransaction method) get_or_create_remote_user() (galaxy.web.framework.webapp.GalaxyWebTransaction method) get_or_create_tool_section() (tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) get_or_create_tool_shed_repository() (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() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method), [1] get_oriented_chopped_blocks_for_region() (in module galaxy.tools.util.maf_utilities) get_oriented_chopped_blocks_with_index_offset_for_region() (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_filenames_by_dataset() (galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper method) (galaxy.model.metadata.JobExternalOutputMetadataWrapper 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_sizes() (galaxy.jobs.JobWrapper method) get_owned() (galaxy.managers.secured.OwnableManagerMixin method) get_owned_workflow() (galaxy.managers.workflows.WorkflowsManager method) get_page() (galaxy.webapps.galaxy.controllers.page.PageController method) 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) (galaxy.jobs.TaskWrapper 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.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_peek() (galaxy.datatypes.genetics.RexpBase method) get_percent() (galaxy.quota.NoQuotaAgent method) (galaxy.quota.QuotaAgent method) get_permissions() (galaxy.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.security) (in module galaxy.webapps.tool_shed.security) get_permitted_libraries() (galaxy.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 tool_shed.util.tool_dependency_util) get_plugin() (galaxy.visualization.plugins.registry.VisualizationsRegistry method) get_plugins() (galaxy.jobs.runners.util.cli.CliInterface method) get_post_job_actions() (galaxy.model.Job method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_precreated_dataset() (in module galaxy.tools.actions.upload_common) get_precreated_datasets() (in module galaxy.tools.actions.upload_common) get_pred_counts() (galaxy.util.topsort.CycleError 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 tool_shed.util.repository_util) get_prior_install_required_dict() (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_user_role() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) (galaxy.webapps.tool_shed.security.RBACAgent method) get_proprietary_tool_panel_elems() (tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager method) get_protocol_from_tool_shed_url() (in module tool_shed.util.common_util) get_published_visualizations() (galaxy.web.base.controller.UsesVisualizationMixin method) get_query_for_setting_metadata_on_repositories() (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.web.base.controller.UsesQuotaMixin method) (in module galaxy.webapps.galaxy.controllers.admin) get_quota_params() (galaxy.web.params.QuotaParamParser method) get_random_bytes() (in module galaxy.web.security) get_raw_data() (galaxy.datatypes.data.Data method) (galaxy.model.DatasetInstance method) get_readable_ctx_date() (in module tool_shed.util.hg_util) get_readme_file_names() (in module tool_shed.util.readme_util) get_readme_files() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) get_readme_files_dict_for_display() (in module tool_shed.util.readme_util) get_ref() (galaxy.tools.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.tools.util.maf_utilities) get_relative_path_to_repository_file() (tool_shed.metadata.metadata_generator.MetadataGenerator method) get_repair_dict() (tool_shed.galaxy_install.repair_repository_manager.RepairRepositoryManager method) get_repo_for_repository() (in module tool_shed.util.hg_util) get_repo_info_dict() (in module tool_shed.util.repository_util) get_repo_info_dict_for_import() (tool_shed.capsule.capsule_manager.ExportRepositoryManager method) get_repo_info_dict_for_repair() (tool_shed.galaxy_install.repair_repository_manager.RepairRepositoryManager method) get_repo_info_dicts() (tool_shed.capsule.capsule_manager.ExportRepositoryManager method) get_repo_info_tuple_contents() (in module tool_shed.util.repository_util) get_repositories() (galaxy.webapps.tool_shed.api.categories.CategoriesController method), [1] get_repositories_by_category() (in module tool_shed.util.repository_util) get_repository_admin_role_name() (in module tool_shed.util.repository_util) get_repository_and_repository_dependencies_from_repo_info_dict() (in module tool_shed.util.repository_util) get_repository_attributes_and_sub_elements() (tool_shed.capsule.capsule_manager.ExportRepositoryManager method) get_repository_by_id() (in module tool_shed.util.repository_util) get_repository_by_name() (in module tool_shed.util.repository_util) get_repository_by_name_and_owner() (in module tool_shed.util.repository_util) get_repository_categories() (in module tool_shed.util.shed_util_common) get_repository_components_for_installation() (tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) get_repository_dependencies() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) (galaxy.webapps.tool_shed.model.Repository method) (in module tool_shed.util.common_util) (in module tool_shed.util.metadata_util) get_repository_dependencies_for_changeset_revision() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) get_repository_dependencies_for_installed_tool_shed_repository() (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() (tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) get_repository_dependency_tups_for_installed_repository() (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 tool_shed.util.repository_util) get_repository_file_contents() (in module tool_shed.util.shed_util_common) get_repository_files() (in module tool_shed.util.shed_util_common) get_repository_for_dependency_relationship() (in module tool_shed.util.repository_util) get_repository_from_refresh_on_change() (in module tool_shed.util.shed_util_common) get_repository_heads() (in module tool_shed.util.hg_util) get_repository_id() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) get_repository_ids() (tool_shed.capsule.capsule_manager.ExportRepositoryManager method) get_repository_ids_requiring_prior_import_or_install() (in module tool_shed.util.repository_util) get_repository_in_tool_shed() (in module tool_shed.util.repository_util) get_repository_info_from_manifest() (tool_shed.capsule.capsule_manager.ImportRepositoryManager method) get_repository_information() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) get_repository_install_dir() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_repository_metadata_by_changeset_revision() (in module tool_shed.util.metadata_util) get_repository_metadata_by_id() (in module tool_shed.util.metadata_util) get_repository_metadata_by_repository_id_changeset_revision() (in module tool_shed.util.metadata_util) get_repository_metadata_revisions_for_review() (in module tool_shed.util.metadata_util) get_repository_owner() (in module tool_shed.util.repository_util) get_repository_owner_from_clone_url() (in module tool_shed.util.repository_util) get_repository_query() (in module tool_shed.util.repository_util) get_repository_reviewer_role() (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) get_repository_revision_install_info() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method), [1] get_repository_status_from_tool_shed() (tool_shed.capsule.capsule_manager.ImportRepositoryManager method) get_repository_tools_tups() (tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) get_repository_tuple_for_installed_repository_manager() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) get_repository_type() (galaxy.webapps.tool_shed.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_repo_info_dict() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) get_required_repo_info_dicts() (tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) get_required_repository_package_env_sh_path() (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.tools.deps.views.DependencyResolversView method) get_resolver_option() (galaxy.tools.deps.DependencyManager method) get_resource_group() (galaxy.jobs.JobToolConfiguration method) get_resource_parameters() (galaxy.jobs.HasResourceParameters 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_revision_label() (in module tool_shed.util.hg_util) get_revision_label_from_ctx() (in module tool_shed.util.hg_util) get_role() (galaxy.security.GalaxyRBACAgent method) (galaxy.web.base.controller.BaseController method) (in module galaxy.webapps.galaxy.controllers.admin) get_role_by_id() (in module tool_shed.util.repository_util) get_roles_for_action() (galaxy.security.GalaxyRBACAgent method) get_runtime_dependent_tool_dependency_tuples() (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.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() (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.tools.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.SplicedAlignment method) get_sequence_reverse_complement() (galaxy.tools.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.SplicedAlignment method) get_sequences_per_file() (galaxy.datatypes.sequence.Sequence static method) get_session() (galaxy.web.framework.openid_manager.OpenIDManager method) get_session_id() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.model.Job method) (galaxy.model.Task method) get_sharable_url() (galaxy.model.tool_shed_install.ToolShedRepository method) get_share_assocs() (galaxy.managers.sharable.SharableModelManager method) get_sharing_roles() (galaxy.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_config_filename() (galaxy.model.tool_shed_install.ToolShedRepository method) get_shed_tool_conf_dict() (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) get_showable_folders() (galaxy.security.GalaxyRBACAgent 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) get_single_status() (galaxy.jobs.runners.util.cli.job.BaseJobExec method) (galaxy.jobs.runners.util.cli.job.slurm.Slurm method) (galaxy.jobs.runners.util.cli.job.torque.Torque method) get_size() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) get_spark_time() (in module galaxy.webapps.reports.controllers.jobs) get_species_in_block() (in module galaxy.tools.util.maf_utilities) get_species_in_maf() (in module galaxy.tools.util.maf_utilities) get_species_names() (galaxy.tools.util.maf_utilities.RegionAlignment method) (galaxy.tools.util.maf_utilities.SplicedAlignment method) get_spliced_region_alignment() (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.web.framework.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.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.slurm.Slurm method) (galaxy.jobs.runners.util.cli.job.slurm_torque.SlurmTorque method) (galaxy.jobs.runners.util.cli.job.torque.Torque method) get_stderr() (galaxy.model.Task method) get_stdout() (galaxy.model.Task method) get_step_handler_by_type() (tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager.StepManager method) get_store_usage_percent() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.objectstore.pulsar.PulsarObjectStore method) (galaxy.objectstore.rods.IRODSObjectStore method) (galaxy.objectstore.s3.S3ObjectStore method) get_stored_accessible_workflow() (galaxy.managers.workflows.WorkflowsManager method) get_stored_workflow() (galaxy.managers.workflows.WorkflowsManager method) (galaxy.web.base.controller.UsesStoredWorkflowMixin method) get_stored_workflow_steps() (galaxy.web.base.controller.UsesStoredWorkflowMixin method) get_structure() (in module galaxy.dataset_collections.structure) get_subsystem() (in module galaxy.jobs.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.web.form_builder) get_table_names_by_path() (galaxy.tools.data.ToolDataTableManager method) get_tables() (galaxy.tools.data.ToolDataTableManager method) get_tag_assoc_class() (galaxy.managers.tags.TagManager method) get_tag_by_id() (galaxy.managers.tags.TagManager method) get_tag_by_name() (galaxy.managers.tags.TagManager method) get_tag_handler() (galaxy.web.base.controller.UsesTagsMixin method) get_tag_handler_by_tag() (tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager.TagManager method) get_tagging_elt_async() (galaxy.webapps.galaxy.controllers.tag.TagsController method) get_tags() (galaxy.managers.taggable.TaggableManagerMixin method) get_tags_str() (galaxy.managers.tags.TagManager method) get_target_install_dir() (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_fname() (in module galaxy.datatypes.data) (in module galaxy.datatypes.sniff) get_tool() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) get_tool_components() (galaxy.tools.ToolBox method) get_tool_conf_watcher() (in module galaxy.tools.toolbox.watcher) get_tool_data_dir_watcher() (in module galaxy.tools.toolbox.watcher) get_tool_def() (galaxy.web.base.controller.UsesVisualizationMixin method) get_tool_dependencies() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) (galaxy.webapps.tool_shed.model.Repository method) (in module tool_shed.util.common_util) get_tool_dependencies_config_contents() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) get_tool_dependency() (in module tool_shed.util.tool_dependency_util) get_tool_dependency_by_name_type_repository() (in module tool_shed.util.tool_dependency_util) get_tool_dependency_by_name_version_type() (in module tool_shed.util.tool_dependency_util) get_tool_dependency_by_name_version_type_repository() (in module tool_shed.util.tool_dependency_util) get_tool_dependency_definition_metadata() (galaxy.webapps.tool_shed.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 tool_shed.util.tool_dependency_util) get_tool_dependency_install_dir() (in module tool_shed.util.tool_dependency_util) get_tool_dependency_tuple_for_installed_repository_manager() (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() (tool_shed.tools.data_table_manager.ShedToolDataTableManager method) get_tool_panel_config_tool_path_install_dir() (in module tool_shed.util.shed_util_common) get_tool_path_by_shed_tool_conf_filename() (in module tool_shed.util.shed_util_common) get_tool_path_install_dir() (in module tool_shed.util.tool_util) get_tool_provided_job_metadata() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) get_tool_relative_path() (galaxy.model.tool_shed_install.ToolShedRepository 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() (galaxy.webapps.tool_shed.api.authenticate.ToolShedAuthenticationController method), [1] get_tool_shed_from_clone_url() (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 tool_shed.util.repository_util) get_tool_shed_repository_ids() (in module tool_shed.util.common_util) get_tool_shed_repository_info_dict() (galaxy.tools.data_manager.manager.DataManager method) get_tool_shed_repository_install_dir() (tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) get_tool_shed_repository_status_label() (in module tool_shed.util.repository_util) get_tool_shed_status_for_installed_repository() (in module tool_shed.util.repository_util) get_tool_shed_url_from_tool_shed_registry() (in module tool_shed.util.common_util) get_tool_source() (in module galaxy.tools.parser) (in module galaxy.tools.parser.factory) get_tool_source_path() (galaxy.tools.locations.dockstore.DockStoreResolver method) (galaxy.tools.locations.ToolLocationResolver method) (galaxy.tools.locations.file.HttpToolResolver method) (galaxy.tools.locations.http.HttpToolResolver method) get_tool_tags() (galaxy.managers.tags.TagManager 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() (galaxy.webapps.tool_shed.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.web.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_tooltip() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule 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_type() (galaxy.workflow.modules.WorkflowModule method) get_type_class() (galaxy.webapps.tool_shed.model.Repository method) get_unique_slug() (galaxy.managers.sharable.SharableModelManager method) get_update_to_changeset_revision_and_ctx_rev() (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 tool_shed.util.metadata_util) get_updated_repository_information() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.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) get_url_params() (galaxy.visualization.plugins.registry.VisualizationsRegistry method) get_usage() (galaxy.quota.NoQuotaAgent method) get_user() (galaxy.model.Job method) (galaxy.web.base.controller.BaseController method) (galaxy.web.framework.webapp.GalaxyWebTransaction method) (galaxy.work.context.WorkRequestContext method) (in module galaxy.webapps.galaxy.controllers.admin) (in module tool_shed.util.shed_util_common) get_user_by_username() (in module tool_shed.util.common_util) get_user_id() (galaxy.model.Job 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.web.base.controller.UsesTagsMixin method) get_valid_by_name() (galaxy.tools.parameters.sanitize.ToolParameterSanitizer class method) get_valid_roles() (galaxy.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.tools.parser.output_actions.FromDataTableOutputActionOption method) (galaxy.tools.parser.output_actions.FromFileToolOutputActionOption method) (galaxy.tools.parser.output_actions.FromParamToolOutputActionOption method) (galaxy.tools.parser.output_actions.NullToolOutputActionOption method) (galaxy.tools.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.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.dataset.HistoryDatasetAssociationListGrid.HistoryColumn method) (galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid.StatusColumn 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.DelayedValueColumn method) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid.DeletedColumn method) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid.ItemCountColumn method) (galaxy.webapps.galaxy.controllers.history.NameColumn method) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid.DatasetsByStateColumn method) (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid.SharedByColumn method) (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid.NameColumn method) (galaxy.webapps.galaxy.controllers.page.PageListGrid.URLColumn method) (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid.HistoryColumn method) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid.StepsColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.CreateTimeColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.JobIdColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.StateColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.ToolColumn method) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.UserColumn method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.CreateTimeColumn method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.UserColumn method) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.WorkflowNameColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.DescriptionColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.NameColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.OwnerColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.RevisionColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.StatusColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.ToolShedColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.ToolShedStatusColumn method) (tool_shed.grids.admin_grids.AdminRepositoryGrid.DeletedColumn method) (tool_shed.grids.admin_grids.GroupGrid.NameColumn method) (tool_shed.grids.admin_grids.GroupGrid.RolesColumn method) (tool_shed.grids.admin_grids.GroupGrid.StatusColumn method) (tool_shed.grids.admin_grids.GroupGrid.UsersColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.DatatypesColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.DeletedColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.DeprecatedColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.IdColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.MaliciousColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.NameColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.OwnerColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.RevisionColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.ToolsColumn method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid.WorkflowsColumn method) (tool_shed.grids.admin_grids.RoleGrid.DescriptionColumn method) (tool_shed.grids.admin_grids.RoleGrid.GroupsColumn method) (tool_shed.grids.admin_grids.RoleGrid.NameColumn method) (tool_shed.grids.admin_grids.RoleGrid.RepositoriesColumn method) (tool_shed.grids.admin_grids.RoleGrid.StatusColumn method) (tool_shed.grids.admin_grids.RoleGrid.TypeColumn method) (tool_shed.grids.admin_grids.RoleGrid.UsersColumn method) (tool_shed.grids.admin_grids.UserGrid.ExternalColumn method) (tool_shed.grids.admin_grids.UserGrid.GroupsColumn method) (tool_shed.grids.admin_grids.UserGrid.LastLoginColumn method) (tool_shed.grids.admin_grids.UserGrid.RolesColumn method) (tool_shed.grids.admin_grids.UserGrid.StatusColumn method) (tool_shed.grids.admin_grids.UserGrid.UserLoginColumn method) (tool_shed.grids.admin_grids.UserGrid.UserNameColumn method) (tool_shed.grids.repository_grids.CategoryGrid.DescriptionColumn method) (tool_shed.grids.repository_grids.CategoryGrid.NameColumn method) (tool_shed.grids.repository_grids.CategoryGrid.RepositoriesColumn method) (tool_shed.grids.repository_grids.DatatypesGrid.DatatypesColumn method) (tool_shed.grids.repository_grids.MatchedRepositoryGrid.DescriptionColumn method) (tool_shed.grids.repository_grids.MatchedRepositoryGrid.NameColumn method) (tool_shed.grids.repository_grids.MatchedRepositoryGrid.RevisionColumn method) (tool_shed.grids.repository_grids.MatchedRepositoryGrid.UserColumn method) (tool_shed.grids.repository_grids.RepositoriesWithInvalidToolsGrid.InvalidToolConfigColumn method) (tool_shed.grids.repository_grids.RepositoryDependenciesGrid.RequiredRepositoryColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.CategoryColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.DeprecatedColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.DescriptionColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.EmailAlertsColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.HeadsColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.LatestInstallableRevisionColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.MetadataRevisionColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.NameColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.TipRevisionColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.TypeColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.UserColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.ChangesetRevisionColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.DownloadableColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.HasRepositoryDependenciesColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.IncludesDatatypesColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.IncludesToolDependenciesColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.IncludesToolsColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.IncludesWorkflowsColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.MaliciousColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.RepositoryNameColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.RepositoryOwnerColumn method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid.RepositoryTypeColumn method) (tool_shed.grids.repository_grids.ToolDependenciesGrid.ToolDependencyColumn method) (tool_shed.grids.repository_grids.ToolsGrid.ToolsColumn method) (tool_shed.grids.repository_grids.ValidCategoryGrid.RepositoriesColumn method) (tool_shed.grids.repository_grids.ValidRepositoryGrid.CategoryColumn method) (tool_shed.grids.repository_grids.ValidRepositoryGrid.InstallableRevisionColumn method) (tool_shed.grids.repository_review_grids.ComponentGrid.DescriptionColumn method) (tool_shed.grids.repository_review_grids.ComponentGrid.NameColumn method) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid.ApprovedColumn method) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid.RatingColumn method) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid.ReviewersColumn method) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid.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_versions() (galaxy.tools.toolbox.lineages.interface.ToolLineage method) (galaxy.tools.toolbox.lineages.ToolLineage method) get_visualization() (galaxy.visualization.plugins.registry.VisualizationsRegistry method) (galaxy.web.base.controller.UsesVisualizationMixin method) get_visualization_config() (galaxy.web.base.controller.UsesVisualizationMixin method) get_visualization_dict() (galaxy.web.base.controller.UsesVisualizationMixin method) get_visualization_revision_dict() (galaxy.web.base.controller.UsesVisualizationMixin method) get_visualization_summary_dict() (galaxy.web.base.controller.UsesVisualizationMixin method) get_visualization_url() (galaxy.visualization.plugins.registry.VisualizationsRegistry 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.web.base.controller.UsesVisualizationMixin method) get_visualizations_shared_with_user() (galaxy.web.base.controller.UsesVisualizationMixin method) get_work_dir_outputs() (galaxy.jobs.runners.BaseJobRunner method) get_workflow() (in module galaxy.webapps.reports.controllers.workflows) get_workflow_data_inputs() (in module tool_shed.util.workflow_util) get_workflow_data_outputs() (in module tool_shed.util.workflow_util) get_workflow_from_dict() (in module tool_shed.util.workflow_util) get_workflow_menu() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] get_workflow_module_name() (in module tool_shed.util.workflow_util) get_workflows_list() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] get_working_directory() (galaxy.model.Task method) getattr_recursive() (in module galaxy.visualization.plugins.utils) getmember() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.CompressedFile method) getmembers() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.CompressedFile method) getmembers_tar() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.CompressedFile method) getmembers_zip() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.CompressedFile method) getMissval() (in module galaxy.datatypes.converters.lped_to_pbed_converter) getname() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.CompressedFile method) getname_tar() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.CompressedFile method) getname_zip() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.CompressedFile method) getSnpeffVersionFromFile() (galaxy.datatypes.text.SnpEffDb method) 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) gie_list() (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) Gif (class in galaxy.datatypes.images) git_execute() (in module galaxy.tools.deps.brew_exts) GitDataResolver (class in galaxy.tools.verify.test_data) 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.page.PageListGrid attribute) (galaxy.webapps.galaxy.controllers.user.UserOpenIDGrid 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) GodockerJobRunner (class in galaxy.jobs.runners.godocker) GolangProxyLauncher (class in galaxy.web.proxy) grant() (galaxy.managers.rbac_secured.AccessDatasetRBACPermission method) (galaxy.managers.rbac_secured.ManageDatasetRBACPermission method) (galaxy.managers.rbac_secured.RBACPermission method) GraphiteMiddleware (class in galaxy.web.framework.middleware.graphite) grd (class in galaxy.datatypes.molecules) grdtgz (class in galaxy.datatypes.molecules) Grid (class in galaxy.web.framework.helpers.grids) grid_fields() (galaxy.model.FormDefinition method) GridAction (class in galaxy.web.framework.helpers.grids) GridColumn (class in galaxy.web.framework.helpers.grids) GridColumnFilter (class in galaxy.web.framework.helpers.grids) GridOperation (class in galaxy.web.framework.helpers.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 galaxy.webapps.tool_shed.controllers.groups) (class in galaxy.webapps.tool_shed.model) group (galaxy.webapps.tool_shed.model.GroupRoleAssociation attribute) (galaxy.webapps.tool_shed.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.webapps.tool_shed.model.GroupRoleAssociation attribute) (galaxy.webapps.tool_shed.model.UserGroupAssociation attribute) group_list_grid (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) (galaxy.webapps.tool_shed.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 galaxy.webapps.tool_shed.model) GroupRolesAPIController (class in galaxy.webapps.galaxy.api.group_roles), [1] groups (galaxy.webapps.tool_shed.model.Role attribute) groups_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) GroupsController (class in galaxy.webapps.tool_shed.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_derived_permissions_for_datasets() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) guess_ext() (in module galaxy.datatypes.sniff) guess_galaxy_port() (galaxy.config.Configuration method) guess_shed_config() (galaxy.model.tool_shed_install.ToolShedRepository method) guess_type() (galaxy.datatypes.tabular.BaseCSV method) GUID_TYPE (galaxy.tools.data_manager.manager.DataManager attribute) GzipDataProvider (class in galaxy.datatypes.dataproviders.external)

H

H5 (class in galaxy.datatypes.binary) Hamamatsu (class in galaxy.datatypes.images) handle_action_shell_file_paths() (tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder.EnvFileBuilder method) handle_bz2() (in module tool_shed.util.commit_util) handle_circular_repository_dependency() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) handle_command() (tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method) handle_comment() (tool_shed.util.xml_util.Py26CommentedTreeBuilder method) handle_complex_command() (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() (tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Repository method) handle_compressed_file() (in module galaxy.datatypes.sniff) handle_controller_exception() (galaxy.web.framework.base.WebApplication method) (galaxy.web.framework.webapp.WebApplication method) handle_current_repository_dependency() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) handle_data() (galaxy.webapps.galaxy.controllers.workflow.SingleTagContentsParser 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_environment_variables() (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() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) handle_found_index_file() (galaxy.tools.data.TabularToolDataTable method) handle_galaxy_url() (in module tool_shed.util.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_missing_data_table_entry() (tool_shed.tools.data_table_manager.ShedToolDataTableManager method) handle_missing_index_file() (in module 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) handle_outputs() (in module galaxy.tools.cwl) (in module galaxy.tools.cwl.runtime_actions) handle_panel_update() (galaxy.tools.ToolBox method) (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) handle_population_failed() (galaxy.model.DatasetCollection method) handle_repository_contents() (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() (tool_shed.metadata.metadata_generator.MetadataGenerator method) handle_repository_install() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) handle_repository_uninstall() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) handle_request() (galaxy.web.framework.base.WebApplication method) (galaxy.webapps.tool_shed.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() (tool_shed.tools.data_table_manager.ShedToolDataTableManager method) handle_signal() (in module galaxy.main) handle_single_execution() (galaxy.tools.Tool 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_dependency_install() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) handle_tool_panel_section() (tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) handle_tool_panel_selection() (tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) handle_tool_shed_repositories() (tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) handle_tool_shed_url_protocol() (in module tool_shed.util.common_util) handle_uploaded_dataset_file() (in module galaxy.datatypes.sniff) handle_user_login() (galaxy.web.framework.webapp.GalaxyWebTransaction method) handle_user_logout() (galaxy.web.framework.webapp.GalaxyWebTransaction method) hapmapmart() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) has_access_permission() (galaxy.managers.datasets.DatasetManager method) has_accessible_folders() (galaxy.security.GalaxyRBACAgent method) has_accessible_library_datasets() (galaxy.security.GalaxyRBACAgent method) has_been_resubmitted() (galaxy.managers.hdas.HDAManager method) has_collections() (galaxy.dataset_collections.matching.CollectionsToMatch method) has_data() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) (galaxy.visualization.data_providers.basic.BaseDataProvider method) (galaxy.visualization.data_providers.genome.BBIDataProvider method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) has_dataprovider() (galaxy.datatypes.data.Data method) has_dataproviders() (in module galaxy.datatypes.dataproviders.decorators) has_doi() (galaxy.managers.citations.BaseCitation method) (galaxy.managers.citations.DoiCitation method) has_env() (galaxy.tools.deps.conda_util.CondaContext method) has_failed_outputs() (galaxy.tools.parameters.output_collect.LegacyToolProvidedMetadata method) (galaxy.tools.parameters.output_collect.NullToolProvidedMetadata method) (galaxy.tools.parameters.output_collect.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) (galaxy.web.stack.UWSGIApplicationStack method) 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) (galaxy.webapps.tool_shed.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.dataset_collections.type_description.CollectionTypeDescription method) has_subcollections_of_type() (galaxy.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.tools.deps.containers) hash() (galaxy.containers.docker_model.DockerAttributeContainer method) hash_dependencies() (galaxy.tools.deps.CachedDependencyManager method) hash_password() (in module galaxy.security.passwords) hash_password_PBKDF2() (in module galaxy.security.passwords) 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 tool_shed.util.shed_util_common) hda_match() (galaxy.tools.parameters.dataset_matcher.DatasetMatcher method) 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] HDASerializer (class in galaxy.managers.hdas) hdca_match() (galaxy.tools.parameters.dataset_matcher.DatasetCollectionMatcher method) 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) Heartbeat (class in galaxy.util.heartbeat) help (galaxy.tools.Tool attribute) help() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) help_by_page (galaxy.tools.Tool attribute) HgController (class in galaxy.webapps.tool_shed.controllers.hg) hgweb_config (galaxy.webapps.tool_shed.util.hgweb_config.HgWebConfigManager attribute) HgWebConfigManager (class in galaxy.webapps.tool_shed.util.hgweb_config) hidden (galaxy.util.pastescript.serve.Command 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) HistoriesController (class in galaxy.webapps.galaxy.api.histories), [1] History (class in galaxy.model) (class in galaxy.webapps.reports.controllers.history) history (galaxy.web.framework.webapp.GalaxyWebTransaction 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_content_type (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) history_data() (galaxy.webapps.galaxy.controllers.history.HistoryController method) 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.security.GalaxyRBACAgent method) history_handle_annotation() (in module galaxy.model.search) history_handle_tag() (in module galaxy.model.search) history_import() (galaxy.webapps.galaxy.controllers.root.RootController method) history_new() (galaxy.webapps.galaxy.controllers.root.RootController method) history_per_user() (galaxy.webapps.reports.controllers.users.Users method) history_set_default_permissions() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) 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] 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) HistoryDatasetAssociation (class in galaxy.model) HistoryDatasetAssociationAnnotationAssociation (class in galaxy.model) HistoryDatasetAssociationDisplayAtAuthorization (class in galaxy.model) HistoryDatasetAssociationHistory (class in galaxy.model) HistoryDatasetAssociationListGrid (class in galaxy.webapps.galaxy.controllers.dataset) HistoryDatasetAssociationListGrid.HistoryColumn (class in galaxy.webapps.galaxy.controllers.dataset) HistoryDatasetAssociationListGrid.StatusColumn (class in galaxy.webapps.galaxy.controllers.dataset) HistoryDatasetAssociationRatingAssociation (class in galaxy.model) HistoryDatasetAssociationSelectionGrid (class in galaxy.webapps.galaxy.controllers.page) HistoryDatasetAssociationSubset (class in galaxy.model) HistoryDatasetAssociationTagAssociation (class in galaxy.model) HistoryDatasetCollectionAnnotationAssociation (class in galaxy.model) HistoryDatasetCollectionAssociation (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) HistoryDatasetView (class in galaxy.model.search) HistoryDeserializer (class in galaxy.managers.histories) HistoryField (class in galaxy.web.form_builder) HistoryFilters (class in galaxy.managers.histories) HistoryListGrid (class in galaxy.webapps.galaxy.controllers.history) HistoryListGrid.DelayedValueColumn (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) 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) 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_directory() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.JobWrapper method) (galaxy.jobs.SharedComputeEnvironment method) home_target (galaxy.jobs.JobWrapper attribute) HomebrewDependency (class in galaxy.tools.deps.resolvers.resolver_mixins) HomebrewDependencyResolver (class in galaxy.tools.deps.resolvers.homebrew) HomebrewRecipe (class in galaxy.tools.deps.brew_util) HomebrewToolShedDependencyResolver (class in galaxy.tools.deps.resolvers.brewed_tool_shed_packages) HomePage (class in galaxy.webapps.reports.controllers.home) homepage_url (galaxy.webapps.tool_shed.model.Repository attribute) host (galaxy.containers.docker.DockerInterface attribute) (galaxy.web.proxy.ProxyMapping attribute) HostAgent (class in galaxy.security) Html (class in galaxy.datatypes.images) (class in galaxy.datatypes.text) html_table (galaxy.datatypes.genetics.RexpBase attribute) HttpsToolResolver (class in galaxy.tools.locations.http) HttpToolResolver (class in galaxy.tools.locations.file) (class in galaxy.tools.locations.http) humanize() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method)

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.tools.data_manager.manager.DataManager attribute) (galaxy.util.jstree.Path attribute) (galaxy.webapps.tool_shed.model.APIKeys attribute) (galaxy.webapps.tool_shed.model.Category attribute) (galaxy.webapps.tool_shed.model.Component attribute) (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.GalaxySession attribute) (galaxy.webapps.tool_shed.model.Group attribute) (galaxy.webapps.tool_shed.model.GroupRoleAssociation attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.RepositoryCategoryAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.RepositoryRoleAssociation attribute) (galaxy.webapps.tool_shed.model.Role attribute) (galaxy.webapps.tool_shed.model.Tag attribute) (galaxy.webapps.tool_shed.model.User attribute) (galaxy.webapps.tool_shed.model.UserGroupAssociation attribute) (galaxy.webapps.tool_shed.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) Idat (class in galaxy.datatypes.binary) IdeasPre (class in galaxy.datatypes.genetics) identifier() (galaxy.tools.wrappers.ElementIdentifierMapper method) 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.DockerCLIInterface method) image_name() (in module galaxy.tools.deps.mulled.util) image_repodigest() (galaxy.containers.docker.DockerInterface method) image_type() (in module galaxy.util.image_util) 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) impl (galaxy.model.custom_types.JSONType attribute) (galaxy.model.custom_types.TrimmedString attribute) (galaxy.model.custom_types.UUIDType attribute) ImplicitCollectionJobs (class in galaxy.model) ImplicitCollectionJobsJobAssociation (class in galaxy.model) ImplicitlyConvertedDatasetAssociation (class in galaxy.model) ImplicitlyCreatedDatasetCollectionInput (class in galaxy.model) import_capsule() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method), [1] (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) import_new_workflow_deprecated() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] import_repository_archive() (tool_shed.capsule.capsule_manager.ImportRepositoryManager method) import_shared_workflow_deprecated() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] import_visualization() (galaxy.web.base.controller.UsesVisualizationMixin method) import_workflow() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method), [1] (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (in module tool_shed.util.workflow_util) import_workflows() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method), [1] imported_macro_paths() (in module galaxy.tools.loader) (in module galaxy.util.xml_macros) importer() (in module galaxy.jobs.dynamic_tool_destination) ImportHistoryTool (class in galaxy.tools) ImportHistoryToolAction (class in galaxy.tools.actions.history_imp_exp) ImportRepositoryManager (class in tool_shed.capsule.capsule_manager) ImportsHistoryMixin (class in galaxy.web.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) 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) includes_data_managers (galaxy.model.tool_shed_install.ToolShedRepository attribute) includes_datatypes (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) includes_tool_dependencies (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) includes_tools (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) includes_tools_for_display_in_tool_panel (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) includes_workflows (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) InconsistentDatabase increase_running_job_count() (galaxy.jobs.handler.JobHandlerQueue method) indent() (in module tool_shed.util.xml_util) index() (galaxy.tools.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController method), [1] (galaxy.webapps.galaxy.api.configuration.ConfigurationController 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.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.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_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.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.data_manager.DataManager 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.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) (galaxy.webapps.tool_shed.api.categories.CategoriesController method), [1] (galaxy.webapps.tool_shed.api.groups.GroupsController method), [1] (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method), [1] (galaxy.webapps.tool_shed.api.repository_revisions.RepositoryRevisionsController method), [1] (galaxy.webapps.tool_shed.api.tools.ToolsController method), [1] (galaxy.webapps.tool_shed.api.users.UsersController method), [1] (galaxy.webapps.tool_shed.controllers.groups.Group method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) (galaxy.webapps.tool_shed.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) indexes() (galaxy.webapps.galaxy.api.genomes.GenomesController method), [1] IndividualTagsColumn (class in galaxy.web.framework.helpers.grids) InfernalCM (class in galaxy.datatypes.msa) Inflector (class in galaxy.util.inflection) info (galaxy.model.LibraryDataset attribute) info() (galaxy.tools.lint.LintContext method) info_text (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) inheritable (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute) init() (in module galaxy.model.mapping) (in module galaxy.model.tool_shed_install.mapping) (in module galaxy.webapps.tool_shed.model.mapping) 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) init_models_from_config() (in module galaxy.config) init_new_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method) initialize() (galaxy.tools.DefaultToolState method) initialize_all_repository_dependencies() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) initiate_repository_installation() (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_connections_by_name (galaxy.model.WorkflowStep attribute) input_paths() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) input_step_types (galaxy.model.Workflow attribute) input_steps (galaxy.model.Workflow attribute) InputDataCollectionModule (class in galaxy.workflow.modules) InputDataModule (class in galaxy.workflow.modules) InputMatchedException InputModule (class in galaxy.workflow.modules) InputParameterModule (class in galaxy.workflow.modules) inputs() (galaxy.webapps.galaxy.api.jobs.JobController method), [1] inputs_defined (galaxy.tools.parser.interface.PagesSource attribute) (galaxy.tools.parser.xml.XmlPagesSource attribute) InputSource (class in galaxy.tools.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.tools.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.DockerCLIInterface method) Install (class in tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler) install() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method), [1] (tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) install_all() (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method) install_and_build_package() (tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) install_and_build_package_via_fabric() (tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) install_conda() (in module galaxy.tools.deps.conda_util) install_conda_target() (in module galaxy.tools.deps.conda_util) install_data_managers() (tool_shed.galaxy_install.tools.data_manager.DataManagerHandler method) install_dependencies() (galaxy.tools.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] install_dependency() (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method) (galaxy.tools.deps.resolvers.InstallableDependencyResolver method) (galaxy.tools.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method), [1] install_environment (galaxy.tools.deps.conda_util.CondaTarget attribute) install_latest_repository_revision() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) install_matched_repository_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute)

install_model (galaxy.managers.context.ProvidesAppContext attribute) install_package() (tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) install_repositories() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) install_repositories_by_revision() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) install_repository() (tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager 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() (tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) install_tool_data_tables() (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() (tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) install_via_fabric() (tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) install_virtualenv() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupVirtualEnv method) installable_description (galaxy.tools.deps.conda_util.CondaContext attribute) (galaxy.tools.deps.installable.InstallableContext attribute) installable_resolvers (galaxy.tools.deps.views.DependencyResolversView attribute) installable_revisions() (galaxy.webapps.tool_shed.model.Repository method) InstallableContext (class in galaxy.tools.deps.installable) InstallableDependencyResolver (class in galaxy.tools.deps.resolvers) installation_complete() (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_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 tool_shed.galaxy_install.installed_repository_manager) InstalledRepositoryMetadataManager (class in tool_shed.galaxy_install.metadata.installed_repository_metadata_manager) InstallEnvironment (class in tool_shed.galaxy_install.tool_dependencies.recipe.install_environment) InstallMatchedRepositoryGrid (class in tool_shed.grids.repository_grids) InstallRepositoryManager (class in tool_shed.galaxy_install.install_manager) InstallToolDependencyManager (class in tool_shed.galaxy_install.install_manager) instance_id (galaxy.web.stack.UWSGIApplicationStack attribute) InstrumentPlugin (class in galaxy.jobs.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) IntegerToolParameter (class in galaxy.tools.parameters.basic) INTENV_REQUEST_FACTORY (galaxy.visualization.plugins.plugin.InteractiveEnvironmentPlugin attribute) InteractiveEnvironmentPlugin (class in galaxy.visualization.plugins.plugin) InteractiveEnvironmentsController (class in galaxy.webapps.galaxy.controllers.interactive_environments) 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) invalidate_external_metadata() (galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper method) (galaxy.jobs.JobWrapper method) (galaxy.model.metadata.JobExternalOutputMetadataWrapper method) InvalidDataManager (class in tool_shed.utility_containers.utility_container_manager) InvalidDataProviderSource 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_step() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] invoke() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] (in module galaxy.util.pastescript.serve) (in module galaxy.workflow.run) Ipynb (class in galaxy.datatypes.text) IQTree (class in galaxy.datatypes.text) IRODSObjectStore (class in galaxy.objectstore.rods) is_a_yaml_with_class() (in module galaxy.tools.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_admin() (galaxy.managers.users.UserManager method) is_admin_user() (galaxy.config.Configuration method) (galaxy.webapps.tool_shed.config.Configuration method) is_anonymous() (galaxy.managers.users.UserManager method) is_binary (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.genetics.RexpBase attribute) (galaxy.datatypes.ngsindex.BowtieIndex attribute) is_binary() (in module galaxy.util) is_bz2() (in module galaxy.datatypes.checkers) (in module galaxy.util.checkers) is_case() (galaxy.tools.parser.output_actions.DatatypeIsInstanceToolOutputActionConditionalWhen method) (galaxy.tools.parser.output_actions.ToolOutputActionConditionalWhen method) (galaxy.tools.parser.output_actions.ValueToolOutputActionConditionalWhen method) is_check_time (galaxy.model.DeferredJob attribute) is_checked() (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.tools.deps.conda_util.CondaContext method) is_current_version() (galaxy.tools.data.ToolDataTable method) is_data_index_sample_file() (in module tool_shed.util.tool_util) is_datasource() (in module galaxy.tools.lint_util) is_deactivated_or_installed (galaxy.model.tool_shed_install.ToolShedRepository attribute) is_deprecated_in_tool_shed (galaxy.model.tool_shed_install.ToolShedRepository attribute) is_destruction_time() (galaxy.containers.docker_swarm_manager.SwarmState 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.util.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() (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.tools.deps.conda_util.CondaContext method) (galaxy.tools.deps.installable.InstallableContext method) is_int() (galaxy.datatypes.tabular.BaseCSV 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_leaf (galaxy.dataset_collections.structure.Leaf attribute) (galaxy.dataset_collections.structure.Tree attribute) (galaxy.dataset_collections.structure.UnitializedTree attribute) is_level_one_certified() (tool_shed.repository_registry.Registry method) is_malicious() (in module tool_shed.util.metadata_util) is_managed() (galaxy.containers.docker_model.DockerNode method) is_missing_shed_tool() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) is_named_collection_part_name() (galaxy.tools.parser.output_objects.ToolOutputCollectionPart static method) (galaxy.tools.parser.ToolOutputCollectionPart static method) is_new (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.model.WorkflowInvocationStep attribute) is_new() (galaxy.webapps.tool_shed.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 (galaxy.webapps.tool_shed.model.Role attribute) is_runtime_value() (in module galaxy.tools.parameters.basic) is_subcollection_of_type() (galaxy.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.tools.loader_directory) is_tool_module_type() (in module galaxy.workflow.modules) is_tool_shed_client() (in module tool_shed.util.repository_util) is_true() (in module galaxy.web.framework.helpers) is_uuid() (in module galaxy.util) is_valid (galaxy.webapps.tool_shed.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) isdir() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.CompressedFile method) isdir_tar() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.CompressedFile method) isdir_zip() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.CompressedFile method) isfile() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.CompressedFile method) isinstance_datatype() (galaxy.managers.datasets.DatasetAssociationFilterParser method) item_has_tag() (galaxy.managers.tags.TagManager method) item_permission_map_for_add() (galaxy.security.GalaxyRBACAgent method) item_permission_map_for_manage() (galaxy.security.GalaxyRBACAgent method) item_permission_map_for_modify() (galaxy.security.GalaxyRBACAgent method) item_to_api_value() (galaxy.model.search.SearchQuery method) ItemAccessibilityException ItemDeletionException ItemOwnershipException ItemRatingAssociation (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) ItemRatings (class in galaxy.webapps.tool_shed.util.ratings_util) items() (galaxy.dataset_collections.matching.CollectionsToMatch method) (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.jobs.runners.util.Bunch 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 galaxy.webapps.tool_shed.model) ItemTagAssocInfo (class in galaxy.managers.tags) iter() (galaxy.datatypes.metadata.MetadataSpecCollection method) (galaxy.model.metadata.MetadataSpecCollection method) iter_blocks_split_by_species() (in module galaxy.tools.util.maf_utilities) iter_blocks_split_by_src() (in module galaxy.tools.util.maf_utilities) iter_components_by_src() (in module galaxy.tools.util.maf_utilities) iter_components_by_src_start() (in module galaxy.tools.util.maf_utilities) iter_fasta_alignment() (in module galaxy.tools.util.maf_utilities) iter_headers() (in module galaxy.datatypes.sniff) 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

Job (class in galaxy.model) job_count() (galaxy.jobs.rule_helper.RuleHelper method) job_destination (galaxy.jobs.JobWrapper attribute) job_failed() (galaxy.tools.SetMetadataTool method) (galaxy.tools.Tool method) job_hash() (galaxy.jobs.rule_helper.RuleHelper method) job_info() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy 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_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.jobs.metrics.instrumenters.collectl.CollectlPlugin method) (galaxy.jobs.metrics.instrumenters.InstrumentPlugin method) (galaxy.jobs.metrics.instrumenters.core.CorePlugin method) (galaxy.jobs.metrics.instrumenters.cpuinfo.CpuInfoPlugin method) (galaxy.jobs.metrics.instrumenters.env.EnvPlugin method) (galaxy.jobs.metrics.instrumenters.meminfo.MemInfoPlugin method) (galaxy.jobs.metrics.instrumenters.uname.UnamePlugin method) JOB_RESOURCE_CONDITIONAL_XML (galaxy.jobs.JobConfiguration 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.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_wrapper() (galaxy.jobs.handler.JobHandlerQueue method) JobConfiguration (class in galaxy.jobs) JobContext (class in galaxy.tools.parameters.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.datatypes.metadata) (class in galaxy.model.metadata) JobFilesAPIController (class in galaxy.webapps.galaxy.api.job_files), [1] JobHandler (class in galaxy.jobs.handler) 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.tools.deps.containers) JobInstrumenter (class in galaxy.jobs.metrics)

JobLike (class in galaxy.model) JobManager (class in galaxy.jobs.manager) JobMappingException JobMetricFormatter (class in galaxy.jobs.metrics.formatting) JobMetricNumeric (class in galaxy.model) JobMetrics (class in galaxy.jobs.metrics) JobMetricText (class in galaxy.model) JobNotReadyException JobParameter (class in galaxy.model) JobRunnerMapper (class in galaxy.jobs.mapper) Jobs (class in galaxy.webapps.reports.controllers.jobs) jobs (galaxy.model.WorkflowInvocationStep attribute) jobs() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) 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) 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) Jpg (class in galaxy.datatypes.images) js() (in module galaxy.web.framework.helpers) JS_APP_MAKO_FILEPATH (galaxy.web.base.controller.JSAppLauncher attribute) js_helper() (in module galaxy.web.framework.helpers) JSAppLauncher (class in galaxy.web.base.controller) Json (class in galaxy.datatypes.text) json() (galaxy.webapps.tool_shed.api.tools.ToolsController method), [1] (in module galaxy.web) (in module galaxy.web.framework.decorators) json_fix() (in module galaxy.util.json) 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.tools.parameters.output_collect) jsonData() (galaxy.util.jstree.JSTree method) (galaxy.util.jstree.Node method) JsonFileProxyIpc (class in galaxy.web.proxy) Jsonld (class in galaxy.datatypes.triples) 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)

K

key (galaxy.containers.ContainerInterface attribute) (galaxy.webapps.tool_shed.model.APIKeys attribute) key_is_current_repositorys_key() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) keys() (galaxy.jobs.runners.util.Bunch method) (galaxy.tools.wrappers.DatasetCollectionWrapper method) (galaxy.util.bunch.Bunch method) (galaxy.util.odict.odict method)

kill_command() (in module galaxy.tools.deps.docker_util) kill_pid() (in module galaxy.jobs.runners.util) (in module galaxy.jobs.runners.util.kill) known_outputs() (galaxy.tools.parser.output_objects.ToolOutputCollection method) KubernetesJobRunner (class in galaxy.jobs.runners.kubernetes)

L

label (galaxy.containers.docker_model.DockerServiceConstraint attribute) (galaxy.tools.parameters.grouping.Conditional attribute) label() (galaxy.tools.parameters.grouping.Repeat method) (galaxy.tools.parameters.grouping.Section method) label_add() (galaxy.containers.docker_model.DockerNode method) 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.webapps.tool_shed.model.GalaxySession attribute) last_check (galaxy.model.DeferredJob attribute) LastzCoverage (class in galaxy.datatypes.coverage) latest_export (galaxy.model.History attribute) launch_proxy_command() (galaxy.web.proxy.GolangProxyLauncher method) (galaxy.web.proxy.NodeProxyLauncher method) (galaxy.web.proxy.ProxyLauncher method) Lav (class in galaxy.datatypes.sequence) 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) LDAP (class in galaxy.auth.providers.ldap_ad) ldap_search() (galaxy.auth.providers.ldap_ad.LDAP method) 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.dataset_collections.structure) LegacyToolProvidedMetadata (class in galaxy.tools.parameters.output_collect) legal_values (galaxy.tools.parameters.basic.BooleanToolParameter attribute) legend (galaxy.web.framework.helpers.grids.Grid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) LengthValidator (class in galaxy.tools.parameters.validation) LibrariesController (class in galaxy.webapps.galaxy.api.libraries), [1] Library (class in galaxy.model) (class in galaxy.webapps.galaxy.controllers.library) library_dataset_name_filter() (in module galaxy.model.search) library_extended_metadata_filter() (in module galaxy.model.search) library_folder_parent_library_id_filter() (in module galaxy.model.search) library_is_public() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) library_is_unrestricted() (galaxy.security.GalaxyRBACAgent method) library_path (galaxy.model.LibraryFolder attribute) library_path_filter() (in module galaxy.model.search) LibraryContentsController (class in galaxy.webapps.galaxy.api.library_contents), [1] LibraryDataset (class in galaxy.model) LibraryDatasetCollectionAnnotationAssociation (class in galaxy.model) LibraryDatasetCollectionAssociation (class in galaxy.model) LibraryDatasetCollectionRatingAssociation (class in galaxy.model) LibraryDatasetCollectionTagAssociation (class in galaxy.model) LibraryDatasetDatasetAssociation (class in galaxy.model) LibraryDatasetDatasetAssociationPermissions (class in galaxy.model) LibraryDatasetDatasetAssociationTagAssociation (class in galaxy.model) LibraryDatasetDatasetInfoAssociation (class in galaxy.model) LibraryDatasetDatasetView (class in galaxy.model.search) LibraryDatasetExtendMetadataController (class in galaxy.webapps.galaxy.api.extended_metadata), [1] LibraryDatasetPermissions (class in galaxy.model) 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) LibraryManager (class in galaxy.managers.libraries) LibraryPermissions (class in galaxy.model) LibraryView (class in galaxy.model.search) 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.tools.util.maf_utilities) 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) LinkageStudies (class in galaxy.datatypes.genetics) lint() (galaxy.tools.lint.LintContext method) lint_citations() (in module galaxy.tools.linters.citations) lint_command() (in module galaxy.tools.linters.command) lint_general() (in module galaxy.tools.linters.general) lint_help() (in module galaxy.tools.linters.help) lint_inputs() (in module galaxy.tools.linters.inputs) lint_output() (in module galaxy.tools.linters.outputs) lint_repeats() (in module galaxy.tools.linters.inputs) lint_stdio() (in module galaxy.tools.linters.stdio) lint_tool_source() (in module galaxy.tools.lint) lint_tool_source_with() (in module galaxy.tools.lint) lint_tsts() (in module galaxy.tools.linters.tests) lint_xml() (in module galaxy.tools.lint) lint_xml_order() (in module galaxy.tools.linters.xml_order) lint_xml_with() (in module galaxy.tools.lint) LintContext (class in galaxy.tools.lint) list() (galaxy.managers.base.ModelManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) (galaxy.webapps.galaxy.controllers.library.Library method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) (tool_shed.managers.groups.GroupManager method) list_accessible() (galaxy.managers.secured.AccessibleManagerMixin method) list_as_xml() (galaxy.webapps.galaxy.controllers.history.HistoryController method) list_by_owner() (tool_shed.managers.repositories.RepoManager method) list_datasets_for_selection() (galaxy.webapps.galaxy.controllers.page.PageController method) list_dependencies() (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method) (galaxy.tools.deps.resolvers.ListableDependencyResolver method) (galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependencyResolver 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_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_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.tools.deps.resolvers) ListDatasetCollectionType (class in galaxy.dataset_collections.types.list) listify (tool_shed.utility_containers.utility_container_manager.RepositoryDependency attribute) (tool_shed.utility_containers.utility_container_manager.ToolDependency attribute) listify() (in module galaxy.util) ListParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) live_pidfile() (in module galaxy.util.pastescript.serve) load() (galaxy.util.aliaspickler.AliasPickleModule method) (in module galaxy.util.xml_macros) load_app_properties() (in module galaxy.util.properties) load_certified_level_one_repository_and_suite_tuple() (tool_shed.repository_registry.Registry method) load_datatype_converters() (galaxy.datatypes.registry.Registry method) load_datatype_sniffers() (galaxy.datatypes.registry.Registry method) load_datatypes() (galaxy.datatypes.registry.Registry method) load_dependency_relationships() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager 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_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_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() (tool_shed.galaxy_install.datatypes.custom_datatype_manager.CustomDatatypeLoader method) load_installed_datatypes() (tool_shed.galaxy_install.datatypes.custom_datatype_manager.CustomDatatypeLoader method) load_installed_display_applications() (tool_shed.galaxy_install.datatypes.custom_datatype_manager.CustomDatatypeLoader method) load_invalid_tool() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) load_item() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) load_job_proxy() (in module galaxy.tools.cwl.parser) load_lib_tools() (in module galaxy.tools.special_tools) load_manager_from_elem() (galaxy.tools.data_manager.manager.DataManagers method) load_module_sections() (in module galaxy.workflow.modules) load_plugins() (in module galaxy.util.plugin_config) load_proprietary_converters_and_display_applications() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) load_proprietary_datatypes() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager 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() (tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager.StepManager method) load_tag_handlers() (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.tools.loader) load_tool_elements_from_path() (in module galaxy.tools.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() (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.tools.loader_directory) load_tool_with_refereces() (in module galaxy.tools.loader) load_tour() (galaxy.tours.ToursRegistry method) load_tours() (galaxy.tours.ToursRegistry method) load_versioned_deps() (in module galaxy.tools.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) loadapp() (in module galaxy.util.pastescript.loadwsgi) loadfilter() (in module galaxy.util.pastescript.loadwsgi) loads() (galaxy.util.aliaspickler.AliasPickleModule method) loadserver() (in module galaxy.util.pastescript.loadwsgi) local_extra_dirs() (in module galaxy.objectstore) 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) LocFileEventHandler (class in galaxy.tools.toolbox.watcher) lock (galaxy.tools.toolbox.lineages.interface.ToolLineage attribute) (galaxy.tools.toolbox.lineages.ToolLineage attribute) LOG (galaxy.jobs.error_level.StdioErrorLevel attribute) 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_results() (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.WorkflowStep method) log_tempfile (module) log_user_action_async() (galaxy.webapps.galaxy.controllers.user.User method) 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.root.RootController method) (galaxy.webapps.galaxy.controllers.user.User method) logout() (galaxy.webapps.galaxy.controllers.user.User method) logs_command() (in module galaxy.tools.deps.docker_util) long_description (galaxy.webapps.tool_shed.model.Repository attribute) looks_like_a_cwl_artifact() (in module galaxy.tools.loader_directory) looks_like_a_tool_cwl() (in module galaxy.tools.loader_directory) looks_like_a_tool_xml() (in module galaxy.tools.loader_directory) looks_like_a_tool_yaml() (in module galaxy.tools.loader_directory) LowerTriangleDistanceMatrix (class in galaxy.datatypes.mothur) Lped (class in galaxy.datatypes.genetics)

M

Maf (class in galaxy.datatypes.sequence) maf_index_by_uid() (in module galaxy.tools.util.maf_utilities) MafCustomTrack (class in galaxy.datatypes.sequence) main() (in module galaxy.containers.docker_swarm_manager) (in module galaxy.datatypes.converters.bedgraph_to_array_tree_converter) (in module galaxy.datatypes.converters.bgzip) (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_coverage) (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_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_array_tree_converter) (in module galaxy.datatypes.converters.wiggle_to_simple_converter) (in module galaxy.main) (in module galaxy.tools.deps.brew_exts) (in module galaxy.tools.deps.mulled.mulled_build) (in module galaxy.tools.deps.mulled.mulled_build_channel) (in module galaxy.tools.deps.mulled.mulled_build_files) (in module galaxy.tools.deps.mulled.mulled_build_tool) (in module galaxy.tools.deps.mulled.mulled_search) (in module galaxy.tools.imp_exp.export_history) (in module galaxy.tools.imp_exp.unpack_tar_gz_archive) make_backup() (galaxy.webapps.tool_shed.util.hgweb_config.HgWebConfigManager method) make_body_iterable() (galaxy.web.framework.base.WebApplication method) (galaxy.web.framework.webapp.WebApplication method) make_catching_iter() (galaxy.web.framework.middleware.error.ErrorMiddleware method) make_copy() (galaxy.datatypes.metadata.FileParameter method) (galaxy.datatypes.metadata.MetadataParameter method) (galaxy.model.metadata.FileParameter method) (galaxy.model.metadata.MetadataParameter method) make_dataset_public() (galaxy.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() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MakeDirectory method) make_file() (galaxy.web.framework.base.FieldStorage method) make_filter() (in module galaxy.web.framework.middleware.translogger) make_folder_public() (galaxy.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.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) make_non_importable() (galaxy.managers.sharable.SharableModelManager method) make_public() (galaxy.managers.libraries.LibraryManager method) make_same_length() (in module tool_shed.util.search_util) make_self_default_handler() (galaxy.jobs.JobConfiguration method) make_static() (in module galaxy.web.framework.middleware.static) make_tag_string_list() (galaxy.model.HasTags method) make_temp_fname() (in module galaxy.tools.verify) MakeDirectory (class in tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) MakeInstall (class in 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) MAKO_TEMPLATE (galaxy.visualization.plugins.plugin.ScriptVisualizationPlugin attribute) MalformedContents MalformedId MalformedYMLException malicious (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) MAlist (class in galaxy.datatypes.genetics) manage_categories() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) manage_category_grid (galaxy.webapps.tool_shed.controllers.admin.AdminController attribute) manage_components() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) manage_data_manager() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) manage_data_table() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) manage_email_alerts() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) manage_repositories_ready_for_review() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) manage_repositories_reviewed_by_me() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) manage_repositories_with_invalid_tests() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) manage_repositories_with_reviews() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) manage_repositories_without_reviews() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) manage_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) manage_repository_admins() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) manage_repository_reviews() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) manage_repository_reviews_of_revision() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) manage_repository_tool_dependencies() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) manage_role_associations() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) manage_roles_and_groups_for_user() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) manage_tool_dependencies() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) manage_user_info() (galaxy.webapps.tool_shed.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) manage_users_and_roles_for_group() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) ManageCategoryGrid (class in tool_shed.grids.admin_grids) ManageDatasetRBACPermission (class in galaxy.managers.rbac_secured) manager (galaxy.managers.base.HasAModelManager attribute) manager_dependency() (galaxy.tools.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method), [1] manager_requirements() (galaxy.tools.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_collection_type() (in module galaxy.dataset_collections.type_description) map_port() (galaxy.containers.Container method) map_tool_to_destination() (in module galaxy.jobs.dynamic_tool_destination) map_wrap() (in module galaxy.objectstore.s3_multipart_upload) MappableDependencyResolver (class in galaxy.tools.deps.resolvers) mapped_over_output_actions (galaxy.jobs.actions.post.ActionBox attribute) mapping() (galaxy.webapps.galaxy.api.datatypes.DatatypesController method), [1] MAPPING_PRESET (galaxy.tools.parameters.sanitize.ToolParameterSanitizer attribute) 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() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) mark_deleted() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) (galaxy.model.Job method) mark_node_idle() (galaxy.containers.docker_swarm_manager.SwarmState method) mark_services_handled() (galaxy.containers.docker_swarm_manager.SwarmState method) mark_spawning_node_ready() (galaxy.containers.docker_swarm_manager.SwarmState method) mark_spawning_node_state() (galaxy.containers.docker_swarm_manager.SwarmState method) mark_spawning_node_timeout() (galaxy.containers.docker_swarm_manager.SwarmState method) mark_tool_dependency_installed() (tool_shed.galaxy_install.install_manager.InstallToolDependencyManager method) mark_undeleted() (galaxy.model.DatasetInstance method) mark_unhidden() (galaxy.model.DatasetInstance method) 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) mask_password_from_url() (in module galaxy.util) match (galaxy.tools.parameters.output_collect.DiscoveredFile attribute) match() (galaxy.tools.parameters.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 (galaxy.webapps.tool_shed.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.data.Data method) matches_requirement() (galaxy.tools.deps.resolvers.RequirementMapping method) matches_selector() (galaxy.datatypes.dataproviders.hierarchy.XMLDataProvider method) MatchingCollections (class in galaxy.dataset_collections.matching) MauveXmfa (class in galaxy.datatypes.msa) MAX (galaxy.jobs.error_level.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_LINES_RETURNED (galaxy.visualization.data_providers.basic.ColumnDataProvider attribute) max_optional_metadata_filesize (galaxy.datatypes.data.Data attribute) MAX_SEQUENCE_SIZE (galaxy.tools.util.maf_utilities.RegionAlignment attribute) 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) MemePsp (class in galaxy.datatypes.sequence) MEMEXml (class in galaxy.datatypes.xml) MemInfoPlugin (class in galaxy.jobs.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) MergeCollectionTool (class in galaxy.tools) merged_environment_name() (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method) message (galaxy.util.pastescript.serve.BadCommand attribute) (galaxy.util.pastescript.serve.Command.BadCommand attribute) message_exception() (galaxy.web.base.controller.BaseUIController method) MessageApplicationStack (class in galaxy.web.stack) MessageException MessageJobHandler (class in galaxy.jobs.manager) MessageJobQueue (class in galaxy.jobs.manager) Metadata (class in tool_shed.repository_types.metadata) metadata (galaxy.model.DatasetInstance attribute) (galaxy.tools.cwl.schema.ProcessDefinition attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) MetaData (in module galaxy.tools.deps.conda_compat) metadata() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method), [1] metadata_revisions (galaxy.webapps.tool_shed.model.Repository attribute) metadata_spec (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.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.CRAM attribute) (galaxy.datatypes.binary.Cel attribute) (galaxy.datatypes.binary.CompressedArchive attribute) (galaxy.datatypes.binary.CompressedZipArchive attribute) (galaxy.datatypes.binary.Cool attribute) (galaxy.datatypes.binary.DMND attribute) (galaxy.datatypes.binary.ExcelXls attribute) (galaxy.datatypes.binary.Fast5Archive attribute) (galaxy.datatypes.binary.Fast5ArchiveBz2 attribute) (galaxy.datatypes.binary.Fast5ArchiveGz attribute) (galaxy.datatypes.binary.GeminiSQLite attribute) (galaxy.datatypes.binary.GenericAsn1Binary attribute) (galaxy.datatypes.binary.H5 attribute) (galaxy.datatypes.binary.ICM attribute) (galaxy.datatypes.binary.Idat attribute) (galaxy.datatypes.binary.IdpDB attribute) (galaxy.datatypes.binary.MzSQlite attribute) (galaxy.datatypes.binary.NetCDF 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.PostgresqlArchive attribute) (galaxy.datatypes.binary.RData attribute) (galaxy.datatypes.binary.SQlite attribute) (galaxy.datatypes.binary.Scf attribute) (galaxy.datatypes.binary.SearchGuiArchive attribute) (galaxy.datatypes.binary.Sff attribute) (galaxy.datatypes.binary.Sra attribute) (galaxy.datatypes.binary.TwoBit attribute) (galaxy.datatypes.binary.Xlsx attribute) (galaxy.datatypes.blast.BlastDomainDb attribute) (galaxy.datatypes.blast.BlastNucDb attribute) (galaxy.datatypes.blast.BlastProtDb attribute) (galaxy.datatypes.blast.BlastXml 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.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.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.ScIdx attribute) (galaxy.datatypes.interval.Wiggle 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.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.proteomics.Analyze75 attribute) (galaxy.datatypes.proteomics.ConsensusXML attribute) (galaxy.datatypes.proteomics.FeatureXML attribute) (galaxy.datatypes.proteomics.IdXML attribute) (galaxy.datatypes.proteomics.ImzML attribute) (galaxy.datatypes.proteomics.MascotDat 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.MzXML 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.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.UniProtXML attribute) (galaxy.datatypes.proteomics.Wiff attribute) (galaxy.datatypes.proteomics.XHunterAslFormat 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.FastaGz attribute) (galaxy.datatypes.sequence.Fastq attribute) (galaxy.datatypes.sequence.FastqBz2 attribute) (galaxy.datatypes.sequence.FastqCSSanger attribute) (galaxy.datatypes.sequence.FastqCSSangerBz2 attribute) (galaxy.datatypes.sequence.FastqCSSangerGz attribute) (galaxy.datatypes.sequence.FastqGz attribute) (galaxy.datatypes.sequence.FastqIllumina attribute) (galaxy.datatypes.sequence.FastqIlluminaBz2 attribute) (galaxy.datatypes.sequence.FastqIlluminaGz attribute) (galaxy.datatypes.sequence.FastqSanger attribute) (galaxy.datatypes.sequence.FastqSangerBz2 attribute) (galaxy.datatypes.sequence.FastqSangerGz attribute) (galaxy.datatypes.sequence.FastqSolexa attribute) (galaxy.datatypes.sequence.FastqSolexaBz2 attribute) (galaxy.datatypes.sequence.FastqSolexaGz 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.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.Pileup attribute) (galaxy.datatypes.tabular.Sam 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.Html attribute) (galaxy.datatypes.text.IQTree attribute) (galaxy.datatypes.text.Ipynb attribute) (galaxy.datatypes.text.Json attribute) (galaxy.datatypes.text.Obo 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)

MetadataCollection (class in galaxy.datatypes.metadata) (class in galaxy.model.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 tool_shed.metadata.metadata_generator) MetadataInDataTableColumnValidator (class in galaxy.tools.parameters.validation) MetadataInFileColumnValidator (class in galaxy.tools.parameters.validation) MetadataParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) 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.tools.parser.output_actions) MetadataType (class in galaxy.model.custom_types) MetadataValidator (class in galaxy.tools.parameters.validation) MetadataValueFilter (class in galaxy.tools.parser.output_actions) metric_query() (galaxy.jobs.rule_helper.RuleHelper method) metrics (galaxy.model.JobLike attribute) 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.webapps.tool_shed.model.migrate.check) (in module tool_shed.galaxy_install.migrate.check) MigrateTools (class in galaxy.model.tool_shed_install) MigrateToolsApplication (class in tool_shed.galaxy_install.migrate.common) mime_type() (galaxy.datatypes.display_applications.parameters.DisplayDataValueWrapper method) (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper method) mimeparse (module) 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.util.none_like.NoneDataset method) missing_repository_dependencies (galaxy.model.tool_shed_install.ToolShedRepository attribute) missing_test_components (galaxy.webapps.tool_shed.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 mkstemp() (log_tempfile.TempFile method) mkstemp_ln() (in module galaxy.util) model (galaxy.managers.context.ProvidesAppContext attribute) model_class (galaxy.managers.base.ModelFilterParser attribute) (galaxy.managers.base.ModelManager 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.pages.PageManager attribute) (galaxy.managers.roles.RoleManager attribute) (galaxy.managers.users.AdminUserFilterParser attribute) (galaxy.managers.users.UserManager 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.dataset.HistoryDatasetAssociationListGrid 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.user.UserOpenIDGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.LibraryDatasetsSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.TracksterSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationListGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) model_manager_class (galaxy.managers.base.HasAModelManager attribute) (galaxy.managers.datasets.DatasetDeserializer 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.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 ModelFilterParser (class in galaxy.managers.base) ModelManager (class in galaxy.managers.base) ModelMapping (class in galaxy.model.base) ModelOperationToolAction (class in galaxy.tools.actions.model_operations) ModelSerializer (class in galaxy.managers.base) ModelSerializingError ModelValidator (class in galaxy.managers.base) modify_environ() (galaxy.tools.deps.brew_exts.EnvAction method) ModuleDependencyResolver (class in galaxy.tools.deps.resolvers.modules) modulize() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) 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.NullToolConfWatcher method) (galaxy.tools.toolbox.watcher.ToolConfWatcher method) (galaxy.tools.toolbox.watcher.ToolDataWatcher method) (galaxy.tools.toolbox.watcher.ToolWatcher 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) most_recent() (galaxy.managers.histories.HistoryManager method) move_directory_files() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MoveDirectoryFiles method) move_file() (in module tool_shed.util.basic_util) move_merge() (in module galaxy.util) MoveDirectoryFiles (class in tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) MoveFile (class in 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.tools.deps.mulled.util) MulledDockerContainerResolver (class in galaxy.tools.deps.container_resolvers.mulled) multi_select_email_alerts() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) MulticolFilterColumn (class in galaxy.web.framework.helpers.grids) multimap() (in module galaxy.objectstore.s3_multipart_upload) multipart_upload() (in module galaxy.objectstore.s3_multipart_upload) MultipleDependencyResolver (class in galaxy.tools.deps.resolvers) MultipleSplitterFilter (class in galaxy.tools.parameters.dynamic_options) (class in galaxy.tools.parser.output_actions) multiply() (galaxy.dataset_collections.structure.Leaf method) (galaxy.dataset_collections.structure.Tree method) (galaxy.dataset_collections.structure.UnitializedTree method) (galaxy.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 (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) my_writable_repositories_missing_tool_test_components_grid (galaxy.webapps.tool_shed.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) MzXML (class in galaxy.datatypes.proteomics)

N

N3 (class in galaxy.datatypes.triples) name (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.model.LibraryDataset attribute) (galaxy.tools.parameters.output_collect.JsonCollectedDatasetMatch attribute) (galaxy.web.stack.ApplicationStack attribute) (galaxy.web.stack.PasteApplicationStack attribute) (galaxy.web.stack.UWSGIApplicationStack attribute) (galaxy.web.stack.WeblessApplicationStack attribute) (galaxy.webapps.tool_shed.model.Category attribute) (galaxy.webapps.tool_shed.model.Component attribute) (galaxy.webapps.tool_shed.model.Group attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.Role attribute) (galaxy.webapps.tool_shed.model.Tag 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) name() (galaxy.datatypes.util.gff_util.GFFFeature method) NameColumn (class in galaxy.webapps.galaxy.controllers.history) NamedTemporaryFile() (log_tempfile.TempFile method) Names (class in galaxy.datatypes.mothur) needs_shell_quoting() (in module galaxy.tools.cwl) (in module galaxy.tools.cwl.cwltool_deps) Neo4j (class in galaxy.datatypes.neo4j) Neo4jDB (class in galaxy.datatypes.neo4j) Neo4jDBzip (class in galaxy.datatypes.neo4j) 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_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.web.framework.webapp.GalaxyWebTransaction method) new_metadata_required_for_utilities() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager 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 (galaxy.webapps.tool_shed.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 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() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) next_line_starts_with() (galaxy.datatypes.proteomics.Msp static method) 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) (galaxy.webapps.tool_shed.model.User attribute) NicerConfigParser (class in galaxy.util.properties) NicerConfigParser.InterpolateWrapper (class in galaxy.util.properties) NO_ERROR (galaxy.jobs.error_level.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_swarm.DockerSwarmInterface method) node_edge_dataprovider() (galaxy.datatypes.graph.Sif method) (galaxy.datatypes.graph.Xgmml method) node_inspect() (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) node_ls() (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) node_ps() (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) node_update() (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) NoDefault (class in galaxy.util.pastescript.serve) NodeProxyLauncher (class in galaxy.web.proxy) nodes() (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) nodes_requested() (galaxy.containers.docker_swarm_manager.SwarmState method) NON_DATA_CONNECTION (galaxy.model.WorkflowStepConnection attribute) non_data_connection (galaxy.model.WorkflowStepConnection attribute) non_private_roles (galaxy.webapps.tool_shed.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 (tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager attribute) NoneDataset (class in galaxy.util.none_like) NoopHandler (class in galaxy.jobs.manager) NoOpLazyProcess (class in galaxy.util.lazy_process) NoopQueue (class in galaxy.jobs) NoOptionsValidator (class in galaxy.tools.parameters.validation) NoProviderAvailable NoQuotaAgent (class in galaxy.quota) not_implemented() (galaxy.web.base.controller.BaseAPIController method) NotFoundCommand (class in galaxy.util.pastescript.serve) NotImplemented NotTested (class in tool_shed.utility_containers) now() (in module galaxy.model.mapping) (in module galaxy.model.orm.now) (in module galaxy.model.tool_shed_install.mapping) (in module galaxy.webapps.tool_shed.model) (in module galaxy.webapps.tool_shed.model.mapping) Nrrd (class in galaxy.datatypes.images) NTriples (class in galaxy.datatypes.triples) nullable_basestring() (galaxy.managers.base.ModelValidator method) NullContainer (class in galaxy.tools.deps.containers) NullContainerFinder (class in galaxy.tools.deps.containers) NullDatasetPathRewriter (class in galaxy.jobs.datasets) NullDependency (class in galaxy.tools.deps.resolvers) NullDependencyManager (class in galaxy.tools.deps) NullJobInstrumenter (class in galaxy.jobs.metrics) NullToolConfWatcher (class in galaxy.tools.toolbox.watcher) NullToolOutputActionOption (class in galaxy.tools.parser.output_actions) NullToolProvidedMetadata (class in galaxy.tools.parameters.output_collect) NullToolTagManager (class in galaxy.tools.toolbox.tags) NullWatcher (class in galaxy.tools.toolbox.watcher) num_page_links (galaxy.web.framework.helpers.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.dataset.HistoryDatasetAssociationListGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.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)

O

OBFS (class in galaxy.datatypes.molecules) object_store (galaxy.model.Dataset attribute) object_to_string() (in module galaxy.util) ObjectAttributeInvalidException ObjectAttributeMissingException ObjectInvalid ObjectNotFound ObjectStore (class in galaxy.objectstore) ObjectStorePopulator (class in galaxy.tools.actions) Obo (class in galaxy.datatypes.text) odict (class in galaxy.util.odict) oidlog() (in module galaxy.web.framework.openid_manager) ok_to_display() (galaxy.security.GalaxyRBACAgent method) Oligos (class in galaxy.datatypes.mothur) on_any_event() (galaxy.tools.toolbox.watcher.LocFileEventHandler method) (galaxy.tools.toolbox.watcher.ToolFileEventHandler method) on_text_for_names() (in module galaxy.tools.actions) one() (galaxy.managers.base.ModelManager method) op (galaxy.containers.docker_model.DockerServiceConstraint attribute) open() (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() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) open_logs() (galaxy.util.heartbeat.Heartbeat method) open_or_build_maf_index() (in module galaxy.tools.util.maf_utilities) open_repository_files_folder() (in module tool_shed.util.shed_util_common) open_tar() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.CompressedFile method) open_zip() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.CompressedFile method) openid_associate() (galaxy.webapps.galaxy.controllers.user.User method) openid_auth() (galaxy.webapps.galaxy.controllers.user.User method) openid_process() (galaxy.webapps.galaxy.controllers.user.User method) OpenIDManager (class in galaxy.web.framework.openid_manager) OpenIDProvider (class in galaxy.openid.providers) OpenIDProviders (class in galaxy.openid.providers) openids_list() (galaxy.webapps.galaxy.controllers.user.User method) OpenObject (class in galaxy.visualization.plugins.utils) 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.dataset.HistoryDatasetAssociationListGrid 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.user.UserOpenIDGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationListGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.grids.admin_grids.AdminRepositoryGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.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_map (galaxy.containers.ContainerInterface attribute) (galaxy.containers.docker.DockerInterface attribute) (galaxy.containers.docker_swarm.DockerSwarmCLIInterface attribute) option_type (in module galaxy.tools.parser.output_actions) optional (galaxy.workflow.modules.InputParameterModule attribute) optional() (in module galaxy.dependencies) options (galaxy.util.jstree.Path attribute) order_components_for_import() (tool_shed.capsule.capsule_manager.ExportRepositoryManager method) order_components_for_installation() (tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) order_contents_on (galaxy.managers.containers.DatasetCollectionAsContainerManagerMixin attribute) (galaxy.managers.containers.LibraryFolderAsContainerManagerMixin attribute) order_repositories_for_installation() (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) OrderedSet (class in galaxy.util.oset) ordinalize() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) orient_block_by_region() (in module galaxy.tools.util.maf_utilities) Otu (class in galaxy.datatypes.mothur) output_names() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) output_paths() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) OutputCollections (class in galaxy.tools.actions) OutputParameterJSONTool (class in galaxy.tools) outputs() (galaxy.webapps.galaxy.api.jobs.JobController method), [1] OutputsToWorkingDirectoryPathRewriter (class in galaxy.jobs.datasets) Owl (class in galaxy.datatypes.xml) OwnableManagerMixin (class in galaxy.managers.secured) OwnerAnnotationColumn (class in galaxy.web.framework.helpers.grids) OwnerColumn (class in galaxy.web.framework.helpers.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 tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler) package_gff_feature() (in module galaxy.visualization.data_providers.genome) package_name (galaxy.tools.deps.mulled.util.Target attribute) package_specifier (galaxy.tools.deps.conda_util.CondaTarget attribute) package_tool() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) packages (galaxy.tools.deps.requirements.ToolRequirements attribute) pad() (galaxy.util.pastescript.serve.Command method) Page (class in galaxy.model) PageAllPublishedGrid (class in galaxy.webapps.galaxy.controllers.page) PageAnnotationAssociation (class in galaxy.model) 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) PageRevisionsController (class in galaxy.webapps.galaxy.api.page_revisions), [1] PageRevisionView (class in galaxy.model.search) 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.tools.parser.interface) PagesSource (class in galaxy.tools.parser.interface) PageTagAssociation (class in galaxy.model) PageUserShareAssociation (class in galaxy.model) PageView (class in galaxy.model.search) PairedDatasetCollectionType (class in galaxy.dataset_collections.types.paired) PairwiseDistanceMatrix (class in galaxy.datatypes.mothur) PAM (class in galaxy.auth.providers.pam_auth) panel_entry_per_tool() (in module 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.jobs) 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) ParamikoShell (class in galaxy.jobs.runners.util.cli.shell.rsh) ParamModifierParser (class in galaxy.visualization.plugins.config_parser) ParamParser (class in galaxy.visualization.plugins.config_parser) Params (class in galaxy.util) params (galaxy.tools.parameters.wrapped.WrappedParameters 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.tools.parser.output_actions) parent (galaxy.datatypes.metadata.MetadataCollection attribute) (galaxy.model.metadata.MetadataCollection attribute) parent_container() (galaxy.managers.containers.ContainableModelMixin method) parent_id (galaxy.webapps.tool_shed.model.Tag attribute) parent_library (galaxy.model.LibraryFolder attribute) parent_path (galaxy.tools.deps.conda_util.CondaContext attribute) (galaxy.tools.deps.installable.InstallableContext 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.tools.parser.interface.ToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) parse_args() (galaxy.util.pastescript.serve.Command method) parse_bool() (galaxy.managers.base.ModelFilterParser method) parse_cast_attribute() (in module galaxy.tools.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.TabularToolDataTable method) parse_columns_from_line() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) parse_command() (galaxy.tools.parser.cwl.CwlToolSource method) (galaxy.tools.Tool method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_compare_type() (in module galaxy.tools.parser.output_actions) parse_config() (galaxy.visualization.plugins.resource_parser.ResourceParser method) parse_configs() (galaxy.dependencies.ConditionalDependencies method) parse_containers_config() (in module galaxy.containers) parse_conversion_tuples() (galaxy.tools.parser.interface.InputSource method) (galaxy.tools.parser.xml.XmlInputSource method) parse_date() (galaxy.managers.base.ModelFilterParser method) parse_dependency_options() (in module galaxy.config) parse_description() (galaxy.tools.parser.cwl.CwlToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_destination_params() (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.pbs.PBSJobRunner method) parse_display() (galaxy.tools.parser.interface.PageSource method) (galaxy.tools.parser.xml.XmlPageSource method) parse_display_interface() (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_docker_env_pass_through() (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) parse_dynamic_options() (in module galaxy.tools.parameters.basic) parse_dynamic_options_elem() (galaxy.tools.parser.interface.InputSource method) (galaxy.tools.parser.xml.XmlInputSource method) parse_edam_operations() (galaxy.tools.parser.cwl.CwlToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_edam_topics() (galaxy.tools.parser.cwl.CwlToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_entry_point() (galaxy.visualization.plugins.config_parser.VisualizationsConfigParser method) parse_environment_variables() (galaxy.tools.parser.cwl.CwlToolSource method) (galaxy.tools.Tool method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_error_level() (galaxy.tools.parser.xml.StdioParser method) parse_external_id() (in module galaxy.jobs.runners.util.external) parse_file() (galaxy.visualization.plugins.config_parser.VisualizationsConfigParser method) parse_file_fields() (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.web.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.tools.parser.cwl.CwlToolSource method) (galaxy.tools.Tool method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.interface.InputSource method) (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.xml.XmlInputSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_hidden() (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) parse_home_target() (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) parse_id() (galaxy.tools.parser.cwl.CwlToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_id_list() (galaxy.managers.base.ModelFilterParser method) parse_input_elem() (galaxy.tools.Tool method) parse_input_pages() (galaxy.tools.parser.cwl.CwlToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_input_sources() (galaxy.tools.parser.cwl.CwlPageSource method) (galaxy.tools.parser.interface.PageSource method) (galaxy.tools.parser.xml.XmlPageSource method) (galaxy.tools.parser.yaml.YamlPageSource method) parse_input_type() (galaxy.tools.parser.xml.XmlInputSource method) (galaxy.tools.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_interpreter() (galaxy.tools.parser.cwl.CwlToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_is_multi_byte() (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_label() (galaxy.tools.parser.interface.InputSource method) (galaxy.tools.parser.xml.XmlInputSource method) parse_limit_offset() (galaxy.web.base.controller.BaseController method) parse_media_range() (in module mimeparse) parse_mime_type() (in module mimeparse) parse_model_class() (galaxy.visualization.plugins.config_parser.DataSourceParser method) parse_name() (galaxy.tools.parameters.basic.ToolParameter static method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.cwl.CwlToolSource method) (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_nested_inputs_source() (galaxy.tools.parser.interface.InputSource method) (galaxy.tools.parser.xml.XmlInputSource method) (galaxy.tools.parser.yaml.YamlInputSource method) parse_non_hex_float() (in module galaxy.util) parse_optional() (galaxy.tools.parser.interface.InputSource method) (galaxy.tools.parser.xml.XmlInputSource method) parse_order_by() (galaxy.managers.histories.HistoryManager method) (galaxy.managers.history_contents.HistoryContentsManager method) parse_outputs() (galaxy.tools.parser.cwl.CwlToolSource method) (galaxy.tools.Tool method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_package_elem() (in module tool_shed.util.tool_dependency_util) parse_parallelism() (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.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_profile() (galaxy.tools.parser.cwl.CwlToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_provided_metadata_file() (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) parse_provided_metadata_style() (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) parse_redirect_url() (galaxy.tools.Tool method) parse_redirect_url_params_elem() (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) parse_refresh() (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) parse_repository_dependency_tuple() (in module tool_shed.util.common_util) parse_request_param_translation_elem() (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) parse_require_login() (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_requirements_and_containers() (galaxy.tools.parser.cwl.CwlToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_requirements_from_dict() (in module galaxy.tools.deps.requirements) parse_requirements_from_xml() (in module galaxy.tools.deps.requirements) parse_row() (galaxy.datatypes.util.gff_util.GFFIntervalToBEDReaderWrapper method) (galaxy.datatypes.util.gff_util.GFFReaderWrapper method) parse_sanitize() (galaxy.tools.parser.cwl.CwlToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_sanitizer_elem() (galaxy.tools.parser.interface.InputSource method) (galaxy.tools.parser.xml.XmlInputSource method) parse_single_status() (galaxy.jobs.runners.util.cli.job.BaseJobExec 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.tools.util.maf_utilities) parse_static_options() (galaxy.tools.parser.interface.InputSource method) (galaxy.tools.parser.xml.XmlInputSource method) (galaxy.tools.parser.yaml.YamlInputSource method) parse_status() (galaxy.jobs.runners.util.cli.job.BaseJobExec 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.tools.parser.cwl.CwlToolSource method) (galaxy.tools.Tool method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_stdio_exit_codes() (galaxy.tools.parser.xml.StdioParser method) parse_stdio_regexes() (galaxy.tools.parser.xml.StdioParser method) parse_strict_shell() (galaxy.tools.parser.cwl.CwlToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_tags() (galaxy.managers.tags.TagManager method) parse_test_input_source() (galaxy.tools.parser.interface.InputSource method) (galaxy.tools.parser.xml.XmlInputSource method) (galaxy.tools.parser.yaml.YamlInputSource method) parse_tests() (galaxy.visualization.plugins.config_parser.DataSourceParser method) (in module galaxy.tools.test) parse_tests_to_dict() (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_tmp_directory_vars() (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.ToolSource method) parse_tmp_target() (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) parse_to_params() (galaxy.visualization.plugins.config_parser.DataSourceParser method) parse_tool_module() (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) parse_tool_type() (galaxy.tools.parser.cwl.CwlToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) parse_type_id_list() (galaxy.managers.history_contents.HistoryContentsFilters method) parse_validator_elems() (galaxy.tools.parser.interface.InputSource method) (galaxy.tools.parser.xml.XmlInputSource method) parse_value() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) parse_vars() (galaxy.util.pastescript.serve.Command method) parse_version() (galaxy.tools.parser.cwl.CwlToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_version_command() (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_version_command_interpreter() (galaxy.tools.parser.interface.ToolSource method) (galaxy.tools.parser.ToolSource method) (galaxy.tools.parser.xml.XmlToolSource method) (galaxy.tools.parser.yaml.YamlToolSource method) parse_visualization() (galaxy.visualization.plugins.config_parser.VisualizationsConfigParser method) parse_when_input_sources() (galaxy.tools.parser.interface.InputSource method) (galaxy.tools.parser.xml.XmlInputSource method) (galaxy.tools.parser.yaml.YamlInputSource method) parse_xml() (in module galaxy.util) (in module tool_shed.util.xml_util) parse_xml_string() (in module galaxy.util) parse_yaml() (in module galaxy.jobs.dynamic_tool_destination) 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 PassedTest (class in tool_shed.utility_containers) password (galaxy.webapps.tool_shed.model.User attribute) password_manager_for_url() (tool_shed.tool_shed_registry.Registry method) PasswordField (class in galaxy.web.form_builder) PasswordResetToken (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) PasteApplicationStack (class in galaxy.web.stack) Path (class in galaxy.util.jstree) path (galaxy.tools.parameters.output_collect.DiscoveredFile attribute) (galaxy.util.jstree.Path attribute) (galaxy.web.framework.base.Request attribute) path() (galaxy.tools.verify.test_data.FileDataResolver method) paths_as_file() (galaxy.tools.wrappers.HasDatasets method) pause() (galaxy.jobs.JobWrapper method) 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_size (galaxy.datatypes.tabular.BaseCSV attribute) 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) permission_failed_error_class (galaxy.managers.rbac_secured.AccessDatasetRBACPermission attribute) (galaxy.managers.rbac_secured.ManageDatasetRBACPermission attribute) (galaxy.managers.rbac_secured.RBACPermission attribute) permissions (galaxy.tools.parameters.output_collect.JobContext attribute) permissions() (galaxy.webapps.galaxy.controllers.history.HistoryController method) permissions_class (galaxy.managers.rbac_secured.DatasetRBACPermission attribute) (galaxy.managers.rbac_secured.RBACPermission attribute) permitted_actions (galaxy.model.Dataset attribute) (galaxy.model.DatasetInstance attribute) (galaxy.model.Library attribute) (galaxy.security.RBACAgent attribute) (galaxy.webapps.tool_shed.security.RBACAgent attribute) persist_session() (galaxy.web.framework.openid_manager.OpenIDManager method) persist_uploads() (in module galaxy.tools.actions.upload_common) PersistentToolTagManager (class in galaxy.tools.toolbox.tags) pgcalc() (in module galaxy.model.util) Pgm (class in galaxy.datatypes.images) PHAR (class in galaxy.datatypes.molecules) Phe (class in galaxy.datatypes.genetics) Pheno (class in galaxy.datatypes.genetics) 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) Pileup (class in galaxy.datatypes.tabular) 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.jobs.metrics.instrumenters.InstrumentPlugin attribute) (galaxy.jobs.metrics.instrumenters.collectl.CollectlPlugin attribute) (galaxy.jobs.metrics.instrumenters.core.CorePlugin attribute) (galaxy.jobs.metrics.instrumenters.cpuinfo.CpuInfoPlugin attribute) (galaxy.jobs.metrics.instrumenters.env.EnvPlugin attribute) (galaxy.jobs.metrics.instrumenters.meminfo.MemInfoPlugin attribute) (galaxy.jobs.metrics.instrumenters.uname.UnamePlugin attribute) (galaxy.workflow.schedulers.WorkflowSchedulingPlugin attribute) (galaxy.workflow.schedulers.core.CoreWorkflowSchedulingPlugin attribute) plugins_dict() (in module galaxy.util.plugin_config) pluralize() (galaxy.util.inflection.English method) (galaxy.util.inflection.Inflector method) 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_active_workflow_ids() (galaxy.model.WorkflowInvocation static method) pool_name (galaxy.web.stack.ApplicationStack attribute) pools (galaxy.web.stack.ApplicationStack attribute) pop() (galaxy.model.custom_types.MutationList method) (galaxy.util.oset.OrderedSet method) popitem() (galaxy.util.odict.odict method) populate() (galaxy.dataset_collections.builder.BoundCollectionBuilder method) populate_api_routes() (in module galaxy.webapps.galaxy.buildapp) populate_collection_elements() (galaxy.tools.parameters.output_collect.JobContext method) 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_tag_payload() (in module galaxy.util.biostar) populate_tool_dependencies_dicts() (tool_shed.galaxy_install.dependency_display.DependencyDisplayer method) populate_tool_payload() (in module galaxy.util.biostar) populate_tool_shed_info() (galaxy.tools.Tool method) populated (galaxy.model.DatasetCollection attribute) (galaxy.model.DatasetCollectionInstance attribute) populated_optimized (galaxy.model.DatasetCollection attribute) populated_states (galaxy.model.DatasetCollection attribute) (galaxy.model.ImplicitCollectionJobs attribute) PopulatedDisplayApplicationLink (class in galaxy.datatypes.display_applications.application) port (galaxy.web.proxy.ProxyMapping attribute) ports (galaxy.containers.Container attribute) (galaxy.containers.docker_model.DockerContainer attribute) (galaxy.containers.docker_model.DockerService attribute) possible_subcommands (galaxy.util.pastescript.serve.ServeCommand attribute) post_authentication() (galaxy.openid.providers.OpenIDProvider method) post_execute_commands() (galaxy.jobs.metrics.JobInstrumenter method) (galaxy.jobs.metrics.NullJobInstrumenter method) post_execute_instrument() (galaxy.jobs.metrics.instrumenters.collectl.CollectlPlugin method) (galaxy.jobs.metrics.instrumenters.InstrumentPlugin method) (galaxy.jobs.metrics.instrumenters.core.CorePlugin method) (galaxy.jobs.metrics.instrumenters.env.EnvPlugin method) post_task() (galaxy.jobs.runners.godocker.GodockerJobRunner method) 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 galaxy.webapps.tool_shed.model) PostJobActionAssociation (class in galaxy.model) Pphe (class in galaxy.datatypes.genetics) Ppm (class in galaxy.datatypes.images) pre_execute_commands() (galaxy.jobs.metrics.JobInstrumenter method) (galaxy.jobs.metrics.NullJobInstrumenter method) pre_execute_instrument() (galaxy.jobs.metrics.instrumenters.collectl.CollectlPlugin method) (galaxy.jobs.metrics.instrumenters.InstrumentPlugin method) (galaxy.jobs.metrics.instrumenters.core.CorePlugin method) (galaxy.jobs.metrics.instrumenters.cpuinfo.CpuInfoPlugin method) (galaxy.jobs.metrics.instrumenters.env.EnvPlugin method) (galaxy.jobs.metrics.instrumenters.meminfo.MemInfoPlugin method) (galaxy.jobs.metrics.instrumenters.uname.UnamePlugin method) precreate_dataset_collection() (galaxy.managers.collections.DatasetCollectionManager method) precreate_dataset_collection_instance() (galaxy.managers.collections.DatasetCollectionManager method) preferences() (galaxy.managers.users.UserManager method) prefix (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver attribute) prepare() (galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter method) (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter method) (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) prepare_activation_link() (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] (galaxy.webapps.galaxy.controllers.user.User method) prepare_display() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method) prepare_for_install() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) prepare_job() (galaxy.jobs.runners.BaseJobRunner method) prepare_step() (tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager.StepManager method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertDirectoryExecutable method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertDirectoryExists method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertFileExecutable method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertFileExists method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.Autoconf method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.ChangeDirectory method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.Chmod method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadBinary method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadByUrl method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadFile method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MakeDirectory method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MakeInstall method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MoveDirectoryFiles method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.MoveFile method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.RecipeStep method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.RegexReplace method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetEnvironment method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetEnvironmentForInstall method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupPerlEnvironment method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupPythonEnvironment method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupREnvironment method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupRubyEnvironment method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.SetupVirtualEnv method) (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.ShellCommand method) (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) preprocess_volumes() (in module galaxy.tools.deps.containers) 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.webapps.tool_shed.model.GalaxySession attribute) preview_tools_in_changeset() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) previous_changeset_revisions() (galaxy.webapps.tool_shed.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 tool_shed.util.container_util) print_nonsleeping() (galaxy.util.heartbeat.Heartbeat method) print_versioned_deps() (in module galaxy.tools.deps.brew_exts) private (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.Repository attribute) private_component_reviews (galaxy.webapps.tool_shed.model.RepositoryReview attribute) private_id (galaxy.model.Role attribute) (galaxy.webapps.tool_shed.model.Role attribute) private_role() (galaxy.managers.users.UserManager method) privately_share_dataset() (galaxy.security.GalaxyRBACAgent method) proceed_login() (galaxy.webapps.galaxy.controllers.user.User method) 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.tools.cwl.schema.SchemaLoader method) process_install_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_move() (galaxy.tools.data_manager.manager.DataManager method) process_object (galaxy.tools.cwl.schema.ProcessDefinition attribute) (galaxy.tools.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() (tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager.TagManager method) (tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Install method) (tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Package method) (tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.ReadMe method) (tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.RecipeTag method) (tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Repository method) (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) ProcessDefinition (class in galaxy.tools.cwl.schema) produce_outputs() (galaxy.tools.DatabaseOperationTool method) (galaxy.tools.FilterFailedDatasetsTool method) (galaxy.tools.FilterFromFileTool method) (galaxy.tools.FlattenTool method) (galaxy.tools.MergeCollectionTool method) (galaxy.tools.RelabelFromFileTool method) (galaxy.tools.SortTool method) (galaxy.tools.UnzipCollectionTool method) (galaxy.tools.ZipCollectionTool method) produces_collections_with_unknown_structure (galaxy.tools.Tool attribute) ProfileMiddleware (class in galaxy.web.framework.middleware.profile) prohibited_middleware (galaxy.web.stack.ApplicationStack attribute) (galaxy.web.stack.UWSGIApplicationStack attribute) ProteomicsXml (class in galaxy.datatypes.proteomics) protocol (galaxy.web.framework.base.Request attribute) prototype() (galaxy.dataset_collections.registry.DatasetCollectionTypesRegistry method) prototype_elements() (galaxy.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] 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.DockerCLIInterface method) Psd (class in galaxy.datatypes.images) pstats_as_html() (in module galaxy.web.framework.middleware.profile) psyco_full (module) public_actions (galaxy.jobs.actions.post.ActionBox attribute) PublicURLColumn (class in galaxy.web.framework.helpers.grids) publish() (galaxy.managers.sharable.SharableModelManager method) publish_port_list_required (galaxy.containers.ContainerInterface attribute) (galaxy.containers.docker_swarm.DockerSwarmInterface attribute) published() (galaxy.webapps.galaxy.api.histories.HistoriesController method), [1] published_list_grid (galaxy.webapps.galaxy.controllers.history.HistoryController attribute) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController attribute) pull_repository() (in module tool_shed.util.hg_util) PulsarEmbeddedJobRunner (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) 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.webapps.galaxy.controllers.dataset.DatasetInterface method) purge_async() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) purge_category() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) purge_deleted_datasets() (galaxy.webapps.galaxy.controllers.history.HistoryController method) purge_operation (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) purge_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) purged (galaxy.webapps.tool_shed.model.User attribute) put() (galaxy.jobs.handler.DefaultJobDispatcher method) (galaxy.jobs.NoopQueue method) (galaxy.jobs.handler.JobHandlerQueue method) (galaxy.jobs.handler.JobHandlerStopQueue method) (galaxy.jobs.manager.MessageJobQueue method) (galaxy.jobs.runners.BaseJobRunner method) put_stop() (galaxy.jobs.NoopQueue method) Py26CommentedTreeBuilder (class in tool_shed.util.xml_util) Py27CommentedTreeBuilder (class in tool_shed.util.xml_util) PythonObjectParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata)

Q

qp (galaxy.datatypes.display_applications.parameters.DisplayDataValueWrapper attribute) (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper attribute) quality() (in module mimeparse) quality_parsed() (in module mimeparse) 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.tools.deps.mulled.util) QuaySearch (class in galaxy.tools.deps.mulled.mulled_search) query() (galaxy.jobs.rule_helper.RuleHelper method) (galaxy.managers.base.ModelManager method) (galaxy.model.search.GalaxySearchEngine 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.web.base.controller.ExportsHistoryMixin method) queue_history_import() (galaxy.web.base.controller.ImportsHistoryMixin method) queue_job() (galaxy.jobs.runners.BaseJobRunner 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.managers.users.UserManager method) quota_amount() (galaxy.model.HistoryDatasetAssociation method) 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_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) quote_first_command_arg() (galaxy.util.pastescript.serve.Command method)

R

RangeParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) rank_collection_type() (galaxy.dataset_collections.type_description.CollectionTypeDescription method) rank_type_plugin() (galaxy.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) (galaxy.webapps.tool_shed.util.ratings_util.ItemRatings method) rate_repository() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) rating (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation attribute) (galaxy.webapps.tool_shed.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.webapps.tool_shed.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.tools.cwl.schema.SchemaLoader attribute) raw_element_identifiers (galaxy.tools.parameters.output_collect.JsonCollectedDatasetMatch attribute) raw_metadata() (in module galaxy.tools.deps.conda_compat) raw_param_dict() (galaxy.model.Job method) raw_process_reference (galaxy.tools.cwl.schema.ProcessDefinition attribute) raw_process_reference() (galaxy.tools.cwl.schema.SchemaLoader method) raw_set_dataset_state() (galaxy.model.DatasetInstance method) raw_tool_xml_tree() (in module galaxy.tools.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.tools.cwl.schema) RawVcfDataProvider (class in galaxy.visualization.data_providers.genome) RBACAgent (class in galaxy.security) (class in galaxy.webapps.tool_shed.security) RBACPermission (class in galaxy.managers.rbac_secured) RBACPermissionFailedException RData (class in galaxy.datatypes.binary) Rdf (class in galaxy.datatypes.triples) read_build_sites() (in module galaxy.util) read_config() (galaxy.webapps.tool_shed.util.hgweb_config.HgWebConfigManager method) read_dbnames() (in module galaxy.util) read_file() (galaxy.util.properties.NicerConfigParser method) read_lines() (galaxy.web.framework.base.FieldStorage method) read_pidfile() (in module galaxy.util.pastescript.serve) read_unordered_gtf() (in module galaxy.datatypes.util.gff_util) readline() (galaxy.tools.exception_handling.UCSCOutWrapper method) (galaxy.util.ucsc.UCSCOutWrapper method) readlines() (galaxy.datatypes.dataproviders.base.DataProvider method) ReadMe (class in 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_name_for_url() (in module galaxy.util) ready_states (galaxy.model.Dataset attribute) rebuild_toolbox_search_index() (in module galaxy.queue_worker) recalculate_user_disk_usage() (in module galaxy.queue_worker) recipe_cellar_path() (in module galaxy.tools.deps.brew_exts) RecipeContext (class in galaxy.tools.deps.brew_exts) RecipeStep (class in tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) RecipeTag (class in tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler) reclaim_ownership() (galaxy.jobs.JobWrapper method) record_pid() (galaxy.util.pastescript.serve.ServeCommand method) recover() (galaxy.jobs.handler.DefaultJobDispatcher method) (galaxy.jobs.runners.BaseJobRunner 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.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) recover_state() (galaxy.workflow.modules.WorkflowModule method) recursively_stringify_dictionary_keys() (in module galaxy.util) RecursiveNone (class in galaxy.util.none_like) redirect() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) redirect_aware_commmunicate() (in module galaxy.tools.deps.commands) redirecting_io() (in module galaxy.tools.deps.commands) reduce_block_by_primary_genome() (in module galaxy.tools.util.maf_utilities) reference() (galaxy.visualization.genomes.Genomes method) referer (galaxy.webapps.tool_shed.model.GalaxySession attribute) RefTaxonomy (class in galaxy.datatypes.mothur) 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() (galaxy.webapps.tool_shed.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.tools.parameters.output_collect) RegexLineDataProvider (class in galaxy.datatypes.dataproviders.line) RegexReplace (class in 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.tools.util.maf_utilities) register() (galaxy.tools.toolbox.lineages.factory.LineageMap method) (galaxy.tools.toolbox.lineages.LineageMap method) register_cleanup_file_attribute() (galaxy.jobs.runners.AsynchronousJobState method) 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) Registry (class in galaxy.datatypes.registry) (class in tool_shed.repository_registry) (class in tool_shed.repository_types.registry) (class in tool_shed.tool_shed_registry) reindex_tool_search() (galaxy.config.ConfiguresGalaxyMixin method) reinstall_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed 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) reload() (galaxy.datatypes.display_applications.application.DisplayApplication method) (galaxy.tools.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tool_data.ToolData method), [1] (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] 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() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) (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_sanitize_whitelist() (galaxy.config.Configuration 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) remote_addr (galaxy.webapps.tool_shed.model.GalaxySession attribute) remote_host (galaxy.web.framework.base.Request attribute) (galaxy.webapps.tool_shed.model.GalaxySession attribute) remote_hostname (galaxy.web.framework.base.Request attribute) remote_port (galaxy.web.framework.base.Request attribute) remote_repository_url (galaxy.webapps.tool_shed.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 galaxy.webapps.tool_shed.framework.middleware.remoteuser) remove() (galaxy.model.custom_types.MutationList method) remove_category_entry() (tool_shed.repository_registry.Registry method) remove_dir() (in module tool_shed.util.basic_util) remove_display_app() (galaxy.datatypes.data.Data method) remove_entry() (galaxy.tools.data.ToolDataTable method) (tool_shed.repository_registry.Registry method) remove_entry_from_installed_repository_dependencies_of_installed_repositories() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) remove_entry_from_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) remove_entry_from_installed_tool_dependencies_of_installed_repositories() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) remove_entry_from_repository_dependencies_of_installed_repositories() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) remove_entry_from_runtime_tool_dependencies_of_installed_tool_dependencies() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) remove_entry_from_tool_dependencies_of_installed_repositories() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) remove_file() (in module tool_shed.util.hg_util) (tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Repository method) remove_from_data_manager() (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() (tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) remove_guids() (tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) remove_item_tag() (galaxy.managers.tags.TagManager 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 tool_shed.util.common_util) remove_protocol_and_port_from_tool_shed_url() (in module tool_shed.util.common_util) remove_protocol_and_user_from_clone_url() (in module tool_shed.util.common_util) remove_protocol_from_tool_shed_url() (in module tool_shed.util.common_util) (tool_shed.capsule.capsule_manager.ExportRepositoryManager method) remove_protocol_from_url() (in module galaxy.util) remove_repository_contents() (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() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method), [1] remove_tag_async() (galaxy.webapps.galaxy.controllers.tag.TagsController method) remove_tags_from_list() (galaxy.managers.tags.TagManager method) remove_temp_index_file() (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 tool_shed.util.tool_dependency_util) remove_tool_dependency_installation_directory() (in module tool_shed.util.tool_dependency_util) remove_unused_dependency_paths() (galaxy.tools.deps.views.DependencyResolversView method) 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) rename_quota() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) rename_role() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) RenameDatasetAction (class in galaxy.jobs.actions.post) render() (galaxy.visualization.plugins.plugin.VisualizationPlugin method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) render_saved() (galaxy.visualization.plugins.plugin.VisualizationPlugin method) repair_methods() (galaxy.datatypes.data.Data method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.tabular.Pileup method) repair_repository_revision() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method), [1] repair_tool_shed_repository() (tool_shed.galaxy_install.repair_repository_manager.RepairRepositoryManager method) RepairRepositoryManager (class in tool_shed.galaxy_install.repair_repository_manager) Repeat (class in galaxy.tools.parameters.grouping) replace_failed_elements() (galaxy.model.DatasetCollection method) 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) (galaxy.webapps.tool_shed.model.Repository method) RepoManager (class in tool_shed.managers.repositories) Report (class in galaxy.webapps.reports.controllers.root) ReportQueryBuilder (class in galaxy.webapps.reports.controllers.query) ReportsWebApplication (class in galaxy.webapps.reports.buildapp) RepoSearch (class in galaxy.webapps.tool_shed.search.repo_search) repositories (galaxy.webapps.tool_shed.model.Category attribute) (galaxy.webapps.tool_shed.model.Role attribute) repositories_by_user_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repositories_i_can_administer_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repositories_i_own_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repositories_in_category_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repositories_missing_tool_test_components_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repositories_ready_for_review_grid (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController attribute) repositories_reviewed_by_me_grid (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController attribute) repositories_with_invalid_tools_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repositories_with_no_tool_tests_grid (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController attribute) repositories_with_reviews_grid (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController attribute) repositories_without_reviews_grid (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController attribute) RepositoriesByUserGrid (class in tool_shed.grids.repository_grids) RepositoriesController (class in galaxy.webapps.tool_shed.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.webapps.tool_shed.model) (class in tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler) repository (galaxy.webapps.tool_shed.model.RepositoryCategoryAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.RepositoryRoleAssociation attribute) repository() (galaxy.webapps.galaxy.api.toolshed.ToolShedController method), [1] repository_dependencies (galaxy.model.tool_shed_install.ToolShedRepository attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) repository_dependencies() (galaxy.webapps.tool_shed.api.repository_revisions.RepositoryRevisionsController method), [1] repository_dependencies_being_installed (galaxy.model.tool_shed_install.ToolShedRepository attribute) repository_dependencies_grid (galaxy.webapps.tool_shed.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_needed_only_for_compiling_tool_dependency() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) repository_grid (galaxy.webapps.tool_shed.controllers.admin.AdminController attribute) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repository_id (galaxy.webapps.tool_shed.model.RepositoryCategoryAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.RepositoryRoleAssociation attribute) repository_ids_for_setting_metadata() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method), [1] repository_installation_status_updates() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method)

repository_metadata (galaxy.webapps.tool_shed.model.RepositoryReview attribute) repository_metadata_grid (galaxy.webapps.tool_shed.controllers.admin.AdminController attribute) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) repository_review (galaxy.webapps.tool_shed.model.ComponentReview attribute) repository_review_id (galaxy.webapps.tool_shed.model.ComponentReview attribute) repository_reviews_by_user() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) repository_reviews_by_user_grid (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController attribute) repository_was_previously_installed() (in module tool_shed.util.repository_util) RepositoryCategoryAssociation (class in galaxy.webapps.tool_shed.model) RepositoryController (class in galaxy.webapps.tool_shed.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 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 galaxy.webapps.tool_shed.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 galaxy.webapps.tool_shed.model) RepositoryRepositoryDependencyAssociation (class in galaxy.model.tool_shed_install) RepositoryReview (class in galaxy.webapps.tool_shed.model) RepositoryReviewController (class in galaxy.webapps.tool_shed.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 galaxy.webapps.tool_shed.api.repository_revisions), [1] RepositoryRoleAssociation (class in galaxy.webapps.tool_shed.model) RepositorySuccessfulInstallation (class in tool_shed.utility_containers) RepositorySuiteDefinition (class in tool_shed.repository_types.repository_suite_definition) RepoToolModule (class in tool_shed.util.workflow_util) RepoWeighting (class in galaxy.webapps.tool_shed.search.repo_search) RepoWorkflowModuleFactory (class in tool_shed.util.workflow_util) Request (class in galaxy.web.framework.base) RequestIDMiddleware (class in galaxy.web.framework.middleware.request_id) RequestParameterInvalidException RequestParameterMissingException require_admin() (in module galaxy.web) (in module galaxy.web.framework.decorators) require_dataset_ok (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) require_file() (in module galaxy.tools.test) require_login() (in module galaxy.web) (in module galaxy.web.framework.decorators) required_args (galaxy.util.pastescript.serve.Command attribute) requirement_to_recipe() (in module galaxy.tools.deps.brew_util) RequirementMapping (class in galaxy.tools.deps.resolvers) requirements() (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] requirements_to_conda_targets() (in module galaxy.tools.deps.conda_util) requirements_to_dependencies() (galaxy.tools.deps.DependencyManager method) requirements_to_mulled_targets() (in module galaxy.tools.deps.mulled.mulled_build_tool) requirements_to_recipe_contexts() (in module galaxy.tools.deps.brew_util) requirements_to_recipes() (in module galaxy.tools.deps.brew_util) RequirementSpecification (class in galaxy.tools.deps.requirements) requires_config_file (galaxy.util.pastescript.serve.ServeCommand attribute) requires_containerization (galaxy.jobs.JobWrapper attribute) requires_dataset_metadata (galaxy.tools.parameters.validation.MetadataInDataTableColumnValidator attribute) (galaxy.tools.parameters.validation.MetadataInFileColumnValidator 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_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) rerun() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) reselect_tool_panel_section() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) resend_verification() (galaxy.webapps.galaxy.controllers.user.User method) resend_verification_email() (galaxy.webapps.galaxy.controllers.user.User method) reset_all_metadata() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) reset_all_metadata_on_installed_repository() (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_metadata_on_installed_repositories() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method), [1] reset_metadata_on_my_writable_repositories_in_tool_shed() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) reset_metadata_on_repositories() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method), [1] reset_metadata_on_repository() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method), [1] reset_metadata_on_selected_installed_repositories() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) reset_metadata_on_selected_repositories() (tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) reset_metadata_on_selected_repositories_in_tool_shed() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) reset_password() (galaxy.webapps.galaxy.controllers.user.User method) reset_previously_installed_repository() (tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method) reset_repository_metadata() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) reset_tags() (galaxy.tools.toolbox.tags.AbstractToolTagManager method) (galaxy.tools.toolbox.tags.NullToolTagManager method) (galaxy.tools.toolbox.tags.PersistentToolTagManager method) reset_to_install() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) reset_tool_data_tables() (tool_shed.tools.data_table_manager.ShedToolDataTableManager method) reset_user_password() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) resolvable (galaxy.tools.deps.requirements.ToolRequirements attribute) resolve() (galaxy.tools.deps.container_resolvers.ContainerResolver method) (galaxy.tools.deps.container_resolvers.explicit.ExplicitContainerResolver method) (galaxy.tools.deps.container_resolvers.mulled.BuildMulledDockerContainerResolver method) (galaxy.tools.deps.container_resolvers.mulled.BuildMulledSingularityContainerResolver method) (galaxy.tools.deps.container_resolvers.mulled.CachedMulledDockerContainerResolver method) (galaxy.tools.deps.container_resolvers.mulled.CachedMulledSingularityContainerResolver method) (galaxy.tools.deps.container_resolvers.mulled.MulledDockerContainerResolver method) (galaxy.tools.deps.resolvers.DependencyResolver method) (galaxy.tools.deps.resolvers.brewed_tool_shed_packages.HomebrewToolShedDependencyResolver method) (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method) (galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependencyResolver method) (galaxy.tools.deps.resolvers.homebrew.HomebrewDependencyResolver method) (galaxy.tools.deps.resolvers.modules.ModuleDependencyResolver method) resolve_all() (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method) (galaxy.tools.deps.resolvers.MultipleDependencyResolver method) resolve_dependencies (galaxy.tools.deps.containers.Container attribute) resolve_path() (galaxy.config.Configuration method) (in module galaxy.config) (in module galaxy.webapps.reports.config) (in module galaxy.webapps.tool_shed.config) resolver_dependency() (galaxy.tools.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method), [1] resolver_msg (galaxy.tools.deps.resolvers.Dependency attribute) (galaxy.tools.deps.resolvers.NullDependency attribute) resolver_requirements() (galaxy.tools.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method), [1] resolver_type (galaxy.tools.deps.container_resolvers.ContainerResolver attribute) (galaxy.tools.deps.container_resolvers.explicit.ExplicitContainerResolver attribute) (galaxy.tools.deps.container_resolvers.mulled.BuildMulledDockerContainerResolver attribute) (galaxy.tools.deps.container_resolvers.mulled.BuildMulledSingularityContainerResolver attribute) (galaxy.tools.deps.container_resolvers.mulled.CachedMulledDockerContainerResolver attribute) (galaxy.tools.deps.container_resolvers.mulled.CachedMulledSingularityContainerResolver attribute) (galaxy.tools.deps.container_resolvers.mulled.MulledDockerContainerResolver attribute) (galaxy.tools.deps.resolvers.brewed_tool_shed_packages.HomebrewToolShedDependencyResolver attribute) (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver attribute) (galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependencyResolver attribute) (galaxy.tools.deps.resolvers.homebrew.HomebrewDependencyResolver attribute) (galaxy.tools.deps.resolvers.modules.ModuleDependencyResolver attribute) (galaxy.tools.deps.resolvers.tool_shed_packages.ToolShedPackageDependencyResolver attribute) (galaxy.tools.deps.resolvers.unlinked_tool_shed_packages.UnlinkedToolShedPackageDependencyResolver attribute) resolves_simple_dependencies (galaxy.tools.deps.resolvers.DependencyResolver attribute) (galaxy.tools.deps.resolvers.tool_shed_packages.ToolShedPackageDependencyResolver attribute) ResourceParser (class in galaxy.visualization.plugins.resource_parser) Response (class in galaxy.web.framework.base) 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) resume_paused_jobs() (galaxy.model.History method) (galaxy.webapps.galaxy.controllers.history.HistoryController method) retag_async() (galaxy.webapps.galaxy.controllers.tag.TagsController method) RetryActionExecutor (class in galaxy.jobs.runners.util.retry) return_code (galaxy.util.pastescript.serve.Command attribute) reverse() (galaxy.util.odict.odict method) reversed_lower_upper_bounded_changelog() (in module tool_shed.util.hg_util) reversed_upper_bounded_changelog() (in module tool_shed.util.hg_util) ReverseSortColumn (class in galaxy.web.framework.helpers.grids) review_tool_migration_stages() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) reviewed_repositories_i_own() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) reviewed_repositories_i_own_grid (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController attribute) ReviewedRepositoriesIOwnGrid (class in tool_shed.grids.repository_review_grids) reviewers (galaxy.webapps.tool_shed.model.Repository attribute) reviews (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) revision() (galaxy.webapps.tool_shed.model.Repository method) revision_update_available (galaxy.model.tool_shed_install.ToolShedRepository attribute) revoke() (galaxy.managers.rbac_secured.AccessDatasetRBACPermission method) (galaxy.managers.rbac_secured.ManageDatasetRBACPermission method) (galaxy.managers.rbac_secured.RBACPermission method) rewrite_dataset_path() (galaxy.jobs.datasets.DatasetPathRewriter method) (galaxy.jobs.datasets.NullDatasetPathRewriter method) (galaxy.jobs.datasets.OutputsToWorkingDirectoryPathRewriter method) (galaxy.jobs.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) RNADotPlotMatrix (class in galaxy.datatypes.sequence) Roadmaps (class in galaxy.datatypes.assembly) rods_connect() (in module galaxy.objectstore.rods) Role (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) role (galaxy.webapps.tool_shed.model.GroupRoleAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryRoleAssociation attribute) (galaxy.webapps.tool_shed.model.UserRoleAssociation attribute) role_id (galaxy.webapps.tool_shed.model.GroupRoleAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryRoleAssociation attribute) (galaxy.webapps.tool_shed.model.UserRoleAssociation attribute) role_list_grid (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) (galaxy.webapps.tool_shed.controllers.admin.AdminController 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.webapps.tool_shed.model.Repository attribute) roles_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) 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.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.ProtXML attribute) (galaxy.datatypes.proteomics.TandemXML attribute) (galaxy.datatypes.proteomics.TraML attribute) (galaxy.datatypes.proteomics.UniProtXML attribute) Root (in module galaxy.web.base.controller) root_container_class (galaxy.managers.history_contents.HistoryContentsManager 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.tools.linters.help) rst_to_html() (in module galaxy.util) RuleHelper (class in galaxy.jobs.rule_helper) RuleValidator (class in galaxy.jobs.dynamic_tool_destination) run() (galaxy.containers.docker.DockerCLIInterface method) (galaxy.containers.docker_swarm_manager.SwarmManager method) (galaxy.jobs.metrics.collectl.cli.CollectlCli method) (galaxy.jobs.transfer_manager.TransferManager method) (galaxy.util.heartbeat.Heartbeat method) (galaxy.util.pastescript.serve.Command method) (galaxy.util.pastescript.serve.NotFoundCommand method) (in module galaxy.util.pastescript.serve) (tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader.AsynchronousReader 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_stats() (galaxy.webapps.reports.controllers.home.HomePage method) runner_name (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) runner_states (galaxy.jobs.runners.JobState attribute) RunnerParams (class in galaxy.jobs.runners) running (galaxy.jobs.runners.AsynchronousJobState attribute) (galaxy.util.lazy_process.LazyProcess attribute) (galaxy.util.lazy_process.NoOpLazyProcess attribute) RuntimeException RuntimeValue (class in galaxy.tools.parameters.basic)

S

S3ObjectStore (class in galaxy.objectstore.s3) sa_session (galaxy.managers.context.ProvidesAppContext attribute) (galaxy.security.GalaxyRBACAgent attribute) (galaxy.security.HostAgent attribute) (galaxy.tools.Tool attribute) (galaxy.tools.toolbox.BaseGalaxyToolBox attribute) (galaxy.tools.toolbox.base.BaseGalaxyToolBox attribute) (galaxy.webapps.tool_shed.security.CommunityRBACAgent attribute) (galaxy.webapps.tool_shed.util.shed_statistics.ShedCounter attribute) (tool_shed.galaxy_install.migrate.common.MigrateToolsApplication attribute) (tool_shed.repository_registry.Registry attribute) Sabund (class in galaxy.datatypes.mothur) safe_dumps() (in module galaxy.util.json) safe_str_cmp() (in module galaxy.util) SafeStringWrapper (class in galaxy.util.object_wrapper) Sakura (class in galaxy.datatypes.images) Sam (class in galaxy.datatypes.tabular) SamDataProvider (class in galaxy.visualization.data_providers.genome) samtools_dataprovider() (galaxy.datatypes.binary.Bam method) SamtoolsDataProvider (class in galaxy.datatypes.dataproviders.dataset) sangerQualities() (galaxy.datatypes.sequence.BaseFastq static 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) sanitize_whitelist() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) save() (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) save_form_definition() (galaxy.webapps.galaxy.controllers.forms.Forms method) save_to_step() (galaxy.workflow.modules.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) save_visualization() (galaxy.web.base.controller.UsesVisualizationMixin method) save_widget_field() (galaxy.web.base.controller.UsesFormDefinitionsMixin method) save_workflow() (in module tool_shed.util.workflow_util) save_workflow_as() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) saved() (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) ScannerError Scf (class in galaxy.datatypes.binary) schedule() (galaxy.workflow.schedulers.ActiveWorkflowSchedulingPlugin method) (galaxy.workflow.schedulers.core.CoreWorkflowSchedulingPlugin method) SchemaLoader (class in galaxy.tools.cwl.schema) scheme (galaxy.tools.locations.dockstore.DockStoreResolver attribute) (galaxy.tools.locations.ToolLocationResolver attribute) (galaxy.tools.locations.file.HttpToolResolver attribute) (galaxy.tools.locations.http.HttpToolResolver attribute) (galaxy.tools.locations.http.HttpsToolResolver attribute) ScIdx (class in galaxy.datatypes.interval) ScriptVisualizationPlugin (class in galaxy.visualization.plugins.plugin) SDF (class in galaxy.datatypes.molecules) search() (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] (galaxy.webapps.galaxy.api.toolshed.ToolShedController method), [1] (galaxy.webapps.tool_shed.search.repo_search.RepoSearch method) (galaxy.webapps.tool_shed.search.tool_search.ToolSearch 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.tools.deps.mulled.mulled_search.QuaySearch method) search_repository_metadata() (in module tool_shed.util.search_util) 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.jobs.metrics.formatting) Section (class in galaxy.tools.parameters.grouping) secure() (galaxy.managers.folders.FolderManager method) (galaxy.managers.libraries.LibraryManager method) SecureShell (class in galaxy.jobs.runners.util.cli.shell.rsh) security_check() (galaxy.web.base.controller.SharableItemSecurityMixin method) (in module galaxy.managers.base) SecurityHelper (class in galaxy.web.security) select_day() (galaxy.webapps.reports.controllers.query.ReportQueryBuilder method) select_files_to_delete() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) select_month() (galaxy.webapps.reports.controllers.query.ReportQueryBuilder method) select_previous_review() (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) SelectField (class in galaxy.web.form_builder) SelectParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) 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) send_control_task() (in module galaxy.queue_worker) send_file() (in module galaxy.web.framework.base) send_local_control_task() (in module galaxy.queue_worker) send_mail() (in module galaxy.util) send_message() (galaxy.web.stack.ApplicationStack method) (galaxy.web.stack.MessageApplicationStack method) send_redirect() (galaxy.web.framework.base.Response method) send_report() (galaxy.tools.errors.ErrorReporter method) send_to_owner() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) send_verification_email() (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] (galaxy.webapps.galaxy.controllers.user.User method) Sentry (class in galaxy.web.framework.middleware.sentry) sentry_dsn_public (galaxy.config.Configuration attribute) (galaxy.webapps.reports.config.Configuration attribute) (galaxy.webapps.tool_shed.config.Configuration attribute) sep() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SimpleComputeEnvironment method) sep2tabs() (in module galaxy.datatypes.sniff) 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) serialize() (galaxy.managers.base.ModelSerializer method) (galaxy.managers.datasets.DatasetAssociationSerializer method) (galaxy.managers.hdas.HDASerializer method) (galaxy.managers.users.CurrentUserSerializer 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_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_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_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_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) serve_ready_history_export() (galaxy.web.base.controller.ExportsHistoryMixin method) ServeCommand (class in galaxy.util.pastescript.serve) server_name_template (galaxy.web.stack.ApplicationStack attribute) (galaxy.web.stack.UWSGIApplicationStack attribute) server_starttime (in module galaxy.web.framework.base) ServesStaticPluginMixin (class in galaxy.visualization.plugins.plugin) ServesTemplatesPluginMixin (class in galaxy.visualization.plugins.plugin) service() (galaxy.containers.docker_swarm.DockerSwarmInterface method) service_create() (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) service_inspect() (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) service_ls() (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) service_ps() (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) service_rm() (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) service_tasks() (galaxy.containers.docker_swarm.DockerSwarmInterface method) services() (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_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_csrf_token (galaxy.web.framework.webapp.GalaxyWebTransaction attribute) session_key (galaxy.webapps.tool_shed.model.GalaxySession attribute) set() (galaxy.managers.datasets.DatasetRBACPermissions method) (galaxy.managers.rbac_secured.DatasetRBACPermission 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() (tool_shed.metadata.metadata_generator.MetadataGenerator method) set_all_dataset_permissions() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) set_all_library_permissions() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) set_allow_push() (galaxy.webapps.tool_shed.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_basic_defaults() (in module galaxy.jobs.splitters.basic) set_changeset_revision() (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.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_content_type() (galaxy.web.framework.base.Response method) set_cookie() (galaxy.web.framework.webapp.GalaxyWebTransaction method) set_copied_from_job_id() (galaxy.model.Job method) set_cors_headers() (galaxy.web.framework.webapp.GalaxyWebTransaction method) set_cpus() (galaxy.containers.docker_model.DockerService method) set_current() (galaxy.managers.histories.HistoryManager method) set_current_by_id() (galaxy.managers.histories.HistoryManager method) set_dataset_permission() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) set_dataset_permissions() (galaxy.security.HostAgent method) set_dataset_state() (galaxy.model.DatasetInstance method) set_datatypes_registry() (in module galaxy.model) set_dbkey() (galaxy.model.DatasetInstance 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_element() (galaxy.jobs.metrics.JobMetrics method) set_destination_conf_file() (galaxy.jobs.metrics.JobMetrics method) set_destination_instrumenter() (galaxy.jobs.metrics.JobMetrics method) set_disk_usage() (galaxy.model.GalaxySession method) (galaxy.model.User method) (galaxy.webapps.tool_shed.model.User method) set_edit() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) set_email_alerts() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) set_entity_group_associations() (galaxy.security.GalaxyRBACAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) set_entity_quota_associations() (galaxy.quota.QuotaAgent method) set_entity_role_associations() (galaxy.security.GalaxyRBACAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) set_entity_user_associations() (galaxy.security.GalaxyRBACAgent method) (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) set_environment() (tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.SetEnvironment method) set_extra_files_path() (galaxy.model.Dataset method) set_file_name() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) set_filter() (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_from_dict() (galaxy.model.DatasetCollection method) (galaxy.model.DatasetCollectionInstance method) set_handler() (galaxy.model.Job method) set_history() (galaxy.web.framework.webapp.GalaxyWebTransaction method) (galaxy.work.context.WorkRequestContext method) set_id() (galaxy.model.Task method) set_image() (galaxy.containers.docker_model.DockerService method) set_image_paths() (in module tool_shed.util.shed_util_common) set_imported() (galaxy.model.Job method) set_index_file() (galaxy.datatypes.binary.CRAM method) set_info() (galaxy.model.Job method) (galaxy.model.LibraryDataset method) (galaxy.model.Task method) set_information() (galaxy.webapps.galaxy.api.users.UserAPIController method), [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) (galaxy.webapps.tool_shed.model.ItemRatingAssociation method) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation method) set_item_extended_metadata_obj() (galaxy.web.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.datatypes.metadata.JobExternalOutputMetadataWrapper method) (galaxy.model.metadata.JobExternalOutputMetadataWrapper 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.LibraryDataset method) set_library_item_permission() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) set_malicious() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) set_max_optional_metadata_filesize() (galaxy.datatypes.data.Data method) set_message() (galaxy.web.framework.webapp.GalaxyWebTransaction method) set_meta() (galaxy.datatypes.assembly.Velvet method) (galaxy.datatypes.binary.Bam method) (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.binary.Bcf method) (galaxy.datatypes.binary.Biom2 method) (galaxy.datatypes.binary.CRAM method) (galaxy.datatypes.binary.Fast5Archive method) (galaxy.datatypes.binary.GeminiSQLite method) (galaxy.datatypes.binary.IdpDB method) (galaxy.datatypes.binary.MzSQlite method) (galaxy.datatypes.binary.PostgresqlArchive method) (galaxy.datatypes.binary.SQlite 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.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.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.qualityscore.QualityScoreSOLiD method) (galaxy.datatypes.sequence.BaseFastq method) (galaxy.datatypes.sequence.DotBracket 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.Sam 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.Ipynb method) (galaxy.datatypes.text.SnpEffDb method) (galaxy.datatypes.text.SnpSiftDbNSFP method) (galaxy.model.DatasetInstance method) set_meta_with_tool_provided() (in module galaxy_ext.metadata.set_metadata) set_metadata() (galaxy.model.DatasetInstance method) (in module galaxy_ext.metadata.set_metadata) set_metadata_defaults() (galaxy.tools.actions.DefaultToolAction method) set_name() (galaxy.model.LibraryDataset method) set_non_data_connection() (galaxy.model.WorkflowStepConnection method) set_object_store_id() (galaxy.tools.actions.ObjectStorePopulator method) set_only_if_compiling_contained_td() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) set_output_datasets() (galaxy.model.Job method) set_output_library_datasets() (galaxy.model.Job method) set_param_filename() (galaxy.model.Job method) set_parameters() (galaxy.model.Job method) (galaxy.model.Task method) set_params() (galaxy.model.Job method) set_parent() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataCollection method) set_parent_container() (galaxy.managers.containers.ContainableModelMixin method) set_password() (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] set_password_cleartext() (galaxy.model.User method) (galaxy.webapps.tool_shed.model.User method) set_peek() (galaxy.datatypes.binary.Ab1 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.CompressedArchive method) (galaxy.datatypes.binary.CompressedZipArchive method) (galaxy.datatypes.binary.Cool method) (galaxy.datatypes.binary.ExcelXls method) (galaxy.datatypes.binary.Fast5Archive method) (galaxy.datatypes.binary.GeminiSQLite method) (galaxy.datatypes.binary.H5 method) (galaxy.datatypes.binary.ICM method) (galaxy.datatypes.binary.IdpDB 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.blast.BlastXml 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.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.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.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.proteomics.MascotDat method) (galaxy.datatypes.proteomics.Mgf method) (galaxy.datatypes.proteomics.ProteomicsXml method) (galaxy.datatypes.proteomics.SPLib method) (galaxy.datatypes.proteomics.SPLibNoIndex method) (galaxy.datatypes.proteomics.ThermoRAW 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.Html 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.model.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] set_permissions_old() (galaxy.webapps.galaxy.api.libraries.LibrariesController method), [1] set_position() (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() (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.web.base.controller.SharableMixin method) set_public_with_single_manager() (galaxy.managers.datasets.DatasetRBACPermissions method) set_quota_default() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) set_range() (galaxy.tools.util.maf_utilities.RegionAlignment method) set_raw_data() (galaxy.datatypes.data.Data method) (galaxy.datatypes.data.Text method) (galaxy.model.DatasetInstance method) set_relative_install_dir() (tool_shed.metadata.metadata_generator.MetadataGenerator method) set_repository() (tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) (tool_shed.metadata.metadata_generator.MetadataGenerator method) (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) set_repository_attributes() (in module tool_shed.util.repository_util) set_repository_clone_url() (tool_shed.metadata.metadata_generator.MetadataGenerator method) set_repository_files_dir() (tool_shed.metadata.metadata_generator.MetadataGenerator 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_shed_config_filename() (galaxy.model.tool_shed_install.ToolShedRepository method) set_size() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) set_slug() (galaxy.managers.sharable.SharableModelManager method) set_slug_async() (galaxy.web.base.controller.SharableMixin method) set_state() (galaxy.model.Job method) (galaxy.model.Task method) set_stderr() (galaxy.model.Task method) set_stdout() (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.managers.tags.TagManager method) (galaxy.web.base.controller.UsesTagsMixin method) set_task_runner_external_id() (galaxy.model.Task method) set_task_runner_name() (galaxy.model.Task method) set_tool_dependency_attributes() (in module 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.web.framework.webapp.GalaxyWebTransaction method) (galaxy.work.context.WorkRequestContext method) set_user_id() (galaxy.model.Job method) set_user_pref_async() (galaxy.webapps.galaxy.controllers.user.User method) 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 tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) (class in tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler) SetEnvironmentForInstall (class in 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_external_metadata() (galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper method) (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.model.metadata.JobExternalOutputMetadataWrapper method) setup_i18n() (galaxy.web.framework.webapp.GalaxyWebTransaction method) setup_input_connections_by_name() (galaxy.model.WorkflowStep method) setup_job() (galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper method) setup_logging() (galaxy.main.GalaxyConfigBuilder method) SETUP_NEEDED (galaxy.web.framework.openid_manager.OpenIDManager attribute) setup_proxy() (galaxy.web.proxy.ProxyManager method) SetupPerlEnvironment (class in tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) SetupPythonEnvironment (class in tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) SetupREnvironment (class in tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) SetupRubyEnvironment (class in tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) SetupVirtualEnv (class in 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) sharable_owner() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) sharable_repository() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) sharable_repository_revision() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) SharableItemSecurityMixin (class in galaxy.web.base.controller) SharableMixin (class in galaxy.web.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.web.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_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_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) sharing() (galaxy.web.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)

sharing_roles() (galaxy.managers.users.UserManager method) SharingStatusColumn (class in galaxy.web.framework.helpers.grids) shed_category() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method), [1] shed_config_filename (galaxy.model.tool_shed_install.ToolShedRepository attribute) shed_repository() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method), [1] shed_search() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method), [1] shed_tool_data_path (galaxy.webapps.tool_shed.config.Configuration attribute) ShedCounter (class in galaxy.webapps.tool_shed.util.shed_statistics) ShedToolDataTableManager (class in tool_shed.tools.data_table_manager) shell (galaxy.jobs.JobWrapper attribute) (galaxy.tools.deps.containers.Container attribute) shell() (in module galaxy.tools.deps.commands) shell_commands() (galaxy.tools.deps.resolvers.Dependency method) (galaxy.tools.deps.resolvers.NullDependency method) (galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency method) (galaxy.tools.deps.resolvers.resolver_mixins.HomebrewDependency method) shell_process() (in module galaxy.tools.deps.commands) ShellCommand (class in tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) ShellJobRunner (class in galaxy.jobs.runners.cli) short_name (galaxy.tools.deps.requirements.RequirementSpecification attribute) should_burst() (galaxy.jobs.rule_helper.RuleHelper method) show() (galaxy.tools.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.dataset_collections.DatasetCollectionsController method), [1] (galaxy.webapps.galaxy.api.datasets.DatasetsController 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.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.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.toolshed.ToolShedController 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] (galaxy.webapps.tool_shed.api.categories.CategoriesController method), [1] (galaxy.webapps.tool_shed.api.groups.GroupsController method), [1] (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method), [1] (galaxy.webapps.tool_shed.api.repository_revisions.RepositoryRevisionsController method), [1] (galaxy.webapps.tool_shed.api.users.UsersController method), [1] show_dependencies() (galaxy.tools.deps.views.DependencyResolversView method) show_error_message() (galaxy.web.framework.webapp.GalaxyWebTransaction 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_item_checkboxes (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.TracksterSelectionGrid attribute) (tool_shed.grids.repository_grids.DockerImageGrid attribute) show_jobs_summary() (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method), [1] show_library_item() (galaxy.security.GalaxyRBACAgent method) show_message() (galaxy.web.framework.webapp.GalaxyWebTransaction method) show_ok_message() (galaxy.web.framework.webapp.GalaxyWebTransaction method) show_params() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) show_status() (galaxy.util.pastescript.serve.ServeCommand method) show_tools() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method), [1] show_warn_message() (galaxy.web.framework.webapp.GalaxyWebTransaction method) shrink_stream_by_size() (in module galaxy.util) shrink_string_by_size() (in module galaxy.util) shutdown() (galaxy.app.UniverseApplication 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.objectstore.DistributedObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.objectstore.pulsar.PulsarObjectStore method) (galaxy.queue_worker.GalaxyQueueWorker method) (galaxy.tools.toolbox.watcher.NullToolConfWatcher method) (galaxy.tools.toolbox.watcher.NullWatcher method) (galaxy.tools.toolbox.watcher.ToolConfWatcher method) (galaxy.tools.toolbox.watcher.ToolDataWatcher method) (galaxy.tools.toolbox.watcher.ToolWatcher method) (galaxy.util.heartbeat.Heartbeat method) (galaxy.util.lazy_process.LazyProcess method) (galaxy.util.lazy_process.NoOpLazyProcess method) (galaxy.web.proxy.ProxyManager method) (galaxy.web.stack.ApplicationStack method) (galaxy.web.stack.MessageApplicationStack method) (galaxy.web.stack.UWSGIApplicationStack method) (galaxy.webapps.galaxy.config_watchers.ConfigWatchers method) (galaxy.webapps.reports.app.UniverseApplication method) (galaxy.webapps.tool_shed.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.galaxy_install.migrate.common.MigrateToolsApplication method) (tool_shed.galaxy_install.update_repository_manager.UpdateRepositoryManager method) Sif (class in galaxy.datatypes.graph) SIFGraphDataProvider (class in galaxy.datatypes.graph) simple_mapping() (in module galaxy.model.mapping) SimpleComputeEnvironment (class in galaxy.jobs) SimpleGraph (class in galaxy.util.simplegraph) SimpleGraphEdge (class in galaxy.util.simplegraph) SimpleGraphNode (class in galaxy.util.simplegraph) 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) SingularityContainer (class in galaxy.tools.deps.containers) singularize() (galaxy.util.inflection.English method) (galaxy.util.inflection.Inflector method) sites (galaxy.security.HostAgent attribute) size() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.objectstore.pulsar.PulsarObjectStore method) (galaxy.objectstore.rods.IRODSObjectStore method) (galaxy.objectstore.s3.S3ObjectStore method) size_string() (in module tool_shed.util.basic_util) size_to_bytes() (in module galaxy.util) skip() (galaxy.managers.base.ModelSerializer method) SkipAttribute skipped() (in module galaxy.tools.util.galaxyops) sleep() (galaxy.util.sleeper.Sleeper method) (tool_shed.galaxy_install.update_repository_manager.Sleeper method) Sleeper (class in galaxy.util.sleeper) (class in tool_shed.galaxy_install.update_repository_manager) slice_collections() (galaxy.dataset_collections.matching.MatchingCollections method) sliced_collection_type() (galaxy.dataset_collections.structure.Leaf method) slots_delta() (galaxy.containers.docker_swarm_manager.SwarmState method) slots_needed() (galaxy.containers.docker_swarm_manager.SwarmState method) slugify() (in module galaxy.util.biostar) 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) SMILES (class in galaxy.datatypes.molecules) sniff() (galaxy.datatypes.assembly.Amos method) (galaxy.datatypes.assembly.Roadmaps method) (galaxy.datatypes.assembly.Sequences 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.CRAM method) (galaxy.datatypes.binary.Cel method) (galaxy.datatypes.binary.Cool method) (galaxy.datatypes.binary.DMND method) (galaxy.datatypes.binary.ExcelXls method) (galaxy.datatypes.binary.Fast5Archive method) (galaxy.datatypes.binary.Fast5ArchiveBz2 method) (galaxy.datatypes.binary.Fast5ArchiveGz method) (galaxy.datatypes.binary.GeminiSQLite method) (galaxy.datatypes.binary.H5 method) (galaxy.datatypes.binary.ICM method) (galaxy.datatypes.binary.Idat method) (galaxy.datatypes.binary.IdpDB method) (galaxy.datatypes.binary.MzSQlite method) (galaxy.datatypes.binary.NetCDF 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.PostgresqlArchive method) (galaxy.datatypes.binary.RData method) (galaxy.datatypes.binary.SQlite method) (galaxy.datatypes.binary.SearchGuiArchive method) (galaxy.datatypes.binary.Sff method) (galaxy.datatypes.binary.Sra method) (galaxy.datatypes.binary.TwoBit method) (galaxy.datatypes.binary.Xlsx method) (galaxy.datatypes.blast.BlastXml method) (galaxy.datatypes.constructive_solid_geometry.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.genetics.rgSampleList 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.Bed 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.Gff3 method) (galaxy.datatypes.interval.Gtf method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.ScIdx method) (galaxy.datatypes.interval.Wiggle 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.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.proteomics.MascotDat method) (galaxy.datatypes.proteomics.Mgf method) (galaxy.datatypes.proteomics.Ms2 method) (galaxy.datatypes.proteomics.Msp method) (galaxy.datatypes.proteomics.ProteomicsXml 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.FastaGz method) (galaxy.datatypes.sequence.FastqBz2 method) (galaxy.datatypes.sequence.FastqGz 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.Pileup method) (galaxy.datatypes.tabular.Sam method) (galaxy.datatypes.tabular.Vcf method) (galaxy.datatypes.tabular.VcfGz method) (galaxy.datatypes.text.Arff method) (galaxy.datatypes.text.Biom1 method) (galaxy.datatypes.text.Html method) (galaxy.datatypes.text.IQTree 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) 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) sort() (galaxy.tools.parameters.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) sort_block_components_by_block() (in module galaxy.tools.util.maf_utilities) sort_by_attr() (galaxy.security.GalaxyRBACAgent method) (in module galaxy.web.base.controller) (in module galaxy.webapps.tool_shed.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) SortTool (class in galaxy.tools) source_dataset_chain (galaxy.model.DatasetInstance attribute) source_library_dataset (galaxy.model.DatasetInstance attribute) spawning_nodes() (galaxy.containers.docker_swarm_manager.SwarmState method) spec (galaxy.datatypes.metadata.MetadataCollection attribute) (galaxy.model.metadata.MetadataCollection attribute) SpecificationAwareDependencyResolver (class in galaxy.tools.deps.resolvers) SpecificationPatternDependencyResolver (class in galaxy.tools.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.tools.deps.requirements.RequirementSpecification attribute) SPLib (class in galaxy.datatypes.proteomics) SPLibNoIndex (class in galaxy.datatypes.proteomics) SplicedAlignment (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_dataset_collection_instance() (in module galaxy.dataset_collections.subcollections) split_output_name() (galaxy.tools.parser.output_objects.ToolOutputCollectionPart static method) (galaxy.tools.parser.ToolOutputCollectionPart static method) split_params() (in module galaxy.jobs.runners.util.cli) split_tag() (in module galaxy.tools.deps.mulled.util) splitLinebyWhitespaces() (galaxy.visualization.data_providers.phyloviz.nexusparser.Nexus_Parser method) 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) SquareDistanceMatrix (class in galaxy.datatypes.mothur) Sra (class in galaxy.datatypes.binary) src_merge() (in module galaxy.tools.util.maf_utilities) src_split() (in module galaxy.tools.util.maf_utilities) SSH_NEW_KEY_STRING (galaxy.jobs.runners.util.cli.shell.rsh.SecureShell attribute) 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.dataset.HistoryDatasetAssociationListGrid 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) (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.tools.util.maf_utilities.SplicedAlignment attribute) start() (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.tools.toolbox.watcher.NullToolConfWatcher method) (galaxy.tools.toolbox.watcher.NullWatcher method) (galaxy.tools.toolbox.watcher.ToolConfWatcher method) (galaxy.tools.toolbox.watcher.ToolDataWatcher method) (galaxy.tools.toolbox.watcher.ToolWatcher method) (galaxy.web.stack.ApplicationStack method) (galaxy.web.stack.MessageApplicationStack method) (galaxy.web.stack.UWSGIApplicationStack method) (galaxy.webapps.galaxy.config_watchers.ConfigWatchers method) (galaxy.webapps.reports.controllers.jobs.Timer method) (galaxy.workflow.scheduling_manager.WorkflowRequestMonitor method) start_process() (galaxy.util.lazy_process.LazyProcess method) (galaxy.util.lazy_process.NoOpLazyProcess 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.DatasetCollection attribute) (galaxy.model.DatasetCollectionInstance attribute) (galaxy.model.DatasetInstance attribute) state_counts() (galaxy.managers.history_contents.HistoryContentsManager method) StateColumn (class in galaxy.web.framework.helpers.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.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.jobs.metrics.collectl.stats) StatsdMiddleware (class in galaxy.web.framework.middleware.statsd) status() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method), [1] (galaxy.webapps.galaxy.api.toolshed.ToolShedController method), [1] 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.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.ToolMetaParameterException attribute) (galaxy.exceptions.ToolMissingException attribute) (galaxy.exceptions.UnknownContentsType attribute) stderr() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) StdioErrorLevel (class in galaxy.jobs.error_level) StdioParser (class in galaxy.tools.parser.xml) stdout() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) step_by_index() (galaxy.model.Workflow method) step_invocation_for_step_id() (galaxy.model.WorkflowInvocation method) step_invocations_by_step_id() (galaxy.model.WorkflowInvocation method) step_states_by_step_id() (galaxy.model.WorkflowInvocation method) StepManager (class in tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager) 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.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) (in module galaxy.datatypes.converters.wiggle_to_simple_converter) stop_job() (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.condor.CondorJobRunner method) (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) (galaxy.jobs.runners.godocker.GodockerJobRunner method) (galaxy.jobs.runners.kubernetes.KubernetesJobRunner method) (galaxy.jobs.runners.local.LocalJobRunner method) (galaxy.jobs.runners.pbs.PBSJobRunner method) (galaxy.jobs.runners.tasks.TaskedJobRunner method) STOP_SIGNAL (galaxy.jobs.handler.JobHandlerQueue attribute) (galaxy.jobs.handler.JobHandlerStopQueue attribute) StorableObject (class in galaxy.model) store_jobtemplate() (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) stored_list_grid (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface attribute) (galaxy.webapps.galaxy.controllers.history.HistoryController attribute) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController attribute) stored_workflow (galaxy.managers.workflows.CreatedWorkflow attribute) StoredWorkflow (class in galaxy.model) StoredWorkflowAllPublishedGrid (class in galaxy.webapps.galaxy.controllers.workflow) StoredWorkflowAnnotationAssociation (class in galaxy.model) (class in galaxy.webapps.tool_shed.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) stream() (galaxy.util.streamball.StreamBall method) (galaxy.util.streamball.ZipBall method) stream_template_mako() (galaxy.web.framework.webapp.GalaxyWebTransaction method) stream_to_file() (in module galaxy.datatypes.sniff) stream_to_open_named_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_replace() (galaxy.util.inflection.Base method) string_standard_ops() (galaxy.managers.base.ModelFilterParser method) string_to_object() (in module galaxy.util) StringFunctionFilter (class in galaxy.tools.parser.output_actions) stringify() (in module tool_shed.util.basic_util) stringify_dictionary_keys() (in module galaxy.util) strip_path() (in module tool_shed.util.basic_util) stripwd() (in module galaxy.model.orm.logging_connection_proxy) structure (galaxy.dataset_collections.matching.MatchingCollections attribute) structure() (galaxy.webapps.galaxy.controllers.history.HistoryController method) structure_regexp (galaxy.datatypes.sequence.DotBracket attribute) (galaxy.datatypes.tabular.ConnectivityTable attribute) stub_label() (galaxy.tools.toolbox.panel.ToolPanelElements method) stub_tool() (galaxy.tools.toolbox.panel.ToolPanelElements method) stub_workflow() (galaxy.tools.toolbox.panel.ToolPanelElements method) subcollection_mapping_type() (galaxy.dataset_collections.matching.MatchingCollections method) subcollection_type_description() (galaxy.dataset_collections.type_description.CollectionTypeDescription method) subcontainer_class (galaxy.managers.containers.ContainerManagerMixin attribute) (galaxy.managers.containers.DatasetCollectionAsContainerManagerMixin attribute) (galaxy.managers.containers.LibraryFolderAsContainerManagerMixin attribute) (galaxy.managers.history_contents.HistoryContentsManager attribute) subcontainer_class_manager_class (galaxy.managers.history_contents.HistoryContentsManager attribute) subcontainer_class_type_name (galaxy.managers.history_contents.HistoryContentsManager attribute) subcontainers() (galaxy.managers.containers.ContainerManagerMixin method) (galaxy.managers.history_contents.HistoryContentsManager method) submission_params() (in module galaxy.jobs.runners.util.condor) submit() (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.util.cli.job.BaseJobExec method) (galaxy.jobs.runners.util.cli.job.slurm.Slurm method) (galaxy.jobs.runners.util.cli.job.torque.Torque method) submodules() (in module galaxy.util.submodules) subprocess() (galaxy.datatypes.dataproviders.external.SubprocessDataProvider method) SubprocessDataProvider (class in galaxy.datatypes.dataproviders.external) 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) SubWorkflowModule (class in galaxy.workflow.modules) SUCCESS (galaxy.web.framework.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) 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_volumes (galaxy.containers.ContainerInterface attribute) (galaxy.containers.docker_swarm.DockerSwarmInterface attribute) SwarmManager (class in galaxy.containers.docker_swarm_manager) SwarmState (class in galaxy.containers.docker_swarm_manager) sweepster() (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) SwiftObjectStore (class in galaxy.objectstore.s3) switch_to_history() (galaxy.webapps.galaxy.controllers.history.HistoryController method) sync_database_with_file_system() (tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.SyncDatabase method) SyncDatabase (class in tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler) synchronized() (in module galaxy.util) 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.webapps.tool_shed.model.APIKeys attribute) (galaxy.webapps.tool_shed.model.Category attribute) (galaxy.webapps.tool_shed.model.Component attribute) (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.GalaxySession attribute) (galaxy.webapps.tool_shed.model.Group attribute) (galaxy.webapps.tool_shed.model.GroupRoleAssociation attribute) (galaxy.webapps.tool_shed.model.PasswordResetToken attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.RepositoryCategoryAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.RepositoryRoleAssociation attribute) (galaxy.webapps.tool_shed.model.Role attribute) (galaxy.webapps.tool_shed.model.Tag attribute) (galaxy.webapps.tool_shed.model.User attribute) (galaxy.webapps.tool_shed.model.UserGroupAssociation attribute) (galaxy.webapps.tool_shed.model.UserRoleAssociation attribute) tableize() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) 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 galaxy.webapps.tool_shed.model) tag (galaxy.tools.parser.output_actions.BooleanFilter attribute) (galaxy.tools.parser.output_actions.ColumnReplaceFilter attribute) (galaxy.tools.parser.output_actions.ColumnStripFilter attribute) (galaxy.tools.parser.output_actions.DatatypeIsInstanceToolOutputActionConditionalWhen attribute) (galaxy.tools.parser.output_actions.FormatToolOutputAction attribute) (galaxy.tools.parser.output_actions.FromDataTableOutputActionOption attribute) (galaxy.tools.parser.output_actions.FromFileToolOutputActionOption attribute) (galaxy.tools.parser.output_actions.FromParamToolOutputActionOption attribute) (galaxy.tools.parser.output_actions.InsertColumnToolOutputActionOptionFilter attribute) (galaxy.tools.parser.output_actions.MetadataToolOutputAction attribute) (galaxy.tools.parser.output_actions.MetadataValueFilter attribute) (galaxy.tools.parser.output_actions.MultipleSplitterFilter attribute) (galaxy.tools.parser.output_actions.NullToolOutputActionOption attribute) (galaxy.tools.parser.output_actions.ParamValueToolOutputActionOptionFilter attribute) (galaxy.tools.parser.output_actions.StringFunctionFilter attribute) (galaxy.tools.parser.output_actions.ToolOutputAction attribute) (galaxy.tools.parser.output_actions.ToolOutputActionConditional attribute) (galaxy.tools.parser.output_actions.ToolOutputActionConditionalWhen attribute) (galaxy.tools.parser.output_actions.ToolOutputActionGroup attribute) (galaxy.tools.parser.output_actions.ToolOutputActionOption attribute) (galaxy.tools.parser.output_actions.ToolOutputActionOptionFilter attribute) (galaxy.tools.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_for_tool() (in module galaxy.util.biostar) 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) 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_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] TagManager (class in galaxy.managers.tags) (class in tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager) tags_used() (galaxy.managers.users.UserManager method) TagsController (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.tools.deps.brew_exts.RecipeContext attribute) Target (class in galaxy.tools.deps.mulled.util) Task (class in galaxy.model) task_add() (galaxy.containers.docker_model.DockerNode method) (galaxy.containers.docker_model.DockerService method) task_count (galaxy.containers.docker_model.DockerNode attribute) task_inspect() (galaxy.containers.docker_swarm.DockerSwarmCLIInterface method) task_suspend() (galaxy.jobs.runners.godocker.GodockerJobRunner method) TaskedJobRunner (class in galaxy.jobs.runners.tasks) TaskMetricNumeric (class in galaxy.model) TaskMetricText (class in galaxy.model) TaskPathRewriter (class in galaxy.jobs.datasets) tasks (galaxy.containers.docker_model.DockerNode attribute) TaskWrapper (class in galaxy.jobs) Taxonomy (class in galaxy.datatypes.tabular) TaxonomySummary (class in galaxy.datatypes.mothur) TempFile (class in log_tempfile) TempfileDataProvider (class in galaxy.datatypes.dataproviders.external) TempFileHandler (class in galaxy.tools.util.maf_utilities) template (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.web.base.controller.JSAppLauncher method) template_context (galaxy.web.framework.webapp.GalaxyWebTransaction attribute) template_macro_params() (in module galaxy.tools.loader) (in module galaxy.util.xml_macros) TEMPLATE_PATHS_CONFIG (galaxy.visualization.plugins.registry.VisualizationsRegistry attribute) TemplateCommand (class in tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) templates() (in module galaxy.web.framework.helpers) terminal_states (galaxy.model.Dataset attribute) (galaxy.model.Job attribute) (galaxy.model.TransferJob attribute) test_data() (galaxy.tools.test.ToolTestBuilder method) test_data_iter() (in module galaxy.tools.test) test_files (galaxy.datatypes.genetics.LinkageStudies attribute) TestCollectionDef (class in galaxy.tools.parser.interface) TestCollectionOutputDef (class in galaxy.tools.parser.interface) TestDataResolver (class in galaxy.tools.verify.test_data) tests (galaxy.tools.Tool attribute) Text (class in galaxy.datatypes.data) text_data() (galaxy.managers.hdas.HDAManager method) TextArea (class in galaxy.web.form_builder) TextColumn (class in galaxy.web.framework.helpers.grids) TextField (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) Timer (class in galaxy.webapps.reports.controllers.jobs) times_downloaded (galaxy.webapps.tool_shed.model.Repository attribute) tip() (galaxy.webapps.tool_shed.model.Repository method) TipOnly (class in tool_shed.repository_types.metadata) title (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.dataset.HistoryDatasetAssociationListGrid 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.user.UserOpenIDGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.LibraryDatasetsSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.TracksterSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.VisualizationListGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.DatatypesGrid attribute) (tool_shed.grids.repository_grids.DeprecatedRepositoriesIOwnGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithInvalidToolsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesByUserGrid attribute) (tool_shed.grids.repository_grids.RepositoriesICanAdministerGrid attribute) (tool_shed.grids.repository_grids.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_plural (galaxy.tools.parameters.grouping.Repeat attribute) (galaxy.tools.parameters.grouping.Section attribute) (galaxy.tools.parameters.grouping.UploadDataset attribute) titleize() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) 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.tools.cwl) (in module galaxy.tools.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.WorkflowRequest method) (galaxy.model.tool_shed_install.ToolShedRepository method) (galaxy.model.tool_shed_install.ToolVersion method) (galaxy.tools.Tool method) (galaxy.tools.data.TabularToolDataField method) (galaxy.tools.data.TabularToolDataTable method) (galaxy.tools.deps.dependencies.DependenciesDescription method) (galaxy.tools.deps.requirements.ContainerDescription method) (galaxy.tools.deps.requirements.RequirementSpecification method) (galaxy.tools.deps.requirements.ToolRequirement 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.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.parser.output_objects.ToolOutput method) (galaxy.tools.parser.output_objects.ToolOutputBase 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.visualization.genomes.Genome 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.webapps.tool_shed.model.Repository method) (galaxy.webhooks.Webhook 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.tools.cwl) (in module galaxy.tools.cwl.representation) to_hda_representative() (galaxy.model.HistoryDatasetCollectionAssociation method) to_history_dataset_association() (galaxy.model.LibraryDatasetDatasetAssociation method) to_html_string() (in module tool_shed.util.basic_util) 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.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.TextToolParameter 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) to_list() (galaxy.tools.deps.requirements.ToolRequirements 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.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.tools.deps.brew_exts.EnvAction 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)

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.SelectToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) to_tool_path() (galaxy.tools.fetcher.ToolLocationFetcher method) to_unicode() (in module galaxy.web.framework.helpers) to_xml() (in module galaxy.tools.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.webapps.tool_shed.model.PasswordResetToken attribute) Tool (class in galaxy.tools) (class in tool_shed.utility_containers.utility_container_manager) tool (galaxy.tools.parser.output_actions.ToolOutputAction attribute) (galaxy.tools.parser.output_actions.ToolOutputActionConditional attribute) (galaxy.tools.parser.output_actions.ToolOutputActionGroup attribute) (galaxy.tools.parser.output_actions.ToolOutputActionOption attribute) (galaxy.tools.parser.output_actions.ToolOutputActionOptionFilter attribute) tool() (galaxy.tools.cwl.schema.SchemaLoader method) tool_class (in module galaxy.tools) tool_config_paths (galaxy.webapps.galaxy.config_watchers.ConfigWatchers attribute) tool_data_path_files (galaxy.tools.data.ToolDataPathFiles attribute) tool_data_paths (galaxy.webapps.galaxy.config_watchers.ConfigWatchers attribute) tool_data_table (galaxy.tools.parameters.dynamic_options.DynamicOptions attribute) tool_data_table_items() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method) tool_dependencies_being_installed (galaxy.model.tool_shed_install.ToolShedRepository attribute) tool_dependencies_grid (galaxy.webapps.tool_shed.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_is_orphan() (tool_shed.galaxy_install.dependency_display.DependencyDisplayer method) tool_dependency_status_updates() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) tool_directory() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) tool_error_messages() (galaxy.webapps.reports.controllers.tools.Tools method) tool_errors() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) 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.tools.util.maf_utilities) tool_help() (galaxy.webapps.galaxy.controllers.root.RootController method) tool_ids (galaxy.tools.toolbox.lineages.interface.ToolLineage attribute) (galaxy.tools.toolbox.lineages.ToolLineage attribute) tool_ids_by_requirements (galaxy.tools.deps.views.DependencyResolversView attribute) tool_json() (galaxy.webapps.galaxy.api.toolshed.ToolShedController method), [1] tool_lineages() (galaxy.webapps.galaxy.api.configuration.ConfigurationController method), [1] tool_output_to_structure() (in module galaxy.dataset_collections.structure) tool_panel_contents() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) tool_per_month() (galaxy.webapps.reports.controllers.jobs.Jobs method) tool_provided_metadata() (galaxy.tools.Tool method) tool_proxy (galaxy.tools.parser.cwl.CwlToolSource attribute) tool_proxy() (in module galaxy.tools.cwl) (in module galaxy.tools.cwl.parser) tool_requirements (galaxy.tools.Tool attribute) tool_requirements_status (galaxy.tools.Tool attribute) tool_search() (galaxy.webapps.galaxy.controllers.root.RootController method) tool_shed (module) tool_shed.capsule (module) tool_shed.capsule.capsule_manager (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.datatypes (module) tool_shed.galaxy_install.datatypes.custom_datatype_manager (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.install_manager (module) tool_shed.galaxy_install.installed_repository_manager (module) tool_shed.galaxy_install.metadata (module) tool_shed.galaxy_install.metadata.installed_repository_metadata_manager (module) tool_shed.galaxy_install.migrate (module) tool_shed.galaxy_install.migrate.check (module) tool_shed.galaxy_install.migrate.common (module) tool_shed.galaxy_install.repair_repository_manager (module) tool_shed.galaxy_install.repository_dependencies (module) tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager (module) tool_shed.galaxy_install.tool_dependencies (module) tool_shed.galaxy_install.tool_dependencies.env_manager (module) tool_shed.galaxy_install.tool_dependencies.recipe (module) tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader (module) tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder (module) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment (module) tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager (module) tool_shed.galaxy_install.tool_dependencies.recipe.step_handler (module) tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler (module) tool_shed.galaxy_install.tool_migration_manager (module) tool_shed.galaxy_install.tools (module) tool_shed.galaxy_install.tools.data_manager (module) tool_shed.galaxy_install.tools.tool_panel_manager (module) tool_shed.galaxy_install.update_repository_manager (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.tool_shed_registry (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.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.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_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.workflow_util (module) tool_shed.util.xml_util (module) tool_shed.utility_containers (module) tool_shed.utility_containers.utility_container_manager (module) tool_shed_decode() (in module tool_shed.util.encoding_util) tool_shed_encode() (in module tool_shed.util.encoding_util) tool_shed_from_repository_clone_url() (tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) tool_shed_is_this_tool_shed() (in module tool_shed.util.shed_util_common) tool_shed_path_name (galaxy.model.tool_shed_install.ToolShedRepository attribute) tool_shed_repository (galaxy.tools.Tool attribute) tool_tag_manager() (in module galaxy.tools.toolbox.tags) tool_type (galaxy.tools.AsyncDataSourceTool attribute) (galaxy.tools.DataDestinationTool attribute) (galaxy.tools.DataManagerTool attribute) (galaxy.tools.DataSourceTool attribute) (galaxy.tools.ExportHistoryTool attribute) (galaxy.tools.FilterFailedDatasetsTool attribute) (galaxy.tools.FilterFromFileTool attribute) (galaxy.tools.FlattenTool attribute) (galaxy.tools.ImportHistoryTool attribute) (galaxy.tools.MergeCollectionTool attribute) (galaxy.tools.OutputParameterJSONTool attribute) (galaxy.tools.RelabelFromFileTool attribute) (galaxy.tools.SetMetadataTool attribute) (galaxy.tools.SortTool attribute) (galaxy.tools.Tool attribute) (galaxy.tools.UnzipCollectionTool attribute) (galaxy.tools.ZipCollectionTool attribute) tool_version_list_grid (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) tool_versions (galaxy.tools.Tool attribute) (galaxy.tools.toolbox.lineages.ToolLineage attribute) (galaxy.tools.toolbox.lineages.interface.ToolLineage attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) tool_versions_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) ToolAction (class in galaxy.tools.actions) ToolBox (class in galaxy.tools) toolbox_requirements_status (galaxy.tools.deps.views.DependencyResolversView attribute) ToolBoxSearch (class in galaxy.tools.search) ToolConfWatcher (class in galaxy.tools.toolbox.watcher) ToolData (class in galaxy.webapps.galaxy.api.tool_data), [1] ToolDataPathFiles (class in galaxy.tools.data) ToolDataTable (class in galaxy.tools.data) ToolDataTableManager (class in galaxy.tools.data) (in module tool_shed.tools.data_table_manager) ToolDataWatcher (class in galaxy.tools.toolbox.watcher) 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) ToolErrorLog (class in galaxy.tools) ToolEvaluator (class in galaxy.tools.evaluation) ToolExecutionCache (class in galaxy.tools.actions) ToolFileEventHandler (class in galaxy.tools.toolbox.watcher) ToolInfo (class in galaxy.tools.deps.containers) 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.tools.fetcher) ToolLocationResolver (class in galaxy.tools.locations) ToolMetadataDatasetCollector (class in galaxy.tools.parameters.output_collect) ToolMetaParameterException ToolMigrationManager (class in tool_shed.galaxy_install.tool_migration_manager) ToolMissingException ToolModule (class in galaxy.workflow.modules) ToolNotFoundException ToolOutput (class in galaxy.tools.parser.output_objects) ToolOutputAction (class in galaxy.tools.parser.output_actions) ToolOutputActionConditional (class in galaxy.tools.parser.output_actions) ToolOutputActionConditionalWhen (class in galaxy.tools.parser.output_actions) ToolOutputActionGroup (class in galaxy.tools.parser.output_actions) ToolOutputActionOption (class in galaxy.tools.parser.output_actions) ToolOutputActionOptionFilter (class in galaxy.tools.parser.output_actions) ToolOutputBase (class in galaxy.tools.parser.output_objects) ToolOutputCollection (class in galaxy.tools.parser.output_objects) ToolOutputCollectionPart (class in galaxy.tools.parser) (class in galaxy.tools.parser.output_objects) ToolOutputCollectionStructure (class in galaxy.tools.parser.output_objects) ToolPanelElements (class in galaxy.tools.toolbox.panel) ToolPanelManager (class in 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.tools.parameters.output_collect) ToolProvidedMetadataDatasetCollection (class in galaxy.tools.parser.output_collection_def) ToolRequirement (class in galaxy.tools.deps.requirements) ToolRequirements (class in galaxy.tools.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 (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) ToolsController (class in galaxy.webapps.galaxy.api.tools), [1] (class in galaxy.webapps.tool_shed.api.tools), [1] ToolSearch (class in galaxy.webapps.tool_shed.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) ToolShedAuthenticationController (class in galaxy.webapps.tool_shed.api.authenticate), [1] ToolShedController (class in galaxy.webapps.galaxy.api.toolshed), [1] ToolShedDependency (class in galaxy.tools.deps.resolvers.galaxy_packages) ToolShedPackageDependencyResolver (class in galaxy.tools.deps.resolvers.tool_shed_packages) ToolShedRepositoriesController (class in galaxy.webapps.galaxy.api.tool_shed_repositories), [1] ToolShedRepository (class in galaxy.model.tool_shed_install) ToolShedUtilityContainerManager (class in tool_shed.utility_containers) ToolSource (class in galaxy.tools.parser) (class in galaxy.tools.parser.interface) ToolStdioExitCode (class in galaxy.tools.parser.interface) ToolStdioRegex (class in galaxy.tools.parser.interface) ToolTagAssociation (class in galaxy.model) ToolTestBuilder (class in galaxy.tools.test) ToolValidator (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) 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) (galaxy.webapps.tool_shed.model.User attribute) total_size() (in module galaxy.model.custom_types) tour_contents() (galaxy.tours.ToursRegistry method) tour_loader() (in module galaxy.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) TraceLoggerProxy (class in galaxy.model.orm.logging_connection_proxy) track() (galaxy.jobs.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) TraML (class in galaxy.datatypes.proteomics) transaction_chooser() (galaxy.web.framework.webapp.WebApplication method) 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_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.dataset_collections.structure) TrimmedString (class in galaxy.model.custom_types) Triples (class in galaxy.datatypes.triples) truncate() (galaxy.datatypes.dataproviders.base.DataProvider method) (in module galaxy.web.framework.helpers) 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.tools.parameters.grouping.Conditional attribute) (galaxy.tools.parameters.grouping.Repeat attribute) (galaxy.tools.parameters.grouping.Section attribute) (galaxy.tools.parameters.grouping.UploadDataset attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.Role attribute) (galaxy.webapps.tool_shed.model.Tag 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.util.workflow_util.RepoToolModule attribute) type() (galaxy.managers.base.ModelValidator method) type_id (galaxy.model.HistoryDatasetAssociation attribute) (galaxy.model.HistoryDatasetCollectionAssociation attribute) type_key (galaxy.tools.data.TabularToolDataTable attribute) types (galaxy.model.DefaultQuotaAssociation attribute) (galaxy.model.FormDefinition attribute) (galaxy.model.Role attribute) (galaxy.model.WorkflowRequestInputParameter attribute) (galaxy.webapps.tool_shed.model.Role attribute)

U

UCI (class in galaxy.model) ucsc_links() (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.interval.CustomTrack method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.Wiggle method) UCSCLimitException, [1] UCSCOutWrapper (class in galaxy.tools.exception_handling) (class in galaxy.util.ucsc) UCSCTrackHub (class in galaxy.datatypes.tracks) umask_fix_perms() (in module galaxy.util) unaccent() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) UnamePlugin (class in galaxy.jobs.metrics.instrumenters.uname) uncompress() (in module tool_shed.util.commit_util) undeletable() (galaxy.model.DatasetInstance method) undelete() (galaxy.managers.deletable.DeletableManagerMixin 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() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) undelete_operation (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) undelete_repository() (galaxy.webapps.tool_shed.controllers.admin.AdminController method) underscore() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector 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) uninstall() (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method) uninstall_dependencies() (galaxy.tools.deps.views.DependencyResolversView method) (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] uninstall_environments() (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method) uninstall_repository() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method), [1] (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) uninstall_tool_dependencies() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) uninstallable_resolvers (galaxy.tools.deps.views.DependencyResolversView attribute) uninstalled_repository_dependencies (galaxy.model.tool_shed_install.ToolShedRepository attribute) uninstalled_tool_dependencies (galaxy.model.tool_shed_install.ToolShedRepository attribute) 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) UnitializedTree (class in galaxy.dataset_collections.structure) UniverseApplication (class in galaxy.app) (class in galaxy.webapps.reports.app) (class in galaxy.webapps.tool_shed.app) unknown_starttag() (galaxy.webapps.galaxy.controllers.workflow.SingleTagContentsParser method) UnknownContentsType UnlinkedToolShedPackageDependencyResolver (class in galaxy.tools.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) unpack_chunks() (in module tool_shed.util.hg_util) unpack_groups() (in module tool_shed.util.hg_util) unpack_patches() (in module tool_shed.util.hg_util) unpublish() (galaxy.managers.sharable.SharableModelManager method) Unrestricted (class in tool_shed.repository_types.unrestricted) unset_item_extended_metadata_obj() (galaxy.web.base.controller.UsesExtendedMetadataMixin method) unshare_with() (galaxy.managers.sharable.SharableModelManager method) UnspecifiedBuildValidator (class in galaxy.tools.parameters.validation) unstructured_path_rewriter() (galaxy.jobs.ComputeEnvironment method) (galaxy.jobs.SimpleComputeEnvironment method) unused_dependency_paths (galaxy.tools.deps.views.DependencyResolversView attribute) unused_dependency_paths() (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method) unused_port() (in module galaxy.util.sockets) unversioned_install() (in module galaxy.tools.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.model.DatasetInstance method) (galaxy.model.WorkflowInvocation method) (galaxy.model.WorkflowInvocationStep method) (galaxy.util.Params method) (galaxy.util.odict.odict method) (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.quotas.QuotaAPIController 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] (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method), [1] (galaxy.webapps.tool_shed.api.repository_revisions.RepositoryRevisionsController method), [1] (tool_shed.managers.groups.GroupManager method) (tool_shed.managers.repositories.RepoManager method) update_circular_repository_dependencies() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method) update_existing_tool_dependency() (tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method) update_files() (galaxy.tools.data.ToolDataPathFiles method) update_from_file() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.DiskObjectStore method) (galaxy.objectstore.NestedObjectStore method) (galaxy.objectstore.ObjectStore method) (galaxy.objectstore.pulsar.PulsarObjectStore method) (galaxy.objectstore.rods.IRODSObjectStore method) (galaxy.objectstore.s3.S3ObjectStore method) update_in_shed_tool_config() (tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method) update_invocation_step() (galaxy.managers.workflows.WorkflowsManager method) (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] update_or_append() (galaxy.tools.toolbox.panel.ToolPanelElements method) update_proxy() (galaxy.web.proxy.ProxyManager method) update_repository() (galaxy.tools.verify.test_data.GitDataResolver method) (in module tool_shed.util.hg_util) (in module tool_shed.util.repository_util) update_repository_dependencies_metadata() (tool_shed.metadata.metadata_generator.MetadataGenerator method) update_repository_record() (tool_shed.galaxy_install.update_repository_manager.UpdateRepositoryManager method) update_requests() (galaxy.web.proxy.JsonFileProxyIpc method) (galaxy.web.proxy.SqliteProxyIpc method) update_shed_config() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) update_time (galaxy.webapps.tool_shed.model.Category attribute) (galaxy.webapps.tool_shed.model.ComponentReview attribute) (galaxy.webapps.tool_shed.model.GalaxySession attribute) (galaxy.webapps.tool_shed.model.Group attribute) (galaxy.webapps.tool_shed.model.GroupRoleAssociation attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.RepositoryMetadata attribute) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.RepositoryRoleAssociation attribute) (galaxy.webapps.tool_shed.model.Role attribute) (galaxy.webapps.tool_shed.model.User attribute) (galaxy.webapps.tool_shed.model.UserGroupAssociation attribute) (galaxy.webapps.tool_shed.model.UserRoleAssociation attribute) update_to_changeset_revision() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) update_tool_panel_dict() (tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method) update_tool_shed_repository_status() (tool_shed.galaxy_install.install_manager.InstallRepositoryManager method) update_tool_shed_status_for_installed_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) update_tour() (galaxy.webapps.galaxy.api.tours.ToursController method), [1] update_watch_data_table_paths() (galaxy.webapps.galaxy.config_watchers.ConfigWatchers method) update_workflow_from_dict() (galaxy.managers.workflows.WorkflowContentsManager method) updated_changeset_revisions() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) UpdateRepositoryManager (class in tool_shed.galaxy_install.update_repository_manager) updates() (galaxy.webapps.tool_shed.api.repositories.RepositoriesController method), [1] upgrade_available (galaxy.model.tool_shed_install.ToolShedRepository attribute) upload() (galaxy.webapps.tool_shed.controllers.upload.UploadController method) upload_capsule() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) (tool_shed.capsule.capsule_manager.ImportRepositoryManager method) upload_directory() (galaxy.webapps.tool_shed.controllers.upload.UploadController method) upload_import_workflow() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) upload_options (galaxy.model.LibraryDataset attribute) upload_tar() (in module tool_shed.util.repository_content_util) UploadController (class in galaxy.webapps.tool_shed.controllers.upload) UploadDataset (class in galaxy.tools.parameters.grouping) UploadToolAction (class in galaxy.tools.actions.upload) uri (galaxy.tools.cwl.schema.RawProcessReference attribute) url (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper attribute) url_auth() (tool_shed.tool_shed_registry.Registry method) url_download() (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 galaxy.webapps.tool_shed) url_get() (in module galaxy.util) 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) urlize() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) usage (galaxy.util.pastescript.serve.Command attribute) (galaxy.util.pastescript.serve.ServeCommand attribute) use_async (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) use_final (galaxy.webapps.tool_shed.search.repo_search.RepoWeighting attribute) use_hide_message (galaxy.web.framework.helpers.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_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.dataset.HistoryDatasetAssociationListGrid attribute) (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid attribute) (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute) (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.visualization.TracksterSelectionGrid attribute) (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute) (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute) (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.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.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.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.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() (tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method) User (class in galaxy.model) (class in galaxy.webapps.galaxy.controllers.user) (class in galaxy.webapps.galaxy.controllers.userskeys) (class in galaxy.webapps.tool_shed.controllers.user) (class in galaxy.webapps.tool_shed.model) user (galaxy.jobs.JobWrapper attribute) (galaxy.web.framework.webapp.GalaxyWebTransaction attribute) (galaxy.webapps.tool_shed.model.GalaxySession attribute) (galaxy.webapps.tool_shed.model.PasswordResetToken attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.UserGroupAssociation attribute) (galaxy.webapps.tool_shed.model.UserRoleAssociation attribute) (galaxy.work.context.WorkRequestContext attribute) user_assoc (galaxy.managers.roles.RoleManager attribute) USER_BOOTSTRAP_KEYS (galaxy.web.base.controller.JSAppLauncher attribute) user_can_administer_repository() (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) user_can_browse_component_review() (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) user_can_do_run_as() (galaxy.managers.context.ProvidesUserContext method) user_can_import_repository_archive() (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) user_can_purge (galaxy.model.Dataset attribute) user_can_review_repositories() (galaxy.webapps.tool_shed.security.CommunityRBACAgent method) user_checks() (galaxy.web.framework.webapp.GalaxyWebTransaction method) user_disk_usage() (galaxy.webapps.reports.controllers.users.Users method) user_ftp_dir (galaxy.managers.context.ProvidesUserContext attribute) user_get_default_permissions() (galaxy.security.GalaxyRBACAgent method) user_id (galaxy.webapps.tool_shed.model.APIKeys attribute) (galaxy.webapps.tool_shed.model.GalaxySession attribute) (galaxy.webapps.tool_shed.model.PasswordResetToken attribute) (galaxy.webapps.tool_shed.model.Repository attribute) (galaxy.webapps.tool_shed.model.RepositoryRatingAssociation attribute) (galaxy.webapps.tool_shed.model.RepositoryReview attribute) (galaxy.webapps.tool_shed.model.UserGroupAssociation attribute) (galaxy.webapps.tool_shed.model.UserRoleAssociation attribute) user_is_admin() (galaxy.managers.context.ProvidesUserContext method) user_list_grid (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute) (galaxy.webapps.tool_shed.controllers.admin.AdminController attribute) user_openid_grid (galaxy.webapps.galaxy.controllers.user.User attribute) user_per_month() (galaxy.webapps.reports.controllers.jobs.Jobs method) (galaxy.webapps.reports.controllers.workflows.Workflows method) user_set_default_permissions() (galaxy.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) UserAction (class in galaxy.model) UserAddress (class in galaxy.model) UserAPIController (class in galaxy.webapps.galaxy.api.users), [1] 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 galaxy.webapps.tool_shed.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.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.webapps.tool_shed.model.User attribute) UserOpenID (class in galaxy.model) UserOpenIDGrid (class in galaxy.webapps.galaxy.controllers.user) UserPreference (class in galaxy.model) UserQuotaAssociation (class in galaxy.model) UserRoleAssociation (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) Users (class in galaxy.webapps.reports.controllers.users) users (galaxy.webapps.tool_shed.model.Group attribute) (galaxy.webapps.tool_shed.model.Role attribute) users_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) UsersController (class in galaxy.webapps.tool_shed.api.users), [1] UserSerializer (class in galaxy.managers.users) uses_tool_shed_dependencies() (galaxy.tools.deps.DependencyManager method) (galaxy.tools.deps.NullDependencyManager method) UsesAnnotations (class in galaxy.model.item_attrs) UsesCreateAndUpdateTime (class in galaxy.model) UsesExtendedMetadataMixin (class in galaxy.web.base.controller) UsesFormDefinitionsMixin (class in galaxy.web.base.controller) UsesHomebrewMixin (class in galaxy.tools.deps.resolvers.resolver_mixins) UsesInstalledRepositoriesMixin (class in galaxy.tools.deps.resolvers.resolver_mixins) UsesItemRatings (class in galaxy.model.item_attrs) UsesLibraryMixin (class in galaxy.web.base.controller) UsesLibraryMixinItems (class in galaxy.web.base.controller) UsesQuotaMixin (class in galaxy.web.base.controller) UsesStoredWorkflowMixin (class in galaxy.web.base.controller) UsesTagsMixin (class in galaxy.web.base.controller) UsesToolDependencyDirMixin (class in galaxy.tools.deps.resolvers.resolver_mixins) UsesVisualizationMixin (class in galaxy.web.base.controller) UtilityContainerManager (class in tool_shed.utility_containers.utility_container_manager) UUIDType (class in galaxy.model.custom_types) uwsgi_app() (in module galaxy.webapps.galaxy.buildapp) (in module galaxy.webapps.reports.buildapp) (in module galaxy.webapps.tool_shed.buildapp) uwsgi_app_factory() (in module galaxy.webapps.galaxy.buildapp) UWSGIApplicationStack (class in galaxy.web.stack) UWSGILogFilter (class in galaxy.web.stack)

V

v1_image_name() (in module galaxy.tools.deps.mulled.util) v2_image_name() (in module galaxy.tools.deps.mulled.util) valid() (galaxy.tools.lint.LintContext method) valid_api_key() (galaxy.managers.users.UserManager method) valid_category_grid (galaxy.webapps.tool_shed.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_hda_match() (galaxy.tools.parameters.dataset_matcher.DatasetMatcher method) valid_input_states (galaxy.model.Dataset attribute) (galaxy.tools.DatabaseOperationTool attribute) (galaxy.tools.Tool attribute) VALID_METHODS (galaxy.datatypes.dataproviders.external.URLDataProvider attribute) valid_operations (galaxy.model.Quota attribute) VALID_PRESET (galaxy.tools.parameters.sanitize.ToolParameterSanitizer attribute) VALID_RENDER_TARGETS (galaxy.visualization.plugins.config_parser.VisualizationsConfigParser attribute) valid_repository_grid (galaxy.webapps.tool_shed.controllers.repository.RepositoryController attribute) valid_update_keys (galaxy.web.proxy.ProxyManager attribute) validate() (galaxy.datatypes.data.Data method) (galaxy.datatypes.genetics.GenomeGraphs method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.metadata.MetadataParameter 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.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.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) validate_and_sanitize_basestring() (in module galaxy.util.validation) validate_and_sanitize_basestring_list() (in module galaxy.util.validation) validate_archive_paths() (tool_shed.capsule.capsule_manager.ImportRepositoryManager method) validate_boolean() (in module galaxy.util.validation) validate_capsule() (tool_shed.capsule.capsule_manager.ImportRepositoryManager method) validate_config() (galaxy.containers.ContainerInterface method) (galaxy.containers.docker.DockerCLIInterface method) (galaxy.containers.docker_swarm.DockerSwarmInterface method) (in module galaxy.jobs.dynamic_tool_destination) validate_email() (in module galaxy.security.validate_user_input) validate_in_users_and_groups() (galaxy.web.base.controller.BaseAPIController method) validate_jsonrpc_request() (in module galaxy.util.json) validate_jsonrpc_response() (in module galaxy.util.json) validate_password() (in module galaxy.security.validate_user_input) validate_publicname() (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) validate_source() (galaxy.datatypes.dataproviders.base.DataProvider method) (galaxy.datatypes.dataproviders.chunk.ChunkDataProvider method) validate_url() (in module galaxy.tools.actions.upload_common) ValidationError (class in galaxy.model) 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.containers.docker_model.DockerNodeLabel attribute) (galaxy.containers.docker_model.DockerServiceConstraint 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_to_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_to_display_text() (galaxy.tools.parameters.basic.ToolParameter method) values() (galaxy.jobs.runners.util.Bunch method) (galaxy.util.bunch.Bunch method) (galaxy.util.odict.odict method) ValueToolOutputActionConditionalWhen (class in galaxy.tools.parser.output_actions) variablize() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) 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) Velvet (class in galaxy.datatypes.assembly) 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) verify() (in module galaxy.tools.verify) verify_archives_in_capsule() (tool_shed.capsule.capsule_manager.ImportRepositoryManager method) verify_assertion() (in module galaxy.tools.verify.asserts) verify_assertions() (in module galaxy.tools.verify.asserts) verify_tools() (in module tool_shed.galaxy_install.migrate.check) version (galaxy.tools.deps.mulled.util.Target attribute) version() (galaxy.webapps.galaxy.api.configuration.ConfigurationController method), [1] (galaxy.webapps.tool_shed.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.tools.deps.mulled.util) versioned_install() (in module galaxy.tools.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() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) view_changeset() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) view_datatypes_registry() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method) view_job() (galaxy.webapps.galaxy.controllers.data_manager.DataManager 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() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) (galaxy.webapps.tool_shed.controllers.repository_review.RepositoryReviewController method) view_repository() (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) view_tool_metadata() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) view_workflow() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (galaxy.webapps.tool_shed.controllers.repository.RepositoryController method) ViewField (class in galaxy.model.search) ViewQueryBaseClass (class in galaxy.model.search) visible (galaxy.tools.parameters.basic.FTPFileToolParameter attribute) (galaxy.tools.parameters.basic.ToolParameter attribute) (galaxy.tools.parameters.grouping.Group attribute) (galaxy.tools.parameters.output_collect.JsonCollectedDatasetMatch attribute) visit_inputs() (galaxy.tools.Tool method) Visualization (class in galaxy.model) 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) 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_from_str() (galaxy.tools.deps.docker_util.DockerVolume static method) volumes_from_str() (galaxy.tools.deps.docker_util.DockerVolume static method) 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_for_toolbox_reload() (galaxy.config.ConfiguresGalaxyMixin method) waiting_for_elements (galaxy.model.DatasetCollection attribute) wake() (galaxy.util.sleeper.Sleeper method) (tool_shed.galaxy_install.update_repository_manager.Sleeper method) walk_collections() (galaxy.dataset_collections.structure.Tree method) walk_over_extra_files() (in module galaxy.tools.parameters.output_collect) walk_over_file_collectors() (in module galaxy.tools.parameters.output_collect) warn() (galaxy.tools.lint.LintContext method) (in module galaxy.tools.util.galaxyops) WARNING (galaxy.jobs.error_level.StdioErrorLevel attribute) watch_directory() (galaxy.tools.toolbox.watcher.NullWatcher method) (galaxy.tools.toolbox.watcher.ToolDataWatcher method) (galaxy.tools.toolbox.watcher.ToolWatcher method) watch_file() (galaxy.tools.toolbox.watcher.NullToolConfWatcher method) (galaxy.tools.toolbox.watcher.NullWatcher method) (galaxy.tools.toolbox.watcher.ToolConfWatcher method) (galaxy.tools.toolbox.watcher.ToolWatcher method) WebApplication (class in galaxy.web.framework.base) (class in galaxy.web.framework.webapp) Webhook (class in galaxy.webhooks) webhook_data() (galaxy.webapps.galaxy.api.webhooks.WebhooksController method), [1] 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.tools.deps.brew_exts) (in module galaxy.tools.deps.commands) (in module galaxy.util) whoami() (galaxy.webapps.galaxy.api.configuration.ConfigurationController method), [1] Wiff (class in galaxy.datatypes.proteomics) Wiggle (class in galaxy.datatypes.interval) wiggle_dataprovider() (galaxy.datatypes.interval.Wiggle method) wiggle_dict_dataprovider() (galaxy.datatypes.interval.Wiggle method) WiggleDataProvider (class in galaxy.datatypes.dataproviders.dataset) with_path_for_job() (galaxy.jobs.datasets.DatasetPath method) workers() (galaxy.web.stack.ApplicationStack method) (galaxy.web.stack.UWSGIApplicationStack method) Workflow (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) (class in tool_shed.utility_containers.utility_container_manager) workflow (galaxy.managers.workflows.CreatedWorkflow attribute) workflow_dict() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] workflow_output_for() (galaxy.model.WorkflowStep method) workflow_outputs (galaxy.model.Workflow attribute) workflow_proxy() (in module galaxy.tools.cwl) workflow_request_to_run_config() (in module galaxy.workflow.run_request) workflow_run_config_to_request() (in module galaxy.workflow.run_request) workflow_tag_handler() (in module galaxy.model.search) workflow_to_dict() (galaxy.managers.workflows.WorkflowContentsManager 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) WorkflowField (class in galaxy.web.form_builder) WorkflowInvocation (class in galaxy.model) WorkflowInvocationOutputDatasetAssociation (class in galaxy.model) WorkflowInvocationOutputDatasetCollectionAssociation (class in galaxy.model) WorkflowInvocationStep (class in galaxy.model) WorkflowInvocationStepJobAssociation (class in galaxy.model) WorkflowInvocationStepOutputDatasetAssociation (class in galaxy.model) WorkflowInvocationStepOutputDatasetCollectionAssociation (class in galaxy.model) WorkflowInvocationToSubworkflowInvocationAssociation (class in galaxy.model) WorkflowMappingField (class in galaxy.web.form_builder) WorkflowModule (class in galaxy.workflow.modules) WorkflowModuleFactory (class in galaxy.workflow.modules) WorkflowModuleInjector (class in galaxy.workflow.modules) WorkflowOutput (class in galaxy.model) WorkflowRequest (class in galaxy.model) WorkflowRequestInputParameter (class in galaxy.model) WorkflowRequestInputStepParmeter (class in galaxy.model)

WorkflowRequestMonitor (class in galaxy.workflow.scheduling_manager) WorkflowRequestStepState (class in galaxy.model) WorkflowRequestToInputDatasetAssociation (class in galaxy.model) WorkflowRequestToInputDatasetCollectionAssociation (class in galaxy.model) WorkflowRunConfig (class in galaxy.workflow.run) (class in galaxy.workflow.run_request) Workflows (class in galaxy.webapps.reports.controllers.workflows) WorkflowsAPIController (class in galaxy.webapps.galaxy.api.workflows), [1] WorkflowSchedulingManager (class in galaxy.workflow.scheduling_manager) WorkflowSchedulingPlugin (class in galaxy.workflow.schedulers) WorkflowSelectionGrid (class in galaxy.webapps.galaxy.controllers.page) WorkflowsManager (class in galaxy.managers.workflows) WorkflowStep (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) WorkflowStepAnnotationAssociation (class in galaxy.model) (class in galaxy.webapps.tool_shed.model) WorkflowStepConnection (class in galaxy.model) (class in galaxy.webapps.tool_shed.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.ComputeEnvironment method) (galaxy.jobs.SharedComputeEnvironment method) WorkRequestContext (class in galaxy.work.context) WorkRequestTagAssociation (class in galaxy.model) 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 galaxy.webapps.tool_shed.buildapp) wrap_in_static() (in module galaxy.webapps.galaxy.buildapp) (in module galaxy.webapps.reports.buildapp) (in module galaxy.webapps.tool_shed.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.converters.interval_to_coverage.CoverageWriter method) (galaxy.datatypes.dataproviders.base.DataProvider method) (galaxy.util.pastescript.serve.LazyWriter method) write_config() (galaxy.webapps.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_executable_script() (galaxy.jobs.runners.BaseJobRunner method) write_from_stream() (galaxy.datatypes.data.Data method) (galaxy.datatypes.data.Text method) (galaxy.model.DatasetInstance method) write_log() (galaxy.web.framework.middleware.translogger.TransLogger method) write_script() (in module galaxy.jobs.runners.util.job_script) write_split_files() (galaxy.datatypes.sequence.Sequence class 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.tools.verify.asserts.xml)

xml_find_text() (in module galaxy.tools.verify.asserts.xml) xml_string (galaxy.tools.data.TabularToolDataTable attribute) xml_text() (in module galaxy.util) xml_to_string() (in module galaxy.util) (in module tool_shed.util.xml_util) XMLDataProvider (class in galaxy.datatypes.dataproviders.hierarchy) XmlInputSource (class in galaxy.tools.parser.xml) XmlPageSource (class in galaxy.tools.parser.xml) XmlPagesSource (class in galaxy.tools.parser.xml) XmlToolSource (class in galaxy.tools.parser.xml) Xpm (class in galaxy.datatypes.images)

Y

YamlInputSource (class in galaxy.tools.parser.yaml)

YamlPageSource (class in galaxy.tools.parser.yaml) YamlToolSource (class in galaxy.tools.parser.yaml)

Z

ZipBall (class in galaxy.util.streamball)

ZipCollectionTool (class in galaxy.tools) zipfile_ok() (tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.CompressedFile method)