Index

_

__init__() (galaxy.app.UniverseApplication method) (galaxy.auth.AuthManager method) (galaxy.auth.providers.ldap_ad.LDAP method) (galaxy.authnz.IdentityProvider method) (galaxy.authnz.managers.AuthnzManager method) (galaxy.authnz.psa_authnz.PSAAuthnz method) (galaxy.authnz.psa_authnz.Strategy method) (galaxy.config.Configuration method) (galaxy.containers.Container method) (galaxy.containers.ContainerInterface method) (galaxy.containers.ContainerVolume method) (galaxy.containers.docker.DockerAPIClient method) (galaxy.containers.docker_model.DockerAttributeContainer method) (galaxy.containers.docker_model.DockerContainer method) (galaxy.containers.docker_model.DockerNode method) (galaxy.containers.docker_model.DockerNodeLabel method) (galaxy.containers.docker_model.DockerService method) (galaxy.containers.docker_model.DockerServiceConstraint method) (galaxy.containers.docker_model.DockerTask method) (galaxy.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.DAA method) (galaxy.datatypes.binary.DMND method) (galaxy.datatypes.binary.Dcd method) (galaxy.datatypes.binary.H5 method) (galaxy.datatypes.binary.Vel 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.sniff.FilePrefix 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.upload_util.UploadProblemException 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.ToolMissingException 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.cgroup.CgroupPlugin 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.hostname.HostnamePlugin 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.chronos.ChronosJobRunner method) (galaxy.jobs.runners.cli.ShellJobRunner method) (galaxy.jobs.runners.condor.CondorJobRunner method) (galaxy.jobs.runners.drmaa.DRMAAJobRunner method) (galaxy.jobs.runners.godocker.GodockerJobRunner method) (galaxy.jobs.runners.kubernetes.KubernetesJobRunner method) (galaxy.jobs.runners.local.LocalJobRunner method) (galaxy.jobs.runners.pbs.PBSJobRunner method) (galaxy.jobs.runners.tasks.TaskedJobRunner method) (galaxy.jobs.runners.util.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.transfer_manager.TransferManager method) (galaxy.main.GalaxyConfigBuilder method) (galaxy.managers.api_keys.ApiKeyManager method) (galaxy.managers.base.HasAModelManager method) (galaxy.managers.base.ModelDeserializer method) (galaxy.managers.base.ModelFilterParser method) (galaxy.managers.base.ModelManager method) (galaxy.managers.base.ModelSerializer method) (galaxy.managers.base.ModelValidator method) (galaxy.managers.citations.BibtexCitation method) (galaxy.managers.citations.CitationCollection method) (galaxy.managers.citations.CitationsManager method) (galaxy.managers.citations.DoiCache method) (galaxy.managers.citations.DoiCitation method) (galaxy.managers.cloud.CloudManager method) (galaxy.managers.collections.DatasetCollectionManager method) (galaxy.managers.configuration.ConfigSerializer method) (galaxy.managers.datasets.DatasetAssociationManager method) (galaxy.managers.datasets.DatasetManager method) (galaxy.managers.datasets.DatasetRBACPermissions method) (galaxy.managers.datasets.DatasetSerializer method) (galaxy.managers.hdas.HDADeserializer method) (galaxy.managers.hdas.HDAManager method) (galaxy.managers.hdas.HDASerializer method) (galaxy.managers.hdcas.DCASerializer method) (galaxy.managers.hdcas.DCESerializer method) (galaxy.managers.hdcas.DCSerializer method) (galaxy.managers.hdcas.HDCAManager method) (galaxy.managers.hdcas.HDCASerializer method) (galaxy.managers.histories.HistoryDeserializer method) (galaxy.managers.histories.HistoryManager method) (galaxy.managers.histories.HistorySerializer method) (galaxy.managers.history_contents.HistoryContentsManager method) (galaxy.managers.history_contents.HistoryContentsSerializer method) (galaxy.managers.jobs.JobSearch method) (galaxy.managers.lddas.LDDAManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.managers.library_datasets.LibraryDatasetsManager method) (galaxy.managers.pages.PageDeserializer method) (galaxy.managers.pages.PageManager method) (galaxy.managers.pages.PageSerializer method) (galaxy.managers.rbac_secured.RBACPermission method) (galaxy.managers.roles.RoleManager method) (galaxy.managers.sharable.SharableModelManager method) (galaxy.managers.sharable.SharableModelSerializer method) (galaxy.managers.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.PSAAssociation method) (galaxy.model.PSACode method) (galaxy.model.PSANonce method) (galaxy.model.PSAPartial 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.UserAuthnzToken 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.ObjectStorePopulator method) (galaxy.objectstore.azure_blob.AzureBlobObjectStore method) (galaxy.objectstore.cloud.Cloud method) (galaxy.objectstore.pithos.PithosObjectStore 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.OutputCollections method) (galaxy.tools.actions.ToolExecutionCache method) (galaxy.tools.cache.ToolCache method) (galaxy.tools.cache.ToolShedRepositoryCache method) (galaxy.tools.cwl.schema.SchemaLoader method) (galaxy.tools.cwl.util.DirectoryUploadTarget method) (galaxy.tools.cwl.util.FileUploadTarget method) (galaxy.tools.cwl.util.ObjectUploadTarget method) (galaxy.tools.data.TabularToolDataField method) (galaxy.tools.data.TabularToolDataTable method) (galaxy.tools.data.ToolDataPathFiles method) (galaxy.tools.data.ToolDataTable method) (galaxy.tools.data.ToolDataTableManager method) (galaxy.tools.data_fetch.UploadConfig method) (galaxy.tools.data_manager.manager.DataManager method) (galaxy.tools.data_manager.manager.DataManagers method) (galaxy.tools.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.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.lmod.LmodDependencyResolver 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.error_reports.ErrorPlugin method) (galaxy.tools.error_reports.ErrorReports method) (galaxy.tools.error_reports.plugins.biostars.BiostarsPlugin method) (galaxy.tools.error_reports.plugins.email.EmailPlugin method) (galaxy.tools.error_reports.plugins.github.GithubPlugin method) (galaxy.tools.error_reports.plugins.influxdb.InfluxDBPlugin method) (galaxy.tools.error_reports.plugins.json.JsonPlugin method) (galaxy.tools.error_reports.plugins.sentry.SentryPlugin method) (galaxy.tools.errors.ErrorReporter method) (galaxy.tools.evaluation.ToolEvaluator method) (galaxy.tools.exception_handling.UCSCOutWrapper method) (galaxy.tools.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.RulesListToolParameter method) (galaxy.tools.parameters.basic.SelectTagParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.TextToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) (galaxy.tools.parameters.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.repositories.ValidationContext method) (galaxy.tools.search.ToolBoxSearch method) (galaxy.tools.test.ParamContext method) (galaxy.tools.test.RootParamContext method) (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.BaseGalaxyToolBox method) (galaxy.tools.toolbox.ToolSection method) (galaxy.tools.toolbox.ToolSectionLabel method) (galaxy.tools.toolbox.base.AbstractToolBox method) (galaxy.tools.toolbox.base.BaseGalaxyToolBox method) (galaxy.tools.toolbox.filters.FilterFactory method) (galaxy.tools.toolbox.lineages.LineageMap method) (galaxy.tools.toolbox.lineages.ToolLineage method) (galaxy.tools.toolbox.lineages.factory.LineageMap method) (galaxy.tools.toolbox.lineages.interface.ToolLineage method) (galaxy.tools.toolbox.lineages.interface.ToolLineageVersion method) (galaxy.tools.toolbox.panel.ToolSection method) (galaxy.tools.toolbox.panel.ToolSectionLabel method) (galaxy.tools.toolbox.tags.PersistentToolTagManager method) (galaxy.tools.toolbox.watcher.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.interactor.GalaxyInteractorApi method) (galaxy.tools.verify.interactor.JobOutputsError method) (galaxy.tools.verify.interactor.RunToolException method) (galaxy.tools.verify.interactor.ToolTestDescription 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.compression_utils.CompressedFile method) (galaxy.util.dbkeys.GenomeBuilds method) (galaxy.util.expressions.ExpressionContext method) (galaxy.util.facts.Facts 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.logging.TraceLogger method) (galaxy.util.logging.fluent_log.FluentTraceLogger 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.renamed_temporary_file.RenamedTemporaryFile method) (galaxy.util.rules_dsl.RuleSet method) (galaxy.util.simplegraph.SimpleGraph method) (galaxy.util.simplegraph.SimpleGraphEdge method) (galaxy.util.simplegraph.SimpleGraphNode method) (galaxy.util.sleeper.Sleeper method) (galaxy.util.streamball.StreamBall method) (galaxy.util.streamball.ZipBall method) (galaxy.util.topsort.CycleError method) (galaxy.util.ucsc.UCSCOutWrapper method) (galaxy.util.watcher.EventHandler method) (galaxy.util.watcher.Watcher method) (galaxy.visualization.data_providers.basic.BaseDataProvider method) (galaxy.visualization.data_providers.basic.ColumnDataProvider method) (galaxy.visualization.data_providers.genome.FeatureLocationIndexDataProvider method) (galaxy.visualization.data_providers.genome.GenomeDataProvider method) (galaxy.visualization.data_providers.genome.SamDataProvider method) (galaxy.visualization.data_providers.phyloviz.PhylovizDataProvider method) (galaxy.visualization.data_providers.phyloviz.baseparser.Base_Parser method) (galaxy.visualization.data_providers.phyloviz.baseparser.Node method) (galaxy.visualization.data_providers.phyloviz.baseparser.PhyloTree method) (galaxy.visualization.data_providers.phyloviz.newickparser.Newick_Parser method) (galaxy.visualization.data_providers.phyloviz.nexusparser.Nexus_Parser method) (galaxy.visualization.data_providers.phyloviz.phyloxmlparser.Phyloxml_Parser method) (galaxy.visualization.data_providers.registry.DataProviderRegistry method) (galaxy.visualization.genomes.Genome method) (galaxy.visualization.genomes.GenomeRegion method) (galaxy.visualization.genomes.Genomes method) (galaxy.visualization.plugins.config_parser.DictParser method) (galaxy.visualization.plugins.config_parser.ListParser method) (galaxy.visualization.plugins.config_parser.VisualizationsConfigParser method) (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) (galaxy.visualization.plugins.plugin.InteractiveEnvironmentPlugin method) (galaxy.visualization.plugins.plugin.VisualizationPlugin method) (galaxy.visualization.plugins.registry.VisualizationsRegistry method) (galaxy.visualization.plugins.resource_parser.ResourceParser method) (galaxy.web.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.profile.ProfileMiddleware method) (galaxy.web.framework.middleware.remoteuser.RemoteUser method) (galaxy.web.framework.middleware.request_id.RequestIDMiddleware method) (galaxy.web.framework.middleware.sentry.Sentry method) (galaxy.web.framework.middleware.sqldebug.SQLDebugMiddleware method) (galaxy.web.framework.middleware.static.CacheableStaticURLParser method) (galaxy.web.framework.middleware.statsd.StatsdMiddleware method) (galaxy.web.framework.middleware.translogger.TransLogger method) (galaxy.web.framework.middleware.xforwardedhost.XForwardedHostMiddleware method) (galaxy.web.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.web.stack.message.ApplicationStackMessage method) (galaxy.web.stack.message.ApplicationStackMessageDispatcher method) (galaxy.web.stack.message.ParamMessage method) (galaxy.web.stack.transport.ApplicationStackTransport method) (galaxy.web.stack.transport.UWSGIFarmMessageTransport method) (galaxy.webapps.config_manage.AppSchema method) (galaxy.webapps.config_manage.GzipFilter method) (galaxy.webapps.config_manage.PrefixFilter method) (galaxy.webapps.config_manage.Schema method) (galaxy.webapps.galaxy.api.annotations.HistoryAnnotationsController method), [1] (galaxy.webapps.galaxy.api.annotations.HistoryContentAnnotationsController method), [1] (galaxy.webapps.galaxy.api.authenticate.AuthenticationController method), [1] (galaxy.webapps.galaxy.api.cloud.CloudController method), [1] (galaxy.webapps.galaxy.api.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.library_datasets.LibraryDatasetsController method), [1] (galaxy.webapps.galaxy.api.metrics.MetricsController method), [1] (galaxy.webapps.galaxy.api.pages.PagesController method), [1] (galaxy.webapps.galaxy.api.plugins.PluginsController method), [1] (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method), [1] (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method), [1] (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] (galaxy.webapps.galaxy.api.tours.ToursController method), [1] (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] (galaxy.webapps.galaxy.api.visualizations.VisualizationsController method), [1] (galaxy.webapps.galaxy.api.webhooks.WebhooksController method), [1] (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] (galaxy.webapps.galaxy.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.reports.framework.grids.CommunityTagsColumn method) (galaxy.webapps.reports.framework.grids.Grid method) (galaxy.webapps.reports.framework.grids.GridAction method) (galaxy.webapps.reports.framework.grids.GridColumn method) (galaxy.webapps.reports.framework.grids.GridColumnFilter method) (galaxy.webapps.reports.framework.grids.GridOperation method) (galaxy.webapps.reports.framework.grids.MulticolFilterColumn method) (galaxy.webapps.reports.framework.grids.OwnerAnnotationColumn method) (galaxy.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.InputProxy method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) (galaxy.workflow.modules.WorkflowModuleFactory method) (galaxy.workflow.modules.WorkflowModuleInjector method) (galaxy.workflow.render.WorkflowCanvas method) (galaxy.workflow.run.WorkflowRunConfig method) (galaxy.workflow.run_request.WorkflowRunConfig method) (galaxy.workflow.schedulers.core.CoreWorkflowSchedulingPlugin method) (galaxy.workflow.scheduling_manager.WorkflowRequestMonitor method) (galaxy.workflow.scheduling_manager.WorkflowSchedulingManager method) (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.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.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.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) AddColumnBasenameRuleDefinition (class in galaxy.util.rules_dsl) AddColumnConcatenateRuleDefinition (class in galaxy.util.rules_dsl) AddColumnGroupTagValueRuleDefinition (class in galaxy.util.rules_dsl) AddColumnMetadataRuleDefinition (class in galaxy.util.rules_dsl) AddColumnRegexRuleDefinition (class in galaxy.util.rules_dsl) AddColumnRownumRuleDefinition (class in galaxy.util.rules_dsl) AddColumnSubstrRuleDefinition (class in galaxy.util.rules_dsl) AddColumnValueRuleDefinition (class in galaxy.util.rules_dsl) AddFilterCompareRuleDefinition (class in galaxy.util.rules_dsl) AddFilterCountRuleDefinition (class in galaxy.util.rules_dsl) AddFilterEmptyRuleDefinition (class in galaxy.util.rules_dsl) AddFilterMatchesRuleDefinition (class in galaxy.util.rules_dsl) AddFilterRegexRuleDefinition (class in galaxy.util.rules_dsl) 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 (class in tool_shed.util.admin_util) admin_api_keys() (galaxy.webapps.galaxy.controllers.userskeys.User method) admin_job_lock() (in module galaxy.queue_worker) admin_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) (galaxy.webapps.reports.framework.grids.GridOperation method) ALLOWED_DATA_SOURCE_ATTRIBUTES (galaxy.visualization.plugins.config_parser.DataSourceParser attribute) ALLOWED_ENTRY_POINT_TYPES (galaxy.visualization.plugins.config_parser.VisualizationsConfigParser attribute) allowed_middleware() (galaxy.web.stack.ApplicationStack method) ALLOWED_MODEL_CLASSES (galaxy.visualization.plugins.config_parser.DataSourceParser attribute) allowed_to_disconnect() (in module galaxy.authnz.psa_authnz) alter_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 (class in galaxy.webapps.config_manage) 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) app_name (galaxy.webapps.config_manage.App attribute) app_properties_from_args() (in module galaxy.util.script) appconfig() (in module galaxy.util.pastescript.loadwsgi) append() (galaxy.datatypes.metadata.MetadataSpecCollection method) (galaxy.model.custom_types.MutationList method) (galaxy.model.metadata.MetadataSpecCollection method) (galaxy.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) (galaxy.web.framework.middleware.sqldebug.SQLDebugMiddleware attribute) application_stack_class() (in module galaxy.web.stack) application_stack_instance() (in module galaxy.web.stack) application_stack_log_filter() (in module galaxy.web.stack) application_stack_log_formatter() (in module galaxy.web.stack) ApplicationStack (class in galaxy.web.stack) ApplicationStackLogFilter (class in galaxy.web.stack) ApplicationStackMessage (class in galaxy.web.stack.message) ApplicationStackMessageDispatcher (class in galaxy.web.stack.message) ApplicationStackTransport (class in galaxy.web.stack.transport) apply() (galaxy.tools.deps.resolvers.RequirementMapping method) (galaxy.util.rules_dsl.AddColumnBasenameRuleDefinition method) (galaxy.util.rules_dsl.AddColumnConcatenateRuleDefinition method) (galaxy.util.rules_dsl.AddColumnGroupTagValueRuleDefinition method) (galaxy.util.rules_dsl.AddColumnMetadataRuleDefinition method) (galaxy.util.rules_dsl.AddColumnRegexRuleDefinition method) (galaxy.util.rules_dsl.AddColumnRownumRuleDefinition method) (galaxy.util.rules_dsl.AddColumnSubstrRuleDefinition method) (galaxy.util.rules_dsl.AddColumnValueRuleDefinition method) (galaxy.util.rules_dsl.AddFilterCompareRuleDefinition method) (galaxy.util.rules_dsl.AddFilterCountRuleDefinition method) (galaxy.util.rules_dsl.AddFilterEmptyRuleDefinition method) (galaxy.util.rules_dsl.AddFilterMatchesRuleDefinition method) (galaxy.util.rules_dsl.AddFilterRegexRuleDefinition method) (galaxy.util.rules_dsl.BaseRuleDefinition method) (galaxy.util.rules_dsl.RemoveColumnsRuleDefinition method) (galaxy.util.rules_dsl.RuleSet method) (galaxy.util.rules_dsl.SortRuleDefinition method) (galaxy.util.rules_dsl.SplitColumnsRuleDefinition method) (galaxy.util.rules_dsl.SwapColumnsRuleDefinition method) apply_action() (galaxy.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) (galaxy.webapps.reports.framework.grids.Grid method) (tool_shed.grids.admin_grids.RoleGrid method) apply_regex() (in module galaxy.util.rules_dsl) apply_rules() (galaxy.managers.collections.DatasetCollectionManager method) ApplyRulesTool (class in galaxy.tools) approve_repository_review() (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) AppSchema (class in galaxy.webapps.config_manage) 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) association (galaxy.authnz.psa_authnz.Storage attribute) ASync (class in galaxy.webapps.galaxy.controllers.async) async_template (galaxy.webapps.reports.framework.grids.Grid attribute) AsyncDataSourceTool (class in galaxy.tools) AsynchronousJobRunner (class in galaxy.jobs.runners) AsynchronousJobState (class in galaxy.jobs.runners) AsynchronousReader (class in 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) Augustus (class in galaxy.datatypes.annotation) authenticate() (galaxy.auth.providers.alwaysreject.AlwaysReject method) (galaxy.auth.providers.AuthProvider method) (galaxy.auth.providers.ldap_ad.LDAP method) (galaxy.auth.providers.localdb.LocalDB method) (galaxy.auth.providers.pam_auth.PAM method) (galaxy.authnz.IdentityProvider method) (galaxy.authnz.managers.AuthnzManager method) (galaxy.authnz.psa_authnz.PSAAuthnz method) authenticate_user() (galaxy.auth.providers.alwaysreject.AlwaysReject method) (galaxy.auth.providers.AuthProvider method) (galaxy.auth.providers.ldap_ad.LDAP method) (galaxy.auth.providers.localdb.LocalDB method) (galaxy.auth.providers.pam_auth.PAM method) AuthenticationController (class in galaxy.webapps.galaxy.api.authenticate), [1] AuthenticationFailed AuthenticationRequired AuthenticationToken (class in galaxy.web.proxy) Authenticator (class in galaxy.auth.util) AuthManager (class in galaxy.auth) AuthnzManager (class in galaxy.authnz.managers) AuthProvider (class in galaxy.auth.providers) auto_propagated_tags (galaxy.model.HasTags attribute) 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_docker_cmd() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) Base_Parser (class in galaxy.visualization.data_providers.phyloviz.baseparser) BASE_URL (galaxy.visualization.plugins.registry.VisualizationsRegistry attribute) BaseAnnotationsController (class in galaxy.webapps.galaxy.api.annotations), [1] BaseAPIController (class in galaxy.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) BaseJsonToolParameter (class in galaxy.tools.parameters.basic) BaseParamParser (class in galaxy.web.params) BaseProvenanceController (class in galaxy.webapps.galaxy.api.provenance), [1] BaseRuleDefinition (class in galaxy.util.rules_dsl) 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) BaseUploadToolAction (class in galaxy.tools.actions.upload) 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) bind_default_handler() (galaxy.web.stack.message.ApplicationStackMessage method) Biom1 (class in galaxy.datatypes.text) Biom2 (class in galaxy.datatypes.binary) biomart() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method) 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) BiostarsPlugin (class in galaxy.tools.error_reports.plugins.biostars) BlastDomainDb (class in galaxy.datatypes.blast) BlastNucDb (class in galaxy.datatypes.blast) BlastProtDb (class in galaxy.datatypes.blast) BlastXml (class in galaxy.datatypes.blast) BlibSQlite (class in galaxy.datatypes.binary) BlockDataProvider (class in galaxy.datatypes.dataproviders.line) blurb (galaxy.datatypes.proteomics.ConsensusXML attribute) (galaxy.datatypes.proteomics.FeatureXML attribute) (galaxy.datatypes.proteomics.IdXML attribute) (galaxy.datatypes.proteomics.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) (class in galaxy.webapps.reports.framework.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_absolute_uri() (galaxy.authnz.psa_authnz.Strategy method) 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) (galaxy.webapps.reports.framework.grids.Grid method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid method) (tool_shed.grids.admin_grids.AdminRepositoryGrid method) (tool_shed.grids.admin_grids.RepositoryMetadataGrid method) (tool_shed.grids.repository_grids.DatatypesGrid method) (tool_shed.grids.repository_grids.DeprecatedRepositoriesIOwnGrid method) (tool_shed.grids.repository_grids.MatchedRepositoryGrid method) (tool_shed.grids.repository_grids.MyWritableRepositoriesGrid method) (tool_shed.grids.repository_grids.MyWritableRepositoriesMissingToolTestComponentsGrid method) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithInvalidToolsGrid method) (tool_shed.grids.repository_grids.RepositoriesByUserGrid method) (tool_shed.grids.repository_grids.RepositoriesICanAdministerGrid method) (tool_shed.grids.repository_grids.RepositoriesIOwnGrid method) (tool_shed.grids.repository_grids.RepositoriesInCategoryGrid method) (tool_shed.grids.repository_grids.RepositoriesMissingToolTestComponentsGrid method) (tool_shed.grids.repository_grids.RepositoriesWithInvalidToolsGrid method) (tool_shed.grids.repository_grids.RepositoryDependenciesGrid method) (tool_shed.grids.repository_grids.RepositoryGrid method) (tool_shed.grids.repository_grids.RepositoryMetadataGrid method) (tool_shed.grids.repository_grids.ToolDependenciesGrid method) (tool_shed.grids.repository_grids.ToolsGrid method) (tool_shed.grids.repository_grids.ValidRepositoryGrid method) (tool_shed.grids.repository_review_grids.RepositoriesReadyForReviewGrid method) (tool_shed.grids.repository_review_grids.RepositoriesReviewedByMeGrid method) (tool_shed.grids.repository_review_grids.RepositoriesWithNoToolTestsGrid method) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid method) (tool_shed.grids.repository_review_grids.RepositoriesWithoutReviewsGrid method) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid method) (tool_shed.grids.repository_review_grids.ReviewedRepositoriesIOwnGrid method) build_invalid_data_managers_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) build_invalid_repository_dependencies_root_folder() (tool_shed.utility_containers.ToolShedUtilityContainerManager method) build_invalid_tool_dependencies_root_folder() (tool_shed.utility_containers.ToolShedUtilityContainerManager method) build_invalid_tools_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method) build_invocations_query() (galaxy.managers.workflows.WorkflowsManager method) build_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_singularity_run_command() (in module galaxy.tools.deps.singularity_util) build_sniff_from_prefix() (in module galaxy.datatypes.sniff) build_state_handlers() (in module galaxy.jobs.runners.state_handler_factory) build_submit_description() (in module galaxy.jobs.runners.util.condor) build_target() (in module galaxy.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) BuildListCollectionTool (class in galaxy.tools) 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) 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_tool_input() (galaxy.managers.jobs.JobSearch method) by_user() (galaxy.managers.datasets.DatasetAssociationManager method) (galaxy.managers.histories.HistoryManager method) (galaxy.managers.sharable.SharableModelManager method) bytes_to_str() (in module galaxy.jobs.dynamic_tool_destination) Bz2DynamicCompressedArchive (class in galaxy.datatypes.binary)

C

cache_job_destination() (galaxy.jobs.mapper.JobRunnerMapper method) cache_tool() (galaxy.tools.cache.ToolCache method) cacheable (galaxy.tools.deps.resolvers.Dependency attribute) CacheableStaticURLParser (class in galaxy.web.framework.middleware.static) cached_id() (in module galaxy.model) 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) callback() (galaxy.authnz.IdentityProvider method) (galaxy.authnz.managers.AuthnzManager method) (galaxy.authnz.psa_authnz.PSAAuthnz method) (galaxy.webapps.galaxy.controllers.authnz.OIDC method) camelize() (galaxy.util.inflection.Base method) (galaxy.util.inflection.Inflector method) can_access_dataset() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) can_access_datasets() (galaxy.security.GalaxyRBACAgent 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) (tool_shed.util.admin_util.Admin method) CgroupPlugin (class in galaxy.jobs.metrics.instrumenters.cgroup) 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) changed() (galaxy.model.UserAuthnzToken class method) ChangeDatatypeAction (class in galaxy.jobs.actions.post) ChangeDirectory (class in tool_shed.galaxy_install.tool_dependencies.recipe.step_handler) changeset2rev() (in module tool_shed.util.hg_util) 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) ChartVisualizationPlugin (class in galaxy.visualization.plugins.plugin) 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) (galaxy.managers.library_datasets.LibraryDatasetsManager method) check_all_jobs() (galaxy.jobs.runners.pbs.PBSJobRunner method) check_and_reload() (galaxy.visualization.genomes.Genomes method) check_and_update_param_values() (galaxy.tools.Tool method) check_and_update_state() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) check_archive() (in module galaxy.tools.imp_exp.unpack_tar_gz_archive) (in module tool_shed.util.commit_util) check_auto_registration() (galaxy.auth.AuthManager method) check_azure_storage() (galaxy.dependencies.ConditionalDependencies method) check_binary() (in module galaxy.datatypes.checkers) (in module galaxy.util.checkers) check_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_docker() (galaxy.dependencies.ConditionalDependencies 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_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_modifiable() (galaxy.managers.library_datasets.LibraryDatasetsManager method) check_mysql_python() (galaxy.dependencies.ConditionalDependencies method) 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_binary() (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.chronos.ChronosJobRunner 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) child_collection_type() (galaxy.dataset_collections.type_description.CollectionTypeDescription method) child_collection_type_description() (galaxy.dataset_collections.type_description.CollectionTypeDescription 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.UninitializedTree 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) ChronosJobRunner (class in galaxy.jobs.runners.chronos) chunk64_dataprovider() (galaxy.datatypes.data.Data method) chunk_dataprovider() (galaxy.datatypes.data.Data method) CHUNKABLE (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.tabular.TabularData attribute) ChunkDataProvider (class in galaxy.datatypes.dataproviders.chunk) circster() (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) CisML (class in galaxy.datatypes.xml) CitationCollection (class in galaxy.managers.citations) citations() (galaxy.webapps.galaxy.api.histories.HistoriesController method), [1] (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] citations_for_tool() (galaxy.managers.citations.CitationsManager method) citations_for_tool_ids() (galaxy.managers.citations.CitationsManager method) CitationsManager (class in galaxy.managers.citations) 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) cleanNewickString() (galaxy.visualization.data_providers.phyloviz.newickparser.Newick_Parser method) cleanTag() (galaxy.visualization.data_providers.phyloviz.phyloxmlparser.Phyloxml_Parser method) cleanup() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.jobs.runners.JobState method) (galaxy.tools.cache.ToolCache method) cleanup_after_job() (galaxy.tools.imp_exp.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) 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_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.UninitializedTree 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) Cloud (class in galaxy.objectstore.cloud) CloudController (class in galaxy.webapps.galaxy.api.cloud), [1] CloudManager (class in galaxy.managers.cloud) 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) code (galaxy.authnz.psa_authnz.Storage attribute) 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_outputs() (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.tools.cwl.representation.TypeRepresentation attribute) (galaxy.util.rules_dsl.RuleSet attribute) (galaxy.workflow.modules.InputDataCollectionModule attribute) collection_types (galaxy.tools.parameters.basic.DataCollectionToolParameter attribute) (galaxy.tools.parameters.DataCollectionToolParameter attribute) collection_wrapper_to_array() (in module galaxy.tools.cwl.representation) collection_wrapper_to_record() (in module galaxy.tools.cwl.representation) 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.interval.ProBed 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) (galaxy.webapps.reports.framework.grids.Grid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.grids.admin_grids.AdminRepositoryGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.ManageCategoryGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.DatatypesGrid attribute) (tool_shed.grids.repository_grids.DeprecatedRepositoriesIOwnGrid attribute) (tool_shed.grids.repository_grids.DockerImageGrid attribute) (tool_shed.grids.repository_grids.EmailAlertsRepositoryGrid attribute) (tool_shed.grids.repository_grids.InstallMatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.MyWritableRepositoriesWithInvalidToolsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesByUserGrid attribute) (tool_shed.grids.repository_grids.RepositoriesICanAdministerGrid attribute) (tool_shed.grids.repository_grids.RepositoriesIOwnGrid attribute) (tool_shed.grids.repository_grids.RepositoriesInCategoryGrid attribute) (tool_shed.grids.repository_grids.RepositoriesMissingToolTestComponentsGrid attribute) (tool_shed.grids.repository_grids.RepositoriesWithInvalidToolsGrid attribute) (tool_shed.grids.repository_grids.RepositoryDependenciesGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ToolDependenciesGrid attribute) (tool_shed.grids.repository_grids.ToolsGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_grids.ValidRepositoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesReadyForReviewGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesReviewedByMeGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithNoToolTestsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithoutReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) (tool_shed.grids.repository_review_grids.ReviewedRepositoriesIOwnGrid attribute) ColumnSetAction (class in galaxy.jobs.actions.post) ColumnStripFilter (class in galaxy.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) (class in galaxy.webapps.reports.framework.grids) CommunityRBACAgent (class in galaxy.webapps.tool_shed.security) CommunityTagManager (class in galaxy.managers.tags) CommunityTagsColumn (class in galaxy.web.framework.helpers.grids) (class in galaxy.webapps.reports.framework.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) complete() (galaxy.authnz.psa_authnz.Strategy 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.annotation.Augustus attribute) (galaxy.datatypes.binary.CompressedArchive attribute) (galaxy.datatypes.binary.Xlsx attribute) (galaxy.datatypes.tabular.Eland attribute) (galaxy.datatypes.tabular.VcfGz attribute) compressed_format (galaxy.datatypes.binary.Bz2DynamicCompressedArchive attribute) (galaxy.datatypes.binary.GzDynamicCompressedArchive attribute) (galaxy.datatypes.tabular.Eland attribute) (galaxy.datatypes.tabular.VcfGz attribute) CompressedArchive (class in galaxy.datatypes.binary) CompressedFile (class in galaxy.util.compression_utils) CompressedZipArchive (class in galaxy.datatypes.binary) compute_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) conf_run_kwopts (galaxy.containers.docker.DockerInterface 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_file_from_args() (in module galaxy.util.script) config_is_ini (galaxy.main.GalaxyConfigBuilder attribute) config_options (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver attribute) (galaxy.tools.deps.resolvers.DependencyResolver attribute) config_paths (galaxy.webapps.config_manage.App 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) 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_run_args() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) container_spec_option_map (galaxy.containers.docker_swarm.DockerSwarmAPIInterface 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) ContainerVolume (class in galaxy.containers) contains_folder() (tool_shed.utility_containers.utility_container_manager.Folder method) contains_repository_dependency() (tool_shed.utility_containers.utility_container_manager.Folder method) contains_required_data() (in module galaxy.authnz.psa_authnz) contains_workflow_parameter() (in module galaxy.tools.parameters.basic) content_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) context_remove() (galaxy.util.logging.fluent_log.FluentTraceLogger method) context_set() (galaxy.util.logging.fluent_log.FluentTraceLogger method) continue_pipeline() (galaxy.authnz.psa_authnz.Strategy 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) Cpt (class in galaxy.datatypes.binary) 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.cloud.Cloud method) (galaxy.objectstore.pithos.PithosObjectStore 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.uploads.UploadsAPIController method), [1] (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] (galaxy.webapps.galaxy.api.visualizations.VisualizationsController method), [1] (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.user.User method) (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method) (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) (tool_shed.util.admin_util.Admin 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) (tool_shed.util.admin_util.Admin 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_random_port_spec() (galaxy.containers.docker_swarm.DockerSwarmAPIInterface static method) create_repo_info_dict() (in module tool_shed.util.repository_util) create_report() (galaxy.tools.errors.ErrorReporter method) create_repository() (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) (tool_shed.util.admin_util.Admin method) create_section() (galaxy.tools.toolbox.AbstractToolBox method) (galaxy.tools.toolbox.base.AbstractToolBox method) create_social_auth() (galaxy.model.UserAuthnzToken class method) create_string_filter() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) create_subworkflow_invocation_for_step() (galaxy.model.WorkflowInvocation method) create_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.model.UserAuthnzToken class method) (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) CuffDiffSQlite (class in galaxy.datatypes.binary) cur_filter_pref_name (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.reports.framework.grids.Grid attribute) cur_sort_key_pref_name (galaxy.web.framework.helpers.grids.Grid attribute) (galaxy.webapps.reports.framework.grids.Grid attribute) current_history_json() (galaxy.webapps.galaxy.controllers.history.HistoryController method) current_state (galaxy.containers.docker_model.DockerTask attribute) current_state_time (galaxy.containers.docker_model.DockerTask attribute) current_user() (galaxy.managers.users.UserManager method) CurrentUserSerializer (class in galaxy.managers.users) cursor_execute() (galaxy.model.orm.logging_connection_proxy.LoggingProxy method) (galaxy.model.orm.logging_connection_proxy.TraceLoggerProxy method) 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

DAA (class in galaxy.datatypes.binary) 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) data_types_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_action_tuples (galaxy.model.DatasetCollection attribute) dataset_collection_description() (in module galaxy.tools.parser.output_collection_def) 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_rewriter (galaxy.jobs.JobWrapper attribute) (galaxy.jobs.TaskWrapper attribute) 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) dataset_wrapper_to_directory_json() (in module galaxy.tools.cwl.representation) dataset_wrapper_to_file_json() (in module galaxy.tools.cwl.representation) DatasetAccessPermissionFailedException DatasetAssociationDeserializer (class in galaxy.managers.datasets) DatasetAssociationFilterParser (class in galaxy.managers.datasets) DatasetAssociationManager (class in galaxy.managers.datasets) DatasetAssociationSerializer (class in galaxy.managers.datasets) DatasetCollection (class in galaxy.model) 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) 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) 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) 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) (class in galaxy.webapps.reports.framework.grids) db_builds (galaxy.managers.context.ProvidesHistoryContext attribute) db_dataset_for() (galaxy.managers.context.ProvidesHistoryContext method) db_next_hid() (in module galaxy.model.mapping) dbkey (galaxy.model.DatasetInstance attribute) (galaxy.tools.parameters.output_collect.JsonCollectedDatasetMatch attribute) DBKeyParameter (class in galaxy.datatypes.metadata) (class in galaxy.model.metadata) DCASerializer (class in galaxy.managers.hdcas) Dcd (class in galaxy.datatypes.binary) DCESerializer (class in galaxy.managers.hdcas) DCSerializer (class in galaxy.managers.hdcas) deactivate (galaxy.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) (in module galaxy.web.stack.message) decode_dataset_user() (in module galaxy.datatypes.display_applications.util) decode_dbkey() (in module galaxy.visualization.genomes) decode_folder_id() (galaxy.managers.folders.FolderManager method) decode_guid() (galaxy.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) (galaxy.webapps.reports.framework.grids.Grid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.grids.admin_grids.AdminRepositoryGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoriesByUserGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) default_handler (galaxy.web.stack.message.ApplicationStackMessage attribute) default_handler() (galaxy.web.stack.message.TaskMessage static method) default_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_port (galaxy.webapps.config_manage.App attribute) default_printer() (in module galaxy.tools.util.galaxyops) default_quota (galaxy.quota.NoQuotaAgent attribute) default_registered_quota (galaxy.quota.QuotaAgent attribute) default_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) (galaxy.webapps.reports.framework.grids.Grid attribute) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute) (tool_shed.grids.admin_grids.GroupGrid attribute) (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.admin_grids.RoleGrid attribute) (tool_shed.grids.admin_grids.UserGrid attribute) (tool_shed.grids.repository_grids.CategoryGrid attribute) (tool_shed.grids.repository_grids.DatatypesGrid attribute) (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryDependenciesGrid attribute) (tool_shed.grids.repository_grids.RepositoryGrid attribute) (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute) (tool_shed.grids.repository_grids.ToolDependenciesGrid attribute) (tool_shed.grids.repository_grids.ToolsGrid attribute) (tool_shed.grids.repository_grids.ValidCategoryGrid attribute) (tool_shed.grids.repository_review_grids.ComponentGrid attribute) (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid attribute) (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute) DEFAULT_SPECS (galaxy.jobs.runners.BaseJobRunner attribute) DEFAULT_TEMPLATE_COLLECTION_SIZE (galaxy.visualization.plugins.plugin.ServesTemplatesPluginMixin attribute) default_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.cloud.Cloud method) (galaxy.objectstore.pithos.PithosObjectStore 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.library_datasets.LibraryDatasetsController method), [1] (galaxy.webapps.galaxy.api.pages.PagesController method), [1] (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method), [1] (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method), [1] (galaxy.webapps.galaxy.api.tool_data.ToolData method), [1] (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method), [1] (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.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_history() (galaxy.tools.verify.interactor.GalaxyInteractorApi 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) (galaxy.webapps.tool_shed.controllers.admin.AdminController attribute) (tool_shed.util.admin_util.Admin 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) (class in galaxy.webapps.reports.framework.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_func() (galaxy.web.stack.message.ApplicationStackMessageDispatcher method) deregister_message_handler() (galaxy.web.stack.ApplicationStack method) (galaxy.web.stack.MessageApplicationStack method) derive_roles_from_access() (galaxy.security.GalaxyRBACAgent method) (galaxy.security.RBACAgent method) desc() (galaxy.tools.parser.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) description_from_tool_object() (in module galaxy.tools.test) descs (galaxy.tools.parser.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_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) desired_state (galaxy.containers.docker_model.DockerTask attribute) destination (galaxy.webapps.config_manage.App attribute) destination_defaults (galaxy.jobs.runners.pulsar.PulsarEmbeddedJobRunner attribute) (galaxy.jobs.runners.pulsar.PulsarLegacyJobRunner attribute) (galaxy.jobs.runners.pulsar.PulsarMQJobRunner attribute) (galaxy.jobs.runners.pulsar.PulsarRESTJobRunner attribute) destination_list (in module galaxy.jobs.dynamic_tool_destination) DESTINATION_PARAMS_SPEC (galaxy.jobs.runners.chronos.ChronosJobRunner attribute) destroy() (galaxy.model.PSAPartial class method) 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.lmod.LmodDependencyResolver 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) DictParser (class in galaxy.visualization.plugins.config_parser) different_revision_defines_tip_only_repository_dependency() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method) difflib (in module galaxy.util.pastescript.serve) dimension (galaxy.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) DirectoryUploadTarget (class in galaxy.tools.cwl.util) disable_commands_in_new_shell() (galaxy.jobs.JobWrapper method) disable_parent_class_sniffing() (in module galaxy.datatypes.sniff) disabled (galaxy.tools.deps.resolvers.DependencyResolver attribute) discard() (galaxy.util.oset.OrderedSet method) disconnect() (galaxy.authnz.IdentityProvider method) (galaxy.authnz.managers.AuthnzManager method) (galaxy.authnz.psa_authnz.PSAAuthnz method) (galaxy.webapps.galaxy.controllers.authnz.OIDC method) (in module galaxy.authnz.psa_authnz) discover_files() (in module galaxy.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) discovered_file_for_unnamed_output() (in module galaxy.tools.parameters.output_collect) 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) dispatch() (galaxy.web.stack.message.ApplicationStackMessageDispatcher method) display (galaxy.util.rules_dsl.RuleSet attribute) display() (galaxy.webapps.galaxy.api.datasets.DatasetsController method), [1] (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.root.RootController method) display_amount (galaxy.model.Quota attribute) display_application() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) display_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.data.Data method) (galaxy.datatypes.sequence.BaseFastq method) (galaxy.datatypes.tabular.TabularData method) (galaxy.datatypes.text.Ipynb method) display_image_in_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method) (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.annotation.Augustus method) (galaxy.datatypes.annotation.SnapHmm method) (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.CuffDiffSQlite method) (galaxy.datatypes.binary.Dcd method) (galaxy.datatypes.binary.ExcelXls method) (galaxy.datatypes.binary.Fast5Archive method) (galaxy.datatypes.binary.GeminiSQLite method) (galaxy.datatypes.binary.GmxBinary method) (galaxy.datatypes.binary.H5 method) (galaxy.datatypes.binary.IdpDB method) (galaxy.datatypes.binary.Loom method) (galaxy.datatypes.binary.NetCDF method) (galaxy.datatypes.binary.PostgresqlArchive method) (galaxy.datatypes.binary.SQlite method) (galaxy.datatypes.binary.Scf method) (galaxy.datatypes.binary.SearchGuiArchive method) (galaxy.datatypes.binary.Sff method) (galaxy.datatypes.binary.Sra method) (galaxy.datatypes.binary.TwoBit method) (galaxy.datatypes.binary.Vel method) (galaxy.datatypes.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.plant_tribes.PlantTribesKsComponents method) (galaxy.datatypes.plant_tribes.Smat 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) (class in galaxy.webapps.reports.framework.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_cmd() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) 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) DockerAPIClient (class in galaxy.containers.docker) DockerAPIInterface (class in galaxy.containers.docker) DockerAttributeContainer (class in galaxy.containers.docker_model) DockerCLIInterface (class in galaxy.containers.docker) DockerContainer (class in galaxy.containers.docker_model) (class in galaxy.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.containers.docker_model) 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.managers.cloud.CloudManager method) (galaxy.webapps.galaxy.api.cloud.CloudController method), [1] (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method), [1] (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) 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] DynamicCompressedArchive (class in galaxy.datatypes.binary) 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.annotation.Augustus attribute) (galaxy.datatypes.annotation.SnapHmm attribute) (galaxy.datatypes.assembly.Amos attribute) (galaxy.datatypes.assembly.Sequences attribute) (galaxy.datatypes.binary.Ab1 attribute) (galaxy.datatypes.binary.Bam attribute) (galaxy.datatypes.binary.BamNative attribute) (galaxy.datatypes.binary.BaseBcf attribute) (galaxy.datatypes.binary.BigBed attribute) (galaxy.datatypes.binary.BigWig attribute) (galaxy.datatypes.binary.CRAM attribute) (galaxy.datatypes.binary.Cel attribute) (galaxy.datatypes.binary.Dcd attribute) (galaxy.datatypes.binary.GeminiSQLite attribute) (galaxy.datatypes.binary.GenericAsn1Binary attribute) (galaxy.datatypes.binary.ICM attribute) (galaxy.datatypes.binary.Idat attribute) (galaxy.datatypes.binary.NetCDF attribute) (galaxy.datatypes.binary.ProBam attribute) (galaxy.datatypes.binary.Scf attribute) (galaxy.datatypes.binary.Sff attribute) (galaxy.datatypes.binary.TwoBit attribute) (galaxy.datatypes.blast.BlastXml attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.data.GenericAsn1 attribute) (galaxy.datatypes.data.Newick attribute) (galaxy.datatypes.data.Nexus attribute) (galaxy.datatypes.images.Image attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.msa.Hmmer attribute) (galaxy.datatypes.msa.Stockholm_1_0 attribute) (galaxy.datatypes.phylip.Phylip attribute) (galaxy.datatypes.proteomics.MascotDat attribute) (galaxy.datatypes.proteomics.Mgf attribute) (galaxy.datatypes.proteomics.PepXmlReport attribute) (galaxy.datatypes.proteomics.ProtXmlReport attribute) (galaxy.datatypes.proteomics.ProteomicsXml attribute) (galaxy.datatypes.proteomics.ThermoRAW attribute) (galaxy.datatypes.proteomics.Wiff attribute) (galaxy.datatypes.qualityscore.QualityScore attribute) (galaxy.datatypes.registry.Registry attribute) (galaxy.datatypes.sequence.Alignment attribute) (galaxy.datatypes.sequence.Axt attribute) (galaxy.datatypes.sequence.DotBracket attribute) (galaxy.datatypes.sequence.Genbank attribute) (galaxy.datatypes.sequence.Lav attribute) (galaxy.datatypes.sequence.Sequence attribute) (galaxy.datatypes.tabular.Sam attribute) (galaxy.datatypes.text.Obo attribute) (galaxy.datatypes.tracks.GeneTrack attribute) (galaxy.datatypes.triples.Triples attribute) (galaxy.datatypes.xml.Phyloxml attribute) (galaxy.datatypes.xml.Sbml attribute) edam_data() (galaxy.webapps.galaxy.api.datatypes.DatatypesController method), [1] edam_format (galaxy.datatypes.assembly.Amos attribute) (galaxy.datatypes.assembly.Roadmaps attribute) (galaxy.datatypes.binary.Ab1 attribute) (galaxy.datatypes.binary.Bam attribute) (galaxy.datatypes.binary.BamNative attribute) (galaxy.datatypes.binary.BaseBcf attribute) (galaxy.datatypes.binary.BigBed attribute) (galaxy.datatypes.binary.BigWig attribute) (galaxy.datatypes.binary.Binary attribute) (galaxy.datatypes.binary.Biom2 attribute) (galaxy.datatypes.binary.CRAM attribute) (galaxy.datatypes.binary.Cel attribute) (galaxy.datatypes.binary.CuffDiffSQlite attribute) (galaxy.datatypes.binary.ExcelXls attribute) (galaxy.datatypes.binary.GeminiSQLite attribute) (galaxy.datatypes.binary.GenericAsn1Binary attribute) (galaxy.datatypes.binary.H5 attribute) (galaxy.datatypes.binary.Idat attribute) (galaxy.datatypes.binary.Loom attribute) (galaxy.datatypes.binary.NetCDF attribute) (galaxy.datatypes.binary.ProBam attribute) (galaxy.datatypes.binary.SQlite attribute) (galaxy.datatypes.binary.Scf attribute) (galaxy.datatypes.binary.Sff attribute) (galaxy.datatypes.binary.TwoBit attribute) (galaxy.datatypes.blast.BlastXml attribute) (galaxy.datatypes.data.Data attribute) (galaxy.datatypes.data.GenericAsn1 attribute) (galaxy.datatypes.data.Newick attribute) (galaxy.datatypes.data.Nexus attribute) (galaxy.datatypes.data.Text attribute) (galaxy.datatypes.images.Bmp attribute) (galaxy.datatypes.images.Eps attribute) (galaxy.datatypes.images.Gif attribute) (galaxy.datatypes.images.Gmaj attribute) (galaxy.datatypes.images.Im attribute) (galaxy.datatypes.images.Image attribute) (galaxy.datatypes.images.Jpg attribute) (galaxy.datatypes.images.Pbm attribute) (galaxy.datatypes.images.Pcd attribute) (galaxy.datatypes.images.Pcx attribute) (galaxy.datatypes.images.Pdf attribute) (galaxy.datatypes.images.Pgm attribute) (galaxy.datatypes.images.Png attribute) (galaxy.datatypes.images.Ppm attribute) (galaxy.datatypes.images.Psd attribute) (galaxy.datatypes.images.Rast attribute) (galaxy.datatypes.images.Rgb attribute) (galaxy.datatypes.images.Tiff attribute) (galaxy.datatypes.images.Xbm attribute) (galaxy.datatypes.images.Xpm attribute) (galaxy.datatypes.interval.Bed attribute) (galaxy.datatypes.interval.Bed12 attribute) (galaxy.datatypes.interval.Bed6 attribute) (galaxy.datatypes.interval.BedGraph attribute) (galaxy.datatypes.interval.BedStrict attribute) (galaxy.datatypes.interval.CustomTrack attribute) (galaxy.datatypes.interval.ENCODEPeak attribute) (galaxy.datatypes.interval.Gff attribute) (galaxy.datatypes.interval.Gff3 attribute) (galaxy.datatypes.interval.Gtf attribute) (galaxy.datatypes.interval.Interval attribute) (galaxy.datatypes.interval.ProBed attribute) (galaxy.datatypes.interval.Wiggle attribute) (galaxy.datatypes.msa.Hmmer attribute) (galaxy.datatypes.msa.Hmmer2 attribute) (galaxy.datatypes.msa.Hmmer3 attribute) (galaxy.datatypes.msa.Stockholm_1_0 attribute) (galaxy.datatypes.phylip.Phylip attribute) (galaxy.datatypes.proteomics.ImzML attribute) (galaxy.datatypes.proteomics.MascotDat attribute) (galaxy.datatypes.proteomics.Mgf attribute) (galaxy.datatypes.proteomics.MzData attribute) (galaxy.datatypes.proteomics.MzIdentML attribute) (galaxy.datatypes.proteomics.MzML attribute) (galaxy.datatypes.proteomics.MzQuantML attribute) (galaxy.datatypes.proteomics.MzXML attribute) (galaxy.datatypes.proteomics.PepXml attribute) (galaxy.datatypes.proteomics.ProteomicsXml attribute) (galaxy.datatypes.proteomics.TandemXML attribute) (galaxy.datatypes.proteomics.ThermoRAW attribute) (galaxy.datatypes.proteomics.TraML attribute) (galaxy.datatypes.proteomics.Wiff attribute) (galaxy.datatypes.qualityscore.QualityScore attribute) (galaxy.datatypes.qualityscore.QualityScore454 attribute) (galaxy.datatypes.qualityscore.QualityScoreIllumina attribute) (galaxy.datatypes.qualityscore.QualityScoreSOLiD attribute) (galaxy.datatypes.qualityscore.QualityScoreSolexa attribute) (galaxy.datatypes.sequence.Axt attribute) (galaxy.datatypes.sequence.BaseFastq attribute) (galaxy.datatypes.sequence.DotBracket attribute) (galaxy.datatypes.sequence.Fasta attribute) (galaxy.datatypes.sequence.Fastq attribute) (galaxy.datatypes.sequence.FastqIllumina attribute) (galaxy.datatypes.sequence.FastqSanger attribute) (galaxy.datatypes.sequence.FastqSolexa attribute) (galaxy.datatypes.sequence.Genbank attribute) (galaxy.datatypes.sequence.Lav attribute) (galaxy.datatypes.sequence.Maf attribute) (galaxy.datatypes.sequence.RNADotPlotMatrix attribute) (galaxy.datatypes.sequence.csFasta attribute) (galaxy.datatypes.tabular.BaseVcf attribute) (galaxy.datatypes.tabular.ConnectivityTable attribute) (galaxy.datatypes.tabular.Pileup attribute) (galaxy.datatypes.tabular.Sam attribute) (galaxy.datatypes.tabular.TabularData attribute) (galaxy.datatypes.text.Arff attribute) (galaxy.datatypes.text.Biom1 attribute) (galaxy.datatypes.text.Html attribute) (galaxy.datatypes.text.Json attribute) (galaxy.datatypes.text.Obo attribute) (galaxy.datatypes.text.SnpEffDb attribute) (galaxy.datatypes.tracks.GeneTrack attribute) (galaxy.datatypes.triples.HDT attribute) (galaxy.datatypes.triples.Jsonld attribute) (galaxy.datatypes.triples.N3 attribute) (galaxy.datatypes.triples.NTriples attribute) (galaxy.datatypes.triples.Rdf attribute) (galaxy.datatypes.triples.Triples attribute) (galaxy.datatypes.triples.Turtle attribute) (galaxy.datatypes.xml.GenericXml attribute) (galaxy.datatypes.xml.Owl attribute) (galaxy.datatypes.xml.Phyloxml attribute) (galaxy.datatypes.xml.Sbml attribute) edam_formats (galaxy.datatypes.registry.Registry attribute) edam_formats() (galaxy.webapps.galaxy.api.datatypes.DatatypesController method), [1] edgelist_for_workflow_steps() (in module galaxy.workflow.steps) edit() (galaxy.webapps.galaxy.controllers.page.PageController method) (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method) edit_category() (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.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_is_set() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataCollection method) element_is_valid() (galaxy.tools.FilterEmptyDatasetsTool method) (galaxy.tools.FilterFailedDatasetsTool method) element_object (galaxy.model.DatasetCollectionElement attribute) element_type (galaxy.model.DatasetCollectionElement attribute) ElementIdentifierMapper (class in galaxy.tools.wrappers) elements_tree_map() (in module galaxy.tools.data_fetch) 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) EmailPlugin (class in galaxy.tools.error_reports.plugins.email) 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.cloud.Cloud method) (galaxy.objectstore.pithos.PithosObjectStore 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) (galaxy.web.stack.message.ApplicationStackMessage 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) endpoint_spec_option_map (galaxy.containers.docker_swarm.DockerSwarmAPIInterface attribute) engine (galaxy.model.Dataset attribute) English (class in galaxy.util.inflection) enqueue() (galaxy.jobs.JobWrapper method) 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_in_working_directory() (galaxy.tools.data_fetch.UploadConfig method) 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) ensure_user_with_email() (galaxy.tools.verify.interactor.GalaxyInteractorApi method) env (galaxy.containers.docker_model.DockerService attribute) 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) 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) ErrorPlugin (class in galaxy.tools.error_reports) (class in galaxy.tools.error_reports.plugins) ErrorReporter (class in galaxy.tools.errors) ErrorReports (class in galaxy.tools.error_reports) errors() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method) errors_per_tool() (galaxy.webapps.reports.controllers.jobs.Jobs method) escape() (in module tool_shed.util.web_util) 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) EventHandler (class in galaxy.util.watcher) 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) example_datatype_registry_for_sample() (in module galaxy.datatypes.registry) ExcelXls (class in galaxy.datatypes.binary) exception_handler() (galaxy.web.framework.middleware.error.ErrorMiddleware method) 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.tools.Tool method) (galaxy.tools.actions.DefaultToolAction method) (galaxy.tools.actions.ToolAction method) (galaxy.tools.actions.data_manager.DataManagerToolAction method) (galaxy.tools.actions.history_imp_exp.ExportHistoryToolAction method) (galaxy.tools.actions.history_imp_exp.ImportHistoryToolAction method) (galaxy.tools.actions.metadata.SetMetadataToolAction method) (galaxy.tools.actions.model_operations.ModelOperationToolAction method) (galaxy.tools.actions.upload.BaseUploadToolAction method) (galaxy.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.cloud.Cloud method) (galaxy.objectstore.pithos.PithosObjectStore 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) expected_app_factories (galaxy.webapps.config_manage.App attribute) expiration_time (galaxy.webapps.tool_shed.model.PasswordResetToken attribute) expire_tool() (galaxy.tools.cache.ToolCache method) 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_files_path_exists() (galaxy.model.Dataset method) (galaxy.model.DatasetInstance method) extra_preferences (galaxy.model.User attribute) extract() (galaxy.util.compression_utils.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) ExtractDatasetCollectionTool (class in galaxy.tools)

F

Facts (class in galaxy.util.facts) facts (galaxy.web.stack.ApplicationStack attribute) (galaxy.web.stack.UWSGIApplicationStack attribute) fail() (galaxy.jobs.JobWrapper method) (galaxy.jobs.TaskWrapper method) (galaxy.model.WorkflowInvocation method) (in module galaxy.tools.util.galaxyops) fail_job() (galaxy.jobs.runners.BaseJobRunner method) (galaxy.jobs.runners.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) 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) Fastq (class in galaxy.datatypes.sequence) FastqCSSanger (class in galaxy.datatypes.sequence) FastqIllumina (class in galaxy.datatypes.sequence) FastqSanger (class in galaxy.datatypes.sequence) FastqSolexa (class in galaxy.datatypes.sequence) FATAL (galaxy.tools.parser.error_level.StdioErrorLevel attribute) FATAL_OOM (galaxy.tools.parser.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() (galaxy.webapps.galaxy.api.tools.ToolsController method), [1] fetch_job_states() (in module galaxy.managers.jobs) fetch_requests() (galaxy.web.proxy.JsonFileProxyIpc method) (galaxy.web.proxy.ProxyIpc method) (galaxy.web.proxy.SqliteProxyIpc method) FetchUploadToolAction (class in galaxy.tools.actions.upload) field (in module galaxy.forms.forms) field_to_field_type() (in module galaxy.tools.cwl.representation) 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) file_append() (tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder.EnvFileBuilder method) file_ext (galaxy.datatypes.annotation.Augustus attribute) (galaxy.datatypes.annotation.SnapHmm attribute) (galaxy.datatypes.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.BlibSQlite 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.Cpt attribute) (galaxy.datatypes.binary.CuffDiffSQlite attribute) (galaxy.datatypes.binary.DAA attribute) (galaxy.datatypes.binary.DMND attribute) (galaxy.datatypes.binary.Dcd attribute) (galaxy.datatypes.binary.ExcelXls attribute) (galaxy.datatypes.binary.Fast5Archive attribute) (galaxy.datatypes.binary.Fast5ArchiveBz2 attribute) (galaxy.datatypes.binary.Fast5ArchiveGz attribute) (galaxy.datatypes.binary.GAFASQLite attribute) (galaxy.datatypes.binary.GeminiSQLite attribute) (galaxy.datatypes.binary.GenericAsn1Binary attribute) (galaxy.datatypes.binary.GmxBinary attribute) (galaxy.datatypes.binary.H5 attribute) (galaxy.datatypes.binary.ICM attribute) (galaxy.datatypes.binary.Idat attribute) (galaxy.datatypes.binary.IdpDB attribute) (galaxy.datatypes.binary.Loom attribute) (galaxy.datatypes.binary.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.ProBam 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.Trr attribute) (galaxy.datatypes.binary.TwoBit attribute) (galaxy.datatypes.binary.Vel attribute) (galaxy.datatypes.binary.Xlsx attribute) (galaxy.datatypes.binary.Xtc 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.ProBed 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.phylip.Phylip attribute) (galaxy.datatypes.plant_tribes.PlantTribesKsComponents attribute) (galaxy.datatypes.plant_tribes.Smat attribute) (galaxy.datatypes.proteomics.Analyze75 attribute) (galaxy.datatypes.proteomics.ConsensusXML attribute) (galaxy.datatypes.proteomics.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.Fastq attribute) (galaxy.datatypes.sequence.FastqCSSanger attribute) (galaxy.datatypes.sequence.FastqIllumina attribute) (galaxy.datatypes.sequence.FastqSanger attribute) (galaxy.datatypes.sequence.FastqSolexa attribute) (galaxy.datatypes.sequence.Genbank attribute) (galaxy.datatypes.sequence.Lav attribute) (galaxy.datatypes.sequence.Maf attribute) (galaxy.datatypes.sequence.MafCustomTrack attribute) (galaxy.datatypes.sequence.MemePsp attribute) (galaxy.datatypes.sequence.RNADotPlotMatrix attribute) (galaxy.datatypes.sequence.SequenceSplitLocations attribute) (galaxy.datatypes.sequence.csFasta attribute) (galaxy.datatypes.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) (galaxy.datatypes.xml.Sbml 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.cloud.Cloud method) (galaxy.objectstore.pulsar.PulsarObjectStore method) (galaxy.objectstore.s3.S3ObjectStore method)

file_size (galaxy.datatypes.sniff.FilePrefix attribute) 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) FilePrefix (class in galaxy.datatypes.sniff) 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) FileUploadTarget (class in galaxy.tools.cwl.util) 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.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) (galaxy.webapps.reports.framework.grids.CommunityTagsColumn method) (galaxy.webapps.reports.framework.grids.DeletedColumn method) (galaxy.webapps.reports.framework.grids.GridColumn method) (galaxy.webapps.reports.framework.grids.MulticolFilterColumn method) (galaxy.webapps.reports.framework.grids.SharingStatusColumn method) (galaxy.webapps.reports.framework.grids.StateColumn method) (galaxy.webapps.reports.framework.grids.TextColumn method) (tool_shed.grids.admin_grids.UserGrid.EmailColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.EmailColumn method) (tool_shed.grids.repository_grids.RepositoryGrid.RepositoryCategoryColumn method) (tool_shed.grids.repository_grids.ValidRepositoryGrid.RepositoryCategoryColumn method) filter_accessible() (galaxy.managers.secured.AccessibleManagerMixin method) filter_actions_after_binary_installation() (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_template (galaxy.auth.util.Authenticator attribute) filter_type (in module galaxy.tools.parser.output_actions) FilterableMixin (class in galaxy.visualization.data_providers.genome) FilterDatasetsTool (class in galaxy.tools) FilteredDataProvider (class in galaxy.datatypes.dataproviders.base) FilteredLineDataProvider (class in galaxy.datatypes.dataproviders.line) FilterEmptyDatasetsTool (class in galaxy.tools) FilterFactory (class in galaxy.tools.toolbox.filters) FilterFailedDatasetsTool (class in galaxy.tools) FilterFromFileTool (class in galaxy.tools) filters (tool_shed.grids.repository_grid_filter_manager.RepositoryGridFilterManager attribute) final() (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_instance_nested() (in module galaxy.util) 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) (galaxy.jobs.runners.chronos.ChronosJobRunner method) finished (galaxy.model.Job attribute) first_dataset_element (galaxy.model.DatasetCollection 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) flat_map() (in module galaxy.util.rules_dsl) flatten() (galaxy.util.Params method) (in module galaxy.web.framework.base) FlattenTool (class in galaxy.tools) float_nan() (in module galaxy.visualization.data_providers.genome) FloatToolParameter (class in galaxy.tools.parameters.basic) FluentTraceLogger (class in galaxy.util.logging.fluent_log) 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_attrs() (in module galaxy.web.framework.helpers.tags) format_bool() (in module galaxy.webapps.galaxy.controllers.page) format_for_summary() (galaxy.tools.verify.interactor.GalaxyInteractorApi method) 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.cgroup.CgroupPlugin 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.hostname.HostnamePlugin 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_api() (galaxy.containers.docker_model.DockerTask class method) from_app() (galaxy.tools.repositories.ValidationContext static method) 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_collection_type() (galaxy.tools.parameters.history_query.HistoryQuery static 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.tools.parser.interface.TestCollectionDef static method) (galaxy.tools.parser.interface.TestCollectionOutputDef 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) (galaxy.tools.error_reports.ErrorPlugin static method) from_id() (galaxy.containers.Container method) (galaxy.containers.docker_model.DockerContainer class method) (galaxy.containers.docker_model.DockerNode class method) (galaxy.containers.docker_model.DockerService class method) from_JSON() (galaxy.datatypes.metadata.MetadataTempFile class method) (galaxy.model.metadata.MetadataTempFile class method) from_json() (galaxy.tools.parameters.basic.BaseURLToolParameter method) (galaxy.tools.parameters.DataCollectionToolParameter method) (galaxy.tools.parameters.DataToolParameter method) (galaxy.tools.parameters.SelectToolParameter method) (galaxy.tools.parameters.basic.BooleanToolParameter method) (galaxy.tools.parameters.basic.ColumnListParameter method) (galaxy.tools.parameters.basic.DataCollectionToolParameter method) (galaxy.tools.parameters.basic.DataToolParameter method) (galaxy.tools.parameters.basic.DrillDownSelectToolParameter method) (galaxy.tools.parameters.basic.FTPFileToolParameter method) (galaxy.tools.parameters.basic.FileToolParameter method) (galaxy.tools.parameters.basic.FloatToolParameter method) (galaxy.tools.parameters.basic.IntegerToolParameter method) (galaxy.tools.parameters.basic.LibraryDatasetToolParameter method) (galaxy.tools.parameters.basic.SelectTagParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) from_JSON_dict() (galaxy.datatypes.metadata.MetadataCollection method) (galaxy.model.metadata.MetadataCollection method) from_label_dictionary() (galaxy.containers.docker_model.DockerNodeLabels class method) from_list() (galaxy.tools.deps.requirements.ToolRequirements static method) from_parameter() (galaxy.tools.parameters.history_query.HistoryQuery static method) from_str() (galaxy.containers.ContainerVolume method) (galaxy.containers.docker_model.DockerServiceConstraint class method) (galaxy.containers.docker_model.DockerVolume class method) (galaxy.visualization.genomes.GenomeRegion static method) from_tool() (galaxy.tools.toolbox.lineages.interface.ToolLineage static method) (galaxy.tools.toolbox.lineages.ToolLineage static method) from_workflow_step() (galaxy.workflow.modules.SubWorkflowModule class method) (galaxy.workflow.modules.ToolModule class method) (galaxy.workflow.modules.WorkflowModule class method) (galaxy.workflow.modules.WorkflowModuleFactory method) (tool_shed.util.workflow_util.RepoToolModule class method) (tool_shed.util.workflow_util.RepoWorkflowModuleFactory method) from_xml() (galaxy.tools.parser.interface.TestCollectionDef static 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

GAFASQLite (class in galaxy.datatypes.binary) galactic_job_json() (in module galaxy.tools.cwl.util) galaxy (galaxy.web.framework.middleware.batch.BatchMiddleware attribute) (module) galaxy.actions (module) galaxy.actions.admin (module) galaxy.actions.library (module) galaxy.app (module) galaxy.auth (module) galaxy.auth.providers (module) galaxy.auth.providers.alwaysreject (module) galaxy.auth.providers.ldap_ad (module) galaxy.auth.providers.localdb (module) galaxy.auth.providers.pam_auth (module) galaxy.auth.util (module) galaxy.authnz (module) galaxy.authnz.managers (module) galaxy.authnz.psa_authnz (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.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.annotation (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.cram_to_bam (module) galaxy.datatypes.converters.fasta_to_len (module) galaxy.datatypes.converters.fasta_to_tabular_converter (module) galaxy.datatypes.converters.fastq_to_fqtoc (module) galaxy.datatypes.converters.fastqsolexa_to_fasta_converter (module) galaxy.datatypes.converters.fastqsolexa_to_qual_converter (module) galaxy.datatypes.converters.gff_to_bed_converter (module) galaxy.datatypes.converters.gff_to_interval_index_converter (module) galaxy.datatypes.converters.interval_to_bed_converter (module) galaxy.datatypes.converters.interval_to_bedstrict_converter (module) galaxy.datatypes.converters.interval_to_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.phylip (module) galaxy.datatypes.plant_tribes (module) galaxy.datatypes.proteomics (module) galaxy.datatypes.qualityscore (module) galaxy.datatypes.registry (module) galaxy.datatypes.sequence (module) galaxy.datatypes.sniff (module) galaxy.datatypes.tabular (module) galaxy.datatypes.text (module) galaxy.datatypes.tracks (module) galaxy.datatypes.triples (module) galaxy.datatypes.upload_util (module) galaxy.datatypes.util (module) galaxy.datatypes.util.generic_util (module) galaxy.datatypes.util.gff_util (module) galaxy.datatypes.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.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.cgroup (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.hostname (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.chronos (module) galaxy.jobs.runners.cli (module) galaxy.jobs.runners.condor (module) galaxy.jobs.runners.drmaa (module) galaxy.jobs.runners.godocker (module) galaxy.jobs.runners.kubernetes (module) galaxy.jobs.runners.local (module) galaxy.jobs.runners.pbs (module) galaxy.jobs.runners.pulsar (module) galaxy.jobs.runners.slurm (module) galaxy.jobs.runners.state_handler_factory (module) galaxy.jobs.runners.state_handlers (module) galaxy.jobs.runners.state_handlers.resubmit (module) galaxy.jobs.runners.tasks (module) galaxy.jobs.runners.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.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.sudo (module) galaxy.jobs.splitters (module) galaxy.jobs.splitters.basic (module) galaxy.jobs.splitters.multi (module) galaxy.jobs.stock_rules (module) galaxy.jobs.transfer_manager (module) galaxy.main (module) galaxy.managers (module) galaxy.managers.annotatable (module) galaxy.managers.api_keys (module) galaxy.managers.base (module) galaxy.managers.citations (module) galaxy.managers.cloud (module) galaxy.managers.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.jobs (module) galaxy.managers.lddas (module) galaxy.managers.libraries (module) galaxy.managers.library_datasets (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.cloud (module) galaxy.objectstore.pithos (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.cache (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.cwl.util (module) galaxy.tools.data (module) galaxy.tools.data_fetch (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.lmod (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.singularity_util (module) galaxy.tools.deps.views (module) galaxy.tools.error_reports (module) galaxy.tools.error_reports.plugins (module) galaxy.tools.error_reports.plugins.biostars (module) galaxy.tools.error_reports.plugins.email (module) galaxy.tools.error_reports.plugins.github (module) galaxy.tools.error_reports.plugins.influxdb (module) galaxy.tools.error_reports.plugins.json (module) galaxy.tools.error_reports.plugins.sentry (module) galaxy.tools.errors (module) galaxy.tools.evaluation (module) galaxy.tools.exception_handling (module) galaxy.tools.execute (module) galaxy.tools.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.error_level (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.repositories (module) galaxy.tools.search (module) galaxy.tools.special_tools (module) galaxy.tools.test (module) galaxy.tools.toolbox (module) galaxy.tools.toolbox.base (module) galaxy.tools.toolbox.filters (module) galaxy.tools.toolbox.integrated_panel (module) galaxy.tools.toolbox.lineages (module) galaxy.tools.toolbox.lineages.factory (module) galaxy.tools.toolbox.lineages.interface (module) galaxy.tools.toolbox.panel (module) galaxy.tools.toolbox.parser (module) galaxy.tools.toolbox.tags (module) galaxy.tools.toolbox.watcher (module) galaxy.tools.util (module) galaxy.tools.util.galaxyops (module) galaxy.tools.util.maf_utilities (module) galaxy.tools.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.interactor (module) galaxy.tools.verify.script (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.create_history_template (module) galaxy.util.dbkeys (module) galaxy.util.dictifiable (module) galaxy.util.expressions (module) galaxy.util.facts (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.logging (module) galaxy.util.logging.fluent_log (module) galaxy.util.monitors (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.path (module) galaxy.util.path.ntpath (module) galaxy.util.path.posixpath (module) galaxy.util.permutations (module) galaxy.util.plugin_config (module) galaxy.util.properties (module) galaxy.util.renamed_temporary_file (module) galaxy.util.rules_dsl (module) galaxy.util.sanitize_html (module) galaxy.util.script (module) galaxy.util.simplegraph (module) galaxy.util.sleeper (module) galaxy.util.sockets (module) galaxy.util.specs (module) galaxy.util.sqlite (module) galaxy.util.streamball (module) galaxy.util.submodules (module) galaxy.util.template (module) galaxy.util.tool_version (module) galaxy.util.topsort (module) galaxy.util.ucsc (module) galaxy.util.validation (module) galaxy.util.watcher (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.interactive_environments (module) galaxy.visualization.plugins.plugin (module) galaxy.visualization.plugins.registry (module) galaxy.visualization.plugins.resource_parser (module) galaxy.visualization.plugins.utils (module) galaxy.visualization.tracks (module) galaxy.web (module) galaxy.web.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.helpers.tags (module) galaxy.web.framework.middleware (module) galaxy.web.framework.middleware.batch (module) galaxy.web.framework.middleware.error (module) galaxy.web.framework.middleware.profile (module) galaxy.web.framework.middleware.remoteuser (module) galaxy.web.framework.middleware.request_id (module) galaxy.web.framework.middleware.sentry (module) galaxy.web.framework.middleware.sqldebug (module) galaxy.web.framework.middleware.static (module) galaxy.web.framework.middleware.statsd (module) galaxy.web.framework.middleware.translogger (module) galaxy.web.framework.middleware.xforwardedhost (module) galaxy.web.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.web.stack.message (module) galaxy.web.stack.transport (module) galaxy.webapps (module) galaxy.webapps.config_manage (module) galaxy.webapps.galaxy (module) galaxy.webapps.galaxy.api (module) galaxy.webapps.galaxy.api.annotations (module), [1] galaxy.webapps.galaxy.api.authenticate (module), [1] galaxy.webapps.galaxy.api.cloud (module), [1] galaxy.webapps.galaxy.api.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.library_datasets (module), [1] galaxy.webapps.galaxy.api.metrics (module), [1] galaxy.webapps.galaxy.api.page_revisions (module), [1] galaxy.webapps.galaxy.api.pages (module), [1] galaxy.webapps.galaxy.api.plugins (module), [1] galaxy.webapps.galaxy.api.provenance (module), [1] galaxy.webapps.galaxy.api.quotas (module), [1] galaxy.webapps.galaxy.api.remote_files (module), [1] galaxy.webapps.galaxy.api.roles (module), [1] galaxy.webapps.galaxy.api.search (module), [1] galaxy.webapps.galaxy.api.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.uploads (module), [1] galaxy.webapps.galaxy.api.users (module), [1] galaxy.webapps.galaxy.api.visualizations (module), [1] galaxy.webapps.galaxy.api.webhooks (module), [1] galaxy.webapps.galaxy.api.workflows (module), [1] galaxy.webapps.galaxy.buildapp (module) galaxy.webapps.galaxy.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.authnz (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.reports.framework (module) galaxy.webapps.reports.framework.grids (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.resources (module) galaxy.workflow.run (module) galaxy.workflow.run_request (module) galaxy.workflow.schedulers (module) galaxy.workflow.schedulers.core (module) galaxy.workflow.scheduling_manager (module) galaxy.workflow.steps (module) galaxy_directory() (in module galaxy.util) galaxy_ext (module) galaxy_ext.metadata (module) galaxy_ext.metadata.set_metadata (module) galaxy_lib_dir (galaxy.jobs.JobWrapper attribute) galaxy_param_type (galaxy.tools.cwl.representation.TypeRepresentation 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) GalaxyInteractorApi (class in galaxy.tools.verify.interactor) GalaxyLargeBinary (class in galaxy.model.custom_types) GalaxyOutput (class in galaxy.tools.cwl.util) 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_hex() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) generate_includes_workflows_img_str() (in module tool_shed.galaxy_install.grids.admin_toolshed_grids) generate_json_error() (galaxy.webapps.galaxy.controllers.root.RootController method) generate_latest_revision_img_str() (in module tool_shed.galaxy_install.grids.admin_toolshed_grids) generate_message_for_invalid_repository_dependencies() (tool_shed.galaxy_install.dependency_display.DependencyDisplayer method) generate_message_for_invalid_tool_dependencies() (tool_shed.galaxy_install.dependency_display.DependencyDisplayer method) generate_message_for_invalid_tools() (in module 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_password() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest 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.managers.datasets.DatasetRBACPermissions method) (galaxy.managers.folders.FolderManager method) (galaxy.managers.lddas.LDDAManager method) (galaxy.managers.libraries.LibraryManager method) (galaxy.managers.library_datasets.LibraryDatasetsManager method) (galaxy.managers.roles.RoleManager method) (galaxy.model.PSAAssociation class method) (galaxy.model.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) (galaxy.webapps.reports.framework.grids.DeletedColumn method) (galaxy.webapps.reports.framework.grids.GridColumn method) (galaxy.webapps.reports.framework.grids.SharingStatusColumn method) (galaxy.webapps.reports.framework.grids.StateColumn method) (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid.DeletedColumn method) get_access_roles() (galaxy.managers.libraries.LibraryManager method) (galaxy.model.Dataset method) (galaxy.model.HistoryDatasetAssociation method) (galaxy.model.Library method) (galaxy.model.LibraryDatasetDatasetAssociation method) get_accessible() (galaxy.managers.secured.AccessibleManagerMixin method) get_accessible_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) (galaxy.webapps.config_manage.AppSchema method) (galaxy.webapps.config_manage.Schema 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_authenticators() (in module galaxy.auth.util) get_available_tracks() (galaxy.datatypes.registry.Registry method) get_ave_item_rating_data() (galaxy.model.item_attrs.UsesItemRatings method) get_base_dir() (galaxy.tools.data.TabularToolDataField method) get_base_path() (galaxy.tools.data.TabularToolDataField method) get_bibtex() (galaxy.managers.citations.DoiCache method) get_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.tools.actions.ToolExecutionCache method) (galaxy.util.dbkeys.GenomeBuilds method) get_chunk() (galaxy.datatypes.binary.BamNative method) (galaxy.datatypes.tabular.ConnectivityTable method) (galaxy.datatypes.tabular.TabularData method) get_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_code() (galaxy.model.PSACode class 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_conf_dict() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) get_config() (in module galaxy.model.orm.scripts) get_config_dict() (galaxy.webapps.galaxy.api.configuration.ConfigurationController method), [1] get_config_form() (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_config_from_disk() (in module 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_container_host() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) get_container_port_mapping() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method) get_containing_repository_for_tool_dependency() (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) (galaxy.webapps.reports.framework.grids.Grid method) (tool_shed.grids.admin_grids.UserGrid method) get_current_repository_metadata_for_changeset_revision() (in module tool_shed.util.metadata_util) get_current_roles() (galaxy.managers.folders.FolderManager method) (galaxy.managers.libraries.LibraryManager method) get_current_thread_object_dict() (in module galaxy.util.heartbeat) get_current_user_roles() (galaxy.managers.context.ProvidesUserContext method) (galaxy.work.context.WorkRequestContext method) get_custom_builds() (galaxy.webapps.galaxy.api.users.UserAPIController method), [1] 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.cloud.Cloud method) (galaxy.objectstore.pithos.PithosObjectStore 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_matcher_factory() (in module galaxy.tools.parameters.dataset_matcher) get_dataset_metadata_key() (galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper method) (galaxy.model.metadata.JobExternalOutputMetadataWrapper method) get_dataset_state() (galaxy.model.DatasetInstance method) get_datasets_for_group() (galaxy.tools.wrappers.DatasetCollectionWrapper method) (galaxy.tools.wrappers.DatasetListWrapper method) get_datasources() (galaxy.model.DatasetInstance method) get_datatype() (galaxy.tools.parameters.grouping.UploadDataset method) get_datatype_by_extension() (galaxy.datatypes.registry.Registry method) get_datatype_class_by_name() (galaxy.datatypes.registry.Registry method) get_datatype_ext() (galaxy.tools.parameters.grouping.UploadDataset method) get_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.SelectTagParameter method) (galaxy.tools.parameters.basic.SelectToolParameter method) (galaxy.tools.parameters.basic.ToolParameter method) get_dependencies_for_metadata_revision() (in module tool_shed.util.metadata_util) get_dependencies_for_repository() (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_destination_list_from_job_config() (in module galaxy.jobs.dynamic_tool_destination) 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_edit_distance() (in module galaxy.jobs.dynamic_tool_destination) 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.SubWorkflowModule method) (galaxy.workflow.modules.ToolModule method) (galaxy.workflow.modules.WorkflowModule method) get_estimated_display_viewport() (galaxy.datatypes.interval.BedGraph method) (galaxy.datatypes.interval.CustomTrack method) (galaxy.datatypes.interval.Gff method) (galaxy.datatypes.interval.Interval method) (galaxy.datatypes.interval.Wiggle method)

get_exit_code() (galaxy.jobs.TaskWrapper method)