Galaxy Project

21.01

Release Notes

Releases

Admin Documentation

Administration
Special topics

Developer Documentation

Development
Galaxy API
Tool Shed API
- API Documentation
Application Documentation

About Project

Project Governance
Issue Management

Galaxy Project

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Index

Index

_ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z

_

__init__() (galaxy.app.ExecutionTimerFactory method)

A

Ab1 (class in galaxy.datatypes.binary)
abs_path() (in module galaxy.tool_util.cwl.util)
abs_path_or_uri() (in module galaxy.tool_util.cwl.util)
absolute_config_path() (in module galaxy.main)
AbstractToolBox (class in galaxy.tools.toolbox)
- (class in galaxy.tools.toolbox.base)
AbstractToolTagManager (class in galaxy.tools.toolbox.tags)
access_entry_point() (galaxy.webapps.galaxy.api.tool_entry_points.ToolEntryPointsAPIController method)
access_entry_point_target() (galaxy.managers.interactivetool.InteractiveToolManager method)
access_token (galaxy.model.CustosAuthnzToken attribute)
AccessDatasetRBACPermission (class in galaxy.managers.rbac_secured)
AccessibleManagerMixin (class in galaxy.managers.secured)
AccNos (class in galaxy.datatypes.mothur)
accumulate_tool_dependencies() (in module galaxy.util.tool_shed.common_util)
acquire() (galaxy.util.filelock.FileLock method)
Action (class in galaxy.security)
- (class in galaxy.workflow.refactor.schema)
- (class in tool_shed.webapp.security)
action (galaxy.jobs.actions.post.RemoveTagDatasetAction attribute)
- (galaxy.jobs.actions.post.TagDatasetAction attribute)
- (galaxy.model.DatasetPermissions attribute)
- (galaxy.model.DefaultHistoryPermissions attribute)
- (galaxy.model.DefaultUserPermissions attribute)
- (galaxy.model.LibraryDatasetDatasetAssociationPermissions attribute)
- (galaxy.model.LibraryDatasetPermissions attribute)
- (galaxy.model.LibraryFolderPermissions attribute)
- (galaxy.model.LibraryPermissions attribute)
- (galaxy.model.UserAction attribute)
- (galaxy.model.WorkflowInvocationStep attribute)
- (galaxy.workflow.refactor.schema.RefactorActionExecution attribute)
action_arguments (galaxy.model.PostJobAction attribute)
action_chains() (galaxy.selenium.has_driver.HasDriver method)
action_class (in module galaxy.workflow.refactor.schema)
action_executions (galaxy.managers.workflows.RefactorResponse attribute)
ACTION_NAME (galaxy.datatypes.display_applications.parameters.DisplayDataValueWrapper attribute)
- (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper attribute)
action_name (galaxy.managers.rbac_secured.AccessDatasetRBACPermission attribute)
- (galaxy.managers.rbac_secured.DatasetRBACPermission attribute)
- (galaxy.managers.rbac_secured.ManageDatasetRBACPermission attribute)
action_name() (galaxy.datatypes.display_applications.parameters.DisplayDataValueWrapper property)
- (galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper property)
action_type (galaxy.model.PostJobAction attribute)
- (galaxy.workflow.refactor.schema.Action attribute)
- (galaxy.workflow.refactor.schema.AddInputAction attribute)
- (galaxy.workflow.refactor.schema.AddStepAction attribute)
- (galaxy.workflow.refactor.schema.ConnectAction attribute)
- (galaxy.workflow.refactor.schema.DisconnectAction attribute)
- (galaxy.workflow.refactor.schema.ExtractInputAction attribute)
- (galaxy.workflow.refactor.schema.ExtractUntypedParameter attribute)
- (galaxy.workflow.refactor.schema.FileDefaultsAction attribute)
- (galaxy.workflow.refactor.schema.FillStepDefaultsAction attribute)
- (galaxy.workflow.refactor.schema.RemoveUnlabeledWorkflowOutputs attribute)
- (galaxy.workflow.refactor.schema.UpdateAnnotationAction attribute)
- (galaxy.workflow.refactor.schema.UpdateCreatorAction attribute)
- (galaxy.workflow.refactor.schema.UpdateLicenseAction attribute)
- (galaxy.workflow.refactor.schema.UpdateNameAction attribute)
- (galaxy.workflow.refactor.schema.UpdateOutputLabelAction attribute)
- (galaxy.workflow.refactor.schema.UpdateReportAction attribute)
- (galaxy.workflow.refactor.schema.UpdateStepLabelAction attribute)
- (galaxy.workflow.refactor.schema.UpdateStepPositionAction attribute)
- (galaxy.workflow.refactor.schema.UpgradeSubworkflowAction attribute)
- (galaxy.workflow.refactor.schema.UpgradeToolAction attribute)
- (in module galaxy.tool_util.parser.output_actions)
ActionBox (class in galaxy.jobs.actions.post)
ActionInputError
actions (galaxy.jobs.actions.post.ActionBox attribute)
- (galaxy.model.Dataset attribute)
- (galaxy.model.Library attribute)
- (galaxy.model.LibraryDataset attribute)
- (galaxy.model.LibraryDatasetDatasetAssociation attribute)
- (galaxy.model.LibraryFolder attribute)
- (galaxy.workflow.refactor.schema.RefactorActions attribute)
activatable_datasets() (galaxy.model.History property)
activatable_library_datasets() (galaxy.model.LibraryFolder property)
activate() (galaxy.managers.users.UserManager method)
- (galaxy.tool_util.deps.conda_util.CondaContext property)
- (galaxy.webapps.galaxy.controllers.user.User method)
activate_operation (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute)
activate_repository() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method)
- (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method)
activation_token (galaxy.model.User attribute)
active (galaxy.managers.jobs.JobLock attribute)
- (galaxy.model.DynamicTool attribute)
- (galaxy.model.User attribute)
active() (galaxy.model.InteractiveToolEntryPoint property)
- (galaxy.model.WorkflowInvocation property)
active_authenticators() (galaxy.auth.AuthManager method)
active_contents() (galaxy.model.History property)
active_counts() (galaxy.managers.history_contents.HistoryContentsManager method)
active_dataset_and_roles_query() (galaxy.model.History property)
active_dataset_collections (galaxy.model.History attribute)
active_datasets (galaxy.model.History attribute)
- (galaxy.model.LibraryFolder attribute)
active_datasets_and_roles() (galaxy.model.History property)
active_folders (galaxy.model.LibraryFolder attribute)
active_folders() (in module galaxy.tools.actions.upload_common)
active_histories (galaxy.model.User attribute)
active_history_associations (galaxy.model.Dataset attribute)
active_history_jobs() (galaxy_test.base.populators.BaseDatasetPopulator method)
active_library_associations (galaxy.model.Dataset attribute)
active_repositories (tool_shed.webapp.model.User attribute)
active_visible_dataset_collections() (galaxy.model.History property)
active_visible_datasets_and_roles() (galaxy.model.History property)
ActiveDirectory (class in galaxy.auth.providers.ldap_ad)
ActiveWorkflowSchedulingPlugin (class in galaxy.workflow.schedulers)
add() (galaxy.managers.citations.CitationCollection method)
- (galaxy.model.dataset_collections.matching.CollectionsToMatch method)
- (galaxy.model.store.SessionlessContext method)
- (galaxy.util.oset.OrderedSet method)
add_api_controller() (galaxy.web.framework.base.WebApplication method)
add_api_controllers() (galaxy.webapps.base.webapp.WebApplication method)
add_boxes() (galaxy.workflow.render.WorkflowCanvas method)
add_category_entry() (tool_shed.repository_registry.Registry method)
add_change_callback() (galaxy.model.database_heartbeat.DatabaseHeartbeat method)
add_changeset() (in module tool_shed.util.hg_util)
add_client_route() (galaxy.web.framework.base.WebApplication method)
add_column() (in module galaxy.model.migrate.versions.util)
add_composite_file() (galaxy.datatypes.data.Data method)
add_connection() (galaxy.model.WorkflowStep method)
- (galaxy.workflow.render.WorkflowCanvas method)
add_custom_build() (galaxy_test.selenium.test_custom_builds.CustomBuildsTestcase method)
add_custom_builds() (galaxy.webapps.galaxy.api.users.UserAPIController method)
add_data_table_watch() (galaxy.datatypes.display_applications.application.DisplayApplication method)
add_dataset() (galaxy.model.dataset_collections.builder.CollectionBuilder method)
- (galaxy.model.History method)
- (galaxy.model.store.DirectoryModelExportStore method)
- (galaxy.model.store.ModelExportStore method)
add_dataset_collection() (galaxy.job_execution.output_collect.BaseJobContext method)
- (galaxy.job_execution.output_collect.SessionlessJobContext method)
- (galaxy.model.History method)
- (galaxy.model.store.DirectoryModelExportStore method)
- (galaxy.model.store.ModelExportStore method)
add_datasets() (galaxy.model.History method)
add_datasets_to_history() (galaxy.job_execution.output_collect.JobContext method)
- (galaxy.model.store.discover.ModelPersistenceContext method)
- (galaxy.model.store.discover.SessionlessModelPersistenceContext method)
add_deserializers() (galaxy.managers.annotatable.AnnotatableDeserializerMixin method)
- (galaxy.managers.base.ModelDeserializer method)
- (galaxy.managers.cloudauthzs.CloudAuthzsDeserializer method)
- (galaxy.managers.datasets.DatasetAssociationDeserializer method)
- (galaxy.managers.deletable.DeletableDeserializerMixin method)
- (galaxy.managers.deletable.PurgableDeserializerMixin method)
- (galaxy.managers.hdas.HDADeserializer method)
- (galaxy.managers.histories.HistoryDeserializer method)
- (galaxy.managers.pages.PageDeserializer method)
- (galaxy.managers.ratable.RatableDeserializerMixin method)
- (galaxy.managers.sharable.SharableModelDeserializer method)
- (galaxy.managers.taggable.TaggableDeserializerMixin method)
- (galaxy.managers.users.UserDeserializer method)
- (galaxy.managers.visualizations.VisualizationDeserializer method)
add_display_app() (galaxy.datatypes.data.Data method)
add_display_application() (galaxy.datatypes.data.Data method)
add_dummy_datasets() (galaxy.workflow.modules.ToolModule method)
- (galaxy.workflow.modules.WorkflowModule method)
add_edge() (galaxy.util.simplegraph.SimpleGraph method)
add_entries() (galaxy.tools.data.ToolDataTable method)
add_entry() (galaxy.tools.data.ToolDataTable method)
- (tool_shed.repository_registry.Registry method)
- (tool_shed.util.hgweb_config.HgWebConfigManager method)
add_entry_to_installed_repository_dependencies_of_installed_repositories() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method)
add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method)
add_entry_to_installed_tool_dependencies_of_installed_repositories() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method)
add_entry_to_repository_dependencies_of_installed_repositories() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method)
add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method)
add_entry_to_tool_dependencies_of_installed_repositories() (galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager method)
add_env_shell_file_paths() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method)
add_error() (galaxy.tools.ToolErrorLog method)
add_exception_handler() (in module galaxy.webapps.galaxy.fast_app)
add_folder() (galaxy.model.LibraryFolder method)
add_galaxy_session() (galaxy.model.History method)
add_handler() (galaxy.web_stack.handlers.ConfiguresHandlers method)
add_history() (galaxy.model.GalaxySession method)
add_implicit_input_collection() (galaxy.model.HistoryDatasetCollectionAssociation method)
add_implicit_output_dataset_collection() (galaxy.model.Job method)
add_index() (in module galaxy.model.migrate.versions.util)
add_input() (galaxy.model.WorkflowInvocation method)
add_input_dataset() (galaxy.model.Job method)
add_input_dataset_collection() (galaxy.model.Job method)
add_input_dataset_collection_element() (galaxy.model.Job method)
add_input_library_dataset() (galaxy.model.Job method)
add_installation_directories_to_tool_dependencies() (tool_shed.galaxy_install.dependency_display.DependencyDisplayer method)
add_item_annotation() (galaxy.model.item_attrs.UsesAnnotations method)
add_job_output_dataset_associations() (galaxy.model.store.DirectoryModelExportStore method)
add_library_dataset() (galaxy.model.LibraryFolder method)
add_library_dataset_to_folder() (galaxy.job_execution.output_collect.JobContext method)
- (galaxy.model.store.discover.ModelPersistenceContext method)
- (galaxy.model.store.discover.SessionlessModelPersistenceContext method)
add_line_to_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method)
add_local_repository() (galaxy.tools.cache.ToolShedRepositoryCache method)
add_manager() (galaxy.tools.data_manager.manager.DataManagers method)
add_metric() (galaxy.model.JobLike method)
add_new_entries_from_config_file() (galaxy.tools.data.ToolDataTableManager method)
add_node() (galaxy.util.simplegraph.SimpleGraph method)
add_option() (galaxy.util.form_builder.SelectField method)
- (galaxy.web.form_builder.SelectField method)
add_output() (galaxy.model.WorkflowInvocation method)
- (galaxy.model.WorkflowInvocationStep method)
add_output_dataset() (galaxy.model.Job method)
add_output_dataset_association() (galaxy.job_execution.output_collect.JobContext method)
- (galaxy.job_execution.output_collect.SessionlessJobContext method)
- (galaxy.model.store.discover.ModelPersistenceContext method)
- (galaxy.model.store.discover.SessionlessModelPersistenceContext method)
add_output_dataset_collection() (galaxy.model.Job method)
add_output_library_dataset() (galaxy.model.Job method)
add_parameter() (galaxy.model.Job method)
add_path() (galaxy.util.zipstream.ZipstreamWrapper method)
add_pending_items() (galaxy.model.History method)
add_post_job_action() (galaxy.model.Job method)
add_repository_registry_entry() (tool_shed.webapp.api.repositories.RepositoriesController method)
add_repository_review_component() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
add_route() (galaxy.web.framework.base.WebApplication method)
add_sample_file_to_defaults (galaxy.config.BaseAppConfiguration attribute)
- (galaxy.config.GalaxyAppConfiguration attribute)
- (tool_shed.webapp.config.ToolShedAppConfiguration attribute)
add_selenium_arguments() (in module galaxy.selenium.cli)
add_sequencer() (in module galaxy.model.migrate.versions.0067_populate_sequencer_table)
add_serializers() (galaxy.managers.annotatable.AnnotatableSerializerMixin method)
- (galaxy.managers.base.ModelSerializer method)
- (galaxy.managers.cloudauthzs.CloudAuthzsSerializer method)
- (galaxy.managers.configuration.AdminConfigSerializer method)
- (galaxy.managers.configuration.ConfigSerializer method)
- (galaxy.managers.datasets.DatasetAssociationSerializer method)
- (galaxy.managers.datasets.DatasetSerializer method)
- (galaxy.managers.deletable.DeletableSerializerMixin method)
- (galaxy.managers.deletable.PurgableSerializerMixin method)
- (galaxy.managers.hdas.HDASerializer method)
- (galaxy.managers.hdcas.DCASerializer method)
- (galaxy.managers.hdcas.DCESerializer method)
- (galaxy.managers.hdcas.DCSerializer method)
- (galaxy.managers.hdcas.HDCASerializer method)
- (galaxy.managers.histories.HistorySerializer method)
- (galaxy.managers.history_contents.HistoryContentsSerializer method)
- (galaxy.managers.pages.PageSerializer method)
- (galaxy.managers.ratable.RatableSerializerMixin method)
- (galaxy.managers.sharable.SharableModelSerializer method)
- (galaxy.managers.taggable.TaggableSerializerMixin method)
- (galaxy.managers.users.UserSerializer method)
- (galaxy.managers.visualizations.VisualizationSerializer method)
add_species() (galaxy.datatypes.util.maf_utilities.RegionAlignment method)
- (galaxy.tools.util.maf_utilities.RegionAlignment method)
add_sreg() (galaxy.openid.openid_manager.OpenIDManager method)
add_steps() (galaxy.workflow.render.WorkflowCanvas method)
add_tag_async() (galaxy.webapps.galaxy.controllers.tag.TagsController method)
add_tags_from_list() (galaxy.model.tags.TagHandler method)
add_tags_to_datasets() (galaxy.model.store.discover.ModelPersistenceContext method)
add_text() (galaxy.workflow.render.WorkflowCanvas method)
add_to_shed_tool_config() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method)
add_to_tool_panel() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method)
add_tool_to_cache() (galaxy.tools.toolbox.AbstractToolBox method)
- (galaxy.tools.toolbox.base.AbstractToolBox method)
add_tool_versions() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method)
add_ui_controller() (galaxy.web.framework.base.WebApplication method)
add_ui_controllers() (galaxy.webapps.base.webapp.WebApplication method)
- (in module galaxy.webapps.reports.buildapp)
- (in module tool_shed.webapp.buildapp)
add_validation_error() (galaxy.model.DatasetInstance method)
add_view() (galaxy.managers.base.ModelSerializer method)
add_visualization_revision() (galaxy.webapps.base.controller.UsesVisualizationMixin method)
addAttributesToRoot() (galaxy.visualization.data_providers.phyloviz.baseparser.PhyloTree method)
addChildNode() (galaxy.visualization.data_providers.phyloviz.baseparser.Node method)
addChildrenToJson() (galaxy.visualization.data_providers.phyloviz.baseparser.Node method)
AddColumnBasenameRuleDefinition (class in galaxy.util.rules_dsl)
AddColumnConcatenateRuleDefinition (class in galaxy.util.rules_dsl)
AddColumnGroupTagValueRuleDefinition (class in galaxy.util.rules_dsl)
AddColumnMetadataRuleDefinition (class in galaxy.util.rules_dsl)
AddColumnRegexRuleDefinition (class in galaxy.util.rules_dsl)
AddColumnRownumRuleDefinition (class in galaxy.util.rules_dsl)
AddColumnSubstrRuleDefinition (class in galaxy.util.rules_dsl)
AddColumnValueRuleDefinition (class in galaxy.util.rules_dsl)
addError() (galaxy_test.base.instrument.StructuredTestDataPlugin method)
addFailure() (galaxy_test.base.instrument.StructuredTestDataPlugin method)
AddFilterCompareRuleDefinition (class in galaxy.util.rules_dsl)
AddFilterCountRuleDefinition (class in galaxy.util.rules_dsl)
AddFilterEmptyRuleDefinition (class in galaxy.util.rules_dsl)
AddFilterMatchesRuleDefinition (class in galaxy.util.rules_dsl)
AddFilterRegexRuleDefinition (class in galaxy.util.rules_dsl)
AddInputAction (class in galaxy.workflow.refactor.schema)
AdditionalValueFilter (class in galaxy.tools.parameters.dynamic_options)
addMiscToJson() (galaxy.visualization.data_providers.phyloviz.baseparser.Node method)
address (galaxy.model.UserAddress attribute)
address() (galaxy.containers.Container property)
- (galaxy.containers.docker_model.DockerContainer property)
- (galaxy.containers.docker_model.DockerService property)
addresses (galaxy.model.User attribute)
AddressField (class in galaxy.util.form_builder)
- (class in galaxy.web.form_builder)
addRoot() (galaxy.visualization.data_providers.phyloviz.baseparser.PhyloTree method)
AddStepAction (class in galaxy.workflow.refactor.schema)
addSuccess() (galaxy_test.base.instrument.StructuredTestDataPlugin method)
adjust_hidden() (galaxy.webapps.galaxy.controllers.history.HistoryController method)
adjust_total_disk_usage() (galaxy.model.User method)
Admin (class in tool_shed.util.admin_util)
ADMIN (galaxy.model.Role.types attribute)
admin_api_keys() (galaxy.webapps.galaxy.controllers.userskeys.User method)
admin_job_lock() (in module galaxy.queue_worker)
admin_login() (galaxy_test.selenium.framework.TestWithSeleniumMixin method)
admin_open() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
admin_role() (tool_shed.webapp.model.Repository property)
admin_users() (galaxy.config.CommonConfigurationMixin property)
AdminActions (class in galaxy.actions.admin)
AdminAppTestCase (class in galaxy_test.selenium.test_admin_app)
AdminConfigSerializer (class in galaxy.managers.configuration)
AdminController (class in tool_shed.webapp.controllers.admin)
AdminGalaxy (class in galaxy.webapps.galaxy.controllers.admin)
AdminRepositoryGrid (class in tool_shed.grids.admin_grids)
AdminRepositoryGrid.DeletedColumn (class in tool_shed.grids.admin_grids)
AdminRequiredException
admins() (galaxy.managers.users.UserManager method)
AdminToolshed (class in galaxy.webapps.galaxy.controllers.admin_toolshed)
AdminUserFilterParser (class in galaxy.managers.users)
AdminWorkflowsApiTestCase (class in galaxy_test.api.test_workflows)
Affybatch (class in galaxy.datatypes.genetics)
after_setting_metadata() (galaxy.datatypes.data.Data method)
aggressive_error_checks() (in module galaxy.tool_util.parser.stdio)
AliasPickleModule (class in galaxy.util.aliaspickler)
AliasUnpickler (class in galaxy.util.aliaspickler)
AlignCheck (class in galaxy.datatypes.mothur)
Alignment (class in galaxy.datatypes.sequence)
AlignReport (class in galaxy.datatypes.mothur)
all() (galaxy.selenium.smart_components.SmartTarget method)
all_control_queues_for_declare() (in module galaxy.queues)
all_entry_points_configured() (galaxy.model.Job property)
all_jobs (galaxy.model.view.HistoryDatasetCollectionJobStateSummary attribute)
all_requirements() (galaxy.tools.ToolBox property)
- (galaxy.webapps.galaxy.api.tools.ToolsController method)
all_roles() (galaxy.model.User method)
- (galaxy.schema.BootstrapAdminUser method)
- (tool_shed.webapp.model.User method)
all_roles_exploiting_cache() (galaxy.model.User method)
all_users() (galaxy.webapps.galaxy.controllers.userskeys.User method)
all_webhooks() (galaxy.webapps.galaxy.api.webhooks.WebhooksController method)
AllegroLOD (class in galaxy.datatypes.genetics)
allow_action() (galaxy.model.security.GalaxyRBACAgent method)
- (galaxy.model.security.HostAgent method)
- (tool_shed.webapp.security.CommunityRBACAgent method)
allow_action_on_libitems() (galaxy.model.security.GalaxyRBACAgent method)
allow_cors() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink property)
allow_datatype_change (galaxy.datatypes.data.Data attribute)
- (galaxy.datatypes.interval.BedStrict attribute)
allow_errored_inputs() (galaxy.tools.DatabaseOperationTool property)
allow_fetching_all_results (galaxy.web.legacy_framework.grids.Grid attribute)
- (tool_shed.grids.repository_grids.RepositoryGrid attribute)
- (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute)
allow_missing_tools (galaxy.managers.workflows.WorkflowUpdateOptions attribute)

allow_push() (tool_shed.webapp.model.Repository method)
allow_user_access() (galaxy.tools.DataManagerTool method)
- (galaxy.tools.Tool method)
allowed() (galaxy.web.framework.helpers.grids.GridOperation method)
- (galaxy.web.legacy_framework.grids.GridOperation method)
ALLOWED_DATA_SOURCE_ATTRIBUTES (galaxy.visualization.plugins.config_parser.DataSourceParser attribute)
ALLOWED_ENTRY_POINT_TYPES (galaxy.visualization.plugins.config_parser.VisualizationsConfigParser attribute)
allowed_middleware() (galaxy.web_stack.ApplicationStack method)
ALLOWED_MODEL_CLASSES (galaxy.visualization.plugins.config_parser.DataSourceParser attribute)
allowed_to_disconnect() (in module galaxy.authnz.psa_authnz)
already_executed() (galaxy.tool_util.verify.script.Results method)
already_successful() (galaxy.tool_util.verify.script.Results method)
alter_column() (in module galaxy.model.migrate.versions.util)
alter_config_and_load_prorietary_datatypes() (galaxy.tool_shed.galaxy_install.datatypes.custom_datatype_manager.CustomDatatypeLoader method)
AlwaysReject (class in galaxy.auth.providers.alwaysreject)
Amos (class in galaxy.datatypes.assembly)
amount() (galaxy.model.Quota property)
Analyze75 (class in galaxy.datatypes.images)
Anndata (class in galaxy.datatypes.binary)
AnnotatableDeserializerMixin (class in galaxy.managers.annotatable)
AnnotatableFilterMixin (class in galaxy.managers.annotatable)
AnnotatableManagerMixin (class in galaxy.managers.annotatable)
AnnotatableSerializerMixin (class in galaxy.managers.annotatable)
annotate() (galaxy.managers.annotatable.AnnotatableManagerMixin method)
annotate_async() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method)
- (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method)
annotation (galaxy.model.HistoryAnnotationAssociation attribute)
- (galaxy.model.HistoryDatasetAssociationAnnotationAssociation attribute)
- (galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation attribute)
- (galaxy.model.LibraryDatasetCollectionAnnotationAssociation attribute)
- (galaxy.model.PageAnnotationAssociation attribute)
- (galaxy.model.StoredWorkflowAnnotationAssociation attribute)
- (galaxy.model.VisualizationAnnotationAssociation attribute)
- (galaxy.model.WorkflowStepAnnotationAssociation attribute)
- (galaxy.workflow.refactor.schema.UpdateAnnotationAction attribute)
annotation() (galaxy.managers.annotatable.AnnotatableManagerMixin method)
- (galaxy.managers.hdas.HDAManager method)
annotation_assoc (galaxy.managers.annotatable.AnnotatableManagerMixin attribute)
- (galaxy.managers.hdas.HDAManager attribute)
- (galaxy.managers.hdcas.HDCAManager attribute)
- (galaxy.managers.histories.HistoryManager attribute)
- (galaxy.managers.pages.PageManager attribute)
- (galaxy.managers.visualizations.VisualizationManager attribute)
annotation_mapping() (in module galaxy.model.mapping)
annotations (galaxy.model.History attribute)
- (galaxy.model.HistoryDatasetAssociation attribute)
- (galaxy.model.HistoryDatasetCollectionAssociation attribute)
- (galaxy.model.LibraryDatasetCollectionAssociation attribute)
- (galaxy.model.Page attribute)
- (galaxy.model.StoredWorkflow attribute)
- (galaxy.model.Visualization attribute)
- (galaxy.model.WorkflowStep attribute)
anon_user_api_value() (galaxy.webapps.galaxy.api.users.UserAPIController method)
anonymous() (galaxy.managers.context.ProvidesUserContext property)
AnonymousHistoriesTestCase (class in galaxy_test.selenium.test_anon_history)
AnvioComposite (class in galaxy.datatypes.anvio)
AnvioContigsDB (class in galaxy.datatypes.anvio)
AnvioDB (class in galaxy.datatypes.anvio)
AnvioGenomesDB (class in galaxy.datatypes.anvio)
AnvioPanDB (class in galaxy.datatypes.anvio)
AnvioProfileDB (class in galaxy.datatypes.anvio)
AnvioSamplesDB (class in galaxy.datatypes.anvio)
AnvioStructureDB (class in galaxy.datatypes.anvio)
any_output_dataset_collection_instances_deleted (galaxy.model.Job attribute)
any_output_dataset_deleted (galaxy.model.Job attribute)
api_delete() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
api_error_message() (in module galaxy.web.framework.decorators)
api_get() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
api_interactor_for_logged_in_user() (galaxy_test.selenium.framework.TestWithSeleniumMixin method)
api_key() (galaxy.webapps.galaxy.api.users.UserAPIController method)
api_key_header() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method)
api_keys (galaxy.model.User attribute)
- (tool_shed.webapp.model.User attribute)
api_keys() (tool_shed.webapp.controllers.user.User method)
api_payload_to_create_params() (in module galaxy.managers.collections_util)
api_post() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
ApiBatchTestCase (class in galaxy_test.api.test_api_batch)
ApiFrameworkTestCase (class in galaxy_test.api.test_framework)
ApiKeyManager (class in galaxy.managers.api_keys)
APIKeys (class in galaxy.model)
- (class in tool_shed.webapp.model)
ApiTestInteractor (class in galaxy_test.base.api)
App (class in galaxy.config.config_manage)
app_factory() (in module galaxy.web.buildapp)
- (in module galaxy.webapps.galaxy.buildapp)
- (in module galaxy.webapps.reports.buildapp)
- (in module tool_shed.webapp.buildapp)
app_kwds() (galaxy.main.GalaxyConfigBuilder method)
app_loop() (in module galaxy.main)
app_name() (galaxy.config.config_manage.App property)
app_properties_from_args() (in module galaxy.util.script)
appconfig() (in module galaxy.util.pastescript.loadwsgi)
append() (galaxy.datatypes.metadata.MetadataSpecCollection method)
- (galaxy.model.custom_types.MutationList method)
- (galaxy.model.metadata.MetadataSpecCollection method)
- (galaxy.tool_util.deps.requirements.ToolRequirements method)
append_line() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder.EnvFileBuilder method)
append_section() (galaxy.tools.toolbox.panel.ToolPanelElements method)
append_tool() (galaxy.tools.toolbox.panel.ToolPanelElements method)
AppInfo (class in galaxy.tool_util.deps.dependencies)
application (galaxy.web.framework.middleware.batch.BatchMiddleware attribute)
- (galaxy.web.framework.middleware.sqldebug.SQLDebugMiddleware attribute)
application_stack_class() (in module galaxy.web_stack)
application_stack_instance() (in module galaxy.web_stack)
application_stack_log_filter() (in module galaxy.web_stack)
application_stack_log_formatter() (in module galaxy.web_stack)
ApplicationStack (class in galaxy.web_stack)
ApplicationStackLogFilter (class in galaxy.web_stack)
ApplicationStackMessage (class in galaxy.web_stack.message)
ApplicationStackMessageDispatcher (class in galaxy.web_stack.message)
ApplicationStackTransport (class in galaxy.web_stack.transport)
apply() (galaxy.tool_util.deps.resolvers.RequirementMapping method)
- (galaxy.util.rules_dsl.AddColumnBasenameRuleDefinition method)
- (galaxy.util.rules_dsl.AddColumnConcatenateRuleDefinition method)
- (galaxy.util.rules_dsl.AddColumnGroupTagValueRuleDefinition method)
- (galaxy.util.rules_dsl.AddColumnMetadataRuleDefinition method)
- (galaxy.util.rules_dsl.AddColumnRegexRuleDefinition method)
- (galaxy.util.rules_dsl.AddColumnRownumRuleDefinition method)
- (galaxy.util.rules_dsl.AddColumnSubstrRuleDefinition method)
- (galaxy.util.rules_dsl.AddColumnValueRuleDefinition method)
- (galaxy.util.rules_dsl.AddFilterCompareRuleDefinition method)
- (galaxy.util.rules_dsl.AddFilterCountRuleDefinition method)
- (galaxy.util.rules_dsl.AddFilterEmptyRuleDefinition method)
- (galaxy.util.rules_dsl.AddFilterMatchesRuleDefinition method)
- (galaxy.util.rules_dsl.AddFilterRegexRuleDefinition method)
- (galaxy.util.rules_dsl.BaseRuleDefinition method)
- (galaxy.util.rules_dsl.RemoveColumnsRuleDefinition method)
- (galaxy.util.rules_dsl.RuleSet method)
- (galaxy.util.rules_dsl.SortRuleDefinition method)
- (galaxy.util.rules_dsl.SplitColumnsRuleDefinition method)
- (galaxy.util.rules_dsl.SwapColumnsRuleDefinition method)
apply_action() (galaxy.tool_util.parser.output_actions.FormatToolOutputAction method)
- (galaxy.tool_util.parser.output_actions.MetadataToolOutputAction method)
- (galaxy.tool_util.parser.output_actions.ToolOutputAction method)
- (galaxy.tool_util.parser.output_actions.ToolOutputActionConditional method)
- (galaxy.tool_util.parser.output_actions.ToolOutputActionConditionalWhen method)
- (galaxy.tool_util.parser.output_actions.ToolOutputActionGroup method)
apply_item_tag() (galaxy.model.tags.TagHandler method)
apply_item_tags() (galaxy.model.tags.TagHandler method)
apply_preferences() (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method)
apply_query_filter() (galaxy.web.framework.helpers.grids.Grid method)
- (galaxy.web.legacy_framework.grids.Grid method)
- (galaxy.webapps.galaxy.controllers.admin.RoleListGrid method)
- (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid method)
- (galaxy.webapps.galaxy.controllers.history.HistoryListGrid method)
- (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid method)
- (galaxy.webapps.galaxy.controllers.page.HistoryDatasetAssociationSelectionGrid method)
- (galaxy.webapps.galaxy.controllers.page.HistorySelectionGrid method)
- (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid method)
- (galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid method)
- (galaxy.webapps.galaxy.controllers.page.PageListGrid method)
- (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid method)
- (galaxy.webapps.galaxy.controllers.visualization.LibraryDatasetsSelectionGrid method)
- (galaxy.webapps.galaxy.controllers.visualization.TracksterSelectionGrid method)
- (galaxy.webapps.galaxy.controllers.visualization.VisualizationAllPublishedGrid method)
- (galaxy.webapps.galaxy.controllers.visualization.VisualizationListGrid method)
- (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid method)
- (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid method)
- (tool_shed.grids.admin_grids.RoleGrid method)
apply_regex() (in module galaxy.util.rules_dsl)
apply_rules() (galaxy.managers.collections.DatasetCollectionManager method)
ApplyRulesTool (class in galaxy.tools)
approve_repository_review() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method)
approved (tool_shed.webapp.model.ComponentReview attribute)
- (tool_shed.webapp.model.RepositoryReview attribute)
approved_states (tool_shed.webapp.model.ComponentReview attribute)
- (tool_shed.webapp.model.RepositoryReview attribute)
AppSchema (class in galaxy.config.schema)
archive() (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method)
archive_dir (galaxy.model.JobImportHistoryArchive attribute)
archive_download() (galaxy.webapps.galaxy.api.histories.HistoriesController method)
archive_export() (galaxy.webapps.galaxy.api.histories.HistoriesController method)
archive_repository_revision() (in module tool_shed.util.hg_util)
Arff (class in galaxy.datatypes.text)
arg_parser() (in module galaxy.tool_util.verify.script)
argv_to_str() (in module galaxy.util.commands)
artifact_class() (in module galaxy.managers.executables)
as_css_class() (galaxy.selenium.components.SelectorTemplate property)
as_dict() (galaxy.model.tool_shed_install.ToolShedRepository method)
- (galaxy.util.simplegraph.SimpleGraph method)
as_display_type() (galaxy.datatypes.data.Data method)
- (galaxy.model.DatasetInstance method)
as_gbrowse_display_file() (galaxy.datatypes.tabular.Tabular method)
as_ucsc_display_file() (galaxy.datatypes.genetics.GenomeGraphs method)
- (galaxy.datatypes.interval.Bed method)
- (galaxy.datatypes.interval.BedGraph method)
- (galaxy.datatypes.interval.Interval method)
- (galaxy.datatypes.tabular.Tabular method)
as_xml() (galaxy.webapps.galaxy.controllers.history.HistoryController method)
asbool() (in module galaxy.util)
assemble_current_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method)
assert_absent() (galaxy.selenium.has_driver.HasDriver method)
- (galaxy.selenium.smart_components.SmartTarget method)
assert_absent_or_hidden() (galaxy.selenium.has_driver.HasDriver method)
- (galaxy.selenium.smart_components.SmartTarget method)
assert_absent_or_hidden_after_transitions() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
- (galaxy.selenium.smart_components.SmartTarget method)
assert_attribute_is() (in module galaxy.tool_util.verify.asserts.xml)
assert_attribute_matches() (in module galaxy.tool_util.verify.asserts.xml)
assert_connected() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method)
assert_custom_builds_in_grid() (galaxy_test.selenium.test_custom_builds.CustomBuildsTestcase method)
assert_directory_executable() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertDirectoryExecutable method)
assert_directory_exists() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertDirectoryExists method)
assert_element_text() (in module galaxy.tool_util.verify.asserts.xml)
assert_element_text_is() (in module galaxy.tool_util.verify.asserts.xml)
assert_element_text_matches() (in module galaxy.tool_util.verify.asserts.xml)
assert_error_code_is() (in module galaxy_test.base.api_asserts)
assert_error_message() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
assert_error_message_contains() (in module galaxy_test.base.api_asserts)
assert_file_executable() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertFileExecutable method)
assert_file_exists() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.AssertFileExists method)
assert_finalized() (galaxy.tools.Tool method)
assert_grid_histories_are() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method)
- (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase method)
assert_grid_histories_sorted_by_owner() (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase method)
assert_has_archive_member() (in module galaxy.tool_util.verify.asserts.archive)
assert_has_changes_and_save() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method)
assert_has_element_with_path() (in module galaxy.tool_util.verify.asserts.xml)
assert_has_h5_attribute() (in module galaxy.tool_util.verify.asserts.hdf5)
assert_has_h5_keys() (in module galaxy.tool_util.verify.asserts.hdf5)
assert_has_key() (in module galaxy_test.base.api_asserts)
assert_has_keys() (in module galaxy_test.base.api_asserts)
assert_has_line() (in module galaxy.tool_util.verify.asserts.text)
assert_has_line_matching() (in module galaxy.tool_util.verify.asserts.text)
assert_has_n_columns() (in module galaxy.tool_util.verify.asserts.tabular)
assert_has_n_elements_with_path() (in module galaxy.tool_util.verify.asserts.xml)
assert_has_n_lines() (in module galaxy.tool_util.verify.asserts.text)
assert_has_size() (in module galaxy.tool_util.verify.asserts.size)
assert_has_text() (in module galaxy.tool_util.verify.asserts.text)
assert_has_text_matching() (in module galaxy.tool_util.verify.asserts.text)
assert_hashes_initialized() (galaxy.tools.cache.ToolCache method)
assert_histories_in_grid() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method)
- (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase method)
assert_history() (galaxy_test.selenium.test_history_multi_view.HistoryMultiViewTestCase method)
assert_initial_history_panel_state_correct() (galaxy_test.selenium.framework.TestWithSeleniumMixin method)
assert_input_mapped() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method)
assert_input_not_mapped() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method)
assert_is_valid_xml() (in module galaxy.tool_util.verify.asserts.xml)
assert_item_dbkey_displayed_as() (galaxy_test.selenium.framework.UsesHistoryItemAssertions method)
assert_item_hid_text() (galaxy_test.selenium.framework.UsesHistoryItemAssertions method)
assert_item_info_includes() (galaxy_test.selenium.framework.UsesHistoryItemAssertions method)
assert_item_name() (galaxy_test.selenium.framework.UsesHistoryItemAssertions method)
assert_item_peek_includes() (galaxy_test.selenium.framework.UsesHistoryItemAssertions method)
assert_item_summary_includes() (galaxy_test.selenium.framework.UsesHistoryItemAssertions method)
assert_message() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
assert_modal_has_text() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method)
assert_no_error_message() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
assert_not_connected() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method)
assert_not_has_keys() (in module galaxy_test.base.api_asserts)
assert_not_has_text() (in module galaxy.tool_util.verify.asserts.text)
assert_object_id_error() (in module galaxy_test.base.api_asserts)
assert_selector() (galaxy.selenium.has_driver.HasDriver method)
assert_selector_absent() (galaxy.selenium.has_driver.HasDriver method)
assert_selector_absent_or_hidden() (galaxy.selenium.has_driver.HasDriver method)
assert_selector_absent_or_hidden_after_transitions() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
assert_status_code_is() (in module galaxy_test.base.api_asserts)
assert_status_code_is_ok() (in module galaxy_test.base.api_asserts)
assert_throws_param_value_error() (in module galaxy.tools.parameters.basic)
assert_tooltip_text() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
assert_warning_message() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
assert_wf_annotation_is() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method)
assert_wf_name_is() (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase method)
assert_xpath() (galaxy.selenium.has_driver.HasDriver method)
AssertDirectoryExecutable (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler)
AssertDirectoryExists (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler)
AssertFileExecutable (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler)
AssertFileExists (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler)
assign_admin_role() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
assign_handler() (galaxy.web_stack.handlers.ConfiguresHandlers method)
assoc_type (galaxy.model.PSAAssociation attribute)
- (galaxy.model.UserAuthnzToken attribute)
associate() (galaxy.managers.base.ModelManager method)
associate_action_dataset_role() (galaxy.model.security.GalaxyRBACAgent method)
associate_components() (galaxy.model.security.GalaxyRBACAgent method)
- (galaxy.security.RBACAgent method)
- (tool_shed.webapp.security.CommunityRBACAgent method)
- (tool_shed.webapp.security.RBACAgent method)
associate_group_role() (galaxy.model.security.GalaxyRBACAgent method)
- (tool_shed.webapp.security.CommunityRBACAgent method)
associate_repository_category() (tool_shed.webapp.security.CommunityRBACAgent method)
associate_user_group() (galaxy.model.security.GalaxyRBACAgent method)
- (tool_shed.webapp.security.CommunityRBACAgent method)
associate_user_role() (galaxy.model.security.GalaxyRBACAgent method)
- (tool_shed.webapp.security.CommunityRBACAgent method)
- (tool_shed.webapp.security.RBACAgent method)
association (galaxy.authnz.psa_authnz.Storage attribute)
ASync (class in galaxy.webapps.galaxy.controllers.async)
async_template (galaxy.web.legacy_framework.grids.Grid attribute)
AsyncDataSourceTool (class in galaxy.tools)
AsynchronousJobRunner (class in galaxy.jobs.runners)
AsynchronousJobState (class in galaxy.jobs.runners)
AsynchronousReader (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader)
attach_identifier() (galaxy.model.SerializationOptions method)
attach_ordered_steps() (in module galaxy.workflow.steps)
attach_stored_workflow() (galaxy.managers.workflows.WorkflowsManager method)
attach_subworkflow_invocation_for_step() (galaxy.model.WorkflowInvocation method)
attempt_create_private_role() (galaxy.model.User method)
attempt_unlink() (in module galaxy.tool_util.deps.brew_exts)
attempt_unlink_all() (in module galaxy.tool_util.deps.brew_exts)
ATTRIBUTE_SPLIT_CHAR (galaxy.visualization.plugins.config_parser.DataSourceParser attribute)
AttributeValueSplitterFilter (class in galaxy.tools.parameters.dynamic_options)
ATTRS_FILENAME_HISTORY (galaxy.model.JobExportHistoryArchive attribute)
Audio (class in galaxy.datatypes.media)
augment_tool_state_for_input_connections() (galaxy.workflow.modules.ToolModule method)
Augustus (class in galaxy.datatypes.annotation)
AUTH_TUPLE (in module galaxy.tool_shed.tool_shed_registry)
authenticate() (galaxy.auth.providers.alwaysreject.AlwaysReject method)
- (galaxy.auth.providers.AuthProvider method)
- (galaxy.auth.providers.ldap_ad.LDAP method)
- (galaxy.auth.providers.localdb.LocalDB method)
- (galaxy.auth.providers.pam_auth.PAM method)
- (galaxy.authnz.custos_authnz.CustosAuthnz method)
- (galaxy.authnz.IdentityProvider method)
- (galaxy.authnz.managers.AuthnzManager method)
- (galaxy.authnz.psa_authnz.PSAAuthnz method)
authenticate_user() (galaxy.auth.providers.alwaysreject.AlwaysReject method)
- (galaxy.auth.providers.AuthProvider method)
- (galaxy.auth.providers.ldap_ad.LDAP method)
- (galaxy.auth.providers.localdb.LocalDB method)
- (galaxy.auth.providers.pam_auth.PAM method)
AuthenticationApiTestCase (class in galaxy_test.api.test_authenticate)
AuthenticationController (class in galaxy.webapps.galaxy.api.authenticate)
AuthenticationFailed
AuthenticationRequired
AuthenticationToken (class in galaxy.web.proxy)
Authenticator (class in galaxy.auth.util)
AuthManager (class in galaxy.auth)
authn (galaxy.model.CloudAuthz attribute)
authn_id (galaxy.model.CloudAuthz attribute)
AuthnzManager (class in galaxy.authnz.managers)
AuthProvider (class in galaxy.auth.providers)
auto_propagated_tags() (galaxy.model.HasTags property)
Autoconf (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler)
available_roles() (galaxy.managers.datasets.DatasetRBACPermissions method)
available_tracks (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid attribute)
- (galaxy.webapps.galaxy.controllers.visualization.LibraryDatasetsSelectionGrid attribute)
average_rating (galaxy.model.History attribute)
- (galaxy.model.Page attribute)
- (galaxy.model.StoredWorkflow attribute)
- (galaxy.model.Visualization attribute)
avg() (galaxy.job_metrics.collectl.stats.StatisticsTracker property)
Axes (class in galaxy.datatypes.mothur)
Axt (class in galaxy.datatypes.sequence)
AzureBlobObjectStore (class in galaxy.objectstore.azure_blob)

B

backdrop (galaxy.tours.TourStep attribute)
backend (galaxy.model.PSAPartial attribute)
BadCommand
BadValue (class in galaxy.tools)
BafTar (class in galaxy.datatypes.binary)
BagArchiveImportModelStore (class in galaxy.model.store)
BagArchiveModelExportStore (class in galaxy.model.store)
BagDirectoryModelExportStore (class in galaxy.model.store)
Bam (class in galaxy.datatypes.binary)
BamDataProvider (class in galaxy.visualization.data_providers.genome)
BamInputSorted (class in galaxy.datatypes.binary)
BamNative (class in galaxy.datatypes.binary)
BamQuerynameSorted (class in galaxy.datatypes.binary)
bare_ampersand (galaxy.managers.pages.PageContentProcessor attribute)
base (galaxy.web.framework.base.Request attribute)
Base64ChunkDataProvider (class in galaxy.datatypes.dataproviders.chunk)
base_dataprovider() (galaxy.datatypes.data.Data method)
base_docker_cmd() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method)
Base_Parser (class in galaxy.visualization.data_providers.phyloviz.baseparser)
BASE_URL (galaxy.visualization.plugins.registry.VisualizationsRegistry attribute)
BaseAction (class in galaxy.workflow.refactor.schema)
BaseAnnotationsController (class in galaxy.webapps.galaxy.api.annotations)
BaseAPIController (class in galaxy.webapps.base.controller)
BaseAppConfiguration (class in galaxy.config)
BaseBcf (class in galaxy.datatypes.binary)
BaseCitation (class in galaxy.managers.citations)
BaseController (class in galaxy.webapps.base.controller)
BaseCSV (class in galaxy.datatypes.tabular)
BaseDataProvider (class in galaxy.visualization.data_providers.basic)
BaseDatasetCollectionPopulator (class in galaxy_test.base.populators)
BaseDatasetCollectionType (class in galaxy.model.dataset_collections.types)
BaseDatasetPopulator (class in galaxy_test.base.populators)
BaseDataToolParameter (class in galaxy.tools.parameters.basic)
BaseDirectoryImportModelStore (class in galaxy.model.store)
BaseExtendedMetadataController (class in galaxy.webapps.galaxy.api.extended_metadata)
BaseFastq (class in galaxy.datatypes.sequence)
BaseField (class in galaxy.util.form_builder)
- (class in galaxy.web.form_builder)
BaseFilesSource (class in galaxy.files.sources)
BaseGalaxyToolBox (class in galaxy.tools.toolbox)
- (class in galaxy.tools.toolbox.base)
BaseGitPlugin (class in galaxy.tools.error_reports.plugins.base_git)
BaseHistories (class in galaxy_test.api.test_histories)
BaseItemTagsController (class in galaxy.webapps.galaxy.api.item_tags)
BaseJobContext (class in galaxy.job_execution.output_collect)
BaseJobExec (class in galaxy.jobs.runners.util.cli.job)
BaseJobMetric (class in galaxy.model)
BaseJobRunner (class in galaxy.jobs.runners)
BaseJsonToolParameter (class in galaxy.tools.parameters.basic)
BaseObjectStore (class in galaxy.objectstore)
BasePageApiTestCase (class in galaxy_test.api.test_pages)
BaseParamParser (class in galaxy.web.params)
BaseProvenanceController (class in galaxy.webapps.galaxy.api.provenance)
BaseRuleDefinition (class in galaxy.util.rules_dsl)
bases_regexp (galaxy.datatypes.sequence.BaseFastq attribute)
- (galaxy.datatypes.sequence.FastqCSSanger attribute)
- (galaxy.datatypes.sequence.FastqSanger attribute)
BaseShellExec (class in galaxy.jobs.runners.util.cli.shell)
basestring() (galaxy.managers.base.ModelValidator method)
basestring_list() (galaxy.managers.base.ModelValidator method)
BaseToolProvidedMetadata (class in galaxy.tool_util.provided_metadata)
BaseTree (class in galaxy.model.dataset_collections.structure)
BaseUIController (class in galaxy.webapps.base.controller)
BaseUploadToolAction (class in galaxy.tools.actions.upload)
BaseURLToolParameter (class in galaxy.tools.parameters.basic)
BaseVcf (class in galaxy.datatypes.tabular)
BaseWatcher (class in galaxy.util.watcher)
BaseWorkflowPopulator (class in galaxy_test.base.populators)
BaseWorkflowsApiTestCase (class in galaxy_test.api.test_workflows)
BasicToolShedFeatures (class in tool_shed.test.functional.test_1000_install_basic_repository)
BatchMiddleware (class in galaxy.web.framework.middleware.batch)
BBIDataProvider (class in galaxy.visualization.data_providers.genome)
Bcf (class in galaxy.datatypes.binary)
BcfUncompressed (class in galaxy.datatypes.binary)
Bed (class in galaxy.datatypes.interval)
Bed12 (class in galaxy.datatypes.interval)
Bed6 (class in galaxy.datatypes.interval)
BedDataProvider (class in galaxy.visualization.data_providers.genome)
BedGraph (class in galaxy.datatypes.interval)
BedStrict (class in galaxy.datatypes.interval)
BedTabixDataProvider (class in galaxy.visualization.data_providers.genome)
before_get() (galaxy.util.properties.NicerConfigParser.InterpolateWrapper method)
before_setting_metadata() (galaxy.datatypes.data.Data method)
BIBTEX_UNSET (galaxy.managers.citations.DoiCitation attribute)
BibtexCitation (class in galaxy.managers.citations)
big_peek_size (galaxy.datatypes.tabular.BaseCSV attribute)
BigBed (class in galaxy.datatypes.binary)
BigBedDataProvider (class in galaxy.visualization.data_providers.genome)
BigWig (class in galaxy.datatypes.binary)
BigWigDataProvider (class in galaxy.datatypes.dataproviders.dataset)
- (class in galaxy.visualization.data_providers.genome)
Binary (class in galaxy.datatypes.binary)
bind_all_addrs (galaxy.web_stack.UWSGIApplicationStack attribute)
bind_and_start() (galaxy.queue_worker.GalaxyQueueWorker method)
bind_default_handler() (galaxy.web_stack.message.ApplicationStackMessage method)
Biom1 (class in galaxy.datatypes.text)
Biom2 (class in galaxy.datatypes.binary)
biomart() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method)
BlastDomainDb (class in galaxy.datatypes.blast)
BlastDomainDb5 (class in galaxy.datatypes.blast)
BlastNucDb (class in galaxy.datatypes.blast)
BlastNucDb5 (class in galaxy.datatypes.blast)
BlastProtDb (class in galaxy.datatypes.blast)
BlastProtDb5 (class in galaxy.datatypes.blast)
BlastXml (class in galaxy.datatypes.blast)
BlibSQlite (class in galaxy.datatypes.binary)
BlockDataProvider (class in galaxy.datatypes.dataproviders.line)
blurb (galaxy.datatypes.media.Wav attribute)
- (galaxy.datatypes.proteomics.ConsensusXML attribute)
- (galaxy.datatypes.proteomics.FeatureXML attribute)
- (galaxy.datatypes.proteomics.IdXML attribute)
- (galaxy.datatypes.proteomics.MascotXML attribute)
- (galaxy.datatypes.proteomics.MzData attribute)
- (galaxy.datatypes.proteomics.MzIdentML attribute)
- (galaxy.datatypes.proteomics.MzML attribute)
- (galaxy.datatypes.proteomics.MzQuantML attribute)
- (galaxy.datatypes.proteomics.MzXML attribute)
- (galaxy.datatypes.proteomics.NmrML attribute)
- (galaxy.datatypes.proteomics.ParamXml attribute)
- (galaxy.datatypes.proteomics.PepXml attribute)
- (galaxy.datatypes.proteomics.ProtXML attribute)
- (galaxy.datatypes.proteomics.QCML attribute)
- (galaxy.datatypes.proteomics.TandemXML attribute)
- (galaxy.datatypes.proteomics.TrafoXML attribute)
- (galaxy.datatypes.proteomics.TraML attribute)
- (galaxy.datatypes.proteomics.UniProtXML attribute)
- (galaxy.datatypes.proteomics.XquestSpecXML attribute)
- (galaxy.datatypes.proteomics.XquestXML attribute)
- (galaxy.datatypes.speech.TextGrid attribute)
- (galaxy.model.HistoryDatasetAssociation attribute)
- (galaxy.model.LibraryDatasetDatasetAssociation attribute)
Bmp (class in galaxy.datatypes.images)
body_renderer() (galaxy.web.framework.middleware.batch.BatchMiddleware method)
bookmarks_from_dataset() (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method)
bool() (galaxy.managers.base.ModelValidator method)
BOOLEAN (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute)
boolean_false() (in module tool_shed.webapp.model.migrate.versions.0013_add_review_tables)
- (in module tool_shed.webapp.model.migrate.versions.0022_add_repository_admin_roles)
BooleanColumn (class in galaxy.web.framework.helpers.grids)
- (class in galaxy.web.legacy_framework.grids)
BooleanFilter (class in galaxy.tool_util.parser.output_actions)
BooleanToolParameter (class in galaxy.tools.parameters.basic)
BoolOptionParser (class in galaxy.util.pastescript.serve)
bootstrap_admin_user (galaxy.model.User attribute)
- (tool_shed.webapp.model.User attribute)
BootstrapAdminUser (class in galaxy.schema)
BoundCollectionBuilder (class in galaxy.model.dataset_collections.builder)
BowtieBaseIndex (class in galaxy.datatypes.ngsindex)
BowtieColorIndex (class in galaxy.datatypes.ngsindex)
BowtieIndex (class in galaxy.datatypes.ngsindex)
BPF (class in galaxy.datatypes.speech)
brew_deps() (in module galaxy.tool_util.deps.brew_exts)
brew_execute() (in module galaxy.tool_util.deps.brew_exts)
brew_head_at_commit() (in module galaxy.tool_util.deps.brew_exts)
brew_head_at_version() (in module galaxy.tool_util.deps.brew_exts)
brew_info() (in module galaxy.tool_util.deps.brew_exts)
brew_versions_info() (in module galaxy.tool_util.deps.brew_exts)
BrewContext (class in galaxy.tool_util.deps.brew_exts)
browse_categories() (tool_shed.webapp.controllers.repository.RepositoryController method)
browse_category() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
browse_component_review() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
browse_components() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method)
browse_custom_datatypes() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
browse_datatypes() (tool_shed.webapp.controllers.repository.RepositoryController method)
browse_deprecated_repositories_i_own() (tool_shed.webapp.controllers.repository.RepositoryController method)
browse_my_writable_repositories() (tool_shed.webapp.controllers.repository.RepositoryController method)
browse_my_writable_repositories_missing_tool_test_components() (tool_shed.webapp.controllers.repository.RepositoryController method)
browse_my_writable_repositories_with_invalid_tools() (tool_shed.webapp.controllers.repository.RepositoryController method)
browse_repositories() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method)
- (tool_shed.webapp.controllers.admin.AdminController method)
- (tool_shed.webapp.controllers.repository.RepositoryController method)
browse_repositories_by_user() (tool_shed.webapp.controllers.repository.RepositoryController method)
browse_repositories_i_can_administer() (tool_shed.webapp.controllers.repository.RepositoryController method)
browse_repositories_i_own() (tool_shed.webapp.controllers.repository.RepositoryController method)
browse_repositories_in_category() (tool_shed.webapp.controllers.repository.RepositoryController method)
browse_repositories_missing_tool_test_components() (tool_shed.webapp.controllers.repository.RepositoryController method)
browse_repositories_with_invalid_tools() (tool_shed.webapp.controllers.repository.RepositoryController method)
browse_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
- (tool_shed.webapp.controllers.repository.RepositoryController method)
browse_repository_dependencies() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
- (tool_shed.webapp.controllers.repository.RepositoryController method)

browse_repository_metadata() (tool_shed.webapp.controllers.admin.AdminController method)
browse_review() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method)
browse_tool_dependencies() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
- (tool_shed.webapp.controllers.repository.RepositoryController method)
browse_tool_shed() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
browse_tools() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
- (tool_shed.webapp.controllers.repository.RepositoryController method)
browse_valid_categories() (tool_shed.webapp.controllers.repository.RepositoryController method)
browse_valid_repositories() (tool_shed.webapp.controllers.repository.RepositoryController method)
browser_url (galaxy.web.framework.base.Request attribute)
bucket_proxy() (galaxy.webapps.galaxy.controllers.root.RootController method)
build() (galaxy.model.dataset_collections.builder.CollectionBuilder method)
- (galaxy.tool_util.deps.mulled.util.Target property)
- (galaxy.tools.evaluation.ToolEvaluator method)
- (galaxy.tools.parameters.basic.ToolParameter class method)
- (galaxy.webapps.galaxy.api.tools.ToolsController method)
build_absolute_uri() (galaxy.authnz.psa_authnz.Strategy method)
build_approved_select_field() (in module tool_shed.grids.util)
build_cache() (galaxy.tool_util.deps.CachedDependencyManager method)
build_case_references() (in module galaxy.tool_util.verify.script)
build_changeset_revision_select_field() (in module tool_shed.grids.util)
build_cli_interface() (in module galaxy.jobs.runners.util.cli.factory)
build_collection() (in module galaxy.model.dataset_collections.builder)
build_command() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method)
- (in module galaxy.jobs.command_factory)
- (in module galaxy.tool_util.deps.docker_util)
build_command_line() (galaxy.job_metrics.collectl.cli.CollectlCli method)
- (galaxy.jobs.runners.BaseJobRunner method)
build_command_list() (galaxy.datatypes.dataproviders.dataset.SamtoolsDataProvider method)
build_container_interfaces() (in module galaxy.containers)
build_data_managers_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method)
build_datatypes_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method)
build_dependency_cache() (galaxy.tools.Tool method)
- (galaxy.webapps.galaxy.api.tools.ToolsController method)
build_dependency_manager() (in module galaxy.tool_util.deps)
build_dependency_shell_commands() (galaxy.tools.Tool method)
build_docker_cache_command() (in module galaxy.tool_util.deps.docker_util)
build_docker_images_command() (in module galaxy.tool_util.deps.docker_util)
build_docker_load_command() (in module galaxy.tool_util.deps.docker_util)
build_docker_run_command() (in module galaxy.tool_util.deps.docker_util)
build_docker_simple_command() (in module galaxy.tool_util.deps.docker_util)
build_drop_trigger() (in module galaxy.model.triggers)
build_elements() (galaxy.model.dataset_collections.builder.CollectionBuilder method)
build_engine() (in module galaxy.model.orm.engine_factory)
build_env() (galaxy.tool_util.deps.brew_exts.EnvAction static method)
build_env_actions() (in module galaxy.tool_util.deps.brew_exts)
build_env_statements() (in module galaxy.tool_util.deps.brew_exts)
build_env_statements_from_recipe_context() (in module galaxy.tool_util.deps.brew_exts)
build_filter_function() (galaxy.tools.toolbox.filters.FilterFactory method)
build_filters() (galaxy.tools.toolbox.filters.FilterFactory method)
build_for_rerun() (galaxy.webapps.galaxy.api.jobs.JobController method)
build_from_current_history() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method)
build_index() (galaxy.tool_util.deps.mulled.mulled_search.QuaySearch method)
- (galaxy.tools.search.ToolBoxSearch method)
- (in module tool_shed.util.shed_index)
build_initial_query() (galaxy.web.framework.helpers.grids.Grid method)
- (galaxy.web.legacy_framework.grids.Grid method)
- (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid method)
- (galaxy.webapps.galaxy.controllers.forms.FormsGrid method)
- (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid method)
- (galaxy.webapps.galaxy.controllers.history.HistoryListGrid method)
- (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid method)
- (galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid method)
- (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid method)
- (galaxy.webapps.galaxy.controllers.visualization.LibraryDatasetsSelectionGrid method)
- (galaxy.webapps.galaxy.controllers.visualization.TracksterSelectionGrid method)
- (galaxy.webapps.galaxy.controllers.visualization.VisualizationAllPublishedGrid method)
- (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid method)
- (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid method)
- (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid method)
- (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid method)
- (tool_shed.grids.admin_grids.AdminRepositoryGrid method)
- (tool_shed.grids.admin_grids.RepositoryMetadataGrid method)
- (tool_shed.grids.repository_grids.DatatypesGrid method)
- (tool_shed.grids.repository_grids.DeprecatedRepositoriesIOwnGrid method)
- (tool_shed.grids.repository_grids.MatchedRepositoryGrid method)
- (tool_shed.grids.repository_grids.MyWritableRepositoriesGrid method)
- (tool_shed.grids.repository_grids.MyWritableRepositoriesMissingToolTestComponentsGrid method)
- (tool_shed.grids.repository_grids.MyWritableRepositoriesWithInvalidToolsGrid method)
- (tool_shed.grids.repository_grids.RepositoriesByUserGrid method)
- (tool_shed.grids.repository_grids.RepositoriesICanAdministerGrid method)
- (tool_shed.grids.repository_grids.RepositoriesInCategoryGrid method)
- (tool_shed.grids.repository_grids.RepositoriesIOwnGrid method)
- (tool_shed.grids.repository_grids.RepositoriesMissingToolTestComponentsGrid method)
- (tool_shed.grids.repository_grids.RepositoriesWithInvalidToolsGrid method)
- (tool_shed.grids.repository_grids.RepositoryDependenciesGrid method)
- (tool_shed.grids.repository_grids.RepositoryGrid method)
- (tool_shed.grids.repository_grids.RepositoryMetadataGrid method)
- (tool_shed.grids.repository_grids.ToolDependenciesGrid method)
- (tool_shed.grids.repository_grids.ToolsGrid method)
- (tool_shed.grids.repository_grids.ValidRepositoryGrid method)
- (tool_shed.grids.repository_review_grids.RepositoriesReadyForReviewGrid method)
- (tool_shed.grids.repository_review_grids.RepositoriesReviewedByMeGrid method)
- (tool_shed.grids.repository_review_grids.RepositoriesWithNoToolTestsGrid method)
- (tool_shed.grids.repository_review_grids.RepositoriesWithoutReviewsGrid method)
- (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid method)
- (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid method)
- (tool_shed.grids.repository_review_grids.ReviewedRepositoriesIOwnGrid method)
build_invalid_data_managers_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method)
build_invalid_repository_dependencies_root_folder() (tool_shed.utility_containers.ToolShedUtilityContainerManager method)
build_invalid_tool_dependencies_root_folder() (tool_shed.utility_containers.ToolShedUtilityContainerManager method)
build_invalid_tools_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method)
build_invocations_query() (galaxy.managers.workflows.WorkflowsManager method)
build_logger() (in module galaxy_test.driver.driver_util)
build_maf_index() (in module galaxy.datatypes.util.maf_utilities)
- (in module galaxy.tools.util.maf_utilities)
build_maf_index_species_chromosomes() (in module galaxy.datatypes.util.maf_utilities)
- (in module galaxy.tools.util.maf_utilities)
build_module() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method)
build_mulled_singularity_pull_command() (galaxy.tool_util.deps.container_classes.SingularityContainer method)
build_native_uwsgi_app() (in module galaxy.webapps.base.webapp)
build_object_store_from_config() (in module galaxy.objectstore)
build_param_dict() (galaxy.tools.evaluation.ToolEvaluator method)
build_parameter_dict() (galaxy.datatypes.display_applications.application.DisplayApplicationLink method)
build_path() (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method)
build_pg_timestamp_fn() (in module galaxy.model.triggers)
build_pg_trigger() (in module galaxy.model.triggers)
build_pull_command() (galaxy.tool_util.deps.container_classes.DockerContainer method)
- (in module galaxy.tool_util.deps.docker_util)
build_readme_files_dict() (in module tool_shed.util.readme_util)
build_readme_files_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method)
build_redirect_url_params() (galaxy.tools.Tool method)
build_repository_containers() (tool_shed.galaxy_install.utility_containers.GalaxyUtilityContainerManager method)
- (tool_shed.utility_containers.ToolShedUtilityContainerManager method)
build_repository_dependencies_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method)
build_repository_dependency_relationships() (galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method)
build_repository_ids_select_field() (galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager.InstalledRepositoryMetadataManager method)
- (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method)
build_repository_type_select_field() (in module tool_shed.repository_types.util)
build_resolver() (in module galaxy.tool_util.verify.test_data)
build_save_image_command() (in module galaxy.tool_util.deps.docker_util)
build_select_input() (in module galaxy.webapps.galaxy.controllers.admin)
build_shed_tool_conf_select_field() (in module galaxy.tool_shed.util.tool_util)
build_singularity_run_command() (in module galaxy.tool_util.deps.singularity_util)
build_sniff_from_prefix() (in module galaxy.datatypes.sniff)
build_state_handlers() (in module galaxy.jobs.runners.state_handler_factory)
build_submit_description() (in module galaxy.jobs.runners.util.condor)
build_target() (in module galaxy.tool_util.deps.mulled.util)
build_template_error_formatters() (in module galaxy.webapps.util)
build_tests() (galaxy_test.driver.driver_util.TestDriver method)
build_timestamp_trigger() (in module galaxy.model.triggers)
build_tool_dependencies_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method)
build_tool_dependencies_select_field() (in module galaxy.tool_shed.util.tool_dependency_util)
build_tool_panel_section_select_field() (in module galaxy.tool_shed.util.tool_util)
build_tools_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method)
build_tours_registry() (in module galaxy.tours)
build_url() (galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter method)
- (galaxy.selenium.cli.DriverWrapper method)
- (galaxy.selenium.context.GalaxySeleniumContext method)
- (in module galaxy.util)
build_url_map() (in module galaxy.webapps.base.webapp)
build_workflow_from_raw_description() (galaxy.managers.workflows.WorkflowContentsManager method)
build_workflow_run_configs() (in module galaxy.workflow.run_request)
build_workflows_folder() (tool_shed.utility_containers.utility_container_manager.UtilityContainerManager method)
BuildListCollectionTool (class in galaxy.tools)
BuildMulledDockerContainerResolver (class in galaxy.tool_util.deps.container_resolvers.mulled)
BuildMulledSingularityContainerResolver (class in galaxy.tool_util.deps.container_resolvers.mulled)
builds_on_resolution (galaxy.tool_util.deps.container_resolvers.ContainerResolver attribute)
- (galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledDockerContainerResolver attribute)
- (galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledSingularityContainerResolver attribute)
BUILT_IN_VISUALIZATIONS (galaxy.visualization.plugins.registry.VisualizationsRegistry attribute)
Bunch (class in galaxy.util.bunch)
burst() (in module galaxy.jobs.stock_rules)
bwa_repository_long_description (in module tool_shed.test.functional.test_0460_upload_to_repository)
bwa_tool_dependency_repository_long_description (in module tool_shed.test.functional.test_0440_deleting_dependency_definitions)
by_api_key() (galaxy.managers.users.UserManager method)
by_dataset() (galaxy.managers.rbac_secured.DatasetRBACPermission method)
by_email() (galaxy.managers.users.UserManager method)
by_email_like() (galaxy.managers.users.UserManager method)
by_id() (galaxy.managers.base.ModelManager method)
by_ids() (galaxy.managers.base.ModelManager method)
by_role() (galaxy.managers.rbac_secured.DatasetRBACPermission method)
by_roles() (galaxy.managers.rbac_secured.DatasetRBACPermission method)
by_tool_input() (galaxy.managers.jobs.JobSearch method)
by_user() (galaxy.managers.datasets.DatasetAssociationManager method)
- (galaxy.managers.histories.HistoryManager method)
- (galaxy.managers.sharable.SharableModelManager method)
bytes (galaxy.model.Quota attribute)
bytes_to_str() (in module galaxy.jobs.dynamic_tool_destination)
ByteSize (class in galaxy.util.bytesize)
Bz2DynamicCompressedArchive (class in galaxy.datatypes.binary)

C

cache_file_is_writeable() (galaxy.tools.cache.ToolDocumentCache property)
cache_job_destination() (galaxy.jobs.mapper.JobRunnerMapper method)
cache_tool() (galaxy.tools.cache.ToolCache method)
cacheable (galaxy.tool_util.deps.resolvers.Dependency attribute)
CacheableStaticURLParser (class in galaxy.web.framework.middleware.static)
cached (galaxy.tool_util.deps.CachedDependencyManager attribute)
- (galaxy.tool_util.deps.DependencyManager attribute)
- (galaxy.tool_util.deps.NullDependencyManager attribute)
cached_container_description() (galaxy.tool_util.deps.container_resolvers.mulled.MulledDockerContainerResolver method)
- (galaxy.tool_util.deps.container_resolvers.mulled.MulledSingularityContainerResolver method)
cached_id() (in module galaxy.model)
CachedDependencyManager (class in galaxy.tool_util.deps)
CachedMulledDockerContainerResolver (class in galaxy.tool_util.deps.container_resolvers.mulled)
CachedMulledSingularityContainerResolver (class in galaxy.tool_util.deps.container_resolvers.mulled)
calculate_and_set_disk_usage() (galaxy.model.User method)
calculate_disk_usage() (galaxy.model.User method)
calculate_pagination() (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method)
call_hook() (galaxy.tools.Tool method)
CallableSafeStringWrapper (class in galaxy.util.object_wrapper)
callback() (galaxy.authnz.custos_authnz.CustosAuthnz method)
- (galaxy.authnz.IdentityProvider method)
- (galaxy.authnz.managers.AuthnzManager method)
- (galaxy.authnz.psa_authnz.PSAAuthnz method)
- (galaxy.webapps.galaxy.controllers.authnz.OIDC method)
can_access_dataset() (galaxy.model.security.GalaxyRBACAgent method)
- (galaxy.security.RBACAgent method)
can_access_datasets() (galaxy.model.security.GalaxyRBACAgent method)
can_access_entry_point() (galaxy.managers.interactivetool.InteractiveToolManager method)
can_access_entry_points() (galaxy.managers.interactivetool.InteractiveToolManager method)
can_access_job() (galaxy.managers.interactivetool.InteractiveToolManager method)
can_access_library() (galaxy.model.security.GalaxyRBACAgent method)
- (galaxy.security.RBACAgent method)
can_access_library_item() (galaxy.model.security.GalaxyRBACAgent method)
can_add_item() (galaxy.managers.folders.FolderManager method)
can_add_library_item() (galaxy.model.security.GalaxyRBACAgent method)
- (galaxy.security.RBACAgent method)
can_add_to_key_rd_dicts() (tool_shed.dependencies.repository.relation_builder.RelationBuilder method)
can_browse_repository_reviews() (in module tool_shed.util.review_util)
can_change_type() (tool_shed.webapp.model.Repository method)
can_change_type_to() (tool_shed.webapp.model.Repository method)
can_convert_to() (galaxy.model.DatasetInstance method)
can_current_user_add_to_library_item() (galaxy.webapps.base.controller.UsesLibraryMixinItems method)
can_deactivate() (galaxy.model.tool_shed_install.ToolShedRepository property)
can_decompress() (galaxy.util.compression_utils.CompressedFile static method)
can_eliminate_repository_dependency() (in module galaxy.tool_shed.util.shed_util_common)
- (in module tool_shed.util.shed_util_common)
can_eliminate_tool_dependency() (in module galaxy.tool_shed.util.shed_util_common)
- (in module tool_shed.util.shed_util_common)
can_install() (galaxy.model.tool_shed_install.ToolDependency property)
- (galaxy.model.tool_shed_install.ToolShedRepository property)
- (galaxy.tool_util.deps.conda_util.CondaContext method)
- (galaxy.tool_util.deps.installable.InstallableContext method)
can_install_conda() (galaxy.tool_util.deps.conda_util.CondaContext method)
can_list_containers() (galaxy.tool_util.deps.container_resolvers.mulled.MulledDockerContainerResolver property)
- (galaxy.tool_util.deps.container_resolvers.mulled.MulledSingularityContainerResolver property)
can_load_config_file() (galaxy.tools.ToolBox method)
- (galaxy.tools.toolbox.AbstractToolBox method)
- (galaxy.tools.toolbox.base.AbstractToolBox method)
can_manage_dataset() (galaxy.model.security.GalaxyRBACAgent method)
- (galaxy.security.RBACAgent method)
can_manage_library_item() (galaxy.model.security.GalaxyRBACAgent method)
- (galaxy.security.RBACAgent method)
can_map_over() (galaxy.tools.parameters.history_query.HistoryQuery method)
can_match() (galaxy.model.dataset_collections.structure.Tree method)
can_match_type() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method)
can_modify_library_item() (galaxy.model.security.GalaxyRBACAgent method)
- (galaxy.security.RBACAgent method)
can_push() (tool_shed.webapp.security.CommunityRBACAgent method)
can_reinstall_or_activate() (galaxy.model.tool_shed_install.ToolShedRepository property)
can_reset_metadata() (galaxy.model.tool_shed_install.ToolShedRepository property)
can_split() (galaxy.jobs.JobWrapper method)
- (galaxy.jobs.TaskWrapper method)
can_uninstall() (galaxy.model.tool_shed_install.ToolDependency property)
- (galaxy.model.tool_shed_install.ToolShedRepository property)
can_uninstall_dependencies (galaxy.tool_util.deps.container_resolvers.ContainerResolver attribute)
can_uninstall_dependencies() (galaxy.tool_util.deps.resolvers.DependencyResolver property)
can_update() (galaxy.model.tool_shed_install.ToolDependency property)
can_use_tool_config_disk_file() (tool_shed.tools.tool_validator.ToolValidator method)
can_user_assume_authn() (galaxy.authnz.managers.AuthnzManager static method)
CANCEL (galaxy.openid.openid_manager.OpenIDManager attribute)
cancel() (galaxy.model.WorkflowInvocation method)
cancel_history_jobs() (galaxy_test.base.populators.BaseDatasetPopulator method)
cancel_invocation() (galaxy.managers.workflows.WorkflowsManager method)
- (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method)
cancel_job() (galaxy_test.base.populators.BaseDatasetPopulator method)
CANCELLED (galaxy.model.WorkflowInvocation.states attribute)
CancelWorkflowEvaluation
categories (tool_shed.webapp.model.Repository attribute)
CategoriesController (class in tool_shed.webapp.api.categories)
Category (class in tool_shed.webapp.model)
category (tool_shed.webapp.model.RepositoryCategoryAssociation attribute)
category_0060_name (in module tool_shed.test.functional.test_1300_reset_all_metadata)
category_description (in module tool_shed.test.functional.test_0130_datatype_converters)
- (in module tool_shed.test.functional.test_0140_tool_help_images)
- (in module tool_shed.test.functional.test_0150_prior_installation_required)
- (in module tool_shed.test.functional.test_0160_circular_prior_installation_required)
- (in module tool_shed.test.functional.test_0170_complex_prior_installation_required)
- (in module tool_shed.test.functional.test_0310_hg_api_features)
- (in module tool_shed.test.functional.test_0530_repository_admin_feature)
- (in module tool_shed.test.functional.test_0540_get_all_metadata_from_api)
- (in module tool_shed.test.functional.test_0550_metadata_updated_dependencies)
- (in module tool_shed.test.functional.test_1150_datatype_converters)
- (in module tool_shed.test.functional.test_1170_prior_installation_required)
- (in module tool_shed.test.functional.test_1180_circular_prior_installation_required)
- (in module tool_shed.test.functional.test_1190_complex_prior_installation_required)
- (in module tool_shed.test.functional.test_1410_update_manager)
- (in module tool_shed.test.functional.test_1450_installing_datatypes_sniffers)
- (in module tool_shed.test.functional.test_1470_updating_installed_repositories)
category_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute)
category_id (tool_shed.webapp.model.RepositoryCategoryAssociation attribute)
CategoryGrid (class in tool_shed.grids.repository_grids)
CategoryGrid.DescriptionColumn (class in tool_shed.grids.repository_grids)
CategoryGrid.NameColumn (class in tool_shed.grids.repository_grids)
CategoryGrid.RepositoriesColumn (class in tool_shed.grids.repository_grids)
Cel (class in galaxy.datatypes.binary)
cellar_path() (galaxy.tool_util.deps.brew_exts.RecipeContext property)
center() (tool_shed.util.admin_util.Admin method)
CgroupPlugin (class in galaxy.job_metrics.instrumenters.cgroup)
change_datatype() (galaxy.datatypes.registry.Registry method)
- (galaxy.model.DatasetInstance method)
change_entry() (tool_shed.util.hgweb_config.HgWebConfigManager method)
change_ownership_for_run() (galaxy.jobs.JobWrapper method)
change_password() (galaxy.managers.users.UserManager method)
- (galaxy.webapps.galaxy.controllers.user.User method)
- (tool_shed.webapp.controllers.user.User method)
change_repository_name_in_hgrc_file() (in module tool_shed.util.repository_util)
change_state() (galaxy.config_watchers.ConfigWatchers method)
- (galaxy.jobs.JobWrapper method)
- (galaxy.jobs.TaskWrapper method)
change_user_group() (galaxy.util.pastescript.serve.ServeCommand method)
changed() (galaxy.model.UserAuthnzToken class method)
ChangeDatatypeAction (class in galaxy.jobs.actions.post)
ChangeDatatypeTestCase (class in galaxy_test.api.test_workflows)
ChangeDirectory (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler)
ChangePasswordTestCase (class in galaxy_test.selenium.test_change_password)
changeset2rev() (in module tool_shed.util.hg_util)
changeset_revision (galaxy.model.tool_shed_install.ToolShedRepository attribute)
- (tool_shed.webapp.model.RepositoryMetadata attribute)
- (tool_shed.webapp.model.RepositoryReview attribute)
changeset_revision_reviewed_by_user() (in module tool_shed.util.review_util)
ChartVisualizationPlugin (class in galaxy.visualization.plugins.plugin)
check() (galaxy.config.GalaxyAppConfiguration method)
- (galaxy.dependencies.ConditionalDependencies method)
- (galaxy.tools.toolbox.watcher.ToolConfWatcher method)
- (galaxy.webapps.reports.config.Configuration method)
- (tool_shed.webapp.config.ToolShedAppConfiguration method)
check_accessible() (galaxy.managers.folders.FolderManager method)
- (galaxy.managers.libraries.LibraryManager method)
- (galaxy.managers.library_datasets.LibraryDatasetsManager method)
check_all_jobs() (galaxy.jobs.runners.pbs.PBSJobRunner method)
check_and_reload() (galaxy.visualization.genomes.Genomes method)
check_and_update_param_values() (galaxy.tools.Tool method)
check_and_update_state() (galaxy.workflow.modules.ToolModule method)
- (galaxy.workflow.modules.WorkflowModule method)
check_archive() (in module galaxy.tools.imp_exp.unpack_tar_gz_archive)
- (in module tool_shed.util.commit_util)
check_auto_registration() (galaxy.auth.AuthManager method)
check_azure_storage() (galaxy.dependencies.ConditionalDependencies method)
check_binary() (in module galaxy.datatypes.checkers)
- (in module galaxy.util.checkers)
check_block() (galaxy.datatypes.sequence.BaseFastq class method)
check_bz2() (in module galaxy.datatypes.checkers)
- (in module galaxy.util.checkers)
check_change_password() (galaxy.auth.AuthManager method)
check_chronos_python() (galaxy.dependencies.ConditionalDependencies method)
check_config() (galaxy.auth.providers.ldap_ad.LDAP method)
check_count_of_metadata_revisions_associated_with_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
check_csrf_token() (galaxy.webapps.base.webapp.GalaxyWebTransaction method)
check_docker() (galaxy.dependencies.ConditionalDependencies method)
check_drmaa() (galaxy.dependencies.ConditionalDependencies method)
check_example_1() (in module galaxy_test.base.rules_test_data)
check_example_2() (in module galaxy_test.base.rules_test_data)
check_example_3() (in module galaxy_test.base.rules_test_data)
check_example_4() (in module galaxy_test.base.rules_test_data)
check_example_5() (in module galaxy_test.base.rules_test_data)
check_example_6() (in module galaxy_test.base.rules_test_data)
check_exported_repository_dependency() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
check_file_content_for_html_and_images() (in module tool_shed.util.commit_util)
check_file_contents_for_email_alerts() (in module tool_shed.util.commit_util)
check_first_block() (galaxy.datatypes.sequence.BaseFastq class method)
check_fluent_logger() (galaxy.dependencies.ConditionalDependencies method)
check_folder_contents() (galaxy.model.security.GalaxyRBACAgent method)
check_for_entry_points() (galaxy.jobs.JobWrapper method)
check_for_missing_tools() (in module galaxy.util.tool_shed.common_util)
check_for_strings() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
check_for_tool_dependencies() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method)
check_for_updates() (galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController method)
- (in module galaxy.tool_shed.util.repository_util)
- (in module tool_shed.util.repository_util)
- (tool_shed.webapp.controllers.repository.RepositoryController method)
check_for_valid_tools() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
check_fs_anvilfs() (galaxy.dependencies.ConditionalDependencies method)
check_fs_dropboxfs() (galaxy.dependencies.ConditionalDependencies method)
check_fs_s3fs() (galaxy.dependencies.ConditionalDependencies method)
check_fs_webdavfs() (galaxy.dependencies.ConditionalDependencies method)
check_galaxy_repository_db_status() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
check_galaxy_repository_tool_panel_section() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
check_galaxycloudrunner() (galaxy.dependencies.ConditionalDependencies method)
check_gzip() (in module galaxy.datatypes.checkers)
- (in module galaxy.util.checkers)
check_histories() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method)
check_html() (in module galaxy.datatypes.checkers)
- (in module galaxy.util.checkers)
check_if_output_datasets_deleted() (galaxy.model.Job method)
check_image() (in module galaxy.datatypes.checkers)
- (in module galaxy.util.checkers)
check_image_type() (in module galaxy.util.image_util)
check_influxdb() (galaxy.dependencies.ConditionalDependencies method)
check_inputs_ready() (galaxy.tools.actions.model_operations.ModelOperationToolAction method)
- (galaxy.tools.DatabaseOperationTool method)
check_installed_repository_tool_dependencies() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
check_interval() (galaxy.model.DeferredJob property)
check_kamaki() (galaxy.dependencies.ConditionalDependencies method)
check_keras() (galaxy.dependencies.ConditionalDependencies method)
check_limits() (galaxy.jobs.JobWrapper method)
- (galaxy.jobs.runners.AsynchronousJobState method)
check_manageable() (galaxy.managers.folders.FolderManager method)
check_master_api_key() (galaxy.managers.users.UserManager method)
check_modifiable() (galaxy.managers.library_datasets.LibraryDatasetsManager method)
check_modifyable() (galaxy.managers.folders.FolderManager method)
check_mysqlclient() (galaxy.dependencies.ConditionalDependencies method)
check_or_update_tool_shed_status_for_installed_repository() (in module galaxy.tool_shed.util.repository_util)
- (in module tool_shed.util.repository_util)
check_output() (in module galaxy.tool_util.output_checker)
check_output_regex() (in module galaxy.tool_util.output_checker)
check_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
check_page_for_string() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
check_password() (galaxy.auth.AuthManager method)
- (galaxy.model.User method)
- (in module galaxy.security.passwords)
- (tool_shed.webapp.model.User method)
check_password_PBKDF2() (in module galaxy.security.passwords)
check_pbs_python() (galaxy.dependencies.ConditionalDependencies method)
check_pg() (in module galaxy.jobs.runners.util.process_groups)
check_psycopg2_binary() (galaxy.dependencies.ConditionalDependencies method)
check_pygithub() (galaxy.dependencies.ConditionalDependencies method)
check_pykube() (galaxy.dependencies.ConditionalDependencies method)
check_python_gitlab() (galaxy.dependencies.ConditionalDependencies method)
check_python_irodsclient() (galaxy.dependencies.ConditionalDependencies method)
check_python_ldap() (galaxy.dependencies.ConditionalDependencies method)
check_python_pam() (galaxy.dependencies.ConditionalDependencies method)
check_raven() (galaxy.dependencies.ConditionalDependencies method)
check_registration_allowed() (galaxy.auth.AuthManager method)
check_repository_changelog() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
check_repository_dependency() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
check_repository_invalid_tools_for_changeset_revision() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
check_repository_metadata() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
check_repository_tools_for_changeset_revision() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
check_role_dict() (galaxy_test.api.test_roles.RolesApiTestCase static method)
check_run() (galaxy_test.base.populators.BaseDatasetPopulator method)
check_s3fs() (galaxy.dependencies.ConditionalDependencies method)
check_script_integrity() (in module galaxy.jobs.runners.util.job_script)
check_security() (galaxy.managers.workflows.WorkflowsManager method)
check_single_job() (galaxy.jobs.runners.pbs.PBSJobRunner method)
check_statsd() (galaxy.dependencies.ConditionalDependencies method)
check_string_count_in_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
check_string_not_in_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
check_tag_attributes() (tool_shed.dependencies.attribute_handlers.RepositoryDependencyAttributeHandler method)
check_tensorflow() (galaxy.dependencies.ConditionalDependencies method)
check_tool_input_params() (galaxy.tool_shed.tools.tool_validator.ToolValidator method)
check_tool_output() (galaxy.jobs.JobWrapper method)
check_tool_tag_set() (in module galaxy.util.tool_shed.common_util)
check_user_activation() (galaxy.managers.context.ProvidesUserContext method)
check_user_can_add_to_library_item() (galaxy.webapps.base.controller.UsesLibraryMixinItems method)
check_user_library_import_dir() (galaxy.webapps.base.webapp.GalaxyWebTransaction method)
check_watchdog() (galaxy.dependencies.ConditionalDependencies method)
check_watched_item() (galaxy.jobs.runners.AsynchronousJobRunner method)
- (galaxy.jobs.runners.chronos.ChronosJobRunner method)
- (galaxy.jobs.runners.drmaa.DRMAAJobRunner method)
- (galaxy.jobs.runners.godocker.GodockerJobRunner method)
- (galaxy.jobs.runners.kubernetes.KubernetesJobRunner method)
- (galaxy.jobs.runners.univa.UnivaJobRunner method)
check_watched_items() (galaxy.jobs.runners.AsynchronousJobRunner method)
- (galaxy.jobs.runners.cli.ShellJobRunner method)
- (galaxy.jobs.runners.condor.CondorJobRunner method)
- (galaxy.jobs.runners.drmaa.DRMAAJobRunner method)
- (galaxy.jobs.runners.pbs.PBSJobRunner method)
check_workflow_compatible() (galaxy.tools.Tool method)
check_zip() (in module galaxy.datatypes.checkers)
- (in module galaxy.util.checkers)
CheckboxField (class in galaxy.util.form_builder)
- (class in galaxy.web.form_builder)
checkComments() (galaxy.visualization.data_providers.phyloviz.nexusparser.Nexus_Parser method)
child_collection (galaxy.model.DatasetCollectionElement attribute)
child_collection_id (galaxy.model.DatasetCollectionElement attribute)
child_collection_type() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method)
child_collection_type_description() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method)
child_tool_association (galaxy.model.tool_shed_install.ToolVersion attribute)
children (galaxy.model.ExtendedMetadata attribute)
- (galaxy.model.Tag attribute)
- (tool_shed.webapp.model.Tag attribute)
children_known (galaxy.model.dataset_collections.structure.Leaf attribute)
- (galaxy.model.dataset_collections.structure.Tree attribute)
- (galaxy.model.dataset_collections.structure.UninitializedTree attribute)
ChiraSQLite (class in galaxy.datatypes.binary)
Chmod (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler)
choose_one() (galaxy.jobs.rule_helper.RuleHelper method)
- (in module galaxy.jobs.stock_rules)
chop_block_by_region() (in module galaxy.datatypes.util.maf_utilities)
- (in module galaxy.tools.util.maf_utilities)
ChromatinInteractions (class in galaxy.datatypes.interval)
ChromatinInteractionsDataProvider (class in galaxy.visualization.data_providers.genome)
ChromatinInteractionsTabixDataProvider (class in galaxy.visualization.data_providers.genome)
ChromInfo (class in galaxy.datatypes.chrominfo)
chroms() (galaxy.visualization.genomes.Genomes method)
ChronosJobRunner (class in galaxy.jobs.runners.chronos)
chunk64_dataprovider() (galaxy.datatypes.data.Data method)
chunk_dataprovider() (galaxy.datatypes.data.Data method)
CHUNKABLE (galaxy.datatypes.data.Data attribute)
- (galaxy.datatypes.tabular.TabularData attribute)
ChunkDataProvider (class in galaxy.datatypes.dataproviders.chunk)
circster() (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method)
CisML (class in galaxy.datatypes.xml)
CitationCollection (class in galaxy.managers.citations)
citations() (galaxy.webapps.galaxy.api.histories.HistoriesController method)
- (galaxy.webapps.galaxy.api.tools.ToolsController method)
citations_for_tool() (galaxy.managers.citations.CitationsManager method)
citations_for_tool_ids() (galaxy.managers.citations.CitationsManager method)
CitationsManager (class in galaxy.managers.citations)
city (galaxy.model.UserAddress attribute)
classproperty (class in galaxy.util)
clean() (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver method)
- (galaxy.tool_util.deps.views.DependencyResolversView method)
- (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method)
clean_base_dir() (galaxy.tools.data.TabularToolDataField method)
clean_dependency_relationships() (in module galaxy.tool_shed.util.shed_util_common)
- (in module tool_shed.util.shed_util_common)
clean_multiline_string() (in module galaxy.util)
clean_repository_metadata() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method)
cleanNewickString() (galaxy.visualization.data_providers.phyloviz.newickparser.Newick_Parser method)
cleanTag() (galaxy.visualization.data_providers.phyloviz.phyloxmlparser.Phyloxml_Parser method)
cleanup() (galaxy.jobs.JobWrapper method)
- (galaxy.jobs.runners.JobState method)
- (galaxy.jobs.TaskWrapper method)
- (galaxy.tools.cache.ToolCache method)
cleanup_after_job() (galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper method)
cleanup_external_metadata() (galaxy.metadata.MetadataCollectionStrategy method)
cleanup_from_JSON_dict_filename() (galaxy.datatypes.metadata.MetadataTempFile class method)
- (galaxy.model.metadata.MetadataTempFile class method)
cleanup_job() (galaxy.jobs.JobWrapper property)
clear() (galaxy.managers.rbac_secured.DatasetRBACPermission method)
- (galaxy.model.ImplicitlyConvertedDatasetAssociation method)
- (galaxy.util.odict.odict method)
clear_associated_files() (galaxy.model.DatasetInstance method)
- (galaxy.model.HistoryDatasetAssociation method)
- (galaxy.model.LibraryDatasetDatasetAssociation method)
clear_display_apps() (galaxy.datatypes.data.Data method)
clear_history() (galaxy.webapps.galaxy.controllers.root.RootController method)
clear_input_field_and_write() (galaxy_test.selenium.test_personal_information.ManageInformationTestCase method)
clear_module_extras() (galaxy.model.WorkflowStep method)
clear_tooltips() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
clear_working_directory() (galaxy.jobs.JobWrapper method)
click() (galaxy.selenium.has_driver.HasDriver method)
click_button_new_workflow() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
click_center() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
click_grid_popup_option() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
click_history_option() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
click_history_options() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
click_label() (galaxy.selenium.has_driver.HasDriver method)
click_masthead_shared_data() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
click_masthead_user() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
click_masthead_workflow() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
click_selector() (galaxy.selenium.has_driver.HasDriver method)
click_submit() (galaxy.selenium.has_driver.HasDriver method)
click_xpath() (galaxy.selenium.has_driver.HasDriver method)
client() (galaxy.webapps.base.controller.JSAppLauncher method)
- (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method)
CliInterface (class in galaxy.jobs.runners.util.cli)
clone() (galaxy.model.dataset_collections.structure.Leaf method)
- (galaxy.model.dataset_collections.structure.Tree method)
- (galaxy.model.dataset_collections.structure.UninitializedTree method)
clone_repository() (in module galaxy.tool_shed.util.hg_util)
- (in module tool_shed.util.hg_util)
- (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
CLONING (galaxy.model.tool_shed_install.ToolShedRepository.installation_status attribute)
close() (galaxy.datatypes.util.maf_utilities.TempFileHandler method)
- (galaxy.tools.cache.ToolDocumentCache method)
- (galaxy.tools.util.maf_utilities.TempFileHandler method)
close_file_descriptor() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method)
close_logs() (galaxy.util.heartbeat.Heartbeat method)
Cloud (class in galaxy.objectstore.cloud)
CloudAuthz (class in galaxy.model)
cloudauthz (galaxy.model.User attribute)
- (galaxy.model.UserAuthnzToken attribute)
CloudAuthzController (class in galaxy.webapps.galaxy.api.cloudauthz)
CloudAuthzManager (class in galaxy.managers.cloudauthzs)
cloudauthzs (galaxy.model.User attribute)
CloudAuthzsDeserializer (class in galaxy.managers.cloudauthzs)
CloudAuthzsSerializer (class in galaxy.managers.cloudauthzs)
CloudConfigMixin (class in galaxy.objectstore.cloud)
- (class in galaxy.objectstore.irods)
- (class in galaxy.objectstore.s3)
CloudController (class in galaxy.webapps.galaxy.api.cloud)
CloudImage_table (in module galaxy.model.migrate.versions.0026_cloud_tables)
- (in module galaxy.model.migrate.versions.0050_drop_cloud_tables)
CloudManager (class in galaxy.managers.cloud)
CMAP (class in galaxy.datatypes.tabular)
CML (class in galaxy.datatypes.molecules)
cmp() (in module galaxy.util.object_wrapper)
code (galaxy.authnz.psa_authnz.Storage attribute)
- (galaxy.model.PSACode attribute)
coerce() (galaxy.model.custom_types.MutationDict class method)
- (galaxy.model.custom_types.MutationList class method)
- (galaxy.model.custom_types.MutationObj class method)
- (in module galaxy.util.object_wrapper)
col_name_data_attr_mapping (galaxy.visualization.data_providers.genome.GenomeDataProvider attribute)
- (galaxy.visualization.data_providers.genome.IntervalIndexDataProvider attribute)
- (galaxy.visualization.data_providers.genome.TabixDataProvider attribute)
- (galaxy.visualization.data_providers.genome.VcfDataProvider attribute)
collect_dynamic_outputs() (in module galaxy.job_execution.output_collect)
collect_extra_files() (in module galaxy.job_execution.output_collect)
collect_input_dataset_collections() (galaxy.tools.actions.DefaultToolAction method)
collect_inputs() (galaxy.tool_util.parser.interface.TestCollectionDef method)
collect_primary_datasets() (in module galaxy.job_execution.output_collect)
collect_properties() (galaxy.job_metrics.JobInstrumenter method)
- (galaxy.job_metrics.JobMetrics method)
- (galaxy.job_metrics.NullJobInstrumenter method)
collection (galaxy.model.DatasetCollectionElement attribute)
- (galaxy.model.HistoryDatasetCollectionAssociation attribute)
- (galaxy.model.LibraryDatasetCollectionAssociation attribute)
collection_builder_clear_filters() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
collection_builder_click_paired_item() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
collection_builder_create() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
collection_builder_for() (galaxy.managers.collections.DatasetCollectionManager method)
collection_builder_hide_originals() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
collection_builder_set_name() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
collection_id (galaxy.model.HistoryDatasetCollectionAssociation attribute)
- (galaxy.model.LibraryDatasetCollectionAssociation attribute)
collection_prototype() (galaxy.tool_util.parser.output_objects.ToolOutputCollectionStructure method)
collection_type (galaxy.model.dataset_collections.types.list.ListDatasetCollectionType attribute)
- (galaxy.model.dataset_collections.types.paired.PairedDatasetCollectionType attribute)
- (galaxy.model.DatasetCollection attribute)
- (galaxy.workflow.modules.InputDataCollectionModule attribute)
- (galaxy.workflow.refactor.schema.AddInputAction attribute)
collection_type() (galaxy.tool_util.cwl.representation.TypeRepresentation property)
- (galaxy.util.rules_dsl.RuleSet property)
collection_types() (galaxy.tools.parameters.basic.DataCollectionToolParameter property)
- (galaxy.tools.parameters.DataCollectionToolParameter property)
collection_wrapper_to_array() (in module galaxy.tool_util.cwl.representation)
collection_wrapper_to_record() (in module galaxy.tool_util.cwl.representation)
CollectionBuilder (class in galaxy.model.dataset_collections.builder)
CollectionBuildersTestCase (class in galaxy_test.selenium.test_collection_builders)
collections_properties() (galaxy.model.store.BaseDirectoryImportModelStore method)
- (galaxy.model.store.ModelImportStore method)
CollectionsToMatch (class in galaxy.model.dataset_collections.matching)
CollectionTypeDescription (class in galaxy.model.dataset_collections.type_description)
CollectionTypeDescriptionFactory (class in galaxy.model.dataset_collections.type_description)
CollectlCli (class in galaxy.job_metrics.collectl.cli)
CollectlPlugin (class in galaxy.job_metrics.instrumenters.collectl)
collector() (galaxy.model.store.discover.DiscoveredFile property)
- (galaxy.model.store.discover.DiscoveredFileError property)
ColorToolParameter (class in galaxy.tools.parameters.basic)
column_dataprovider() (galaxy.datatypes.binary.Bam method)
- (galaxy.datatypes.tabular.Sam method)
- (galaxy.datatypes.tabular.TabularData method)
COLUMN_NAMES (galaxy.datatypes.dataproviders.dataset.BigWigDataProvider attribute)
- (galaxy.datatypes.dataproviders.dataset.GenomicRegionDataProvider attribute)
- (galaxy.datatypes.dataproviders.dataset.IntervalDataProvider attribute)
- (galaxy.datatypes.dataproviders.dataset.WiggleDataProvider attribute)
column_names (galaxy.datatypes.interval.Bed attribute)
- (galaxy.datatypes.interval.ChromatinInteractions attribute)
- (galaxy.datatypes.interval.ENCODEPeak attribute)
- (galaxy.datatypes.interval.Gff attribute)
- (galaxy.datatypes.interval.Gff3 attribute)
- (galaxy.datatypes.interval.Gtf attribute)
- (galaxy.datatypes.interval.ProBed attribute)
- (galaxy.datatypes.molecules.InChI attribute)
- (galaxy.datatypes.molecules.SMILES attribute)
- (galaxy.datatypes.tabular.BaseVcf attribute)
column_repository_long_description (in module tool_shed.test.functional.test_1430_repair_installed_repository)
column_spec_to_index() (galaxy.tools.parameters.dynamic_options.DynamicOptions method)
ColumnarDataProvider (class in galaxy.datatypes.dataproviders.column)
ColumnDataProvider (class in galaxy.visualization.data_providers.basic)
ColumnListParameter (class in galaxy.tools.parameters.basic)
ColumnParameter (class in galaxy.datatypes.metadata)
- (class in galaxy.model.metadata)
ColumnReplaceFilter (class in galaxy.tool_util.parser.output_actions)
columns (galaxy.web.framework.helpers.grids.Grid attribute)
- (galaxy.web.legacy_framework.grids.Grid attribute)
- (galaxy.webapps.galaxy.controllers.admin.GroupListGrid attribute)
- (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid attribute)
- (galaxy.webapps.galaxy.controllers.admin.RoleListGrid attribute)
- (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid attribute)
- (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute)
- (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute)
- (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid attribute)
- (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute)
- (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid attribute)
- (galaxy.webapps.galaxy.controllers.page.HistoryDatasetAssociationSelectionGrid attribute)
- (galaxy.webapps.galaxy.controllers.page.HistorySelectionGrid attribute)
- (galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid attribute)
- (galaxy.webapps.galaxy.controllers.page.PageListGrid attribute)
- (galaxy.webapps.galaxy.controllers.page.PageSelectionGrid attribute)
- (galaxy.webapps.galaxy.controllers.page.VisualizationSelectionGrid attribute)
- (galaxy.webapps.galaxy.controllers.page.WorkflowSelectionGrid attribute)
- (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid attribute)
- (galaxy.webapps.galaxy.controllers.visualization.LibraryDatasetsSelectionGrid attribute)
- (galaxy.webapps.galaxy.controllers.visualization.TracksterSelectionGrid attribute)
- (galaxy.webapps.galaxy.controllers.visualization.VisualizationAllPublishedGrid attribute)
- (galaxy.webapps.galaxy.controllers.visualization.VisualizationListGrid attribute)
- (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute)
- (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid attribute)
- (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute)
- (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute)
- (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute)
- (tool_shed.grids.admin_grids.AdminRepositoryGrid attribute)
- (tool_shed.grids.admin_grids.GroupGrid attribute)
- (tool_shed.grids.admin_grids.ManageCategoryGrid attribute)
- (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute)
- (tool_shed.grids.admin_grids.RoleGrid attribute)
- (tool_shed.grids.admin_grids.UserGrid attribute)
- (tool_shed.grids.repository_grids.CategoryGrid attribute)
- (tool_shed.grids.repository_grids.DatatypesGrid attribute)
- (tool_shed.grids.repository_grids.DeprecatedRepositoriesIOwnGrid attribute)
- (tool_shed.grids.repository_grids.DockerImageGrid attribute)
- (tool_shed.grids.repository_grids.EmailAlertsRepositoryGrid attribute)
- (tool_shed.grids.repository_grids.InstallMatchedRepositoryGrid attribute)
- (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute)
- (tool_shed.grids.repository_grids.MyWritableRepositoriesGrid attribute)
- (tool_shed.grids.repository_grids.MyWritableRepositoriesMissingToolTestComponentsGrid attribute)
- (tool_shed.grids.repository_grids.MyWritableRepositoriesWithInvalidToolsGrid attribute)
- (tool_shed.grids.repository_grids.RepositoriesByUserGrid attribute)
- (tool_shed.grids.repository_grids.RepositoriesICanAdministerGrid attribute)
- (tool_shed.grids.repository_grids.RepositoriesInCategoryGrid attribute)
- (tool_shed.grids.repository_grids.RepositoriesIOwnGrid attribute)
- (tool_shed.grids.repository_grids.RepositoriesMissingToolTestComponentsGrid attribute)
- (tool_shed.grids.repository_grids.RepositoriesWithInvalidToolsGrid attribute)
- (tool_shed.grids.repository_grids.RepositoryDependenciesGrid attribute)
- (tool_shed.grids.repository_grids.RepositoryGrid attribute)
- (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute)
- (tool_shed.grids.repository_grids.ToolDependenciesGrid attribute)
- (tool_shed.grids.repository_grids.ToolsGrid attribute)
- (tool_shed.grids.repository_grids.ValidCategoryGrid attribute)
- (tool_shed.grids.repository_grids.ValidRepositoryGrid attribute)
- (tool_shed.grids.repository_review_grids.ComponentGrid attribute)
- (tool_shed.grids.repository_review_grids.RepositoriesReadyForReviewGrid attribute)
- (tool_shed.grids.repository_review_grids.RepositoriesReviewedByMeGrid attribute)
- (tool_shed.grids.repository_review_grids.RepositoriesWithNoToolTestsGrid attribute)
- (tool_shed.grids.repository_review_grids.RepositoriesWithoutReviewsGrid attribute)
- (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid attribute)
- (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute)
- (tool_shed.grids.repository_review_grids.ReviewedRepositoriesIOwnGrid attribute)
ColumnSetAction (class in galaxy.jobs.actions.post)
ColumnStripFilter (class in galaxy.tool_util.parser.output_actions)
ColumnTypesParameter (class in galaxy.datatypes.metadata)
- (class in galaxy.model.metadata)
commaify() (in module galaxy.util)
Command (class in galaxy.util.pastescript.serve)
command() (galaxy.util.pastescript.serve.ServeCommand method)
Command.BadCommand
command_line (galaxy.model.Job attribute)
- (galaxy.model.Task attribute)
command_list() (in module galaxy.tool_util.deps.docker_util)
command_shell() (in module galaxy.tool_util.deps.docker_util)
command_version() (galaxy.model.Job property)
CommandLineException, [1]
commands_in_new_shell() (galaxy.jobs.JobWrapper property)
comment (tool_shed.webapp.model.ComponentReview attribute)
- (tool_shed.webapp.model.RepositoryRatingAssociation attribute)
comment_lines (galaxy.datatypes.proteomics.Dta attribute)
- (galaxy.datatypes.proteomics.Dta2d attribute)
- (galaxy.datatypes.proteomics.Edta attribute)
- (galaxy.datatypes.proteomics.ProtXmlReport attribute)
commit_and_push() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
commit_changeset() (in module tool_shed.util.hg_util)
commit_for_version() (in module galaxy.tool_util.deps.brew_exts)
common_columns (galaxy.managers.history_contents.HistoryContentsManager attribute)
common_prefix_dir() (galaxy.util.compression_utils.CompressedFile property)
common_problems() (galaxy.webapps.galaxy.api.jobs.JobController method)
CommonConfigurationMixin (class in galaxy.config)
CommunityRatingColumn (class in galaxy.web.framework.helpers.grids)
- (class in galaxy.web.legacy_framework.grids)
CommunityRBACAgent (class in tool_shed.webapp.security)
CommunityTagHandler (class in galaxy.model.tags)
CommunityTagsColumn (class in galaxy.web.framework.helpers.grids)
- (class in galaxy.web.legacy_framework.grids)
CommunityWebApplication (class in tool_shed.webapp.buildapp)
compare_changeset_revisions() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method)
compare_data_manager() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method)
compare_datatypes() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method)
compare_endswith() (in module galaxy.tool_util.parser.output_actions)
compare_eq() (in module galaxy.tool_util.parser.output_actions)
compare_gt() (in module galaxy.tool_util.parser.output_actions)
compare_gte() (in module galaxy.tool_util.parser.output_actions)
compare_in() (in module galaxy.tool_util.parser.output_actions)
compare_lt() (in module galaxy.tool_util.parser.output_actions)
compare_lte() (in module galaxy.tool_util.parser.output_actions)
compare_neq() (in module galaxy.tool_util.parser.output_actions)
compare_re_search() (in module galaxy.tool_util.parser.output_actions)
compare_readme_files() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method)
compare_repository_dependencies() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method)
compare_startswith() (in module galaxy.tool_util.parser.output_actions)
compare_tool_dependencies() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method)
compare_urls() (in module galaxy.util)
compare_values() (galaxy.model.custom_types.JSONType method)
compare_workflows() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method)
compile_drop_materialized_view() (in module galaxy.model.view.utils)
complete() (galaxy.authnz.psa_authnz.Strategy method)
Component (class in galaxy.selenium.components)
- (class in tool_shed.webapp.model)
component (tool_shed.webapp.model.ComponentReview attribute)
component_grid (tool_shed.webapp.controllers.repository_review.RepositoryReviewController attribute)
component_id (tool_shed.webapp.model.ComponentReview attribute)
component_overlaps_region() (in module galaxy.datatypes.util.maf_utilities)
- (in module galaxy.tools.util.maf_utilities)
component_reviews (tool_shed.webapp.model.RepositoryReview attribute)
ComponentGrid (class in tool_shed.grids.repository_review_grids)
ComponentGrid.DescriptionColumn (class in tool_shed.grids.repository_review_grids)
ComponentGrid.NameColumn (class in tool_shed.grids.repository_review_grids)
ComponentReview (class in tool_shed.webapp.model)
components() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy property)
components_are_associated() (galaxy.security.RBACAgent method)
composite_files (galaxy.datatypes.data.Data attribute)
composite_type (galaxy.datatypes.anvio.AnvioComposite attribute)
- (galaxy.datatypes.assembly.Velvet attribute)
- (galaxy.datatypes.blast.BlastDomainDb attribute)
- (galaxy.datatypes.blast.BlastDomainDb5 attribute)
- (galaxy.datatypes.blast.BlastNucDb attribute)
- (galaxy.datatypes.blast.BlastNucDb5 attribute)
- (galaxy.datatypes.blast.BlastProtDb attribute)
- (galaxy.datatypes.blast.BlastProtDb5 attribute)
- (galaxy.datatypes.blast.LastDb attribute)
- (galaxy.datatypes.data.Data attribute)
- (galaxy.datatypes.genetics.IdeasPre attribute)
- (galaxy.datatypes.genetics.RexpBase attribute)
- (galaxy.datatypes.genetics.Rgenetics attribute)
- (galaxy.datatypes.gis.Shapefile attribute)
- (galaxy.datatypes.images.Analyze75 attribute)
- (galaxy.datatypes.molecules.OBFS attribute)
- (galaxy.datatypes.msa.HmmerPress attribute)
- (galaxy.datatypes.neo4j.Neo4jDB attribute)
- (galaxy.datatypes.neo4j.Neo4jDBzip attribute)
- (galaxy.datatypes.ngsindex.BowtieIndex attribute)
- (galaxy.datatypes.proteomics.ImzML attribute)
- (galaxy.datatypes.proteomics.SPLib attribute)
- (galaxy.datatypes.proteomics.Wiff attribute)
- (galaxy.datatypes.text.SnpSiftDbNSFP attribute)
- (galaxy.datatypes.tracks.UCSCTrackHub attribute)

compressed (galaxy.datatypes.annotation.Augustus attribute)
- (galaxy.datatypes.binary.CompressedArchive attribute)
- (galaxy.datatypes.binary.Xlsx attribute)
- (galaxy.datatypes.tabular.Eland attribute)
- (galaxy.datatypes.tabular.VcfGz attribute)
- (galaxy.model.JobExportHistoryArchive attribute)
compressed_format (galaxy.datatypes.binary.Bz2DynamicCompressedArchive attribute)
- (galaxy.datatypes.binary.GzDynamicCompressedArchive attribute)
- (galaxy.datatypes.tabular.Eland attribute)
- (galaxy.datatypes.tabular.VcfGz attribute)
CompressedArchive (class in galaxy.datatypes.binary)
CompressedFile (class in galaxy.util.compression_utils)
CompressedZipArchive (class in galaxy.datatypes.binary)
compute_collection_info() (galaxy.workflow.modules.WorkflowModule method)
compute_fasta_length() (in module galaxy.datatypes.converters.fasta_to_len)
compute_outputs() (galaxy.jobs.JobWrapper method)
compute_runtime_state() (galaxy.workflow.modules.ToolModule method)
- (galaxy.workflow.modules.WorkflowModule method)
ComputeEnvironment (class in galaxy.jobs)
concat_messages() (tool_shed.tools.tool_validator.ToolValidator method)
ConcreteObjectStore (class in galaxy.objectstore)
cond_plural() (galaxy.util.inflection.Inflector method)
conda_build_available() (galaxy.tool_util.deps.conda_util.CondaContext property)
conda_build_target_str() (in module galaxy.tool_util.deps.mulled.util)
conda_info() (galaxy.tool_util.deps.conda_util.CondaContext method)
conda_version() (galaxy.tool_util.deps.conda_util.CondaContext property)
CondaContext (class in galaxy.tool_util.deps.conda_util)
CondaDependencyResolver (class in galaxy.tool_util.deps.resolvers.conda)
CondaSearch (class in galaxy.tool_util.deps.mulled.mulled_search)
CondaTarget (class in galaxy.tool_util.deps.conda_util)
Conditional (class in galaxy.tools.parameters.grouping)
CONDITIONAL (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute)
ConditionalDependencies (class in galaxy.dependencies)
ConditionalWhen (class in galaxy.tools.parameters.grouping)
condor_stop() (in module galaxy.jobs.runners.util.condor)
condor_submit() (in module galaxy.jobs.runners.util.condor)
CondorJobRunner (class in galaxy.jobs.runners.condor)
conf_defaults (galaxy.containers.ContainerInterface attribute)
- (galaxy.containers.docker.DockerCLIInterface attribute)
- (galaxy.containers.docker.DockerInterface attribute)
- (galaxy.containers.docker_swarm.DockerSwarmInterface attribute)
conf_run_kwopts (galaxy.containers.docker.DockerInterface attribute)
config (galaxy.model.CloudAuthz attribute)
- (galaxy.model.VisualizationRevision attribute)
- (galaxy.model.WorkflowStep attribute)
config_directories_from_setting() (in module galaxy.util)
config_directory() (galaxy.jobs.ComputeEnvironment method)
- (galaxy.jobs.SimpleComputeEnvironment method)
config_elems_to_xml_file() (galaxy.tool_shed.galaxy_install.tools.tool_panel_manager.ToolPanelManager method)
config_exception() (in module galaxy.jobs)
config_file_from_args() (in module galaxy.util.script)
config_is_ini() (galaxy.main.GalaxyConfigBuilder property)
config_options (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver attribute)
- (galaxy.tool_util.deps.resolvers.DependencyResolver attribute)
config_paths() (galaxy.config.config_manage.App property)
config_to_dict() (in module galaxy.objectstore)
ConfigDoesNotAllowException
ConfigSerializer (class in galaxy.managers.configuration)
Configuration (class in galaxy.webapps.reports.config)
- (in module galaxy.config)
- (in module tool_shed.webapp.config)
ConfigurationApiTestCase (class in galaxy_test.api.test_configuration)
ConfigurationController (class in galaxy.webapps.galaxy.api.configuration)
- (class in tool_shed.webapp.api.configuration)
ConfigurationError, [1], [2]
configure() (galaxy_test.base.instrument.StructuredTestDataPlugin method)
configure_and_load() (galaxy.tools.data.RefgenieToolDataTable method)
- (galaxy.tools.data.TabularToolDataTable method)
configure_entry_point() (galaxy.managers.interactivetool.InteractiveToolManager method)
configure_entry_points() (galaxy.managers.interactivetool.InteractiveToolManager method)
configure_fluent_log() (galaxy.app.UniverseApplication method)
configure_logging() (in module galaxy.config)
configure_provider() (galaxy.managers.cloud.CloudManager static method)
configured (galaxy.model.InteractiveToolEntryPoint attribute)
configured_pools() (galaxy.web_stack.ApplicationStack property)
- (galaxy.web_stack.UWSGIApplicationStack property)
- (galaxy.web_stack.WeblessApplicationStack property)
ConfiguredFileSources (class in galaxy.files)
ConfiguredFileSourcesConfig (class in galaxy.files)
ConfiguresGalaxyMixin (class in galaxy.config)
ConfiguresHandlers (class in galaxy.web_stack.handlers)
ConfigWatchers (class in galaxy.config_watchers)
Conflict
connect() (galaxy.jobs.runners.util.cli.shell.rsh.ParamikoShell method)
- (in module galaxy.util.sqlite)
ConnectAction (class in galaxy.workflow.refactor.schema)
ConnectedValue (class in galaxy.tools.parameters.basic)
connection() (galaxy.queue_worker.ControlTask property)
connection_configuration() (galaxy.tool_util.deps.container_classes.DockerContainer property)
- (galaxy.tool_util.deps.container_classes.SingularityContainer property)
connection_drop_forced (galaxy.workflow.refactor.schema.RefactorActionExecutionMessageTypeEnum attribute)
connection_from_config() (in module galaxy.queues)
connections (galaxy.model.WorkflowStepInput attribute)
ConnectivityTable (class in galaxy.datatypes.tabular)
ConsensusTaxonomy (class in galaxy.datatypes.mothur)
ConsensusXML (class in galaxy.datatypes.proteomics)
constraint() (galaxy.containers.docker_model.DockerNodeLabel property)
constraint_add() (galaxy.containers.docker_model.DockerService method)
constraint_string() (galaxy.containers.docker_model.DockerNodeLabel property)
constraints() (galaxy.containers.docker_model.DockerNodeLabels property)
- (galaxy.containers.docker_model.DockerService property)
contact_owner() (tool_shed.webapp.controllers.repository.RepositoryController method)
contained() (galaxy.managers.containers.ContainerManagerMixin method)
- (galaxy.managers.history_contents.HistoryContentsManager method)
contained_class (galaxy.managers.containers.ContainerManagerMixin attribute)
- (galaxy.managers.containers.DatasetCollectionAsContainerManagerMixin attribute)
- (galaxy.managers.containers.LibraryFolderAsContainerManagerMixin attribute)
- (galaxy.managers.history_contents.HistoryContentsManager attribute)
contained_class_manager_class (galaxy.managers.history_contents.HistoryContentsManager attribute)
contained_class_type_name (galaxy.managers.history_contents.HistoryContentsManager attribute)
Container (class in galaxy.containers)
- (class in galaxy.tool_util.deps.container_classes)
container (galaxy.model.Job attribute)
container_class (galaxy.containers.ContainerInterface attribute)
- (galaxy.containers.docker.DockerInterface attribute)
- (galaxy.containers.docker_swarm.DockerSwarmInterface attribute)
container_description() (galaxy.tool_util.deps.containers.ResolvedContainerDescription property)
container_from_element() (in module galaxy.tool_util.deps.requirements)
container_ids() (galaxy.web.proxy.ProxyMapping property)
container_info (galaxy.model.JobContainerAssociation attribute)
container_interface() (galaxy.web.proxy.ProxyMapping property)
container_monitor_command() (galaxy.jobs.JobWrapper method)
container_name (galaxy.model.JobContainerAssociation attribute)
container_resolver() (galaxy.tool_util.deps.containers.ResolvedContainerDescription property)
container_run_args() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method)
container_spec_option_map (galaxy.containers.docker_swarm.DockerSwarmAPIInterface attribute)
container_testing() (in module galaxy.tool_util.deps.mulled.mulled_update_singularity_containers)
container_type (galaxy.containers.ContainerInterface attribute)
- (galaxy.containers.docker.DockerAPIInterface attribute)
- (galaxy.containers.docker.DockerCLIInterface attribute)
- (galaxy.containers.docker_swarm.DockerSwarmAPIInterface attribute)
- (galaxy.containers.docker_swarm.DockerSwarmCLIInterface attribute)
- (galaxy.model.JobContainerAssociation attribute)
- (galaxy.tool_util.deps.container_classes.DockerContainer attribute)
- (galaxy.tool_util.deps.container_classes.SingularityContainer attribute)
- (galaxy.tool_util.deps.container_resolvers.explicit.ExplicitSingularityContainerResolver attribute)
- (galaxy.tool_util.deps.container_resolvers.explicit.FallbackContainerResolver attribute)
- (galaxy.tool_util.deps.container_resolvers.explicit.FallbackNoRequirementsSingularityContainerResolver attribute)
- (galaxy.tool_util.deps.container_resolvers.explicit.FallbackSingularityContainerResolver attribute)
- (galaxy.tool_util.deps.container_resolvers.explicit.RequiresGalaxyEnvironmentSingularityContainerResolver attribute)
ContainerCLIError
ContainerDependency (class in galaxy.tool_util.deps.resolvers)
ContainerDescription (class in galaxy.tool_util.deps.requirements)
ContainerFinder (class in galaxy.tool_util.deps.containers)
ContainerImageNotFound
ContainerInterface (class in galaxy.containers)
ContainerInterfaceConfig (class in galaxy.containers)
containerize_command() (galaxy.tool_util.deps.container_classes.Container method)
- (galaxy.tool_util.deps.container_classes.DockerContainer method)
- (galaxy.tool_util.deps.container_classes.SingularityContainer method)
ContainerManagerMixin (class in galaxy.managers.containers)
ContainerNotFound
ContainerPort (class in galaxy.containers)
ContainerRegistry (class in galaxy.tool_util.deps.containers)
ContainerResolutionAPIController (class in galaxy.webapps.galaxy.api.container_resolution)
ContainerResolutionView (class in galaxy.tool_util.deps.views)
ContainerResolver (class in galaxy.tool_util.deps.container_resolvers)
ContainerRunError
containers_config_file() (galaxy.containers.ContainerInterface property)
ContainerVolume (class in galaxy.containers)
contains_collection() (galaxy.model.HistoryDatasetCollectionAssociation method)
contains_folder() (tool_shed.utility_containers.utility_container_manager.Folder method)
contains_repository_dependency() (tool_shed.utility_containers.utility_container_manager.Folder method)
contains_required_data() (in module galaxy.authnz.psa_authnz)
contains_workflow_parameter() (in module galaxy.tools.parameters.basic)
content (galaxy.model.FormValues attribute)
- (galaxy.model.PageRevision attribute)
- (galaxy.tours.TourStep attribute)
content_format (galaxy.model.PageRevision attribute)
content_id (galaxy.workflow.refactor.schema.UpgradeSubworkflowAction attribute)
content_id() (galaxy.model.WorkflowStep property)
content_type (galaxy.model.HistoryDatasetAssociation attribute)
- (galaxy.model.HistoryDatasetCollectionAssociation attribute)
contents() (galaxy.managers.containers.ContainerManagerMixin method)
- (galaxy.managers.history_contents.HistoryContentsManager method)
- (galaxy.webapps.galaxy.api.dataset_collections.DatasetCollectionsController method)
contents_count() (galaxy.managers.history_contents.HistoryContentsManager method)
contents_iter() (galaxy.model.History method)
contents_near() (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method)
contents_query() (galaxy.managers.history_contents.HistoryContentsManager method)
context (galaxy.model.UserAction attribute)
context_remove() (galaxy.util.custom_logging.fluent_log.FluentTraceLogger method)
context_set() (galaxy.util.custom_logging.fluent_log.FluentTraceLogger method)
continue_pipeline() (galaxy.authnz.psa_authnz.Strategy method)
control_queues() (galaxy.queue_worker.ControlTask property)
control_queues_from_config() (in module galaxy.queues)
controller_name (galaxy.webapps.galaxy.api.annotations.HistoryAnnotationsController attribute)
- (galaxy.webapps.galaxy.api.annotations.HistoryContentAnnotationsController attribute)
- (galaxy.webapps.galaxy.api.annotations.WorkflowAnnotationsController attribute)
- (galaxy.webapps.galaxy.api.extended_metadata.HistoryDatasetExtendMetadataController attribute)
- (galaxy.webapps.galaxy.api.extended_metadata.LibraryDatasetExtendMetadataController attribute)
- (galaxy.webapps.galaxy.api.item_tags.HistoryContentTagsController attribute)
- (galaxy.webapps.galaxy.api.item_tags.HistoryTagsController attribute)
- (galaxy.webapps.galaxy.api.item_tags.WorkflowTagsController attribute)
- (galaxy.webapps.galaxy.api.provenance.HDAProvenanceController attribute)
- (galaxy.webapps.galaxy.api.provenance.LDDAProvenanceController attribute)
ControllerUnavailable
ControlTask (class in galaxy.queue_worker)
convert_bed_coords_to_gff() (in module galaxy.datatypes.util.gff_util)
convert_bytes() (in module galaxy.objectstore)
convert_dataset() (galaxy.datatypes.data.Data method)
- (galaxy.datatypes.dataproviders.dataset.ConvertedDatasetDataProvider method)
- (galaxy.model.DatasetInstance method)
convert_gff_coords_to_bed() (in module galaxy.datatypes.util.gff_util)
convert_legacy_destinations() (galaxy.jobs.JobConfiguration method)
convert_newlines() (in module galaxy.datatypes.sniff)
convert_newlines_sep2tabs() (in module galaxy.datatypes.sniff)
convert_permitted_action_strings() (galaxy.security.RBACAgent method)
- (tool_shed.webapp.security.RBACAgent method)
convert_statjob_to_bunches() (galaxy.jobs.runners.pbs.PBSJobRunner method)
convert_to_csv() (in module galaxy.datatypes.converters.tabular_csv)
convert_to_tsv() (in module galaxy.datatypes.converters.tabular_csv)
converted() (galaxy.webapps.galaxy.api.datasets.DatasetsController method)
ConvertedDatasetDataProvider (class in galaxy.datatypes.dataproviders.dataset)
converter_safe() (galaxy.tools.parameters.basic.DataToolParameter method)
- (galaxy.tools.parameters.DataToolParameter method)
ConverterDependencyException
converters() (galaxy.webapps.galaxy.api.datatypes.DatatypesController method)
cookie_path() (galaxy.webapps.base.webapp.GalaxyWebTransaction property)
cookies (galaxy.web.framework.base.Request attribute)
Cool (class in galaxy.datatypes.binary)
copied_from_history_dataset_association (galaxy.model.HistoryDatasetAssociation attribute)
- (galaxy.model.LibraryDatasetDatasetAssociation attribute)
copied_from_history_dataset_association_id (galaxy.model.HistoryDatasetAssociation attribute)
- (galaxy.model.LibraryDatasetDatasetAssociation attribute)
copied_from_history_dataset_collection_association (galaxy.model.HistoryDatasetCollectionAssociation attribute)
copied_from_history_dataset_collection_association_id (galaxy.model.HistoryDatasetCollectionAssociation attribute)
copied_from_job_id (galaxy.model.Job attribute)
copied_from_library_dataset_dataset_association (galaxy.model.HistoryDatasetAssociation attribute)
- (galaxy.model.LibraryDatasetDatasetAssociation attribute)
copied_from_library_dataset_dataset_association_id (galaxy.model.HistoryDatasetAssociation attribute)
- (galaxy.model.LibraryDatasetDatasetAssociation attribute)
copied_to_history_dataset_associations (galaxy.model.HistoryDatasetAssociation attribute)
- (galaxy.model.LibraryDatasetDatasetAssociation attribute)
copied_to_history_dataset_collection_associations (galaxy.model.HistoryDatasetCollectionAssociation attribute)
copied_to_library_dataset_dataset_associations (galaxy.model.HistoryDatasetAssociation attribute)
- (galaxy.model.LibraryDatasetDatasetAssociation attribute)
copy() (galaxy.datatypes.util.gff_util.GFFFeature method)
- (galaxy.datatypes.util.gff_util.GFFInterval method)
- (galaxy.managers.base.ModelManager method)
- (galaxy.managers.collections.DatasetCollectionManager method)
- (galaxy.managers.datasets.DatasetManager method)
- (galaxy.managers.hdas.HDAManager method)
- (galaxy.managers.histories.HistoryManager method)
- (galaxy.managers.pages.PageManager method)
- (galaxy.model.DatasetCollection method)
- (galaxy.model.History method)
- (galaxy.model.HistoryDatasetAssociation method)
- (galaxy.model.HistoryDatasetCollectionAssociation method)
- (galaxy.model.ItemTagAssociation method)
- (galaxy.model.JobParameter method)
- (galaxy.model.LibraryDatasetDatasetAssociation method)
- (galaxy.model.Visualization method)
- (galaxy.model.VisualizationRevision method)
- (galaxy.model.Workflow method)
- (galaxy.model.WorkflowOutput method)
- (galaxy.model.WorkflowStepConnection method)
- (galaxy.model.WorkflowStepInput method)
- (galaxy.tool_util.cwl.cwltool_deps.LoadingContext method)
- (galaxy.tool_util.cwl.cwltool_deps.RuntimeContext method)
- (galaxy.tool_util.deps.requirements.ToolRequirement method)
- (galaxy.tools.DefaultToolState method)
- (galaxy.tools.toolbox.panel.ToolSection method)
- (galaxy.tools.toolbox.ToolSection method)
- (galaxy.util.odict.odict method)
- (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method)
- (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method)
copy_attributes() (galaxy.model.DatasetInstance method)
- (galaxy.model.HistoryDatasetAssociation method)
copy_database_template() (in module galaxy_test.driver.driver_util)
copy_dataset_permissions() (galaxy.job_execution.output_collect.PermissionProvider method)
- (galaxy.model.security.GalaxyRBACAgent method)
- (galaxy.model.store.discover.PermissionProvider method)
- (galaxy.model.store.discover.UnusedPermissionProvider method)
copy_datasets() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method)
copy_disk_sample_files_to_dir() (tool_shed.tools.tool_validator.ToolValidator method)
copy_file_from_manifest() (in module galaxy.tool_shed.util.hg_util)
- (in module tool_shed.util.hg_util)
copy_from() (galaxy.model.HistoryDatasetAssociation method)
copy_hda_to_library_folder() (galaxy.webapps.base.controller.UsesLibraryMixinItems method)
copy_history() (galaxy_test.selenium.test_history_multi_view.HistoryMultiViewTestCase method)
copy_item_annotation() (galaxy.model.item_attrs.UsesAnnotations method)
copy_ldda() (galaxy.managers.hdas.HDAManager method)
copy_library_permissions() (galaxy.model.security.GalaxyRBACAgent method)
copy_list() (in module galaxy.model)
copy_review() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method)
copy_safe_peek (galaxy.datatypes.data.Data attribute)
- (galaxy.datatypes.images.Gmaj attribute)
- (galaxy.datatypes.images.Laj attribute)
copy_sample_file() (in module galaxy.tool_shed.util.tool_util)
copy_sample_files() (in module galaxy.tool_shed.util.tool_util)
copy_tags_from() (galaxy.model.HasTags method)
- (galaxy.model.StoredWorkflow method)
copy_tags_to() (galaxy.model.HistoryDatasetAssociation method)
copy_to() (galaxy.model.WorkflowStep method)
copy_to_collection() (galaxy.model.DatasetCollectionElement method)
copy_value() (galaxy.model.custom_types.JSONType method)
CorePlugin (class in galaxy.job_metrics.instrumenters.core)
CoreWorkflowSchedulingPlugin (class in galaxy.workflow.schedulers.core)
count_data_lines() (galaxy.datatypes.data.Text method)
count_lines() (in module galaxy.datatypes.molecules)
count_repositories_in_category() (in module tool_shed.util.shed_util_common)
count_special_lines() (in module galaxy.datatypes.util.generic_util)
country (galaxy.model.UserAddress attribute)
CountTable (class in galaxy.datatypes.mothur)
Cpt (class in galaxy.datatypes.binary)
CpuInfoPlugin (class in galaxy.job_metrics.instrumenters.cpuinfo)
cpus() (galaxy.containers.docker_model.DockerNode property)
- (galaxy.containers.docker_model.DockerService property)
- (galaxy.containers.docker_model.DockerTask property)
CRAM (class in galaxy.datatypes.binary)
create() (galaxy.managers.base.ModelManager method)
- (galaxy.managers.collections.DatasetCollectionManager method)
- (galaxy.managers.datasets.DatasetManager method)
- (galaxy.managers.folders.FolderManager method)
- (galaxy.managers.hdas.HDAManager method)
- (galaxy.managers.libraries.LibraryManager method)
- (galaxy.managers.pages.PageManager method)
- (galaxy.managers.roles.RoleManager method)
- (galaxy.managers.users.UserManager method)
- (galaxy.objectstore.BaseObjectStore method)
- (galaxy.objectstore.ObjectStore method)
- (galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController method)
- (galaxy.webapps.galaxy.api.cloudauthz.CloudAuthzController method)
- (galaxy.webapps.galaxy.api.dataset_collections.DatasetCollectionsController method)
- (galaxy.webapps.galaxy.api.dynamic_tools.DynamicToolsController method)
- (galaxy.webapps.galaxy.api.extended_metadata.BaseExtendedMetadataController method)
- (galaxy.webapps.galaxy.api.folder_contents.FolderContentsController method)
- (galaxy.webapps.galaxy.api.folders.FoldersController method)
- (galaxy.webapps.galaxy.api.forms.FormDefinitionAPIController method)
- (galaxy.webapps.galaxy.api.groups.GroupAPIController method)
- (galaxy.webapps.galaxy.api.histories.HistoriesController method)
- (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method)
- (galaxy.webapps.galaxy.api.item_tags.BaseItemTagsController method)
- (galaxy.webapps.galaxy.api.job_files.JobFilesAPIController method)
- (galaxy.webapps.galaxy.api.job_ports.JobPortsAPIController method)
- (galaxy.webapps.galaxy.api.jobs.JobController method)
- (galaxy.webapps.galaxy.api.libraries.LibrariesController method)
- (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method)
- (galaxy.webapps.galaxy.api.metrics.MetricsController method)
- (galaxy.webapps.galaxy.api.page_revisions.PageRevisionsController method)
- (galaxy.webapps.galaxy.api.pages.PagesController method)
- (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method)
- (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method)
- (galaxy.webapps.galaxy.api.roles.FastAPIRoles method)
- (galaxy.webapps.galaxy.api.roles.RoleAPIController method)
- (galaxy.webapps.galaxy.api.search.SearchController method)
- (galaxy.webapps.galaxy.api.tools.ToolsController method)
- (galaxy.webapps.galaxy.api.uploads.UploadsAPIController method)
- (galaxy.webapps.galaxy.api.users.UserAPIController method)
- (galaxy.webapps.galaxy.api.visualizations.VisualizationsController method)
- (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method)
- (galaxy.webapps.galaxy.controllers.page.PageController method)
- (galaxy.webapps.galaxy.controllers.user.User method)
- (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method)
- (tool_shed.managers.groups.GroupManager method)
- (tool_shed.managers.repositories.RepoManager method)
- (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
- (tool_shed.webapp.api.categories.CategoriesController method)
- (tool_shed.webapp.api.groups.GroupsController method)
- (tool_shed.webapp.api.repositories.RepositoriesController method)
- (tool_shed.webapp.api.users.UsersController method)
- (tool_shed.webapp.controllers.user.User method)
create_and_write_tmp_file() (in module galaxy.util.tool_shed.xml_util)
create_api_key() (galaxy.managers.api_keys.ApiKeyManager method)
- (galaxy.managers.users.UserManager method)
- (galaxy.webapps.base.controller.CreatesApiKeysMixin method)
create_applet_tag_peek() (in module galaxy.datatypes.images)
create_archive() (in module galaxy.tools.imp_exp.export_history)
create_category() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
- (tool_shed.webapp.controllers.admin.AdminController method)
create_changeset_revision() (tool_shed.webapp.api.repositories.RepositoriesController method)
create_collection() (galaxy.tools.actions.OutputCollections method)
create_compiler_class() (in module galaxy.util.template)
create_component() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method)
create_dataset() (galaxy.model.store.discover.ModelPersistenceContext method)
create_dataset_collection() (galaxy.managers.collections.DatasetCollectionManager method)
create_dataset_request() (galaxy_test.base.populators.LibraryPopulator method)
create_dynamic_tool() (galaxy.tools.ToolBox method)
- (galaxy.tools.toolbox.AbstractToolBox method)
- (galaxy.tools.toolbox.base.AbstractToolBox method)
create_element() (in module galaxy.util.tool_shed.xml_util)
create_entry_points() (galaxy.managers.interactivetool.InteractiveToolManager method)
create_env_var_dict() (galaxy.tool_shed.galaxy_install.tool_dependencies.env_manager.EnvManager method)
create_extended_metadata() (galaxy.webapps.base.controller.UsesExtendedMetadataMixin method)
create_extra_files_path() (galaxy.model.Dataset method)
create_file() (galaxy.datatypes.dataproviders.external.TempfileDataProvider method)
create_for_history() (galaxy.model.JobExportHistoryArchive static method)
create_form() (galaxy.webapps.galaxy.controllers.forms.Forms method)
create_galaxy_docker_image() (tool_shed.webapp.controllers.repository.RepositoryController method)
create_group() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method)
- (tool_shed.util.admin_util.Admin method)
create_hdca() (galaxy.job_execution.output_collect.JobContext method)
- (galaxy.model.store.discover.SessionlessModelPersistenceContext method)
create_hgrc_file() (in module tool_shed.util.hg_util)
create_history() (galaxy_test.selenium.test_histories_list.SavedHistoriesTestCase method)
- (galaxy_test.selenium.test_published_histories_grid.HistoryGridTestCase method)
create_interactivetool() (galaxy.managers.interactivetool.InteractiveToolManager method)
create_item_slug() (galaxy.webapps.base.controller.SharableMixin method)
create_job() (in module galaxy.tools.actions.upload_common)
create_library_folder() (galaxy.job_execution.output_collect.JobContext method)
- (galaxy.model.store.discover.ModelPersistenceContext method)
- (galaxy.model.store.discover.SessionlessModelPersistenceContext method)
create_list_filter() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method)
create_list_from_pairs() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method)
create_list_in_history() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method)
create_list_of_list_in_history() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method)
create_list_of_pairs_in_history() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method)
create_list_payload() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method)
create_log_file() (galaxy.jobs.runners.godocker.GodockerJobRunner method)
create_mako_template_lookup() (galaxy.webapps.base.webapp.WebApplication method)
create_nested_collection() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method)
create_new_current() (galaxy.webapps.galaxy.controllers.history.HistoryController method)
create_new_user() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method)
- (tool_shed.util.admin_util.Admin method)
create_numeric_filter() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method)
create_or_update_env_shell_file() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder.EnvFileBuilder static method)
create_or_update_repository_metadata() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method)
create_or_update_tool_dependency() (in module galaxy.tool_shed.util.tool_dependency_util)
create_or_update_tool_shed_repository() (in module galaxy.tool_shed.util.repository_util)
- (in module tool_shed.util.repository_util)
create_or_update_tool_shed_repository_record() (galaxy.tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager method)
create_or_update_tool_shed_repository_records() (galaxy.tool_shed.galaxy_install.tool_migration_manager.ToolMigrationManager method)
create_or_update_workflow_output() (galaxy.model.WorkflowStep method)
create_or_verify_database() (in module galaxy.model.migrate.check)
- (in module galaxy.model.tool_shed_install.migrate.check)
- (in module tool_shed.webapp.model.migrate.check)
create_pair_in_history() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method)
create_pair_payload() (galaxy_test.base.populators.BaseDatasetCollectionPopulator method)
create_panel_section() (in module galaxy.queue_worker)
create_paramfile() (in module galaxy.tools.actions.upload_common)
create_private_user_role() (galaxy.model.security.GalaxyRBACAgent method)
- (galaxy.security.RBACAgent method)
- (tool_shed.webapp.security.CommunityRBACAgent method)
- (tool_shed.webapp.security.RBACAgent method)
create_quota() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method)
- (galaxy_test.base.populators.BaseDatasetPopulator method)
create_random_port_spec() (galaxy.containers.docker_swarm.DockerSwarmAPIInterface static method)
create_repo_info_dict() (in module tool_shed.util.repository_util)
create_report() (galaxy.tools.errors.ErrorReporter method)
create_repository() (in module tool_shed.util.repository_util)
- (tool_shed.webapp.controllers.repository.RepositoryController method)
create_repository_admin_role() (in module tool_shed.util.repository_util)
create_repository_dependency() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
create_repository_dependency_objects() (galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager method)
create_repository_dict_for_proprietary_datatypes() (galaxy.tool_shed.galaxy_install.datatypes.custom_datatype_manager.CustomDatatypeLoader method)
create_repository_review() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
create_review() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method)
create_role() (galaxy.model.security.GalaxyRBACAgent method)
- (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method)
- (galaxy_test.base.populators.BaseDatasetPopulator method)
- (tool_shed.util.admin_util.Admin method)
create_section() (galaxy.tools.toolbox.AbstractToolBox method)
- (galaxy.tools.toolbox.base.AbstractToolBox method)
create_sequencer_form_definition() (in module galaxy.model.migrate.versions.0067_populate_sequencer_table)
create_social_auth() (galaxy.model.UserAuthnzToken class method)
create_string_filter() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method)
create_subworkflow_invocation_for_step() (galaxy.model.WorkflowInvocation method)
create_table() (in module galaxy.model.migrate.versions.util)
create_tag_filter() (galaxy.managers.taggable.TaggableFilterMixin method)
create_tag_handler_session() (galaxy.model.tags.TagHandler method)
create_temporary_tool_dependencies_config() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Repository method)
create_time (galaxy.model.APIKeys attribute)
- (galaxy.model.CloudAuthz attribute)
- (galaxy.model.DataManagerHistoryAssociation attribute)
- (galaxy.model.DataManagerJobAssociation attribute)
- (galaxy.model.Dataset attribute)
- (galaxy.model.DatasetCollection attribute)
- (galaxy.model.DatasetPermissions attribute)
- (galaxy.model.DefaultQuotaAssociation attribute)
- (galaxy.model.DeferredJob attribute)
- (galaxy.model.DynamicTool attribute)
- (galaxy.model.Event attribute)
- (galaxy.model.FormDefinition attribute)
- (galaxy.model.FormDefinitionCurrent attribute)
- (galaxy.model.FormValues attribute)
- (galaxy.model.GalaxySession attribute)
- (galaxy.model.GalaxySessionToHistoryAssociation attribute)
- (galaxy.model.Group attribute)
- (galaxy.model.GroupQuotaAssociation attribute)
- (galaxy.model.GroupRoleAssociation attribute)
- (galaxy.model.History attribute)
- (galaxy.model.HistoryDatasetAssociation attribute)
- (galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization attribute)
- (galaxy.model.HistoryDatasetCollectionAssociation attribute)
- (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute)
- (galaxy.model.Job attribute)
- (galaxy.model.JobStateHistory attribute)
- (galaxy.model.Library attribute)
- (galaxy.model.LibraryDataset attribute)
- (galaxy.model.LibraryDatasetDatasetAssociation attribute)
- (galaxy.model.LibraryDatasetDatasetAssociationPermissions attribute)
- (galaxy.model.LibraryDatasetPermissions attribute)
- (galaxy.model.LibraryFolder attribute)
- (galaxy.model.LibraryFolderPermissions attribute)
- (galaxy.model.LibraryPermissions attribute)
- (galaxy.model.MetadataFile attribute)
- (galaxy.model.Page attribute)
- (galaxy.model.PageRevision attribute)
- (galaxy.model.Quota attribute)
- (galaxy.model.Role attribute)
- (galaxy.model.StoredWorkflow attribute)
- (galaxy.model.Task attribute)
- (galaxy.model.tool_shed_install.RepositoryDependency attribute)
- (galaxy.model.tool_shed_install.RepositoryRepositoryDependencyAssociation attribute)
- (galaxy.model.tool_shed_install.ToolDependency attribute)
- (galaxy.model.tool_shed_install.ToolShedRepository attribute)
- (galaxy.model.tool_shed_install.ToolVersion attribute)
- (galaxy.model.TransferJob attribute)
- (galaxy.model.User attribute)
- (galaxy.model.UserAction attribute)
- (galaxy.model.UserAddress attribute)
- (galaxy.model.UserGroupAssociation attribute)
- (galaxy.model.UserQuotaAssociation attribute)
- (galaxy.model.UserRoleAssociation attribute)
- (galaxy.model.Visualization attribute)
- (galaxy.model.VisualizationRevision attribute)
- (galaxy.model.Workflow attribute)
- (galaxy.model.WorkflowInvocation attribute)
- (galaxy.model.WorkflowInvocationStep attribute)
- (galaxy.model.WorkflowStep attribute)
- (tool_shed.webapp.model.APIKeys attribute)
- (tool_shed.webapp.model.Category attribute)
- (tool_shed.webapp.model.ComponentReview attribute)
- (tool_shed.webapp.model.GalaxySession attribute)
- (tool_shed.webapp.model.Group attribute)
- (tool_shed.webapp.model.GroupRoleAssociation attribute)
- (tool_shed.webapp.model.Repository attribute)
- (tool_shed.webapp.model.RepositoryMetadata attribute)
- (tool_shed.webapp.model.RepositoryRatingAssociation attribute)
- (tool_shed.webapp.model.RepositoryReview attribute)
- (tool_shed.webapp.model.RepositoryRoleAssociation attribute)
- (tool_shed.webapp.model.Role attribute)
- (tool_shed.webapp.model.User attribute)
- (tool_shed.webapp.model.UserGroupAssociation attribute)
- (tool_shed.webapp.model.UserRoleAssociation attribute)
create_timestamps() (in module galaxy.model.migrate.versions.0165_add_content_update_time)
create_tool() (galaxy.managers.tools.DynamicToolManager method)
- (galaxy.tools.ToolBox method)
- (galaxy.tools.toolbox.AbstractToolBox method)
- (galaxy.tools.toolbox.base.AbstractToolBox method)
- (galaxy_test.base.populators.BaseDatasetPopulator method)
create_tool_dependency_objects() (in module galaxy.tool_shed.util.tool_dependency_util)
create_tool_dependency_with_initialized_env_sh_file() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler.Repository method)
create_tool_filter() (galaxy.managers.tools.ToolFilterMixin method)
create_tool_from_path() (galaxy_test.base.populators.BaseDatasetPopulator method)
create_tool_from_source() (in module galaxy.tools)
create_unique_slug() (galaxy.managers.sharable.SharableModelManager method)
create_user() (galaxy.authnz.custos_authnz.CustosAuthnz method)
- (galaxy.authnz.managers.AuthnzManager method)
- (galaxy.model.UserAuthnzToken class method)
- (galaxy.webapps.galaxy.controllers.authnz.OIDC method)
create_user_in_galaxy() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
create_user_role() (galaxy.model.security.GalaxyRBACAgent method)
- (tool_shed.webapp.security.CommunityRBACAgent method)
- (tool_shed.webapp.security.RBACAgent method)
create_visualization() (galaxy.webapps.base.controller.UsesVisualizationMixin method)
create_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method)
create_workflow_response() (galaxy_test.base.populators.BaseWorkflowPopulator method)
create_working_directory_for_job() (in module galaxy.job_execution.setup)
created_from_basename (galaxy.model.Dataset attribute)
created_from_basename() (galaxy.model.DatasetInstance property)
- (galaxy.model.store.discover.JsonCollectedDatasetMatch property)
created_time (galaxy.model.GenomeIndexToolData attribute)
- (galaxy.model.InteractiveToolEntryPoint attribute)
- (galaxy.model.JobContainerAssociation attribute)
created_with_galaxy_version() (galaxy.jobs.JobWrapper property)
CreatedWorkflow (class in galaxy.managers.workflows)
CreatesApiKeysMixin (class in galaxy.webapps.base.controller)
CreateView (class in galaxy.model.view.utils)
creating_job() (galaxy.managers.datasets.DatasetAssociationManager method)
- (galaxy.model.DatasetInstance property)
creating_job_associations (galaxy.model.HistoryDatasetAssociation attribute)
- (galaxy.model.HistoryDatasetCollectionAssociation attribute)
- (galaxy.model.LibraryDatasetDatasetAssociation attribute)
creator (galaxy.workflow.refactor.schema.UpdateCreatorAction attribute)
creator_metadata (galaxy.model.Workflow attribute)
csFasta (class in galaxy.datatypes.sequence)
css() (in module galaxy.web.framework.helpers)
CSV (class in galaxy.datatypes.tabular)
ctx_rev (galaxy.model.tool_shed_install.ToolShedRepository attribute)
CuffDiffSQlite (class in galaxy.datatypes.binary)
cur_filter_pref_name (galaxy.web.framework.helpers.grids.Grid attribute)
- (galaxy.web.legacy_framework.grids.Grid attribute)
cur_sort_key_pref_name (galaxy.web.framework.helpers.grids.Grid attribute)
- (galaxy.web.legacy_framework.grids.Grid attribute)
current (galaxy.model.FormDefinition attribute)
current_history (galaxy.model.GalaxySession attribute)
current_history() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
current_history_id (galaxy.model.GalaxySession attribute)
current_history_id() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
current_history_json() (galaxy.webapps.galaxy.controllers.history.HistoryController method)
current_state() (galaxy.containers.docker_model.DockerTask property)
current_state_time() (galaxy.containers.docker_model.DockerTask property)
current_user() (galaxy.managers.users.UserManager method)
CurrentUserSerializer (class in galaxy.managers.users)
CustomBuildsTestcase (class in galaxy_test.selenium.test_custom_builds)
CustomDatatypeLoader (class in galaxy.tool_shed.galaxy_install.datatypes.custom_datatype_manager)
CustomTrack (class in galaxy.datatypes.interval)
custos_auth (galaxy.model.User attribute)
CustosAuthnz (class in galaxy.authnz.custos_authnz)
CustosAuthnzToken (class in galaxy.model)
cut_and_decode() (galaxy.managers.folders.FolderManager method)
cut_the_prefix() (galaxy.managers.folders.FolderManager method)
CwlPageSource (class in galaxy.tool_util.parser.cwl)
CwlToolSource (class in galaxy.tool_util.parser.cwl)
CwlWorkflowOutput (class in galaxy.tool_util.cwl.runnable)
CycleError

D

DAA (class in galaxy.datatypes.binary)
daemonize() (galaxy.util.pastescript.serve.ServeCommand method)
DaemonizeException
Data (class in galaxy.datatypes.data)
DATA (galaxy.model.Dataset.conversion_messages attribute)
- (galaxy.model.DatasetInstance.conversion_messages attribute)
data (galaxy.model.ExtendedMetadata attribute)
- (galaxy.model.PSAPartial attribute)
DATA (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute)
DATA_COLLECTON (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute)
data_conversion_status() (galaxy.managers.hdas.HDAManager method)
data_line_offset (galaxy.datatypes.tabular.SraManifest attribute)
- (galaxy.datatypes.tabular.TabularData attribute)
data_manager_association (galaxy.model.Job attribute)
data_manager_config_elems_to_xml_file() (galaxy.tool_shed.galaxy_install.tools.data_manager.DataManagerHandler method)
data_manager_configs() (galaxy.config_watchers.ConfigWatchers property)
data_manager_histories (galaxy.model.User attribute)
data_manager_id (galaxy.model.DataManagerJobAssociation attribute)
data_manager_tar_file (in module tool_shed.test.functional.test_1460_data_managers)
data_managers_list() (galaxy.webapps.galaxy.controllers.data_manager.DataManager method)
data_managers_path() (galaxy.tool_shed.galaxy_install.tools.data_manager.DataManagerHandler property)
data_source_redirect() (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method)
data_sources (galaxy.datatypes.binary.Bam attribute)
- (galaxy.datatypes.binary.BigBed attribute)
- (galaxy.datatypes.binary.BigWig attribute)
- (galaxy.datatypes.data.Data attribute)
- (galaxy.datatypes.interval.Bed attribute)
- (galaxy.datatypes.interval.BedGraph attribute)
- (galaxy.datatypes.interval.ChromatinInteractions attribute)
- (galaxy.datatypes.interval.ENCODEPeak attribute)
- (galaxy.datatypes.interval.Gff attribute)
- (galaxy.datatypes.interval.Interval attribute)
- (galaxy.datatypes.interval.Wiggle attribute)
- (galaxy.datatypes.tabular.BaseVcf attribute)
- (galaxy.datatypes.tabular.Pileup attribute)
- (galaxy.datatypes.tabular.Sam attribute)
data_tables_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method)
data_types_list() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method)
database_conf() (in module galaxy_test.driver.driver_util)
DATABASE_OPERATION (galaxy.selenium.navigates_galaxy.WAIT_TYPES attribute)
DatabaseHeartbeat (class in galaxy.model.database_heartbeat)
DatabaseOperationTool (class in galaxy.tools)
DataCollectionToolParameter (class in galaxy.tools.parameters)
- (class in galaxy.tools.parameters.basic)
DataDestinationTool (class in galaxy.tools)
DataIn (class in galaxy.datatypes.genetics)
DataManager (class in galaxy.tools.data_manager.manager)
- (class in galaxy.webapps.galaxy.controllers.data_manager)
- (class in tool_shed.utility_containers.utility_container_manager)
DataManagerHandler (class in galaxy.tool_shed.galaxy_install.tools.data_manager)
DataManagerHistoryAssociation (class in galaxy.model)
DataManagerJobAssociation (class in galaxy.model)
DataManagers (class in galaxy.tools.data_manager.manager)
DataManagerTool (class in galaxy.tools)
DataManagerToolAction (class in galaxy.tools.actions.data_manager)
DataMeta (class in galaxy.datatypes.data)
DataMetaFilter (class in galaxy.tools.parameters.dynamic_options)
DataProvider (class in galaxy.datatypes.dataproviders.base)
dataprovider() (galaxy.datatypes.data.Data method)
dataprovider_factory() (in module galaxy.datatypes.dataproviders.decorators)
DataProviderRegistry (class in galaxy.visualization.data_providers.registry)
dataproviders (galaxy.datatypes.binary.Bam attribute)
- (galaxy.datatypes.binary.SQlite attribute)
- (galaxy.datatypes.data.Data attribute)
- (galaxy.datatypes.data.Text attribute)
- (galaxy.datatypes.graph.Sif attribute)
- (galaxy.datatypes.graph.Xgmml attribute)
- (galaxy.datatypes.interval.Gff attribute)
- (galaxy.datatypes.interval.Interval attribute)
- (galaxy.datatypes.interval.Wiggle attribute)
- (galaxy.datatypes.tabular.BaseCSV attribute)
- (galaxy.datatypes.tabular.BaseVcf attribute)
- (galaxy.datatypes.tabular.CSV attribute)
- (galaxy.datatypes.tabular.Pileup attribute)
- (galaxy.datatypes.tabular.Sam attribute)
- (galaxy.datatypes.tabular.Tabular attribute)
- (galaxy.datatypes.tabular.TabularData attribute)
- (galaxy.datatypes.tabular.TSV attribute)
- (galaxy.datatypes.xml.GenericXml attribute)
Dataset (class in galaxy.model)
dataset (galaxy.model.DatasetHash attribute)
- (galaxy.model.DatasetPermissions attribute)
- (galaxy.model.DatasetSource attribute)
- (galaxy.model.GenomeIndexToolData attribute)
- (galaxy.model.HistoryDatasetAssociation attribute)
- (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute)
- (galaxy.model.JobExportHistoryArchive attribute)
- (galaxy.model.JobToInputDatasetAssociation attribute)
- (galaxy.model.JobToInputLibraryDatasetAssociation attribute)
- (galaxy.model.JobToOutputDatasetAssociation attribute)
- (galaxy.model.JobToOutputLibraryDatasetAssociation attribute)
- (galaxy.model.LibraryDatasetDatasetAssociation attribute)
- (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute)
- (galaxy.model.WorkflowInvocationStepOutputDatasetAssociation attribute)
- (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute)
dataset() (galaxy.model.DatasetCollectionElement property)
- (galaxy.model.JobExternalOutputMetadata property)
Dataset.conversion_messages (class in galaxy.model)
Dataset.states (class in galaxy.model)
dataset_access_mapping() (galaxy.model.security.GalaxyRBACAgent method)
dataset_action_tuples() (galaxy.model.DatasetCollection property)
dataset_actions (galaxy.model.Role attribute)
dataset_collection (galaxy.model.ImplicitlyCreatedDatasetCollectionInput attribute)
- (galaxy.model.JobToImplicitOutputDatasetCollectionAssociation attribute)
- (galaxy.model.JobToInputDatasetCollectionAssociation attribute)
- (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute)
- (galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation attribute)
- (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute)
dataset_collection_description() (in module galaxy.tool_util.parser.output_collection_def)
dataset_collection_element (galaxy.model.JobToInputDatasetCollectionElementAssociation attribute)
dataset_collection_element_id (galaxy.model.JobToInputDatasetCollectionElementAssociation attribute)
dataset_collection_id (galaxy.model.DatasetCollectionElement attribute)
- (galaxy.model.ImplicitlyCreatedDatasetCollectionInput attribute)
- (galaxy.model.JobToImplicitOutputDatasetCollectionAssociation attribute)
- (galaxy.model.JobToInputDatasetCollectionAssociation attribute)
- (galaxy.model.JobToOutputDatasetCollectionAssociation attribute)
- (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute)
- (galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation attribute)
- (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute)
dataset_collection_instance (galaxy.model.JobToOutputDatasetCollectionAssociation attribute)
dataset_collection_populator() (galaxy_test.selenium.framework.TestWithSeleniumMixin property)
dataset_collections (galaxy.model.History attribute)
- (galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation attribute)
- (galaxy.model.HistoryDatasetCollectionRatingAssociation attribute)
- (galaxy.model.HistoryDatasetCollectionTagAssociation attribute)
- (galaxy.model.LibraryDatasetCollectionAnnotationAssociation attribute)
- (galaxy.model.LibraryDatasetCollectionRatingAssociation attribute)
- (galaxy.model.LibraryDatasetCollectionTagAssociation attribute)
- (galaxy.model.LibraryFolder attribute)
dataset_collector() (in module galaxy.job_execution.output_collect)
dataset_collector_descriptions() (galaxy.tool_util.parser.output_objects.ToolOutputCollection property)
dataset_collector_descriptions_from_elem() (in module galaxy.tool_util.parser.output_collection_def)
dataset_collector_descriptions_from_list() (in module galaxy.tool_util.parser.output_collection_def)
dataset_collector_descriptions_from_output_dict() (in module galaxy.tool_util.parser.output_collection_def)
dataset_column_dataprovider() (galaxy.datatypes.tabular.Sam method)
- (galaxy.datatypes.tabular.TabularData method)
dataset_content_needs_grooming() (galaxy.datatypes.binary.Bam method)
- (galaxy.datatypes.binary.BamInputSorted method)
- (galaxy.datatypes.binary.BamQuerynameSorted method)
- (galaxy.datatypes.data.Data method)
dataset_dict_dataprovider() (galaxy.datatypes.tabular.Sam method)
- (galaxy.datatypes.tabular.TabularData method)
dataset_elements() (galaxy.model.DatasetCollection property)
dataset_id (galaxy.model.DatasetHash attribute)
- (galaxy.model.DatasetPermissions attribute)
- (galaxy.model.DatasetSource attribute)
- (galaxy.model.GenomeIndexToolData attribute)
- (galaxy.model.HistoryDatasetAssociation attribute)
- (galaxy.model.JobExportHistoryArchive attribute)
- (galaxy.model.JobToInputDatasetAssociation attribute)
- (galaxy.model.JobToOutputDatasetAssociation attribute)
- (galaxy.model.LibraryDatasetDatasetAssociation attribute)
- (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute)
- (galaxy.model.WorkflowInvocationStepOutputDatasetAssociation attribute)
- (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute)
dataset_info() (galaxy.webapps.reports.controllers.system.System method)
dataset_instance() (galaxy.model.DatasetCollectionElement property)
dataset_instances() (galaxy.model.DatasetCollection property)
- (galaxy.model.DatasetCollectionElement property)
- (galaxy.model.DatasetCollectionInstance property)
dataset_is_private_to_user() (galaxy.model.security.GalaxyRBACAgent method)
dataset_is_public() (galaxy.model.security.GalaxyRBACAgent method)
- (galaxy.security.RBACAgent method)
dataset_is_unrestricted() (galaxy.model.security.GalaxyRBACAgent method)
dataset_ldda (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute)
dataset_make_primary() (galaxy.webapps.galaxy.controllers.root.RootController method)
dataset_path_rewriter() (galaxy.jobs.JobWrapper property)
- (galaxy.jobs.TaskWrapper property)
dataset_path_rewrites() (in module galaxy.job_execution.datasets)
dataset_permission_map_for_access() (galaxy.model.security.GalaxyRBACAgent method)
dataset_populator() (galaxy_test.selenium.framework.TestWithSeleniumMixin property)
dataset_source_id (galaxy.model.DatasetSourceHash attribute)
dataset_states_and_extensions_summary() (galaxy.model.DatasetCollection property)
dataset_storage_info() (galaxy_test.base.populators.BaseDatasetPopulator method)
dataset_to_param() (in module galaxy_test.api.test_tools)
dataset_type (galaxy.visualization.data_providers.genome.BamDataProvider attribute)
- (galaxy.visualization.data_providers.genome.BBIDataProvider attribute)
- (galaxy.visualization.data_providers.genome.BedDataProvider attribute)
- (galaxy.visualization.data_providers.genome.ChromatinInteractionsDataProvider attribute)
- (galaxy.visualization.data_providers.genome.ENCODEPeakDataProvider attribute)
- (galaxy.visualization.data_providers.genome.GenomeDataProvider attribute)
- (galaxy.visualization.data_providers.genome.IntervalDataProvider attribute)
- (galaxy.visualization.data_providers.genome.IntervalIndexDataProvider attribute)
- (galaxy.visualization.data_providers.genome.RawGFFDataProvider attribute)
- (galaxy.visualization.data_providers.genome.SamDataProvider attribute)
- (galaxy.visualization.data_providers.genome.TabixDataProvider attribute)
- (galaxy.visualization.data_providers.genome.VcfDataProvider attribute)
- (galaxy.visualization.data_providers.genome.VcfTabixDataProvider attribute)
- (galaxy.visualization.data_providers.phyloviz.PhylovizDataProvider attribute)
dataset_version (galaxy.model.JobToInputDatasetAssociation attribute)
dataset_wrapper_to_directory_json() (in module galaxy.tool_util.cwl.representation)
dataset_wrapper_to_file_json() (in module galaxy.tool_util.cwl.representation)
DatasetAccessPermissionFailedException
DatasetAssociationDeserializer (class in galaxy.managers.datasets)
DatasetAssociationFilterParser (class in galaxy.managers.datasets)
DatasetAssociationManager (class in galaxy.managers.datasets)
DatasetAssociationSerializer (class in galaxy.managers.datasets)
DatasetCollection (class in galaxy.model)
DatasetCollection.populated_states (class in galaxy.model)
DatasetCollectionApiTestCase (class in galaxy_test.api.test_dataset_collections)
DatasetCollectionAsContainerManagerMixin (class in galaxy.managers.containers)
DatasetCollectionDescription (class in galaxy.tool_util.parser.output_collection_def)
DatasetCollectionElement (class in galaxy.model)
DatasetCollectionInstance (class in galaxy.model)
DatasetCollectionManager (class in galaxy.managers.collections)
DatasetCollectionPopulator (class in galaxy_test.base.populators)
DatasetCollectionsController (class in galaxy.webapps.galaxy.api.dataset_collections)
DatasetCollectionType (class in galaxy.model.dataset_collections.types)
DatasetCollectionTypesRegistry (class in galaxy.model.dataset_collections.registry)
DatasetCollectionWrapper (class in galaxy.tools.wrappers)
DatasetCollector (class in galaxy.job_execution.output_collect)
DatasetColumnarDataProvider (class in galaxy.datatypes.dataproviders.dataset)
DatasetDataProvider (class in galaxy.datatypes.dataproviders.dataset)
DatasetDictDataProvider (class in galaxy.datatypes.dataproviders.dataset)
DatasetEmptyValidator (class in galaxy.tools.parameters.validation)
DatasetExtraFilesPathEmptyValidator (class in galaxy.tools.parameters.validation)
DatasetFilenameWrapper (class in galaxy.tools.wrappers)
DatasetFilenameWrapper.MetadataWrapper (class in galaxy.tools.wrappers)
DatasetHash (class in galaxy.model)
DatasetInstance (class in galaxy.model)
DatasetInstance.conversion_messages (class in galaxy.model)
DatasetInstance.states (class in galaxy.model)
DatasetInstance.validated_states (class in galaxy.model)
DatasetInterface (class in galaxy.webapps.galaxy.controllers.dataset)
DatasetListWrapper (class in galaxy.tools.wrappers)
DatasetManagePermissionFailedException
DatasetManager (class in galaxy.managers.datasets)
DatasetOkValidator (class in galaxy.tools.parameters.validation)
DatasetPath (class in galaxy.job_execution.datasets)
DatasetPathRewriter (class in galaxy.job_execution.datasets)
DatasetPermissions (class in galaxy.model)
DatasetPopulator (class in galaxy_test.base.populators)
DatasetRBACPermission (class in galaxy.managers.rbac_secured)
DatasetRBACPermissions (class in galaxy.managers.datasets)
datasets (galaxy.model.History attribute)
- (galaxy.model.LibraryFolder attribute)
datasets_are_public() (galaxy.model.security.GalaxyRBACAgent method)
datasets_properties() (galaxy.model.store.BaseDirectoryImportModelStore method)
- (galaxy.model.store.ModelImportStore method)
DatasetsApiTestCase (class in galaxy_test.api.test_datasets)
DatasetsController (class in galaxy.webapps.galaxy.api.datasets)
DatasetSerializer (class in galaxy.managers.datasets)
DatasetSource (class in galaxy.model)
DatasetSourceHash (class in galaxy.model)
DatasetSubprocessDataProvider (class in galaxy.datatypes.dataproviders.dataset)
DataSourceParser (class in galaxy.visualization.plugins.config_parser)
DataSourceTool (class in galaxy.tools)
DataSourceToolAction (class in galaxy.tools.actions.data_source)
DataToolParameter (class in galaxy.tools.parameters)
- (class in galaxy.tools.parameters.basic)
Datatype (class in galaxy.webapps.base.controller)
- (class in tool_shed.utility_containers.utility_container_manager)
datatype() (galaxy.model.DatasetInstance property)
datatype_for_extension() (in module galaxy.model)
DatatypeIsInstanceToolOutputActionConditionalWhen (class in galaxy.tool_util.parser.output_actions)
datatypes_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute)
DatatypesApiTestCase (class in galaxy_test.api.test_datatypes)
DatatypesController (class in galaxy.webapps.galaxy.api.datatypes)
DatatypesGrid (class in tool_shed.grids.repository_grids)
DatatypesGrid.DatatypesColumn (class in tool_shed.grids.repository_grids)
DatatypeValidation (class in galaxy.datatypes.data)
date_string_re (galaxy.managers.base.ModelFilterParser attribute)
DateTimeColumn (class in galaxy.web.framework.helpers.grids)
- (class in galaxy.web.legacy_framework.grids)
db_builds() (galaxy.managers.context.ProvidesHistoryContext property)
db_dataset_for() (galaxy.managers.context.ProvidesHistoryContext method)
db_next_hid() (in module galaxy.model.mapping)
DB_PREASSIGN (galaxy.web_stack.handlers.HANDLER_ASSIGNMENT_METHODS attribute)
DB_SELF (galaxy.web_stack.handlers.HANDLER_ASSIGNMENT_METHODS attribute)
DB_SKIP_LOCKED (galaxy.web_stack.handlers.HANDLER_ASSIGNMENT_METHODS attribute)
DB_TRANSACTION_ISOLATION (galaxy.web_stack.handlers.HANDLER_ASSIGNMENT_METHODS attribute)
dbkey (galaxy.model.Visualization attribute)
- (galaxy.model.VisualizationRevision attribute)
dbkey() (galaxy.model.DatasetInstance property)
- (galaxy.model.store.discover.JsonCollectedDatasetMatch property)
DBKeyParameter (class in galaxy.datatypes.metadata)
- (class in galaxy.model.metadata)
DCASerializer (class in galaxy.managers.hdcas)
Dcd (class in galaxy.datatypes.binary)
DCESerializer (class in galaxy.managers.hdcas)
DCSerializer (class in galaxy.managers.hdcas)
deactivate() (galaxy.managers.tools.DynamicToolManager method)
- (galaxy.tool_util.deps.conda_util.CondaContext property)
deactivate_dynamic_tool() (galaxy_test.base.populators.BaseDatasetPopulator method)
deactivate_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
DEACTIVATED (galaxy.model.tool_shed_install.ToolShedRepository.installation_status attribute)
debug_handler() (in module tool_shed.util.shed_index)
debugging (galaxy.webapps.galaxy.api.metrics.MetricsController attribute)
declare_queues() (galaxy.queue_worker.ControlTask property)
- (galaxy.queue_worker.GalaxyQueueWorker property)
decode() (galaxy.tools.DefaultToolState method)
- (in module galaxy.web_stack.message)
decode_dataset_user() (in module galaxy.datatypes.display_applications.util)
decode_dbkey() (in module galaxy.visualization.genomes)
decode_folder_id() (galaxy.managers.folders.FolderManager method)
decode_guid() (galaxy.security.idencoding.IdEncodingHelper method)
decode_id() (galaxy.security.idencoding.IdEncodingHelper method)
- (galaxy.webapps.base.controller.BaseController method)
- (galaxy.webapps.galaxy.api.configuration.ConfigurationController method)
- (in module galaxy.managers.base)
decode_query_ids() (galaxy.model.search.SearchQuery method)
- (galaxy.model.search.ViewQueryBaseClass method)
decode_runtime_state() (galaxy.workflow.modules.ToolModule method)
- (galaxy.workflow.modules.WorkflowModule method)
decode_type_id() (galaxy.managers.history_contents.HistoryContentsFilters method)
decoder() (in module galaxy.tools.cache)
deep_test_search() (in module galaxy.tool_util.deps.mulled.get_tests)
default (galaxy.model.Quota attribute)
- (galaxy.workflow.refactor.schema.AddInputAction attribute)
default() (galaxy.model.custom_types.SafeJsonEncoder method)
- (galaxy.webapps.galaxy.controllers.async.ASync method)
- (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method)
- (galaxy.webapps.galaxy.controllers.root.RootController method)
- (galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner method)
default_app_name (galaxy.web_stack.ApplicationStack attribute)
DEFAULT_BASE_HANDLER_POOLS (galaxy.jobs.JobConfiguration attribute)
- (galaxy.web_stack.handlers.ConfiguresHandlers attribute)
- (galaxy.workflow.scheduling_manager.WorkflowSchedulingManager attribute)
default_build_pulsar_app (galaxy.jobs.runners.pulsar.PulsarEmbeddedJobRunner attribute)
- (galaxy.jobs.runners.pulsar.PulsarEmbeddedMQJobRunner attribute)
DEFAULT_CHUNK_SIZE (galaxy.datatypes.dataproviders.chunk.ChunkDataProvider attribute)
default_collection_type (galaxy.workflow.modules.InputDataCollectionModule attribute)
DEFAULT_COMMENT_CHAR (galaxy.datatypes.dataproviders.line.FilteredLineDataProvider attribute)
default_compute_environment() (galaxy.jobs.JobWrapper method)
DEFAULT_CONFIG (galaxy.web.framework.middleware.batch.BatchMiddleware attribute)
default_config_file_name (galaxy.config.GalaxyAppConfiguration attribute)
- (tool_shed.webapp.config.ToolShedAppConfiguration attribute)
DEFAULT_CONTENT_FORMAT (galaxy.model.PageRevision attribute)
default_default_value (galaxy.workflow.modules.InputParameterModule attribute)
default_deserializer() (galaxy.managers.base.ModelDeserializer method)
DEFAULT_ENTRY_FN (galaxy.webapps.base.controller.JSAppLauncher attribute)
default_exit_code_file() (in module galaxy.job_execution.output_collect)
default_filter (galaxy.web.framework.helpers.grids.Grid attribute)
- (galaxy.web.legacy_framework.grids.Grid attribute)
- (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute)
- (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute)
- (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid attribute)
- (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute)
- (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid attribute)
- (galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid attribute)
- (galaxy.webapps.galaxy.controllers.page.PageListGrid attribute)
- (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid attribute)
- (galaxy.webapps.galaxy.controllers.visualization.LibraryDatasetsSelectionGrid attribute)
- (galaxy.webapps.galaxy.controllers.visualization.VisualizationAllPublishedGrid attribute)
- (galaxy.webapps.galaxy.controllers.visualization.VisualizationListGrid attribute)
- (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute)
- (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid attribute)
- (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute)
- (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute)
- (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute)
- (tool_shed.grids.repository_grids.RepositoriesByUserGrid attribute)
- (tool_shed.grids.repository_grids.RepositoryGrid attribute)
- (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute)
default_handler (galaxy.web_stack.message.ApplicationStackMessage attribute)
default_handler() (galaxy.web_stack.message.TaskMessage static method)
DEFAULT_HANDLER_TAG (galaxy.web_stack.handlers.ConfiguresHandlers attribute)
default_interactive (galaxy.util.pastescript.serve.Command attribute)
DEFAULT_INVALID_CHAR (galaxy.tools.parameters.sanitize.ToolParameterSanitizer attribute)
default_is_multi_byte (galaxy.tool_util.parser.interface.ToolSource attribute)
- (galaxy.tool_util.parser.ToolSource attribute)
default_job_file() (galaxy.jobs.runners.JobState static method)
default_job_tool_configuration() (galaxy.jobs.JobConfiguration property)
default_length() (galaxy.selenium.navigates_galaxy.WaitType property)
default_loader() (in module galaxy.tool_util.cwl.cwltool_deps)
DEFAULT_MAX_OPEN_FILES (galaxy.datatypes.util.maf_utilities.TempFileHandler attribute)
- (galaxy.tools.util.maf_utilities.TempFileHandler attribute)
default_merge_type (galaxy.model.WorkflowStepInput attribute)
default_name (galaxy.model.History attribute)
- (galaxy.util.dbkeys.GenomeBuilds attribute)
DEFAULT_NWORKERS (galaxy.jobs.JobConfiguration attribute)
default_optional (galaxy.tool_util.parser.interface.InputSource attribute)
- (galaxy.workflow.modules.InputModule attribute)
- (galaxy.workflow.modules.InputParameterModule attribute)
default_order_by (galaxy.managers.containers.ContainerManagerMixin attribute)
- (galaxy.managers.history_contents.HistoryContentsManager attribute)
DEFAULT_PARAM_TYPE (galaxy.visualization.plugins.config_parser.ParamParser attribute)
default_parameter_type (galaxy.workflow.modules.InputParameterModule attribute)
default_password (galaxy.selenium.navigates_galaxy.NavigatesGalaxy attribute)
default_pbs_server() (galaxy.jobs.runners.pbs.PBSJobRunner property)
default_permissions (galaxy.model.History attribute)
- (galaxy.model.User attribute)
default_permissions() (galaxy.managers.users.UserManager method)
default_port() (galaxy.config.config_manage.App property)
DEFAULT_POSITION (galaxy.model.WorkflowStep attribute)
default_printer() (in module galaxy.tools.util.galaxyops)
default_quota() (galaxy.quota.NoQuotaAgent property)
default_scatter_type (galaxy.model.WorkflowStepInput attribute)
default_serializer() (galaxy.managers.base.ModelSerializer method)
- (galaxy.managers.configuration.ConfigSerializer method)
default_shed_tool_conf_dict() (galaxy.tools.toolbox.AbstractToolBox method)
- (galaxy.tools.toolbox.base.AbstractToolBox method)
default_sort_key (galaxy.web.framework.helpers.grids.Grid attribute)
- (galaxy.web.legacy_framework.grids.Grid attribute)
- (galaxy.webapps.galaxy.controllers.admin.GroupListGrid attribute)
- (galaxy.webapps.galaxy.controllers.admin.QuotaListGrid attribute)
- (galaxy.webapps.galaxy.controllers.admin.RoleListGrid attribute)
- (galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid attribute)
- (galaxy.webapps.galaxy.controllers.admin.UserListGrid attribute)
- (galaxy.webapps.galaxy.controllers.forms.FormsGrid attribute)
- (galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid attribute)
- (galaxy.webapps.galaxy.controllers.history.HistoryListGrid attribute)
- (galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid attribute)
- (galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid attribute)
- (galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid attribute)
- (galaxy.webapps.galaxy.controllers.page.PageListGrid attribute)
- (galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid attribute)
- (galaxy.webapps.galaxy.controllers.visualization.LibraryDatasetsSelectionGrid attribute)
- (galaxy.webapps.galaxy.controllers.visualization.TracksterSelectionGrid attribute)
- (galaxy.webapps.galaxy.controllers.visualization.VisualizationAllPublishedGrid attribute)
- (galaxy.webapps.galaxy.controllers.visualization.VisualizationListGrid attribute)
- (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid attribute)
- (galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid attribute)
- (galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid attribute)
- (galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid attribute)
- (tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid attribute)
- (tool_shed.grids.admin_grids.GroupGrid attribute)
- (tool_shed.grids.admin_grids.RepositoryMetadataGrid attribute)
- (tool_shed.grids.admin_grids.RoleGrid attribute)
- (tool_shed.grids.admin_grids.UserGrid attribute)
- (tool_shed.grids.repository_grids.CategoryGrid attribute)
- (tool_shed.grids.repository_grids.DatatypesGrid attribute)
- (tool_shed.grids.repository_grids.MatchedRepositoryGrid attribute)
- (tool_shed.grids.repository_grids.RepositoryDependenciesGrid attribute)
- (tool_shed.grids.repository_grids.RepositoryGrid attribute)
- (tool_shed.grids.repository_grids.RepositoryMetadataGrid attribute)
- (tool_shed.grids.repository_grids.ToolDependenciesGrid attribute)
- (tool_shed.grids.repository_grids.ToolsGrid attribute)
- (tool_shed.grids.repository_grids.ValidCategoryGrid attribute)
- (tool_shed.grids.repository_review_grids.ComponentGrid attribute)
- (tool_shed.grids.repository_review_grids.RepositoriesWithReviewsGrid attribute)
- (tool_shed.grids.repository_review_grids.RepositoryReviewsByUserGrid attribute)
DEFAULT_SPECS (galaxy.jobs.runners.BaseJobRunner attribute)
DEFAULT_TEMPLATE_COLLECTION_SIZE (galaxy.visualization.plugins.plugin.ServesTemplatesPluginMixin attribute)
default_timeout() (galaxy.selenium.cli.DriverWrapper property)
default_tool_action (galaxy.tools.DatabaseOperationTool attribute)
- (galaxy.tools.DataManagerTool attribute)
- (galaxy.tools.DataSourceTool attribute)
- (galaxy.tools.Tool attribute)
default_url_path() (in module galaxy.webapps.base.webapp)
default_value (galaxy.model.WorkflowStepInput attribute)
- (galaxy.util.dbkeys.GenomeBuilds attribute)
- (galaxy.workflow.modules.InputParameterModule attribute)
default_value_set (galaxy.model.WorkflowStepInput attribute)
default_verbosity (galaxy.util.pastescript.serve.Command attribute)
- (galaxy.util.pastescript.serve.ServeCommand attribute)
DEFAULT_VERSION (galaxy.tools.data_manager.manager.DataManager attribute)
default_web_host (galaxy_test.selenium.framework.TestWithSeleniumMixin attribute)
default_web_host_for_selenium_tests() (in module galaxy_test.selenium.framework)
DefaultHistoryPermissions (class in galaxy.model)
DefaultJobAction (class in galaxy.jobs.actions.post)
DefaultJobDispatcher (class in galaxy.jobs.handler)
DefaultQuotaAssociation (class in galaxy.model)
DefaultQuotaAssociation.types (class in galaxy.model)
defaults() (galaxy.config.schema.AppSchema property)
- (galaxy.util.properties.NicerConfigParser method)
DefaultToolAction (class in galaxy.tools.actions)
DefaultToolState (class in galaxy.tools)
DefaultUserPermissions (class in galaxy.model)
DefaultWebTransaction (class in galaxy.web.framework.base)
deferred (galaxy.model.GenomeIndexToolData attribute)
deferred_job (galaxy.model.DeferredJob attribute)
deferred_job_id (galaxy.model.GenomeIndexToolData attribute)
DeferredJob (class in galaxy.model)
DeferredJob.states (class in galaxy.model)
defines_new_history() (galaxy.model.store.BaseDirectoryImportModelStore method)
- (galaxy.model.store.ModelImportStore method)
DelayedWorkflowEvaluation
DeletableDeserializerMixin (class in galaxy.managers.deletable)
DeletableFiltersMixin (class in galaxy.managers.deletable)
DeletableManagerMixin (class in galaxy.managers.deletable)
DeletableSerializerMixin (class in galaxy.managers.deletable)
delete() (galaxy.jobs.runners.util.cli.job.BaseJobExec method)
- (galaxy.jobs.runners.util.cli.job.lsf.LSF method)
- (galaxy.jobs.runners.util.cli.job.slurm.Slurm method)
- (galaxy.jobs.runners.util.cli.job.torque.Torque method)
- (galaxy.managers.collections.DatasetCollectionManager method)
- (galaxy.managers.deletable.DeletableManagerMixin method)
- (galaxy.managers.folders.FolderManager method)
- (galaxy.managers.libraries.LibraryManager method)
- (galaxy.managers.users.UserManager method)
- (galaxy.objectstore.BaseObjectStore method)
- (galaxy.objectstore.ObjectStore method)
- (galaxy.tools.cache.ToolDocumentCache method)
- (galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController method)
- (galaxy.webapps.galaxy.api.cloudauthz.CloudAuthzController method)
- (galaxy.webapps.galaxy.api.dynamic_tools.DynamicToolsController method)
- (galaxy.webapps.galaxy.api.extended_metadata.BaseExtendedMetadataController method)
- (galaxy.webapps.galaxy.api.folders.FoldersController method)
- (galaxy.webapps.galaxy.api.group_roles.GroupRolesAPIController method)
- (galaxy.webapps.galaxy.api.group_users.GroupUsersAPIController method)
- (galaxy.webapps.galaxy.api.histories.HistoriesController method)
- (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method)
- (galaxy.webapps.galaxy.api.item_tags.BaseItemTagsController method)
- (galaxy.webapps.galaxy.api.jobs.JobController method)
- (galaxy.webapps.galaxy.api.libraries.LibrariesController method)
- (galaxy.webapps.galaxy.api.library_contents.LibraryContentsController method)
- (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method)
- (galaxy.webapps.galaxy.api.pages.PagesController method)
- (galaxy.webapps.galaxy.api.provenance.BaseProvenanceController method)
- (galaxy.webapps.galaxy.api.quotas.QuotaAPIController method)
- (galaxy.webapps.galaxy.api.tool_data.ToolData method)
- (galaxy.webapps.galaxy.api.users.UserAPIController method)
- (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method)
- (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method)
- (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method)
- (galaxy_test.base.api.ApiTestInteractor method)
- (tool_shed.managers.groups.GroupManager method)
- (tool_shed.managers.repositories.RepoManager method)
delete_async() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method)
delete_custom_build() (galaxy_test.selenium.test_custom_builds.CustomBuildsTestcase method)
delete_custom_builds() (galaxy.webapps.galaxy.api.users.UserAPIController method)
delete_dataset() (galaxy_test.base.populators.BaseDatasetPopulator method)
delete_extended_metadata() (galaxy.webapps.base.controller.UsesExtendedMetadataMixin method)
delete_files_from_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
delete_history() (galaxy.tool_util.verify.interactor.GalaxyInteractorApi method)
- (galaxy_test.base.populators.BaseDatasetPopulator method)
delete_item_annotation() (galaxy.model.item_attrs.UsesAnnotations method)
delete_item_tags() (galaxy.model.tags.TagHandler method)
delete_obj() (in module tool_shed.test.base.test_db_util)
delete_operation (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy attribute)
- (tool_shed.util.admin_util.Admin attribute)
- (tool_shed.webapp.controllers.admin.AdminController attribute)
delete_repository() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
- (tool_shed.webapp.controllers.admin.AdminController method)
delete_repository_metadata() (tool_shed.webapp.controllers.admin.AdminController method)
delete_task() (galaxy.jobs.runners.godocker.GodockerJobRunner method)
delete_unused_dependency_paths() (galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController method)
delete_user_roles() (in module tool_shed.test.base.test_db_util)
deleted (galaxy.model.Dataset attribute)
- (galaxy.model.FormDefinitionCurrent attribute)
- (galaxy.model.Group attribute)
- (galaxy.model.History attribute)
- (galaxy.model.HistoryDatasetAssociation attribute)
- (galaxy.model.HistoryDatasetCollectionAssociation attribute)
- (galaxy.model.ImplicitlyConvertedDatasetAssociation attribute)
- (galaxy.model.InteractiveToolEntryPoint attribute)
DELETED (galaxy.model.Job.states attribute)
deleted (galaxy.model.Library attribute)
- (galaxy.model.LibraryDataset attribute)
- (galaxy.model.LibraryDatasetCollectionAssociation attribute)
- (galaxy.model.LibraryDatasetDatasetAssociation attribute)
- (galaxy.model.LibraryDatasetDatasetInfoAssociation attribute)
- (galaxy.model.LibraryFolder attribute)
- (galaxy.model.LibraryFolderInfoAssociation attribute)
- (galaxy.model.LibraryInfoAssociation attribute)
- (galaxy.model.MetadataFile attribute)
- (galaxy.model.Page attribute)
- (galaxy.model.Quota attribute)
- (galaxy.model.Role attribute)
- (galaxy.model.StoredWorkflow attribute)
DELETED (galaxy.model.Task.states attribute)
deleted (galaxy.model.tool_shed_install.ToolShedRepository attribute)
- (galaxy.model.User attribute)
- (galaxy.model.UserAddress attribute)
- (galaxy.model.view.HistoryDatasetCollectionJobStateSummary attribute)
- (galaxy.model.Visualization attribute)
- (tool_shed.webapp.model.Category attribute)
- (tool_shed.webapp.model.ComponentReview attribute)
- (tool_shed.webapp.model.Group attribute)
- (tool_shed.webapp.model.Repository attribute)
- (tool_shed.webapp.model.RepositoryReview attribute)
- (tool_shed.webapp.model.Role attribute)
- (tool_shed.webapp.model.User attribute)
deleted_datasets() (galaxy.webapps.reports.controllers.system.System method)
deleted_histories() (galaxy.webapps.reports.controllers.system.System method)
DELETED_NEW (galaxy.model.Job.states attribute)
deleted_new (galaxy.model.view.HistoryDatasetCollectionJobStateSummary attribute)
DeleteDatasetAction (class in galaxy.jobs.actions.post)
DeletedColumn (class in galaxy.web.framework.helpers.grids)
- (class in galaxy.web.legacy_framework.grids)
DeleteIntermediatesAction (class in galaxy.jobs.actions.post)
DELETING (galaxy.model.Job.states attribute)
delimiter (galaxy.datatypes.tabular.BaseCSV attribute)
dependencies (galaxy.model.Job attribute)
DependenciesDescription (class in galaxy.tool_util.deps.dependencies)
Dependency (class in galaxy.tool_util.deps.resolvers)
dependency_shell_commands() (galaxy.jobs.JobWrapper property)
- (galaxy.tool_util.deps.CachedDependencyManager method)
- (galaxy.tool_util.deps.DependencyManager method)
- (galaxy.tool_util.deps.NullDependencyManager method)
dependency_type (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependency attribute)
- (galaxy.tool_util.deps.resolvers.galaxy_packages.ToolShedDependency attribute)
- (galaxy.tool_util.deps.resolvers.NullDependency attribute)
- (galaxy.tool_util.deps.resolvers.tool_shed_packages.ToolShedPackageDependencyResolver attribute)
DependencyDisplayer (class in tool_shed.galaxy_install.dependency_display)
DependencyException
DependencyManager (class in galaxy.tool_util.deps)
DependencyResolver (class in galaxy.tool_util.deps.resolvers)
DependencyResolversView (class in galaxy.tool_util.deps.views)
dependent_jobs (galaxy.model.HistoryDatasetAssociation attribute)
- (galaxy.model.LibraryDatasetDatasetAssociation attribute)
deprecate() (tool_shed.webapp.controllers.repository.RepositoryController method)
deprecated (tool_shed.webapp.model.Repository attribute)
deprecated_dirs (galaxy.config.BaseAppConfiguration attribute)
- (galaxy.config.GalaxyAppConfiguration attribute)
deprecated_options (galaxy.config.GalaxyAppConfiguration attribute)
deprecated_repositories_i_own_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute)
DeprecatedMethod
DeprecatedRepositoriesIOwnGrid (class in tool_shed.grids.repository_grids)
deps_error_message() (in module galaxy.tool_util.deps.mulled.mulled_search)
deregister_func() (galaxy.web_stack.message.ApplicationStackMessageDispatcher method)
deregister_message_handler() (galaxy.web_stack.ApplicationStack method)
- (galaxy.web_stack.MessageApplicationStack method)
derive_roles_from_access() (galaxy.model.security.GalaxyRBACAgent method)
- (galaxy.security.RBACAgent method)
desc (galaxy.model.FormDefinition attribute)
- (galaxy.model.UserAddress attribute)
desc() (galaxy.tool_util.parser.stdio.StdioErrorLevel static method)
descendant() (galaxy.selenium.components.SelectorTemplate method)
description (galaxy.managers.roles.RoleDefinitionModel attribute)
- (galaxy.managers.roles.RoleModel attribute)
- (galaxy.model.CloudAuthz attribute)
- (galaxy.model.Library attribute)
- (galaxy.model.LibraryFolder attribute)
- (galaxy.model.Quota attribute)
- (galaxy.model.Role attribute)
- (galaxy.model.tool_shed_install.ToolShedRepository attribute)
- (galaxy.tours.TourCore attribute)
- (galaxy.util.pastescript.serve.Command attribute)
- (galaxy.util.pastescript.serve.ServeCommand attribute)
- (tool_shed.webapp.model.Category attribute)
- (tool_shed.webapp.model.Component attribute)
- (tool_shed.webapp.model.Repository attribute)
- (tool_shed.webapp.model.Role attribute)
description() (galaxy.selenium.components.Label property)
- (galaxy.selenium.components.SelectorTemplate property)
- (galaxy.selenium.components.Target property)
- (galaxy.selenium.components.Text property)
description_from_tool_object() (in module galaxy.tools.test)
descs (galaxy.tool_util.parser.stdio.StdioErrorLevel attribute)
deserialize() (galaxy.managers.base.ModelDeserializer method)
deserialize_and_validate_authn_id() (galaxy.managers.cloudauthzs.CloudAuthzsDeserializer method)
deserialize_annotation() (galaxy.managers.annotatable.AnnotatableDeserializerMixin method)
deserialize_basestring() (galaxy.managers.base.ModelDeserializer method)
deserialize_bool() (galaxy.managers.base.ModelDeserializer method)
deserialize_datatype() (galaxy.managers.datasets.DatasetAssociationDeserializer method)
deserialize_deleted() (galaxy.managers.deletable.DeletableDeserializerMixin method)
deserialize_genome_build() (galaxy.managers.base.ModelDeserializer method)
deserialize_importable() (galaxy.managers.sharable.SharableModelDeserializer method)
deserialize_int() (galaxy.managers.base.ModelDeserializer method)
deserialize_metadata() (galaxy.managers.datasets.DatasetAssociationDeserializer method)
deserialize_metadatum() (galaxy.managers.datasets.DatasetAssociationDeserializer method)
deserialize_published() (galaxy.managers.sharable.SharableModelDeserializer method)

deserialize_purged() (galaxy.managers.deletable.PurgableDeserializerMixin method)
deserialize_rating() (galaxy.managers.ratable.RatableDeserializerMixin method)
deserialize_tags() (galaxy.managers.taggable.TaggableDeserializerMixin method)
deserialize_username() (galaxy.managers.users.UserDeserializer method)
deserialize_users_shared_with() (galaxy.managers.sharable.SharableModelDeserializer method)
designation (galaxy.model.HistoryDatasetAssociation attribute)
- (galaxy.model.LibraryDatasetDatasetAssociation attribute)
designation() (galaxy.model.store.discover.JsonCollectedDatasetMatch property)
desired_state() (galaxy.containers.docker_model.DockerTask property)
destination() (galaxy.config.config_manage.App property)
destination_defaults (galaxy.jobs.runners.pulsar.PulsarEmbeddedJobRunner attribute)
- (galaxy.jobs.runners.pulsar.PulsarLegacyJobRunner attribute)
- (galaxy.jobs.runners.pulsar.PulsarMQJobRunner attribute)
- (galaxy.jobs.runners.pulsar.PulsarRESTJobRunner attribute)
destination_id (galaxy.model.Job attribute)
destination_list (in module galaxy.jobs.dynamic_tool_destination)
destination_params (galaxy.model.Job attribute)
destination_params() (galaxy.webapps.galaxy.api.jobs.JobController method)
DESTINATION_PARAMS_SPEC (galaxy.jobs.runners.chronos.ChronosJobRunner attribute)
destroy() (galaxy.model.PSAPartial class method)
destroyable() (galaxy.containers.docker_model.DockerNode method)
detailsUrl (galaxy.managers.licenses.LicenseMetadataModel attribute)
detect_datatype() (galaxy.managers.datasets.DatasetAssociationManager method)
determine_output_format() (in module galaxy.tools.actions)
deterministic_handler_assignment() (galaxy.web_stack.handlers.ConfiguresHandlers property)
diagnostics() (galaxy.webapps.galaxy.api.tools.ToolsController method)
dialect (galaxy.datatypes.tabular.CSV attribute)
- (galaxy.datatypes.tabular.TSV attribute)
dict() (galaxy.util.bunch.Bunch method)
dict_collection_visible_keys (galaxy.model.DatasetCollection attribute)
- (galaxy.model.DatasetCollectionElement attribute)
- (galaxy.model.DynamicTool attribute)
- (galaxy.model.FormDefinition attribute)
- (galaxy.model.Group attribute)
- (galaxy.model.HasTags attribute)
- (galaxy.model.History attribute)
- (galaxy.model.InteractiveToolEntryPoint attribute)
- (galaxy.model.ItemTagAssociation attribute)
- (galaxy.model.Job attribute)
- (galaxy.model.Library attribute)
- (galaxy.model.Quota attribute)
- (galaxy.model.Role attribute)
- (galaxy.model.StoredWorkflow attribute)
- (galaxy.model.tool_shed_install.ToolShedRepository attribute)
- (galaxy.model.User attribute)
- (galaxy.model.Workflow attribute)
- (galaxy.model.WorkflowInvocation attribute)
- (galaxy.model.WorkflowInvocationOutputDatasetAssociation attribute)
- (galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation attribute)
- (galaxy.model.WorkflowInvocationOutputValue attribute)
- (galaxy.model.WorkflowInvocationStep attribute)
- (galaxy.model.WorkflowInvocationStepOutputDatasetAssociation attribute)
- (galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation attribute)
- (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute)
- (galaxy.model.WorkflowRequestInputParameter attribute)
- (galaxy.model.WorkflowRequestInputStepParameter attribute)
- (galaxy.model.WorkflowRequestStepState attribute)
- (galaxy.model.WorkflowRequestToInputDatasetAssociation attribute)
- (galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation attribute)
- (galaxy.tool_util.deps.container_resolvers.ContainerResolver attribute)
- (galaxy.tool_util.deps.resolvers.conda.CondaDependencyResolver attribute)
- (galaxy.tool_util.deps.resolvers.ContainerDependency attribute)
- (galaxy.tool_util.deps.resolvers.Dependency attribute)
- (galaxy.tool_util.deps.resolvers.DependencyResolver attribute)
- (galaxy.tool_util.deps.resolvers.galaxy_packages.GalaxyPackageDependency attribute)
- (galaxy.tool_util.deps.resolvers.lmod.LmodDependencyResolver attribute)
- (galaxy.tool_util.deps.resolvers.modules.ModuleDependencyResolver attribute)
- (galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages.UnlinkedToolShedPackageDependencyResolver attribute)
- (galaxy.tool_util.parser.output_objects.ToolExpressionOutput attribute)
- (galaxy.tool_util.parser.output_objects.ToolOutput attribute)
- (galaxy.tool_util.parser.output_objects.ToolOutputCollection attribute)
- (galaxy.tools.data.RefgenieToolDataTable attribute)
- (galaxy.tools.data.TabularToolDataField attribute)
- (galaxy.tools.data.TabularToolDataTable attribute)
- (galaxy.tools.parameters.basic.FloatToolParameter attribute)
- (galaxy.tools.parameters.basic.IntegerToolParameter attribute)
- (galaxy.tools.parameters.basic.ToolParameter attribute)
- (galaxy.tools.parameters.grouping.ConditionalWhen attribute)
- (galaxy.tools.parameters.grouping.Group attribute)
- (galaxy.tools.parameters.grouping.Repeat attribute)
- (galaxy.tools.parameters.grouping.Section attribute)
- (galaxy.tools.Tool attribute)
- (galaxy.tools.toolbox.panel.ToolSection attribute)
- (galaxy.tools.toolbox.panel.ToolSectionLabel attribute)
- (galaxy.tools.toolbox.ToolSection attribute)
- (galaxy.tools.toolbox.ToolSectionLabel attribute)
- (tool_shed.webapp.model.Category attribute)
- (tool_shed.webapp.model.ComponentReview attribute)
- (tool_shed.webapp.model.Group attribute)
- (tool_shed.webapp.model.Repository attribute)
- (tool_shed.webapp.model.RepositoryMetadata attribute)
- (tool_shed.webapp.model.RepositoryReview attribute)
- (tool_shed.webapp.model.Role attribute)
- (tool_shed.webapp.model.User attribute)
dict_dataprovider() (galaxy.datatypes.binary.Bam method)
- (galaxy.datatypes.tabular.Sam method)
- (galaxy.datatypes.tabular.TabularData method)
dict_element_visible_keys (galaxy.model.DatasetCollection attribute)
- (galaxy.model.DatasetCollectionElement attribute)
- (galaxy.model.DefaultQuotaAssociation attribute)
- (galaxy.model.DynamicTool attribute)
- (galaxy.model.FormDefinition attribute)
- (galaxy.model.Group attribute)
- (galaxy.model.GroupQuotaAssociation attribute)
- (galaxy.model.HasTags attribute)
- (galaxy.model.History attribute)
- (galaxy.model.InteractiveToolEntryPoint attribute)
- (galaxy.model.ItemTagAssociation attribute)
- (galaxy.model.Job attribute)
- (galaxy.model.Library attribute)
- (galaxy.model.LibraryFolder attribute)
- (galaxy.model.Page attribute)
- (galaxy.model.PageRevision attribute)
- (galaxy.model.Quota attribute)
- (galaxy.model.Role attribute)
- (galaxy.model.StoredWorkflow attribute)
- (galaxy.model.tool_shed_install.ToolShedRepository attribute)
- (galaxy.model.tool_shed_install.ToolVersion attribute)
- (galaxy.model.User attribute)
- (galaxy.model.UserQuotaAssociation attribute)
- (galaxy.model.Workflow attribute)
- (galaxy.model.WorkflowInvocation attribute)
- (galaxy.model.WorkflowInvocationStep attribute)
- (galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation attribute)
- (tool_shed.webapp.model.Category attribute)
- (tool_shed.webapp.model.ComponentReview attribute)
- (tool_shed.webapp.model.Group attribute)
- (tool_shed.webapp.model.Repository attribute)
- (tool_shed.webapp.model.RepositoryMetadata attribute)
- (tool_shed.webapp.model.RepositoryReview attribute)
- (tool_shed.webapp.model.Role attribute)
- (tool_shed.webapp.model.User attribute)
dict_for() (in module galaxy.util.dictifiable)
dict_map() (in module galaxy.model.dataset_collections.structure)
DictClientTestConfig (class in galaxy.tool_util.verify.interactor)
DictDataProvider (class in galaxy.datatypes.dataproviders.column)
DictFileSourcesUserContext (class in galaxy.files)
Dictifiable (class in galaxy.util.dictifiable)
dictify_dataset_collection_instance() (in module galaxy.managers.collections_util)
DictParameter (class in galaxy.datatypes.metadata)
- (class in galaxy.model.metadata)
DictParser (class in galaxy.visualization.plugins.config_parser)
different_revision_defines_tip_only_repository_dependency() (tool_shed.metadata.repository_metadata_manager.RepositoryMetadataManager method)
difflib (in module galaxy.util.pastescript.serve)
dimension() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription property)
direct_match() (galaxy.tools.parameters.history_query.HistoryQuery method)
direction (galaxy.jobs.actions.post.RemoveTagDatasetAction attribute)
- (galaxy.jobs.actions.post.TagDatasetAction attribute)
Directory (class in galaxy.datatypes.data)
directory_hash_id() (in module galaxy.util)
DirectoryImportModelStore1901 (class in galaxy.model.store)
DirectoryImportModelStoreLatest (class in galaxy.model.store)
DirectoryModelExportStore (class in galaxy.model.store)
DirectoryUploadTarget (class in galaxy.tool_util.cwl.util)
DirectoryUriToolParameter (class in galaxy.tools.parameters.basic)
disable_commands_in_new_shell() (galaxy.jobs.JobWrapper method)
disable_parent_class_sniffing() (in module galaxy.datatypes.sniff)
disabled (galaxy.tool_util.deps.resolvers.DependencyResolver attribute)
discard() (galaxy.util.oset.OrderedSet method)
DISCARDED (galaxy.model.Dataset.states attribute)
- (galaxy.model.DatasetInstance.states attribute)
disconnect() (galaxy.authnz.custos_authnz.CustosAuthnz method)
- (galaxy.authnz.IdentityProvider method)
- (galaxy.authnz.managers.AuthnzManager method)
- (galaxy.authnz.psa_authnz.PSAAuthnz method)
- (galaxy.webapps.galaxy.controllers.authnz.OIDC method)
- (in module galaxy.authnz.psa_authnz)
DisconnectAction (class in galaxy.workflow.refactor.schema)
discover_files() (in module galaxy.job_execution.output_collect)
discover_outputs() (galaxy.jobs.JobWrapper method)
- (galaxy.tools.Tool method)
discover_target_directory() (in module galaxy.model.store.discover)
discover_via (galaxy.tool_util.parser.output_collection_def.FilePatternDatasetCollectionDescription attribute)
- (galaxy.tool_util.parser.output_collection_def.ToolProvidedMetadataDatasetCollection attribute)
discovered_file_for_element() (in module galaxy.model.store.discover)
DiscoveredFile (class in galaxy.model.store.discover)
DiscoveredFileError (class in galaxy.model.store.discover)
disk_nice_size() (galaxy.model.History property)
disk_size (galaxy.model.History attribute)
disk_usage (galaxy.model.GalaxySession attribute)
- (galaxy.model.User attribute)
disk_usage() (galaxy.webapps.reports.controllers.system.System method)
DiskObjectStore (class in galaxy.objectstore)
dispatch() (galaxy.web_stack.message.ApplicationStackMessageDispatcher method)
display() (galaxy.util.rules_dsl.RuleSet property)
- (galaxy.webapps.galaxy.api.datasets.DatasetsController method)
- (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method)
- (galaxy.webapps.galaxy.controllers.page.PageController method)
- (galaxy.webapps.galaxy.controllers.root.RootController method)
display_amount() (galaxy.model.Quota property)
display_application() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method)
display_as() (galaxy.webapps.galaxy.controllers.root.RootController method)
display_as_markdown() (galaxy.datatypes.data.Data method)
- (galaxy.datatypes.tabular.TabularData method)
display_at() (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method)
display_by_id() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method)
display_by_username_and_slug() (galaxy.webapps.base.controller.SharableMixin method)
- (galaxy.webapps.galaxy.controllers.dataset.DatasetInterface method)
- (galaxy.webapps.galaxy.controllers.history.HistoryController method)
- (galaxy.webapps.galaxy.controllers.page.PageController method)
- (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method)
- (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method)
display_data() (galaxy.datatypes.binary.BamNative method)
- (galaxy.datatypes.data.Data method)
- (galaxy.datatypes.sequence.BaseFastq method)
- (galaxy.datatypes.tabular.TabularData method)
- (galaxy.datatypes.text.Ipynb method)
display_galaxy_browse_repositories_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
display_image_in_repository() (galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed method)
- (tool_shed.webapp.controllers.repository.RepositoryController method)
display_info() (galaxy.datatypes.data.Data method)
- (galaxy.model.DatasetInstance method)
display_installed_jobs_list_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
display_installed_repository_manage_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
display_manage_repository_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
display_name() (galaxy.datatypes.data.Data method)
- (galaxy.model.DatasetCollectionInstance method)
- (galaxy.model.DatasetInstance method)
- (galaxy.model.LibraryDataset method)
display_peek() (galaxy.datatypes.annotation.Augustus method)
- (galaxy.datatypes.annotation.SnapHmm method)
- (galaxy.datatypes.anvio.AnvioComposite method)
- (galaxy.datatypes.binary.Ab1 method)
- (galaxy.datatypes.binary.Anndata method)
- (galaxy.datatypes.binary.BafTar method)
- (galaxy.datatypes.binary.BamNative method)
- (galaxy.datatypes.binary.BigWig method)
- (galaxy.datatypes.binary.Biom2 method)
- (galaxy.datatypes.binary.CompressedArchive method)
- (galaxy.datatypes.binary.CompressedZipArchive method)
- (galaxy.datatypes.binary.Cool method)
- (galaxy.datatypes.binary.CuffDiffSQlite method)
- (galaxy.datatypes.binary.Dcd method)
- (galaxy.datatypes.binary.ExcelXls method)
- (galaxy.datatypes.binary.Fast5Archive method)
- (galaxy.datatypes.binary.GeminiSQLite method)
- (galaxy.datatypes.binary.GmxBinary method)
- (galaxy.datatypes.binary.H5 method)
- (galaxy.datatypes.binary.IdpDB method)
- (galaxy.datatypes.binary.Loom method)
- (galaxy.datatypes.binary.MCool method)
- (galaxy.datatypes.binary.NcbiTaxonomySQlite method)
- (galaxy.datatypes.binary.NetCDF method)
- (galaxy.datatypes.binary.PostgresqlArchive method)
- (galaxy.datatypes.binary.Scf method)
- (galaxy.datatypes.binary.SearchGuiArchive method)
- (galaxy.datatypes.binary.Sff method)
- (galaxy.datatypes.binary.SQlite method)
- (galaxy.datatypes.binary.Sra method)
- (galaxy.datatypes.binary.TwoBit method)
- (galaxy.datatypes.binary.Vel method)
- (galaxy.datatypes.blast.LastDb method)
- (galaxy.datatypes.constructive_solid_geometry.Ply method)
- (galaxy.datatypes.constructive_solid_geometry.Vtk method)
- (galaxy.datatypes.data.Data method)
- (galaxy.datatypes.genetics.RexpBase method)
- (galaxy.datatypes.genetics.rgTabList method)
- (galaxy.datatypes.gis.Shapefile method)
- (galaxy.datatypes.images.Gmaj method)
- (galaxy.datatypes.images.Laj method)
- (galaxy.datatypes.interval.CustomTrack method)
- (galaxy.datatypes.interval.Gff method)
- (galaxy.datatypes.interval.Interval method)
- (galaxy.datatypes.interval.Wiggle method)
- (galaxy.datatypes.molecules.OBFS method)
- (galaxy.datatypes.msa.Hmmer method)
- (galaxy.datatypes.msa.HmmerPress method)
- (galaxy.datatypes.neo4j.Neo4j method)
- (galaxy.datatypes.ngsindex.BowtieIndex method)
- (galaxy.datatypes.plant_tribes.PlantTribesKsComponents method)
- (galaxy.datatypes.plant_tribes.Smat method)
- (galaxy.datatypes.proteomics.Kroenik method)
- (galaxy.datatypes.proteomics.PepList method)
- (galaxy.datatypes.proteomics.PepXmlReport method)
- (galaxy.datatypes.proteomics.ProtXmlReport method)
- (galaxy.datatypes.proteomics.PSMS method)
- (galaxy.datatypes.proteomics.ThermoRAW method)
- (galaxy.datatypes.sequence.Maf method)
- (galaxy.datatypes.tabular.BaseVcf method)
- (galaxy.datatypes.tabular.Pileup method)
- (galaxy.datatypes.tabular.Sam method)
- (galaxy.datatypes.tabular.TabularData method)
- (galaxy.datatypes.tabular.Taxonomy method)
- (galaxy.datatypes.text.Json method)
- (galaxy.datatypes.tracks.UCSCTrackHub method)
- (galaxy.model.DatasetInstance method)
display_ready() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method)
display_repository_clone_page() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
display_repository_file_contents() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
display_repository_reviews_by_user() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
display_reviewed_repositories_owned_by_user() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
display_structured() (galaxy.webapps.galaxy.controllers.history.HistoryController method)
display_tool() (tool_shed.webapp.controllers.repository.RepositoryController method)
display_url() (galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink method)
displayable() (galaxy.datatypes.interval.Interval method)
- (galaxy.datatypes.tabular.TabularData method)
DisplayApplication (class in galaxy.datatypes.display_applications.application)
DisplayApplicationDataParameter (class in galaxy.datatypes.display_applications.parameters)
DisplayApplicationLink (class in galaxy.datatypes.display_applications.application)
DisplayApplicationParameter (class in galaxy.datatypes.display_applications.parameters)
DisplayApplicationsController (class in galaxy.webapps.galaxy.api.display_applications)
DisplayApplicationTemplateParameter (class in galaxy.datatypes.display_applications.parameters)
DisplayByUsernameAndSlugGridOperation (class in galaxy.web.framework.helpers.grids)
- (class in galaxy.web.legacy_framework.grids)
DisplayDataValueWrapper (class in galaxy.datatypes.display_applications.parameters)
DisplayParameterValueWrapper (class in galaxy.datatypes.display_applications.parameters)
dist_css() (in module galaxy.web.framework.helpers)
dist_js() (in module galaxy.web.framework.helpers)
dist_to_shed (galaxy.model.tool_shed_install.ToolShedRepository attribute)
DistanceMatrix (class in galaxy.datatypes.mothur)
DistributedObjectStore (class in galaxy.objectstore)
DlibSQlite (class in galaxy.datatypes.binary)
DMND (class in galaxy.datatypes.binary)
DNA_COMPLEMENT (galaxy.datatypes.util.maf_utilities.RegionAlignment attribute)
- (galaxy.datatypes.util.maf_utilities.SplicedAlignment attribute)
- (galaxy.tools.util.maf_utilities.RegionAlignment attribute)
- (galaxy.tools.util.maf_utilities.SplicedAlignment attribute)
do_fast_split() (galaxy.datatypes.sequence.Sequence class method)
do_invocation_step_action() (galaxy.workflow.modules.PauseModule method)
- (galaxy.workflow.modules.WorkflowModule method)
do_merge() (in module galaxy.jobs.splitters.basic)
- (in module galaxy.jobs.splitters.multi)
do_not_cache() (in module galaxy.web)
- (in module galaxy.web.framework.decorators)
do_refactor() (galaxy.managers.workflows.WorkflowContentsManager method)
do_slow_split() (galaxy.datatypes.sequence.Sequence class method)
do_split() (in module galaxy.jobs.splitters.basic)
- (in module galaxy.jobs.splitters.multi)
docker_cache_path() (in module galaxy.tool_util.deps.container_classes)
docker_cmd() (galaxy.visualization.plugins.interactive_environments.InteractiveEnvironmentRequest method)
docker_columns() (in module galaxy.containers.docker_decorators)
docker_compatible_realpath() (galaxy.tool_util.cwl.cwltool_deps.StdFsAccess method)
docker_dispatch() (in module galaxy.jobs.stock_rules)
docker_host_args() (in module galaxy.tool_util.deps.dockerfiles)
docker_host_props() (galaxy.tool_util.deps.container_classes.DockerContainer property)
docker_image_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute)
docker_json() (in module galaxy.containers.docker_decorators)
docker_to_singularity() (in module galaxy.tool_util.deps.mulled.mulled_update_singularity_containers)
DockerAPIClient (class in galaxy.containers.docker)
DockerAPIInterface (class in galaxy.containers.docker)
DockerAttributeContainer (class in galaxy.containers.docker_model)
DockerCLIInterface (class in galaxy.containers.docker)
DockerContainer (class in galaxy.containers.docker_model)
- (class in galaxy.tool_util.deps.container_classes)
dockerfile_build() (in module galaxy.tool_util.deps.dockerfiles)
DockerImageGrid (class in tool_shed.grids.repository_grids)
DockerInterface (class in galaxy.containers.docker)
DockerNode (class in galaxy.containers.docker_model)
DockerNodeLabel (class in galaxy.containers.docker_model)
DockerNodeLabels (class in galaxy.containers.docker_model)
DockerService (class in galaxy.containers.docker_model)
DockerServiceConstraint (class in galaxy.containers.docker_model)
DockerServiceConstraints (class in galaxy.containers.docker_model)
DockerSwarmAPIInterface (class in galaxy.containers.docker_swarm)
DockerSwarmCLIInterface (class in galaxy.containers.docker_swarm)
DockerSwarmInterface (class in galaxy.containers.docker_swarm)
DockerTask (class in galaxy.containers.docker_model)
DockerVolume (class in galaxy.containers.docker_model)
DockStoreResolver (class in galaxy.tool_util.locations.dockstore)
docstring_trim() (in module galaxy.util)
doi() (galaxy.managers.citations.DoiCitation method)
DoiCache (class in galaxy.managers.citations)
DoiCitation (class in galaxy.managers.citations)
DOMAIN (galaxy.model.search.HistoryDatasetView attribute)
- (galaxy.model.search.HistoryView attribute)
- (galaxy.model.search.JobView attribute)
- (galaxy.model.search.PageRevisionView attribute)
- (galaxy.model.search.PageView attribute)
- (galaxy.model.search.WorkflowView attribute)
DONE (galaxy.model.TransferJob.states attribute)
DotBracket (class in galaxy.datatypes.sequence)
downgrade() (in module galaxy.model.migrate.versions.0002_metadata_file_table)
- (in module galaxy.model.migrate.versions.0003_security_and_libraries)
- (in module galaxy.model.migrate.versions.0004_indexes_and_defaults)
- (in module galaxy.model.migrate.versions.0005_cleanup_datasets_fix)
- (in module galaxy.model.migrate.versions.0006_change_qual_datatype)
- (in module galaxy.model.migrate.versions.0007_sharing_histories)
- (in module galaxy.model.migrate.versions.0008_galaxy_forms)
- (in module galaxy.model.migrate.versions.0009_request_table)
- (in module galaxy.model.migrate.versions.0010_hda_display_at_authz_table)
- (in module galaxy.model.migrate.versions.0011_v0010_mysql_index_fix)
- (in module galaxy.model.migrate.versions.0012_user_address)
- (in module galaxy.model.migrate.versions.0013_change_lib_item_templates_to_forms)
- (in module galaxy.model.migrate.versions.0014_pages)
- (in module galaxy.model.migrate.versions.0015_tagging)
- (in module galaxy.model.migrate.versions.0016_v0015_mysql_index_fix)
- (in module galaxy.model.migrate.versions.0017_library_item_indexes)
- (in module galaxy.model.migrate.versions.0018_ordered_tags_and_page_tags)
- (in module galaxy.model.migrate.versions.0019_request_library_folder)
- (in module galaxy.model.migrate.versions.0020_library_upload_job)
- (in module galaxy.model.migrate.versions.0021_user_prefs)
- (in module galaxy.model.migrate.versions.0022_visualization_tables)
- (in module galaxy.model.migrate.versions.0023_page_published_and_deleted_columns)
- (in module galaxy.model.migrate.versions.0024_page_slug_unique_constraint)
- (in module galaxy.model.migrate.versions.0025_user_info)
- (in module galaxy.model.migrate.versions.0026_cloud_tables)
- (in module galaxy.model.migrate.versions.0027_request_events)
- (in module galaxy.model.migrate.versions.0028_external_metadata_file_override)
- (in module galaxy.model.migrate.versions.0029_user_actions)
- (in module galaxy.model.migrate.versions.0030_history_slug_column)
- (in module galaxy.model.migrate.versions.0031_community_and_workflow_tags)
- (in module galaxy.model.migrate.versions.0032_stored_workflow_slug_column)
- (in module galaxy.model.migrate.versions.0033_published_cols_for_histories_and_workflows)
- (in module galaxy.model.migrate.versions.0034_page_user_share_association)
- (in module galaxy.model.migrate.versions.0035_item_annotations_and_workflow_step_tags)
- (in module galaxy.model.migrate.versions.0036_add_deleted_column_to_library_template_assoc_tables)
- (in module galaxy.model.migrate.versions.0037_samples_library)
- (in module galaxy.model.migrate.versions.0038_add_inheritable_column_to_library_template_assoc_tables)
- (in module galaxy.model.migrate.versions.0039_add_synopsis_column_to_library_table)
- (in module galaxy.model.migrate.versions.0040_page_annotations)
- (in module galaxy.model.migrate.versions.0041_workflow_invocation)
- (in module galaxy.model.migrate.versions.0042_workflow_invocation_fix)
- (in module galaxy.model.migrate.versions.0043_visualization_sharing_tagging_annotating)
- (in module galaxy.model.migrate.versions.0044_add_notify_column_to_request_table)
- (in module galaxy.model.migrate.versions.0045_request_type_permissions_table)
- (in module galaxy.model.migrate.versions.0046_post_job_actions)
- (in module galaxy.model.migrate.versions.0047_job_table_user_id_column)
- (in module galaxy.model.migrate.versions.0048_dataset_instance_state_column)
- (in module galaxy.model.migrate.versions.0049_api_keys_table)
- (in module galaxy.model.migrate.versions.0050_drop_cloud_tables)
- (in module galaxy.model.migrate.versions.0051_imported_col_for_jobs_table)
- (in module galaxy.model.migrate.versions.0052_sample_dataset_table)
- (in module galaxy.model.migrate.versions.0053_item_ratings)
- (in module galaxy.model.migrate.versions.0054_visualization_dbkey)
- (in module galaxy.model.migrate.versions.0055_add_pja_assoc_for_jobs)
- (in module galaxy.model.migrate.versions.0056_workflow_outputs)
- (in module galaxy.model.migrate.versions.0057_request_notify)
- (in module galaxy.model.migrate.versions.0058_history_import_export)
- (in module galaxy.model.migrate.versions.0059_sample_dataset_file_path)
- (in module galaxy.model.migrate.versions.0060_history_archive_import)
- (in module galaxy.model.migrate.versions.0061_tasks)
- (in module galaxy.model.migrate.versions.0062_user_openid_table)
- (in module galaxy.model.migrate.versions.0063_sequencer_table)
- (in module galaxy.model.migrate.versions.0064_add_run_and_sample_run_association_tables)
- (in module galaxy.model.migrate.versions.0065_add_name_to_form_fields_and_values)
- (in module galaxy.model.migrate.versions.0066_deferred_job_and_transfer_job_tables)
- (in module galaxy.model.migrate.versions.0067_populate_sequencer_table)
- (in module galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services)
- (in module galaxy.model.migrate.versions.0069_rename_sequencer_form_type)
- (in module galaxy.model.migrate.versions.0070_add_info_column_to_deferred_job_table)
- (in module galaxy.model.migrate.versions.0071_add_history_and_workflow_to_sample)
- (in module galaxy.model.migrate.versions.0072_add_pid_and_socket_columns_to_transfer_job_table)
- (in module galaxy.model.migrate.versions.0073_add_ldda_to_implicit_conversion_table)
- (in module galaxy.model.migrate.versions.0074_add_purged_column_to_library_dataset_table)
- (in module galaxy.model.migrate.versions.0075_add_subindex_column_to_run_table)
- (in module galaxy.model.migrate.versions.0076_fix_form_values_data_corruption)
- (in module galaxy.model.migrate.versions.0077_create_tool_tag_association_table)
- (in module galaxy.model.migrate.versions.0078_add_columns_for_disk_usage_accounting)
- (in module galaxy.model.migrate.versions.0079_input_library_to_job_table)
- (in module galaxy.model.migrate.versions.0080_quota_tables)
- (in module galaxy.model.migrate.versions.0081_add_tool_version_to_hda_ldda)
- (in module galaxy.model.migrate.versions.0082_add_tool_shed_repository_table)
- (in module galaxy.model.migrate.versions.0083_add_prepare_files_to_task)
- (in module galaxy.model.migrate.versions.0084_add_ldda_id_to_implicit_conversion_table)
- (in module galaxy.model.migrate.versions.0085_add_task_info)
- (in module galaxy.model.migrate.versions.0086_add_tool_shed_repository_table_columns)
- (in module galaxy.model.migrate.versions.0087_tool_id_guid_map_table)
- (in module galaxy.model.migrate.versions.0088_add_installed_changeset_revison_column)
- (in module galaxy.model.migrate.versions.0089_add_object_store_id_columns)
- (in module galaxy.model.migrate.versions.0090_add_tool_shed_repository_table_columns)
- (in module galaxy.model.migrate.versions.0091_add_tool_version_tables)
- (in module galaxy.model.migrate.versions.0092_add_migrate_tools_table)
- (in module galaxy.model.migrate.versions.0093_add_job_params_col)
- (in module galaxy.model.migrate.versions.0094_add_job_handler_col)
- (in module galaxy.model.migrate.versions.0095_hda_subsets)
- (in module galaxy.model.migrate.versions.0096_openid_provider)
- (in module galaxy.model.migrate.versions.0097_add_ctx_rev_column)
- (in module galaxy.model.migrate.versions.0098_genome_index_tool_data_table)
- (in module galaxy.model.migrate.versions.0099_add_tool_dependency_table)
- (in module galaxy.model.migrate.versions.0100_alter_tool_dependency_table_version_column)
- (in module galaxy.model.migrate.versions.0101_drop_installed_changeset_revision_column)
- (in module galaxy.model.migrate.versions.0102_add_tool_dependency_status_columns)
- (in module galaxy.model.migrate.versions.0103_add_tool_shed_repository_status_columns)
- (in module galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters)
- (in module galaxy.model.migrate.versions.0105_add_cleanup_event_table)
- (in module galaxy.model.migrate.versions.0106_add_missing_indexes)
- (in module galaxy.model.migrate.versions.0107_add_exit_code_to_job_and_task)
- (in module galaxy.model.migrate.versions.0108_add_extended_metadata)
- (in module galaxy.model.migrate.versions.0109_add_repository_dependency_tables)
- (in module galaxy.model.migrate.versions.0110_add_dataset_uuid)
- (in module galaxy.model.migrate.versions.0111_add_job_destinations)
- (in module galaxy.model.migrate.versions.0112_add_data_manager_history_association_and_data_manager_job_association_tables)
- (in module galaxy.model.migrate.versions.0113_update_migrate_tools_table)
- (in module galaxy.model.migrate.versions.0114_update_migrate_tools_table_again)
- (in module galaxy.model.migrate.versions.0115_longer_user_password_field)
- (in module galaxy.model.migrate.versions.0116_drop_update_available_col_add_tool_shed_status_col)
- (in module galaxy.model.migrate.versions.0117_add_user_activation)
- (in module galaxy.model.migrate.versions.0118_add_hda_extended_metadata)
- (in module galaxy.model.migrate.versions.0119_job_metrics)
- (in module galaxy.model.migrate.versions.0120_dataset_collections)
- (in module galaxy.model.migrate.versions.0121_workflow_uuids)
- (in module galaxy.model.migrate.versions.0122_grow_mysql_blobs)
- (in module galaxy.model.migrate.versions.0123_add_workflow_request_tables)
- (in module galaxy.model.migrate.versions.0124_job_state_history)
- (in module galaxy.model.migrate.versions.0125_workflow_step_tracking)
- (in module galaxy.model.migrate.versions.0126_password_reset)
- (in module galaxy.model.migrate.versions.0127_output_collection_adjustments)
- (in module galaxy.model.migrate.versions.0128_session_timeout)
- (in module galaxy.model.migrate.versions.0129_job_external_output_metadata_validity)
- (in module galaxy.model.migrate.versions.0130_change_pref_datatype)
- (in module galaxy.model.migrate.versions.0131_subworkflow_and_input_parameter_modules)
- (in module galaxy.model.migrate.versions.0132_add_lastpasswordchange_to_user)
- (in module galaxy.model.migrate.versions.0133_add_dependency_column_to_job)
- (in module galaxy.model.migrate.versions.0134_hda_set_deleted_if_purged)
- (in module galaxy.model.migrate.versions.0135_add_library_tags)
- (in module galaxy.model.migrate.versions.0136_collection_and_workflow_state)
- (in module galaxy.model.migrate.versions.0137_add_copied_from_job_id_column)
- (in module galaxy.model.migrate.versions.0138_add_hda_version)
- (in module galaxy.model.migrate.versions.0139_add_history_dataset_association_history_table)
- (in module galaxy.model.migrate.versions.0140_add_dataset_version_to_job_to_input_dataset_association_table)
- (in module galaxy.model.migrate.versions.0141_add_oidc_tables)
- (in module galaxy.model.migrate.versions.0142_change_numeric_metric_precision)
- (in module galaxy.model.migrate.versions.0143_add_cloudauthz_tables)
- (in module galaxy.model.migrate.versions.0144_add_cleanup_event_user_table)
- (in module galaxy.model.migrate.versions.0145_add_workflow_step_input)
- (in module galaxy.model.migrate.versions.0146_workflow_paths)
- (in module galaxy.model.migrate.versions.0147_job_messages)
- (in module galaxy.model.migrate.versions.0148_add_checksum_table)
- (in module galaxy.model.migrate.versions.0149_dynamic_tools)
- (in module galaxy.model.migrate.versions.0150_add_create_time_field_for_cloudauthz)
- (in module galaxy.model.migrate.versions.0151_add_worker_process)
- (in module galaxy.model.migrate.versions.0152_add_metadata_file_uuid)
- (in module galaxy.model.migrate.versions.0153_add_custos_authnz_token_table)
- (in module galaxy.model.migrate.versions.0154_created_from_basename)
- (in module galaxy.model.migrate.versions.0155_job_galaxy_version)
- (in module galaxy.model.migrate.versions.0156_add_interactivetools)
- (in module galaxy.model.migrate.versions.0157_rework_dataset_validation)
- (in module galaxy.model.migrate.versions.0158_workflow_reports)
- (in module galaxy.model.migrate.versions.0159_add_job_external_id_index)
- (in module galaxy.model.migrate.versions.0160_hda_set_deleted_if_purged_again)
- (in module galaxy.model.migrate.versions.0161_add_workflow_invocation_output_table)
- (in module galaxy.model.migrate.versions.0162_job_only_pjas)
- (in module galaxy.model.migrate.versions.0163_worker_process_pid)
- (in module galaxy.model.migrate.versions.0164_page_format)
- (in module galaxy.model.migrate.versions.0165_add_content_update_time)
- (in module galaxy.model.migrate.versions.0166_job_state_summary_view)
- (in module galaxy.model.migrate.versions.0167_add_job_to_input_dataset_collection_element_association)
- (in module galaxy.model.migrate.versions.0168_stored_workflow_hidden_col)
- (in module galaxy.model.migrate.versions.0169_add_missing_indexes)
- (in module galaxy.model.migrate.versions.0170_add_more_missing_indexes)
- (in module galaxy.model.migrate.versions.0171_schemaorg_metadata)
- (in module galaxy.model.migrate.versions.0172_it_entrypoint_requires_domain)
- (in module galaxy.tool_shed.galaxy_install.migrate.versions.0001_tools)
- (in module galaxy.tool_shed.galaxy_install.migrate.versions.0002_tools)
- (in module galaxy.tool_shed.galaxy_install.migrate.versions.0003_tools)
- (in module galaxy.tool_shed.galaxy_install.migrate.versions.0004_tools)
- (in module galaxy.tool_shed.galaxy_install.migrate.versions.0005_tools)
- (in module galaxy.tool_shed.galaxy_install.migrate.versions.0006_tools)
- (in module galaxy.tool_shed.galaxy_install.migrate.versions.0007_tools)
- (in module galaxy.tool_shed.galaxy_install.migrate.versions.0008_tools)
- (in module galaxy.tool_shed.galaxy_install.migrate.versions.0009_tools)
- (in module galaxy.tool_shed.galaxy_install.migrate.versions.0010_tools)
- (in module galaxy.tool_shed.galaxy_install.migrate.versions.0011_tools)
- (in module galaxy.tool_shed.galaxy_install.migrate.versions.0012_tools)
- (in module tool_shed.webapp.model.migrate.versions.0001_initial_tables)
- (in module tool_shed.webapp.model.migrate.versions.0002_add_tool_suite_column)
- (in module tool_shed.webapp.model.migrate.versions.0003_review_and_review_association_tables)
- (in module tool_shed.webapp.model.migrate.versions.0004_repository_tables)
- (in module tool_shed.webapp.model.migrate.versions.0005_drop_tool_related_tables)
- (in module tool_shed.webapp.model.migrate.versions.0006_add_email_alerts_column)
- (in module tool_shed.webapp.model.migrate.versions.0007_add_long_description_times_downloaded_columns)
- (in module tool_shed.webapp.model.migrate.versions.0008_add_repository_metadata_table)
- (in module tool_shed.webapp.model.migrate.versions.0009_add_malicious_column)
- (in module tool_shed.webapp.model.migrate.versions.0010_add_new_repo_alert_column)
- (in module tool_shed.webapp.model.migrate.versions.0011_add_tool_versions_column)
- (in module tool_shed.webapp.model.migrate.versions.0012_add_downloadable_column)
- (in module tool_shed.webapp.model.migrate.versions.0013_add_review_tables)
- (in module tool_shed.webapp.model.migrate.versions.0014_add_deprecated_column)
- (in module tool_shed.webapp.model.migrate.versions.0015_add_api_keys_table)
- (in module tool_shed.webapp.model.migrate.versions.0016_add_do_not_test_tools_functionally_correct_errors_columns)
- (in module tool_shed.webapp.model.migrate.versions.0017_add_galaxy_utility_columns_to_repository_metadata_table)
- (in module tool_shed.webapp.model.migrate.versions.0018_add_repository_metadata_flag_columns)
- (in module tool_shed.webapp.model.migrate.versions.0019_add_skip_tool_test_table_and_test_install_error_column)
- (in module tool_shed.webapp.model.migrate.versions.0020_add_repository_type_column)
- (in module tool_shed.webapp.model.migrate.versions.0021_change_repository_type_value)
- (in module tool_shed.webapp.model.migrate.versions.0022_add_repository_admin_roles)
- (in module tool_shed.webapp.model.migrate.versions.0023_add_repository_url_and_hompeage_url)
- (in module tool_shed.webapp.model.migrate.versions.0024_password_reset)
- (in module tool_shed.webapp.model.migrate.versions.0025_session_timeout)
- (in module tool_shed.webapp.model.migrate.versions.0026_add_numeric_revision_column)
Download (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler)
download() (galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController method)
- (galaxy.webapps.galaxy.api.tools.ToolsController method)
- (tool_shed.webapp.controllers.repository.RepositoryController method)
download_binary() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler.DownloadBinary method)
download_command() (in module galaxy.util.commands)
download_dataset_collection() (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method)
download_dataset_from_library() (galaxy_test.selenium.test_library_contents.LibraryContentsTestCase method)
download_field_file() (galaxy.webapps.galaxy.api.tool_data.ToolData method)
download_invocation_bco() (galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController method)
download_output() (in module galaxy.tool_util.cwl.util)
download_to_file() (in module galaxy.util)
download_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method)
downloadable (tool_shed.webapp.model.RepositoryMetadata attribute)
downloadable_revisions (tool_shed.webapp.model.Repository attribute)
DownloadBinary (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler)
DownloadByUrl (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler)
DownloadFile (class in galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler)
drain() (galaxy.containers.docker_model.DockerNode method)
DRF (class in galaxy.datatypes.molecules)
DrillDownSelectToolParameter (class in galaxy.tools.parameters.basic)
drive_test() (in module galaxy_test.driver.driver_util)
DrivenFunctionalTestCase (class in galaxy_test.driver.testcase)
driver() (galaxy.selenium.context.GalaxySeleniumContext property)
DriverWrapper (class in galaxy.selenium.cli)
DRMAAJobRunner (class in galaxy.jobs.runners.drmaa)
drop_column() (in module galaxy.model.migrate.versions.util)
drop_index() (in module galaxy.model.migrate.versions.util)
drop_table() (in module galaxy.model.migrate.versions.util)
drop_timestamp_triggers() (in module galaxy.model.triggers)
drop_timestamps() (in module galaxy.model.migrate.versions.0165_add_content_update_time)
DropboxFilesSource (class in galaxy.files.sources.dropbox)
DropView (class in galaxy.model.view.utils)
dry_run (galaxy.managers.workflows.RefactorResponse attribute)
- (galaxy.managers.workflows.WorkflowUpdateOptions attribute)
- (galaxy.workflow.refactor.schema.RefactorActions attribute)
ds_entry() (galaxy_test.base.populators.BaseDatasetPopulator method)
Dta (class in galaxy.datatypes.proteomics)
Dta2d (class in galaxy.datatypes.proteomics)
dump() (galaxy.util.aliaspickler.AliasPickleModule method)
- (galaxy.util.heartbeat.Heartbeat method)
dump_signal_handler() (galaxy.util.heartbeat.Heartbeat method)
dump_test_information() (in module galaxy_test.selenium.framework)
dump_workflow() (galaxy_test.base.populators.BaseWorkflowPopulator method)
dumps() (galaxy.util.aliaspickler.AliasPickleModule method)
DumpTourCallback (class in galaxy.selenium.scripts.dump_tour)
DuplicatedIdentifierException
DuplicatedSlugException
dynamic_conf_filenames() (galaxy.tools.toolbox.AbstractToolBox method)
- (galaxy.tools.toolbox.base.AbstractToolBox method)
dynamic_confs() (galaxy.tools.toolbox.AbstractToolBox method)
- (galaxy.tools.toolbox.base.AbstractToolBox method)
dynamic_structure() (galaxy.tool_util.parser.output_objects.ToolOutputCollection property)
dynamic_tool (galaxy.model.WorkflowStep attribute)
dynamic_tool_confs() (galaxy.webapps.galaxy.api.configuration.ConfigurationController method)
dynamic_tool_id (galaxy.model.Job attribute)
- (galaxy.model.WorkflowStep attribute)
DynamicCompressedArchive (class in galaxy.datatypes.binary)
DynamicDisplayApplicationBuilder (class in galaxy.datatypes.display_applications.application)
DynamicOptions (class in galaxy.tools.parameters.dynamic_options)
DynamicTool (class in galaxy.model)
DynamicToolManager (class in galaxy.managers.tools)
DynamicToolsController (class in galaxy.webapps.galaxy.api.dynamic_tools)
Dzi (class in galaxy.datatypes.xml)

E

echo() (galaxy.webapps.galaxy.controllers.root.RootController method)
echo_json() (galaxy.webapps.galaxy.controllers.root.RootController method)
edam_data (galaxy.datatypes.annotation.Augustus attribute)
- (galaxy.datatypes.annotation.SnapHmm attribute)
- (galaxy.datatypes.assembly.Amos attribute)
- (galaxy.datatypes.assembly.Sequences attribute)
- (galaxy.datatypes.binary.Ab1 attribute)
- (galaxy.datatypes.binary.BafTar attribute)
- (galaxy.datatypes.binary.Bam attribute)
- (galaxy.datatypes.binary.BamNative attribute)
- (galaxy.datatypes.binary.BaseBcf attribute)
- (galaxy.datatypes.binary.BigBed attribute)
- (galaxy.datatypes.binary.BigWig attribute)
- (galaxy.datatypes.binary.Cel attribute)
- (galaxy.datatypes.binary.CRAM attribute)
- (galaxy.datatypes.binary.Dcd attribute)
- (galaxy.datatypes.binary.GeminiSQLite attribute)
- (galaxy.datatypes.binary.GenericAsn1Binary attribute)
- (galaxy.datatypes.binary.ICM attribute)
- (galaxy.datatypes.binary.Idat attribute)
- (galaxy.datatypes.binary.NetCDF attribute)
- (galaxy.datatypes.binary.ProBam attribute)
- (galaxy.datatypes.binary.Scf attribute)
- (galaxy.datatypes.binary.Sff attribute)
- (galaxy.datatypes.binary.TwoBit attribute)
- (galaxy.datatypes.blast.BlastXml attribute)
- (galaxy.datatypes.data.Data attribute)
- (galaxy.datatypes.data.GenericAsn1 attribute)
- (galaxy.datatypes.data.Newick attribute)
- (galaxy.datatypes.data.Nexus attribute)
- (galaxy.datatypes.images.Image attribute)
- (galaxy.datatypes.interval.Gff attribute)
- (galaxy.datatypes.interval.Interval attribute)
- (galaxy.datatypes.microarrays.Gal attribute)
- (galaxy.datatypes.microarrays.Gpr attribute)
- (galaxy.datatypes.msa.Hmmer attribute)
- (galaxy.datatypes.msa.Msf attribute)
- (galaxy.datatypes.msa.Stockholm_1_0 attribute)
- (galaxy.datatypes.phylip.Phylip attribute)
- (galaxy.datatypes.proteomics.MascotDat attribute)
- (galaxy.datatypes.proteomics.Mgf attribute)
- (galaxy.datatypes.proteomics.MzTab attribute)
- (galaxy.datatypes.proteomics.PepXmlReport attribute)
- (galaxy.datatypes.proteomics.ProteomicsXml attribute)
- (galaxy.datatypes.proteomics.ProtXmlReport attribute)
- (galaxy.datatypes.proteomics.ThermoRAW attribute)
- (galaxy.datatypes.proteomics.Wiff attribute)
- (galaxy.datatypes.qualityscore.QualityScore attribute)
- (galaxy.datatypes.sequence.Alignment attribute)
- (galaxy.datatypes.sequence.Axt attribute)
- (galaxy.datatypes.sequence.DotBracket attribute)
- (galaxy.datatypes.sequence.Genbank attribute)
- (galaxy.datatypes.sequence.Lav attribute)
- (galaxy.datatypes.sequence.Sequence attribute)
- (galaxy.datatypes.tabular.Sam attribute)
- (galaxy.datatypes.text.Obo attribute)
- (galaxy.datatypes.tracks.GeneTrack attribute)
- (galaxy.datatypes.triples.Triples attribute)
- (galaxy.datatypes.xml.Phyloxml attribute)
- (galaxy.datatypes.xml.Sbml attribute)
edam_data() (galaxy.datatypes.registry.Registry property)
- (galaxy.webapps.galaxy.api.datatypes.DatatypesController method)
edam_format (galaxy.datatypes.assembly.Amos attribute)
- (galaxy.datatypes.assembly.Roadmaps attribute)
- (galaxy.datatypes.binary.Ab1 attribute)
- (galaxy.datatypes.binary.BafTar attribute)
- (galaxy.datatypes.binary.Bam attribute)
- (galaxy.datatypes.binary.BamNative attribute)
- (galaxy.datatypes.binary.BaseBcf attribute)
- (galaxy.datatypes.binary.BigBed attribute)
- (galaxy.datatypes.binary.BigWig attribute)
- (galaxy.datatypes.binary.Binary attribute)
- (galaxy.datatypes.binary.Biom2 attribute)
- (galaxy.datatypes.binary.Cel attribute)
- (galaxy.datatypes.binary.CRAM attribute)
- (galaxy.datatypes.binary.CuffDiffSQlite attribute)
- (galaxy.datatypes.binary.ExcelXls attribute)
- (galaxy.datatypes.binary.GeminiSQLite attribute)
- (galaxy.datatypes.binary.GenericAsn1Binary attribute)
- (galaxy.datatypes.binary.H5 attribute)
- (galaxy.datatypes.binary.Idat attribute)
- (galaxy.datatypes.binary.Loom attribute)
- (galaxy.datatypes.binary.NetCDF attribute)
- (galaxy.datatypes.binary.ProBam attribute)
- (galaxy.datatypes.binary.Scf attribute)
- (galaxy.datatypes.binary.Sff attribute)
- (galaxy.datatypes.binary.SQlite attribute)
- (galaxy.datatypes.binary.TwoBit attribute)
- (galaxy.datatypes.blast.BlastXml attribute)
- (galaxy.datatypes.data.Data attribute)
- (galaxy.datatypes.data.GenericAsn1 attribute)
- (galaxy.datatypes.data.Newick attribute)
- (galaxy.datatypes.data.Nexus attribute)
- (galaxy.datatypes.data.Text attribute)
- (galaxy.datatypes.images.Bmp attribute)
- (galaxy.datatypes.images.Eps attribute)
- (galaxy.datatypes.images.Gif attribute)
- (galaxy.datatypes.images.Gmaj attribute)
- (galaxy.datatypes.images.Im attribute)
- (galaxy.datatypes.images.Image attribute)
- (galaxy.datatypes.images.Jpg attribute)
- (galaxy.datatypes.images.Pbm attribute)
- (galaxy.datatypes.images.Pcd attribute)
- (galaxy.datatypes.images.Pcx attribute)
- (galaxy.datatypes.images.Pdf attribute)
- (galaxy.datatypes.images.Pgm attribute)
- (galaxy.datatypes.images.Png attribute)
- (galaxy.datatypes.images.Ppm attribute)
- (galaxy.datatypes.images.Psd attribute)
- (galaxy.datatypes.images.Rast attribute)
- (galaxy.datatypes.images.Rgb attribute)
- (galaxy.datatypes.images.Tiff attribute)
- (galaxy.datatypes.images.Xbm attribute)
- (galaxy.datatypes.images.Xpm attribute)
- (galaxy.datatypes.interval.Bed attribute)
- (galaxy.datatypes.interval.Bed12 attribute)
- (galaxy.datatypes.interval.Bed6 attribute)
- (galaxy.datatypes.interval.BedGraph attribute)
- (galaxy.datatypes.interval.BedStrict attribute)
- (galaxy.datatypes.interval.CustomTrack attribute)
- (galaxy.datatypes.interval.ENCODEPeak attribute)
- (galaxy.datatypes.interval.Gff attribute)
- (galaxy.datatypes.interval.Gff3 attribute)
- (galaxy.datatypes.interval.Gtf attribute)
- (galaxy.datatypes.interval.Interval attribute)
- (galaxy.datatypes.interval.ProBed attribute)
- (galaxy.datatypes.interval.Wiggle attribute)
- (galaxy.datatypes.microarrays.Gal attribute)
- (galaxy.datatypes.microarrays.Gpr attribute)
- (galaxy.datatypes.msa.Hmmer attribute)
- (galaxy.datatypes.msa.Hmmer2 attribute)
- (galaxy.datatypes.msa.Hmmer3 attribute)
- (galaxy.datatypes.msa.Msf attribute)
- (galaxy.datatypes.msa.Stockholm_1_0 attribute)
- (galaxy.datatypes.phylip.Phylip attribute)
- (galaxy.datatypes.proteomics.ImzML attribute)
- (galaxy.datatypes.proteomics.MascotDat attribute)
- (galaxy.datatypes.proteomics.Mgf attribute)
- (galaxy.datatypes.proteomics.MzData attribute)
- (galaxy.datatypes.proteomics.MzIdentML attribute)
- (galaxy.datatypes.proteomics.MzML attribute)
- (galaxy.datatypes.proteomics.MzQuantML attribute)
- (galaxy.datatypes.proteomics.MzXML attribute)
- (galaxy.datatypes.proteomics.PepXml attribute)
- (galaxy.datatypes.proteomics.ProteomicsXml attribute)
- (galaxy.datatypes.proteomics.TandemXML attribute)
- (galaxy.datatypes.proteomics.ThermoRAW attribute)
- (galaxy.datatypes.proteomics.TraML attribute)
- (galaxy.datatypes.proteomics.Wiff attribute)
- (galaxy.datatypes.qualityscore.QualityScore attribute)
- (galaxy.datatypes.qualityscore.QualityScore454 attribute)
- (galaxy.datatypes.qualityscore.QualityScoreIllumina attribute)
- (galaxy.datatypes.qualityscore.QualityScoreSolexa attribute)
- (galaxy.datatypes.qualityscore.QualityScoreSOLiD attribute)
- (galaxy.datatypes.sequence.Axt attribute)
- (galaxy.datatypes.sequence.BaseFastq attribute)
- (galaxy.datatypes.sequence.csFasta attribute)
- (galaxy.datatypes.sequence.DotBracket attribute)
- (galaxy.datatypes.sequence.Fasta attribute)
- (galaxy.datatypes.sequence.Fastg attribute)
- (galaxy.datatypes.sequence.Fastq attribute)
- (galaxy.datatypes.sequence.FastqIllumina attribute)
- (galaxy.datatypes.sequence.FastqSanger attribute)
- (galaxy.datatypes.sequence.FastqSolexa attribute)
- (galaxy.datatypes.sequence.Genbank attribute)
- (galaxy.datatypes.sequence.Lav attribute)
- (galaxy.datatypes.sequence.Maf attribute)
- (galaxy.datatypes.sequence.RNADotPlotMatrix attribute)
- (galaxy.datatypes.tabular.BaseVcf attribute)
- (galaxy.datatypes.tabular.ConnectivityTable attribute)
- (galaxy.datatypes.tabular.Pileup attribute)
- (galaxy.datatypes.tabular.Sam attribute)
- (galaxy.datatypes.tabular.TabularData attribute)
- (galaxy.datatypes.text.Arff attribute)
- (galaxy.datatypes.text.Biom1 attribute)
- (galaxy.datatypes.text.Html attribute)
- (galaxy.datatypes.text.Json attribute)
- (galaxy.datatypes.text.Obo attribute)
- (galaxy.datatypes.text.SnpEffDb attribute)
- (galaxy.datatypes.tracks.GeneTrack attribute)
- (galaxy.datatypes.triples.HDT attribute)
- (galaxy.datatypes.triples.Jsonld attribute)
- (galaxy.datatypes.triples.N3 attribute)
- (galaxy.datatypes.triples.NTriples attribute)
- (galaxy.datatypes.triples.Rdf attribute)
- (galaxy.datatypes.triples.Triples attribute)
- (galaxy.datatypes.triples.Turtle attribute)
- (galaxy.datatypes.xml.GenericXml attribute)
- (galaxy.datatypes.xml.Owl attribute)
- (galaxy.datatypes.xml.Phyloxml attribute)
- (galaxy.datatypes.xml.Sbml attribute)
edam_formats() (galaxy.datatypes.registry.Registry property)
- (galaxy.webapps.galaxy.api.datatypes.DatatypesController method)
edgelist_for_workflow_steps() (in module galaxy.workflow.steps)
edit() (galaxy.webapps.galaxy.controllers.page.PageController method)
- (galaxy.webapps.galaxy.controllers.visualization.VisualizationController method)
edit_category() (tool_shed.webapp.controllers.admin.AdminController method)
edit_category_entry() (tool_shed.repository_registry.Registry method)
edit_component() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method)
edit_content() (galaxy.webapps.galaxy.controllers.page.PageController method)
edit_form() (galaxy.webapps.galaxy.controllers.forms.Forms method)
edit_info() (tool_shed.webapp.controllers.user.User method)
edit_quota() (galaxy.webapps.galaxy.controllers.admin.AdminGalaxy method)
edit_repository_categories() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
edit_repository_information() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
edit_review() (tool_shed.webapp.controllers.repository_review.RepositoryReviewController method)
edit_username() (tool_shed.webapp.controllers.user.User method)
editable_keys (galaxy.model.HistoryDatasetCollectionAssociation attribute)
- (galaxy.model.LibraryDatasetCollectionAssociation attribute)
editor() (galaxy.webapps.galaxy.controllers.workflow.WorkflowController method)
Edr (class in galaxy.datatypes.binary)
Edta (class in galaxy.datatypes.proteomics)
effective_collection_type() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method)
effective_collection_type_description() (galaxy.model.dataset_collections.type_description.CollectionTypeDescription method)
effective_output_name() (galaxy.tool_util.parser.output_objects.ToolOutputCollectionPart property)
- (galaxy.tool_util.parser.ToolOutputCollectionPart property)
Eigenstratgeno (class in galaxy.datatypes.genetics)
Eigenstratpca (class in galaxy.datatypes.genetics)
Eland (class in galaxy.datatypes.tabular)
ElandMulti (class in galaxy.datatypes.tabular)
elapsed() (galaxy.util.ExecutionTimer property)
- (galaxy.util.StructuredExecutionTimer property)
elem() (galaxy.tool_util.parser.interface.InputSource method)
- (galaxy.tool_util.parser.xml.XmlInputSource method)
element (galaxy.tours.TourStep attribute)
element_as_dict() (galaxy.datatypes.dataproviders.hierarchy.XMLDataProvider method)
element_count (galaxy.model.DatasetCollection attribute)
element_identifier (galaxy.model.DatasetCollectionElement attribute)
element_identifier() (galaxy.tools.wrappers.DatasetCollectionWrapper property)
- (galaxy.tools.wrappers.DatasetFilenameWrapper property)
element_identifiers() (galaxy.model.store.discover.JsonCollectedDatasetMatch property)
element_index (galaxy.model.DatasetCollectionElement attribute)
element_is_set() (galaxy.datatypes.metadata.MetadataCollection method)
- (galaxy.model.metadata.MetadataCollection method)
- (galaxy.tools.wrappers.DatasetFilenameWrapper.MetadataWrapper method)
element_is_valid() (galaxy.tools.FilterEmptyDatasetsTool method)
- (galaxy.tools.FilterFailedDatasetsTool method)
element_locator() (galaxy.selenium.components.Label property)
- (galaxy.selenium.components.SelectorTemplate property)
- (galaxy.selenium.components.Target property)
- (galaxy.selenium.components.Text property)
element_object() (galaxy.model.DatasetCollectionElement property)
element_type() (galaxy.model.DatasetCollectionElement property)
ElementIdentifierMapper (class in galaxy.tools.wrappers)
elements (galaxy.model.DatasetCollection attribute)
elements_no_end_tag (galaxy.managers.pages.PageContentProcessor attribute)
elements_tree_map() (in module galaxy.tools.data_fetch)
ELEMENTS_UNINITIALIZED (galaxy.managers.collections.DatasetCollectionManager attribute)
ElibSQlite (class in galaxy.datatypes.binary)
email (galaxy.model.PSACode attribute)
- (galaxy.model.User attribute)
- (galaxy.schema.BootstrapAdminUser attribute)
- (tool_shed.webapp.model.User attribute)
email() (galaxy.files.DictFileSourcesUserContext property)
- (galaxy.files.ProvidesUserFileSourcesUserContext property)
email_alerts (tool_shed.webapp.model.Repository attribute)
email_alerts_repository_grid (tool_shed.webapp.controllers.repository.RepositoryController attribute)
EmailAction (class in galaxy.jobs.actions.post)
EmailAlertsRepositoryGrid (class in tool_shed.grids.repository_grids)
EmailErrorReporter (class in galaxy.tools.errors)
EmailPlugin (class in galaxy.tools.error_reports.plugins.email)
emboss_repository_long_description (in module tool_shed.test.functional.test_0470_tool_dependency_repository_type)
EMPTY (galaxy.model.Dataset.states attribute)
- (galaxy.model.DatasetInstance.states attribute)
empty() (galaxy.model.History property)
- (galaxy.objectstore.BaseObjectStore method)
- (galaxy.objectstore.ObjectStore method)
EmptyTextfieldValidator (class in galaxy.tools.parameters.validation)
enable_email_alerts() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
enabled_container_types() (galaxy.tool_util.deps.DependencyManager property)
encode() (galaxy.datatypes.dataproviders.chunk.Base64ChunkDataProvider method)
- (galaxy.datatypes.dataproviders.chunk.ChunkDataProvider method)
- (galaxy.tools.DefaultToolState method)
- (galaxy.web_stack.message.ApplicationStackMessage method)
encode_all_ids() (galaxy.security.idencoding.IdEncodingHelper method)
- (galaxy.webapps.base.controller.BaseController method)
encode_dataset_user() (in module galaxy.datatypes.display_applications.util)
encode_dict_ids() (galaxy.security.idencoding.IdEncodingHelper method)
encode_guid() (galaxy.security.idencoding.IdEncodingHelper method)
encode_id() (galaxy.security.idencoding.IdEncodingHelper method)
encode_runtime_state() (galaxy.workflow.modules.WorkflowModule method)
encode_type_id() (galaxy.webapps.galaxy.api.history_contents.HistoryContentsController method)
EncodedDatabaseIdField (class in galaxy.schema.fields)
ENCODEPeak (class in galaxy.datatypes.interval)
ENCODEPeakDataProvider (class in galaxy.visualization.data_providers.genome)
ENCODEPeakTabixDataProvider (class in galaxy.visualization.data_providers.genome)
encoder() (in module galaxy.tools.cache)
end() (galaxy.datatypes.util.maf_utilities.SplicedAlignment property)
- (galaxy.tools.util.maf_utilities.SplicedAlignment property)
endpoint_spec_option_map (galaxy.containers.docker_swarm.DockerSwarmAPIInterface attribute)
engine (galaxy.model.Dataset attribute)
engine_false() (in module galaxy.model.migrate.versions.util)
engine_true() (in module galaxy.model.migrate.versions.util)
enqueue() (galaxy.jobs.JobWrapper method)
- (galaxy.jobs.manager.JobManager method)
- (galaxy.jobs.manager.NoopManager method)
enqueue_output() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment.InstallEnvironment method)
ensure_brew_on_path() (in module galaxy.tool_util.deps.brew_exts)
ensure_conda_build_installed_if_needed() (galaxy.tool_util.deps.conda_util.CondaContext method)
ensure_configs_directory() (in module galaxy.job_execution.setup)
ensure_cwltool_available() (in module galaxy.tool_util.cwl.cwltool_deps)
ensure_history_annotation_area_displayed() (galaxy.selenium.navigates_galaxy.NavigatesGalaxy method)
ensure_in_working_directory() (galaxy.tools.data_fetch.UploadConfig method)
ensure_installed() (in module galaxy.tool_util.deps.installable)
ensure_port_cleanup() (in module galaxy.util.pastescript.serve)
ensure_pykube() (in module galaxy.jobs.runners.util.pykube_util)
ensure_raw_description() (galaxy.managers.workflows.WorkflowContentsManager method)
ensure_registered (galaxy_test.selenium.framework.TestWithSeleniumMixin attribute)
- (galaxy_test.selenium.test_collection_builders.CollectionBuildersTestCase attribute)
- (galaxy_test.selenium.test_history_copy_elements.HistoryCopyElementsTestCase attribute)
- (galaxy_test.selenium.test_history_multi_view.HistoryMultiViewTestCase attribute)
- (galaxy_test.selenium.test_history_panel.HistoryPanelTestCase attribute)
- (galaxy_test.selenium.test_history_panel_collections.HistoryPanelCollectionsTestCase attribute)
- (galaxy_test.selenium.test_history_panel_pagination.HistoryPanelPaginationTestCase attribute)
- (galaxy_test.selenium.test_history_structure.HistoryStructureTestCase attribute)
- (galaxy_test.selenium.test_jupyter.JupyterTestCase attribute)
- (galaxy_test.selenium.test_pages.PagesTestCase attribute)
- (galaxy_test.selenium.test_tool_form.LoggedInToolFormTestCase attribute)
- (galaxy_test.selenium.test_workflow_editor.WorkflowEditorTestCase attribute)
- (galaxy_test.selenium.test_workflow_management.WorkflowManagementTestCase attribute)
- (galaxy_test.selenium.test_workflow_run.WorkflowRunTestCase attribute)

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

F

Facts (class in galaxy.util.facts)
facts() (galaxy.web_stack.ApplicationStack property)
- (galaxy.web_stack.UWSGIApplicationStack property)
fail() (galaxy.jobs.JobWrapper method)
- (galaxy.jobs.TaskWrapper method)
- (galaxy.model.WorkflowInvocation method)
- (in module galaxy.tools.util.galaxyops)
fail_job() (galaxy.jobs.runners.BaseJobRunner method)
- (galaxy.jobs.runners.pbs.PBSJobRunner method)
FAILED (galaxy.model.DatasetCollection.populated_states attribute)
- (galaxy.model.ImplicitCollectionJobs.populated_states attribute)
- (galaxy.model.Job.states attribute)
failed (galaxy.model.view.HistoryDatasetCollectionJobStateSummary attribute)
FAILED (galaxy.model.WorkflowInvocation.states attribute)
failed() (galaxy.tool_util.lint.LintContext method)
FAILED_METADATA (galaxy.model.Dataset.states attribute)
- (galaxy.model.DatasetInstance.states attribute)
FailedTest (class in tool_shed.utility_containers)
FAILURE (galaxy.openid.openid_manager.OpenIDManager attribute)
failure() (in module galaxy.jobs.runners.state_handlers.resubmit)
failure_count() (galaxy.tool_util.verify.script.Results property)
fake_dataset_association (galaxy.model.FakeDatasetAssociation attribute)
FakeDatasetAssociation (class in galaxy.model)
FallbackContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit)
FallbackNoRequirementsContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit)
FallbackNoRequirementsSingularityContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit)
FallbackSingularityContainerResolver (class in galaxy.tool_util.deps.container_resolvers.explicit)
Fast5Archive (class in galaxy.datatypes.binary)
Fast5ArchiveBz2 (class in galaxy.datatypes.binary)
Fast5ArchiveGz (class in galaxy.datatypes.binary)
Fasta (class in galaxy.datatypes.sequence)
fasta_path (galaxy.model.GenomeIndexToolData attribute)
FastaDataProvider (class in galaxy.datatypes.dataproviders.dataset)
FastAPIJobs (class in galaxy.webapps.galaxy.api.jobs)
FastAPILicenses (class in galaxy.webapps.galaxy.api.licenses)
FastAPIRoles (class in galaxy.webapps.galaxy.api.roles)
FastAPITours (class in galaxy.webapps.galaxy.api.tours)
Fastg (class in galaxy.datatypes.sequence)
Fastq (class in galaxy.datatypes.sequence)
FastqCSSanger (class in galaxy.datatypes.sequence)
FastqIllumina (class in galaxy.datatypes.sequence)
FastqSanger (class in galaxy.datatypes.sequence)
FastqSolexa (class in galaxy.datatypes.sequence)
FATAL (galaxy.tool_util.parser.stdio.StdioErrorLevel attribute)
FATAL_OOM (galaxy.tool_util.parser.stdio.StdioErrorLevel attribute)
fda() (galaxy.model.JobExportHistoryArchive property)
FeatureLocationIndex (class in galaxy.datatypes.tabular)
FeatureLocationIndexDataProvider (class in galaxy.visualization.data_providers.genome)
FeatureXML (class in galaxy.datatypes.proteomics)
feed() (galaxy.managers.pages.PageContentProcessor method)
fetch() (galaxy.webapps.galaxy.api.tools.ToolsController method)
- (galaxy_test.base.populators.BaseDatasetPopulator method)
fetch_job_data() (in module galaxy_test.base.instrument)
fetch_job_states() (in module galaxy.managers.jobs)
fetch_repository_metadata() (tool_shed.test.base.twilltestcase.ShedTwillTestCase method)
fetch_requests() (galaxy.web.proxy.JsonFileProxyIpc method)
- (galaxy.web.proxy.ProxyIpc method)
- (galaxy.web.proxy.SqliteProxyIpc method)
FetchUploadToolAction (class in galaxy.tools.actions.upload)
ffprobe() (in module galaxy.datatypes.media)
FIELD (galaxy.tool_util.cwl.representation.INPUT_TYPE attribute)
field_to_field_type() (in module galaxy.tool_util.cwl.representation)
fields (galaxy.model.FormDefinition attribute)
FIELDS (galaxy.model.search.HistoryDatasetView attribute)
- (galaxy.model.search.HistoryView attribute)
- (galaxy.model.search.JobView attribute)
- (galaxy.model.search.LibraryDatasetDatasetView attribute)
- (galaxy.model.search.LibraryDatasetView attribute)
- (galaxy.model.search.LibraryFolderView attribute)
- (galaxy.model.search.LibraryView attribute)
- (galaxy.model.search.PageRevisionView attribute)
- (galaxy.model.search.PageView attribute)
- (galaxy.model.search.ToolView attribute)
- (galaxy.model.search.ViewQueryBaseClass attribute)
- (galaxy.model.search.WorkflowView attribute)
fields() (galaxy.util.form_builder.AddressField static method)
- (galaxy.web.form_builder.AddressField static method)
file_append() (galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder.EnvFileBuilder method)
file_ext (galaxy.datatypes.annotation.Augustus attribute)
- (galaxy.datatypes.annotation.SnapHmm attribute)
- (galaxy.datatypes.anvio.AnvioComposite attribute)
- (galaxy.datatypes.anvio.AnvioContigsDB attribute)
- (galaxy.datatypes.anvio.AnvioDB attribute)
- (galaxy.datatypes.anvio.AnvioGenomesDB attribute)
- (galaxy.datatypes.anvio.AnvioPanDB attribute)
- (galaxy.datatypes.anvio.AnvioProfileDB attribute)
- (galaxy.datatypes.anvio.AnvioSamplesDB attribute)
- (galaxy.datatypes.anvio.AnvioStructureDB attribute)
- (galaxy.datatypes.assembly.Amos attribute)
- (galaxy.datatypes.assembly.Roadmaps attribute)
- (galaxy.datatypes.assembly.Sequences attribute)
- (galaxy.datatypes.assembly.Velvet attribute)
- (galaxy.datatypes.binary.Ab1 attribute)
- (galaxy.datatypes.binary.Anndata attribute)
- (galaxy.datatypes.binary.BafTar attribute)
- (galaxy.datatypes.binary.Bam attribute)
- (galaxy.datatypes.binary.BamInputSorted attribute)
- (galaxy.datatypes.binary.BamNative attribute)
- (galaxy.datatypes.binary.BamQuerynameSorted attribute)
- (galaxy.datatypes.binary.Bcf attribute)
- (galaxy.datatypes.binary.BcfUncompressed attribute)
- (galaxy.datatypes.binary.BigBed attribute)
- (galaxy.datatypes.binary.BigWig attribute)
- (galaxy.datatypes.binary.Biom2 attribute)
- (galaxy.datatypes.binary.BlibSQlite attribute)
- (galaxy.datatypes.binary.Cel attribute)
- (galaxy.datatypes.binary.ChiraSQLite attribute)
- (galaxy.datatypes.binary.CompressedArchive attribute)
- (galaxy.datatypes.binary.CompressedZipArchive attribute)
- (galaxy.datatypes.binary.Cool attribute)
- (galaxy.datatypes.binary.Cpt attribute)
- (galaxy.datatypes.binary.CRAM attribute)
- (galaxy.datatypes.binary.CuffDiffSQlite attribute)
- (galaxy.datatypes.binary.DAA attribute)
- (galaxy.datatypes.binary.Dcd attribute)
- (galaxy.datatypes.binary.DlibSQlite attribute)
- (galaxy.datatypes.binary.DMND attribute)
- (galaxy.datatypes.binary.Edr attribute)
- (galaxy.datatypes.binary.ElibSQlite attribute)
- (galaxy.datatypes.binary.ExcelXls attribute)
- (galaxy.datatypes.binary.Fast5Archive attribute)
- (galaxy.datatypes.binary.Fast5ArchiveBz2 attribute)
- (galaxy.datatypes.binary.Fast5ArchiveGz attribute)
- (galaxy.datatypes.binary.GAFASQLite attribute)
- (galaxy.datatypes.binary.GeminiSQLite attribute)
- (galaxy.datatypes.binary.GenericAsn1Binary attribute)
- (galaxy.datatypes.binary.GmxBinary attribute)
- (galaxy.datatypes.binary.H5 attribute)
- (galaxy.datatypes.binary.ICM attribute)
- (galaxy.datatypes.binary.Idat attribute)
- (galaxy.datatypes.binary.IdpDB attribute)
- (galaxy.datatypes.binary.Loom attribute)
- (galaxy.datatypes.binary.MashSketch attribute)
- (galaxy.datatypes.binary.MassHunterTar attribute)
- (galaxy.datatypes.binary.MassLynxTar attribute)
- (galaxy.datatypes.binary.MCool attribute)
- (galaxy.datatypes.binary.Meryldb attribute)
- (galaxy.datatypes.binary.MzSQlite attribute)
- (galaxy.datatypes.binary.NcbiTaxonomySQlite attribute)
- (galaxy.datatypes.binary.NetCDF attribute)
- (galaxy.datatypes.binary.OSW attribute)
- (galaxy.datatypes.binary.OxliCountGraph attribute)
- (galaxy.datatypes.binary.OxliGraphLabels attribute)
- (galaxy.datatypes.binary.OxliNodeGraph attribute)
- (galaxy.datatypes.binary.OxliStopTags attribute)
- (galaxy.datatypes.binary.OxliSubset attribute)
- (galaxy.datatypes.binary.OxliTagSet attribute)
- (galaxy.datatypes.binary.Parquet attribute)
- (galaxy.datatypes.binary.PostgresqlArchive attribute)
- (galaxy.datatypes.binary.PQP attribute)
- (galaxy.datatypes.binary.ProBam attribute)
- (galaxy.datatypes.binary.RData attribute)
- (galaxy.datatypes.binary.RMA6 attribute)
- (galaxy.datatypes.binary.Scf attribute)
- (galaxy.datatypes.binary.SearchGuiArchive attribute)
- (galaxy.datatypes.binary.Sff attribute)
- (galaxy.datatypes.binary.SQlite attribute)
- (galaxy.datatypes.binary.SQmass attribute)
- (galaxy.datatypes.binary.Sra attribute)
- (galaxy.datatypes.binary.TdfTar attribute)
- (galaxy.datatypes.binary.Trr attribute)
- (galaxy.datatypes.binary.TwoBit attribute)
- (galaxy.datatypes.binary.Vel attribute)
- (galaxy.datatypes.binary.WiffTar attribute)
- (galaxy.datatypes.binary.Xlsx attribute)
- (galaxy.datatypes.binary.Xtc attribute)
- (galaxy.datatypes.binary.YepTar attribute)
- (galaxy.datatypes.blast.BlastDomainDb attribute)
- (galaxy.datatypes.blast.BlastDomainDb5 attribute)
- (galaxy.datatypes.blast.BlastNucDb attribute)
- (galaxy.datatypes.blast.BlastNucDb5 attribute)
- (galaxy.datatypes.blast.BlastProtDb attribute)
- (galaxy.datatypes.blast.BlastProtDb5 attribute)
- (galaxy.datatypes.blast.BlastXml attribute)
- (galaxy.datatypes.blast.LastDb attribute)
- (galaxy.datatypes.chrominfo.ChromInfo attribute)
- (galaxy.datatypes.constructive_solid_geometry.PlyAscii attribute)
- (galaxy.datatypes.constructive_solid_geometry.PlyBinary attribute)
- (galaxy.datatypes.constructive_solid_geometry.STL attribute)
- (galaxy.datatypes.constructive_solid_geometry.VtkAscii attribute)
- (galaxy.datatypes.constructive_solid_geometry.VtkBinary attribute)
- (galaxy.datatypes.coverage.LastzCoverage attribute)
- (galaxy.datatypes.data.Data attribute)
- (galaxy.datatypes.data.GenericAsn1 attribute)
- (galaxy.datatypes.data.Newick attribute)
- (galaxy.datatypes.data.Nexus attribute)
- (galaxy.datatypes.data.Text attribute)
- (galaxy.datatypes.genetics.Affybatch attribute)
- (galaxy.datatypes.genetics.AllegroLOD attribute)
- (galaxy.datatypes.genetics.DataIn attribute)
- (galaxy.datatypes.genetics.Eigenstratgeno attribute)
- (galaxy.datatypes.genetics.Eigenstratpca attribute)
- (galaxy.datatypes.genetics.Eset attribute)
- (galaxy.datatypes.genetics.Fped attribute)
- (galaxy.datatypes.genetics.Fphe attribute)
- (galaxy.datatypes.genetics.GenomeGraphs attribute)
- (galaxy.datatypes.genetics.GenotypeMatrix attribute)
- (galaxy.datatypes.genetics.IdeasPre attribute)
- (galaxy.datatypes.genetics.ldIndep attribute)
- (galaxy.datatypes.genetics.Lped attribute)
- (galaxy.datatypes.genetics.MAlist attribute)
- (galaxy.datatypes.genetics.MarkerMap attribute)
- (galaxy.datatypes.genetics.Pbed attribute)
- (galaxy.datatypes.genetics.Phe attribute)
- (galaxy.datatypes.genetics.Pheno attribute)
- (galaxy.datatypes.genetics.Pphe attribute)
- (galaxy.datatypes.genetics.RexpBase attribute)
- (galaxy.datatypes.genetics.Rgenetics attribute)
- (galaxy.datatypes.genetics.rgFeatureList attribute)
- (galaxy.datatypes.genetics.rgSampleList attribute)
- (galaxy.datatypes.genetics.rgTabList attribute)
- (galaxy.datatypes.genetics.SNPMatrix attribute)
- (galaxy.datatypes.genetics.Snptest attribute)
- (galaxy.datatypes.gis.Shapefile attribute)
- (galaxy.datatypes.graph.Sif attribute)
- (galaxy.datatypes.graph.Xgmml attribute)
- (galaxy.datatypes.images.Analyze75 attribute)
- (galaxy.datatypes.images.Bmp attribute)
- (galaxy.datatypes.images.Eps attribute)
- (galaxy.datatypes.images.Gif attribute)
- (galaxy.datatypes.images.Gifti attribute)
- (galaxy.datatypes.images.Gmaj attribute)
- (galaxy.datatypes.images.Hamamatsu attribute)
- (galaxy.datatypes.images.Im attribute)
- (galaxy.datatypes.images.Image attribute)
- (galaxy.datatypes.images.Jpg attribute)
- (galaxy.datatypes.images.Laj attribute)
- (galaxy.datatypes.images.Mirax attribute)
- (galaxy.datatypes.images.Nifti1 attribute)
- (galaxy.datatypes.images.Nifti2 attribute)
- (galaxy.datatypes.images.Nrrd attribute)
- (galaxy.datatypes.images.Pbm attribute)
- (galaxy.datatypes.images.Pcd attribute)
- (galaxy.datatypes.images.Pcx attribute)
- (galaxy.datatypes.images.Pdf attribute)
- (galaxy.datatypes.images.Pgm attribute)
- (galaxy.datatypes.images.Png attribute)
- (galaxy.datatypes.images.Ppm attribute)
- (galaxy.datatypes.images.Psd attribute)
- (galaxy.datatypes.images.Rast attribute)
- (galaxy.datatypes.images.Rgb attribute)
- (galaxy.datatypes.images.Sakura attribute)
- (galaxy.datatypes.images.Tck attribute)
- (galaxy.datatypes.images.Tiff attribute)
- (galaxy.datatypes.images.Trk attribute)
- (galaxy.datatypes.images.Xbm attribute)
- (galaxy.datatypes.images.Xpm attribute)
- (galaxy.datatypes.interval.Bed attribute)
- (galaxy.datatypes.interval.Bed12 attribute)
- (galaxy.datatypes.interval.Bed6 attribute)
- (galaxy.datatypes.interval.BedGraph attribute)
- (galaxy.datatypes.interval.BedStrict attribute)
- (galaxy.datatypes.interval.ChromatinInteractions attribute)
- (galaxy.datatypes.interval.CustomTrack attribute)
- (galaxy.datatypes.interval.ENCODEPeak attribute)
- (galaxy.datatypes.interval.Gff attribute)
- (galaxy.datatypes.interval.Gff3 attribute)
- (galaxy.datatypes.interval.Gtf attribute)
- (galaxy.datatypes.interval.Interval attribute)
- (galaxy.datatypes.interval.ProBed attribute)
- (galaxy.datatypes.interval.ScIdx attribute)
- (galaxy.datatypes.int