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galaxy.tool_util package
Subpackages
- galaxy.tool_util.biotools package
BiotoolsMetadataSource
BiotoolsMetadataSourceConfig
get_biotools_metadata_source()
ParsedBiotoolsEntry
- Submodules
- galaxy.tool_util.biotools.interface module
- galaxy.tool_util.biotools.source module
- galaxy.tool_util.client package
- galaxy.tool_util.cwl package
tool_proxy()
tool_proxy_from_persistent_representation()
workflow_proxy()
handle_outputs()
to_cwl_job()
to_galaxy_parameters()
needs_shell_quoting()
- Submodules
- galaxy.tool_util.cwl.cwltool_deps module
CommentedMap
CommentedMap.__init__()
CommentedMap.update()
CommentedMap.insert()
CommentedMap.mlget()
CommentedMap.get()
CommentedMap.non_merged_items()
CommentedMap.pop()
CommentedMap.keys()
CommentedMap.values()
CommentedMap.items()
CommentedMap.merge
CommentedMap.copy()
CommentedMap.add_referent()
CommentedMap.add_yaml_merge()
CommentedMap.update_key_value()
default_loader()
ensure_cwltool_available()
getdefault()
LoadingContext
needs_shell_quoting()
normalizeFilesDirs()
relink_initialworkdir()
resolve_and_validate_document()
RuntimeContext
RuntimeContext.outdir
RuntimeContext.tmpdir
RuntimeContext.tmpdir_prefix
RuntimeContext.stagedir
RuntimeContext.__init__()
RuntimeContext.tmp_outdir_prefix
RuntimeContext.get_outdir()
RuntimeContext.get_tmpdir()
RuntimeContext.get_stagedir()
RuntimeContext.create_tmpdir()
RuntimeContext.create_outdir()
RuntimeContext.copy()
StdFsAccess
visit_class()
yaml_no_ts()
- galaxy.tool_util.cwl.parser module
- galaxy.tool_util.cwl.representation module
- galaxy.tool_util.cwl.runnable module
- galaxy.tool_util.cwl.runtime_actions module
- galaxy.tool_util.cwl.schema module
- galaxy.tool_util.cwl.util module
set_basename_and_derived_properties()
OutputPropertiesType
output_properties()
abs_path_or_uri()
abs_path()
path_or_uri_to_uri()
galactic_job_json()
UploadTarget
FileLiteralTarget
FileUploadTarget
ObjectUploadTarget
DirectoryUploadTarget
GalaxyOutput
tool_response_to_output()
invocation_to_output()
output_to_cwl_json()
download_output()
guess_artifact_type()
- galaxy.tool_util.deps package
build_dependency_manager()
DependencyManager
DependencyManager.cached
DependencyManager.__init__()
DependencyManager.set_enabled_container_types()
DependencyManager.get_destination_info_for_container_type()
DependencyManager.enabled_container_types
DependencyManager.get_resolver_option()
DependencyManager.get_app_option()
DependencyManager.precache
DependencyManager.dependency_shell_commands()
DependencyManager.requirements_to_dependencies()
DependencyManager.uses_tool_shed_dependencies()
DependencyManager.find_dep()
DependencyManager.to_dict()
CachedDependencyManager
NullDependencyManager
- Subpackages
- galaxy.tool_util.deps.container_resolvers package
- galaxy.tool_util.deps.mulled package
- Submodules
- galaxy.tool_util.deps.mulled.get_tests module
- galaxy.tool_util.deps.mulled.mulled_build module
- galaxy.tool_util.deps.mulled.mulled_build_channel module
- galaxy.tool_util.deps.mulled.mulled_build_files module
- galaxy.tool_util.deps.mulled.mulled_build_tool module
- galaxy.tool_util.deps.mulled.mulled_hash module
- galaxy.tool_util.deps.mulled.mulled_list module
- galaxy.tool_util.deps.mulled.mulled_search module
- galaxy.tool_util.deps.mulled.mulled_update_singularity_containers module
- galaxy.tool_util.deps.mulled.util module
- galaxy.tool_util.deps.resolvers package
DependencyResolver
MultipleDependencyResolver
ListableDependencyResolver
MappableDependencyResolver
RequirementMapping
SpecificationAwareDependencyResolver
SpecificationPatternDependencyResolver
Dependency
ContainerDependency
NullDependency
DependencyException
- Submodules
- galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages module
- galaxy.tool_util.deps.resolvers.conda module
- galaxy.tool_util.deps.resolvers.galaxy_packages module
- galaxy.tool_util.deps.resolvers.homebrew module
- galaxy.tool_util.deps.resolvers.lmod module
- galaxy.tool_util.deps.resolvers.modules module
- galaxy.tool_util.deps.resolvers.resolver_mixins module
- galaxy.tool_util.deps.resolvers.tool_shed_packages module
- galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages module
- Submodules
- galaxy.tool_util.deps.brew_exts module
BrewContext
RecipeContext
main()
CommandLineException
versioned_install()
commit_for_version()
print_versioned_deps()
load_versioned_deps()
unversioned_install()
attempt_unlink_all()
attempt_unlink()
brew_execute()
build_env_statements_from_recipe_context()
build_env_statements()
build_env_actions()
EnvAction
brew_head_at_version()
brew_head_at_commit()
git_execute()
execute()
brew_deps()
brew_info()
extended_brew_info()
brew_versions_info()
recipe_cellar_path()
ensure_brew_on_path()
which()
- galaxy.tool_util.deps.brew_util module
- galaxy.tool_util.deps.commands module
- galaxy.tool_util.deps.conda_compat module
- galaxy.tool_util.deps.conda_util module
CondaContext
CondaContext.installable_description
CondaContext.__init__()
CondaContext.conda_version
CondaContext.conda_build_available
CondaContext.ensure_conda_build_installed_if_needed()
CondaContext.conda_info()
CondaContext.is_conda_installed()
CondaContext.can_install_conda()
CondaContext.exec_command()
CondaContext.is_package_installed()
CondaContext.exec_create()
CondaContext.exec_remove()
CondaContext.exec_install()
CondaContext.exec_clean()
CondaContext.exec_search()
CondaContext.export_list()
CondaContext.env_path()
CondaContext.envs_path
CondaContext.has_env()
CondaContext.get_conda_target_installed_path()
CondaContext.deactivate
CondaContext.activate
CondaContext.is_installed()
CondaContext.can_install()
CondaContext.parent_path
CondaTarget
install_conda()
install_conda_target()
requirements_to_conda_targets()
- galaxy.tool_util.deps.container_classes module
ContainerProtocol
Container
Volume
preprocess_volumes()
HasDockerLikeVolumes
DockerContainer
docker_cache_path()
SingularityContainer
SingularityContainer.container_type
SingularityContainer.get_singularity_target_kwds()
SingularityContainer.connection_configuration
SingularityContainer.build_mulled_singularity_pull_command()
SingularityContainer.build_singularity_pull_command()
SingularityContainer.containerize_command()
SingularityContainer.container_info
- galaxy.tool_util.deps.container_volumes module
- galaxy.tool_util.deps.containers module
- galaxy.tool_util.deps.dependencies module
- galaxy.tool_util.deps.docker_util module
- galaxy.tool_util.deps.dockerfiles module
- galaxy.tool_util.deps.installable module
- galaxy.tool_util.deps.requirements module
- galaxy.tool_util.deps.singularity_util module
- galaxy.tool_util.deps.views module
DependencyResolversView
DependencyResolversView.__init__()
DependencyResolversView.index()
DependencyResolversView.show()
DependencyResolversView.reload()
DependencyResolversView.manager_requirements()
DependencyResolversView.resolver_requirements()
DependencyResolversView.manager_dependency()
DependencyResolversView.resolver_dependency()
DependencyResolversView.show_dependencies()
DependencyResolversView.uninstall_dependencies()
DependencyResolversView.unused_dependency_paths
DependencyResolversView.remove_unused_dependency_paths()
DependencyResolversView.install_dependencies()
DependencyResolversView.install_dependency()
DependencyResolversView.installable_resolvers
DependencyResolversView.uninstallable_resolvers
DependencyResolversView.tool_ids_by_requirements
DependencyResolversView.toolbox_requirements_status
DependencyResolversView.summarize_requirements()
DependencyResolversView.summarize_tools()
DependencyResolversView.get_requirements_status()
DependencyResolversView.clean()
ContainerResolutionView
pop_tool_ids()
- galaxy.tool_util.linters package
- Submodules
- galaxy.tool_util.linters.citations module
- galaxy.tool_util.linters.command module
- galaxy.tool_util.linters.cwl module
- galaxy.tool_util.linters.general module
ToolVersionMissing
ToolVersionPEP404
ToolVersionWhitespace
ToolVersionValid
ToolNameMissing
ToolNameWhitespace
ToolNameValid
ToolIDMissing
ToolIDWhitespace
ToolIDValid
ToolProfileInvalid
ToolProfileLegacy
ToolProfileValid
RequirementNameMissing
RequirementVersionMissing
RequirementVersionWhitespace
ResourceRequirementExpression
- galaxy.tool_util.linters.help module
- galaxy.tool_util.linters.inputs module
InputsNum
InputsMissing
InputsMissingDataSource
InputsDatasourceTags
InputsName
InputsNameRedundantArgument
InputsNameEmpty
InputsNameValid
InputsNameDuplicate
InputsNameDuplicateOutput
InputsTypeChildCombination
InputsDataFormat
InputsDataOptionsMultiple
InputsDataOptionsAttrib
InputsDataOptionsFilterAttribFiltersType
InputsDataOptionsFiltersType
InputsDataOptionsFiltersRef
InputsSelectDynamicOptions
InputsSelectOptionsDef
InputsSelectOptionsDefConditional
InputsSelectOptionValueMissing
InputsSelectOptionDuplicateValue
InputsSelectOptionDuplicateText
InputsSelectOptionsMultiple
InputsSelectOptionsDefinesOptions
InputsSelectOptionsDeprecatedAttr
InputsSelectOptionsFromDatasetAndDatatable
InputsSelectOptionsMetaFileKey
InputsBoolDistinctValues
InputsBoolProblematic
InputsSelectSingleCheckboxes
InputsSelectMandatoryCheckboxes
InputsSelectMultipleRadio
InputsSelectOptionalRadio
ValidatorParamIncompatible
ValidatorAttribIncompatible
ValidatorHasText
ValidatorHasNoText
ValidatorExpression
ValidatorExpressionFuture
ValidatorMinMax
ValidatorDatasetMetadataEqualValue
ValidatorDatasetMetadataEqualValueOrJson
ValidatorMetadataCheckSkip
ValidatorTableName
ValidatorMetadataName
ConditionalParamTypeBool
ConditionalParamType
ConditionalParamIncompatibleAttributes
ConditionalWhenMissing
ConditionalOptionMissing
ConditionalOptionMissingBoolean
- galaxy.tool_util.linters.outputs module
- galaxy.tool_util.linters.stdio module
- galaxy.tool_util.linters.tests module
TestsMissing
TestsMissingDatasource
TestsAssertsMultiple
TestsAssertsHasNQuant
TestsAssertsHasSizeQuant
TestsAssertsHasSizeOrValueQuant
TestsExpectNumOutputs
TestsParamInInputs
TestsOutputName
TestsOutputDefined
TestsOutputCorresponding
TestsOutputCollectionCorresponding
TestsOutputCompareAttrib
TestsOutputCheckDiscovered
TestsOutputCollectionCheckDiscovered
TestsOutputCollectionCheckDiscoveredNested
TestsOutputFailing
TestsExpectNumOutputsFailing
TestsHasExpectations
TestsNoValid
TestsValid
- galaxy.tool_util.linters.xml_order module
- galaxy.tool_util.locations package
- galaxy.tool_util.ontologies package
- galaxy.tool_util.parser package
get_input_source()
get_tool_source()
get_tool_source_from_representation()
RequiredFiles
ToolOutputCollectionPart
ToolSource
ToolSource.language
ToolSource.parse_id()
ToolSource.parse_version()
ToolSource.parse_tool_module()
ToolSource.parse_action_module()
ToolSource.parse_tool_type()
ToolSource.parse_name()
ToolSource.parse_description()
ToolSource.parse_edam_operations()
ToolSource.parse_edam_topics()
ToolSource.parse_xrefs()
ToolSource.parse_display_interface()
ToolSource.parse_require_login()
ToolSource.parse_request_param_translation_elem()
ToolSource.parse_command()
ToolSource.parse_expression()
ToolSource.parse_environment_variables()
ToolSource.parse_home_target()
ToolSource.parse_tmp_target()
ToolSource.parse_tmp_directory_vars()
ToolSource.parse_docker_env_pass_through()
ToolSource.parse_interpreter()
ToolSource.parse_interactivetool()
ToolSource.parse_redirect_url_params_elem()
ToolSource.parse_version_command()
ToolSource.parse_version_command_interpreter()
ToolSource.parse_parallelism()
ToolSource.parse_hidden()
ToolSource.parse_sanitize()
ToolSource.parse_refresh()
ToolSource.parse_required_files()
ToolSource.parse_requirements_and_containers()
ToolSource.parse_input_pages()
ToolSource.parse_provided_metadata_style()
ToolSource.parse_provided_metadata_file()
ToolSource.parse_outputs()
ToolSource.parse_strict_shell()
ToolSource.parse_stdio()
ToolSource.parse_help()
ToolSource.parse_profile()
ToolSource.parse_license()
ToolSource.parse_python_template_version()
ToolSource.parse_creator()
ToolSource.macro_paths
ToolSource.source_path
ToolSource.paths_and_modtimes()
ToolSource.parse_tests_to_dict()
ToolSource.to_string()
- Submodules
- galaxy.tool_util.parser.cwl module
CwlToolSource
CwlToolSource.language
CwlToolSource.__init__()
CwlToolSource.source_path
CwlToolSource.tool_proxy
CwlToolSource.parse_tool_type()
CwlToolSource.parse_id()
CwlToolSource.parse_name()
CwlToolSource.parse_command()
CwlToolSource.parse_environment_variables()
CwlToolSource.parse_edam_operations()
CwlToolSource.parse_edam_topics()
CwlToolSource.parse_help()
CwlToolSource.parse_sanitize()
CwlToolSource.parse_strict_shell()
CwlToolSource.parse_stdio()
CwlToolSource.parse_interpreter()
CwlToolSource.parse_version()
CwlToolSource.parse_description()
CwlToolSource.parse_interactivetool()
CwlToolSource.parse_input_pages()
CwlToolSource.parse_outputs()
CwlToolSource.parse_requirements_and_containers()
CwlToolSource.parse_profile()
CwlToolSource.parse_xrefs()
CwlToolSource.parse_license()
CwlToolSource.parse_python_template_version()
CwlToolSource.to_string()
tool_proxy()
- galaxy.tool_util.parser.factory module
- galaxy.tool_util.parser.interface module
AssertionDict
ToolSourceTest
ToolSourceTest.inputs
ToolSourceTest.outputs
ToolSourceTest.output_collections
ToolSourceTest.stdout
ToolSourceTest.stderr
ToolSourceTest.expect_exit_code
ToolSourceTest.expect_failure
ToolSourceTest.expect_test_failure
ToolSourceTest.maxseconds
ToolSourceTest.expect_num_outputs
ToolSourceTest.command
ToolSourceTest.command_version
ToolSourceTests
ToolSource
ToolSource.language
ToolSource.parse_id()
ToolSource.parse_version()
ToolSource.parse_tool_module()
ToolSource.parse_action_module()
ToolSource.parse_tool_type()
ToolSource.parse_name()
ToolSource.parse_description()
ToolSource.parse_edam_operations()
ToolSource.parse_edam_topics()
ToolSource.parse_xrefs()
ToolSource.parse_display_interface()
ToolSource.parse_require_login()
ToolSource.parse_request_param_translation_elem()
ToolSource.parse_command()
ToolSource.parse_expression()
ToolSource.parse_environment_variables()
ToolSource.parse_home_target()
ToolSource.parse_tmp_target()
ToolSource.parse_tmp_directory_vars()
ToolSource.parse_docker_env_pass_through()
ToolSource.parse_interpreter()
ToolSource.parse_interactivetool()
ToolSource.parse_redirect_url_params_elem()
ToolSource.parse_version_command()
ToolSource.parse_version_command_interpreter()
ToolSource.parse_parallelism()
ToolSource.parse_hidden()
ToolSource.parse_sanitize()
ToolSource.parse_refresh()
ToolSource.parse_required_files()
ToolSource.parse_requirements_and_containers()
ToolSource.parse_input_pages()
ToolSource.parse_provided_metadata_style()
ToolSource.parse_provided_metadata_file()
ToolSource.parse_outputs()
ToolSource.parse_strict_shell()
ToolSource.parse_stdio()
ToolSource.parse_help()
ToolSource.parse_profile()
ToolSource.parse_license()
ToolSource.parse_python_template_version()
ToolSource.parse_creator()
ToolSource.macro_paths
ToolSource.source_path
ToolSource.paths_and_modtimes()
ToolSource.parse_tests_to_dict()
ToolSource.to_string()
PagesSource
InputSource
InputSource.default_optional
InputSource.elem()
InputSource.get()
InputSource.get_bool()
InputSource.parse_label()
InputSource.parse_name()
InputSource.parse_input_type()
InputSource.parse_help()
InputSource.parse_sanitizer_elem()
InputSource.parse_validator_elems()
InputSource.parse_optional()
InputSource.parse_dynamic_options_elem()
InputSource.parse_static_options()
InputSource.parse_conversion_tuples()
InputSource.parse_nested_inputs_source()
InputSource.parse_test_input_source()
InputSource.parse_when_input_sources()
InputSource.parse_default()
PageSource
TestCollectionDef
RequiredFiles
TestCollectionOutputDef
- galaxy.tool_util.parser.output_actions module
ToolOutputActionGroup
ToolOutputActionConditionalWhen
ValueToolOutputActionConditionalWhen
DatatypeIsInstanceToolOutputActionConditionalWhen
ToolOutputActionConditional
ToolOutputAction
ToolOutputActionOption
NullToolOutputActionOption
FromFileToolOutputActionOption
FromParamToolOutputActionOption
FromDataTableOutputActionOption
MetadataToolOutputAction
FormatToolOutputAction
ToolOutputActionOptionFilter
ParamValueToolOutputActionOptionFilter
InsertColumnToolOutputActionOptionFilter
MultipleSplitterFilter
ColumnStripFilter
ColumnReplaceFilter
MetadataValueFilter
BooleanFilter
action_type
filter_type
option_type
StringFunctionFilter
parse_cast_attribute()
parse_compare_type()
compare_eq()
compare_neq()
compare_gt()
compare_gte()
compare_lt()
compare_lte()
compare_in()
compare_startswith()
compare_endswith()
compare_re_search()
- galaxy.tool_util.parser.output_collection_def module
- galaxy.tool_util.parser.output_objects module
ChangeFormatModel
ToolOutputBase
ToolOutput
ToolExpressionOutput
ToolOutputCollection
ToolOutputCollection.dict_collection_visible_keys
ToolOutputCollection.__init__()
ToolOutputCollection.known_outputs()
ToolOutputCollection.dynamic_structure
ToolOutputCollection.dataset_collector_descriptions
ToolOutputCollection.to_dict()
ToolOutputCollection.from_dict()
ToolOutputCollection.output_discover_patterns
ToolOutputCollectionStructure
ToolOutputCollectionPart
- galaxy.tool_util.parser.stdio module
- galaxy.tool_util.parser.util module
- galaxy.tool_util.parser.xml module
inject_validates()
destroy_tree()
parse_change_format()
XmlToolSource
XmlToolSource.language
XmlToolSource.__init__()
XmlToolSource.to_string()
XmlToolSource.mem_optimize()
XmlToolSource.parse_version()
XmlToolSource.parse_id()
XmlToolSource.parse_tool_module()
XmlToolSource.parse_action_module()
XmlToolSource.parse_tool_type()
XmlToolSource.parse_name()
XmlToolSource.parse_edam_operations()
XmlToolSource.parse_edam_topics()
XmlToolSource.parse_xrefs()
XmlToolSource.parse_description()
XmlToolSource.parse_display_interface()
XmlToolSource.parse_require_login()
XmlToolSource.parse_request_param_translation_elem()
XmlToolSource.parse_command()
XmlToolSource.parse_expression()
XmlToolSource.parse_environment_variables()
XmlToolSource.parse_home_target()
XmlToolSource.parse_tmp_target()
XmlToolSource.parse_interpreter()
XmlToolSource.parse_version_command()
XmlToolSource.parse_version_command_interpreter()
XmlToolSource.parse_parallelism()
XmlToolSource.parse_interactivetool()
XmlToolSource.parse_hidden()
XmlToolSource.parse_redirect_url_params_elem()
XmlToolSource.parse_sanitize()
XmlToolSource.parse_refresh()
XmlToolSource.parse_required_files()
XmlToolSource.parse_requirements_and_containers()
XmlToolSource.parse_input_pages()
XmlToolSource.parse_provided_metadata_style()
XmlToolSource.parse_provided_metadata_file()
XmlToolSource.parse_outputs()
XmlToolSource.parse_stdio()
XmlToolSource.parse_strict_shell()
XmlToolSource.parse_help()
XmlToolSource.macro_paths
XmlToolSource.source_path
XmlToolSource.parse_tests_to_dict()
XmlToolSource.parse_profile()
XmlToolSource.parse_license()
XmlToolSource.parse_python_template_version()
XmlToolSource.parse_creator()
StdioParser
XmlPagesSource
XmlPageSource
XmlInputSource
XmlInputSource.__init__()
XmlInputSource.parse_input_type()
XmlInputSource.elem()
XmlInputSource.get()
XmlInputSource.get_bool()
XmlInputSource.parse_label()
XmlInputSource.parse_help()
XmlInputSource.parse_sanitizer_elem()
XmlInputSource.parse_validator_elems()
XmlInputSource.parse_dynamic_options_elem()
XmlInputSource.parse_static_options()
XmlInputSource.parse_optional()
XmlInputSource.parse_conversion_tuples()
XmlInputSource.parse_nested_inputs_source()
XmlInputSource.parse_test_input_source()
XmlInputSource.parse_when_input_sources()
XmlInputSource.parse_default()
ParallelismInfo
- galaxy.tool_util.parser.yaml module
YamlToolSource
YamlToolSource.language
YamlToolSource.__init__()
YamlToolSource.source_path
YamlToolSource.parse_tool_type()
YamlToolSource.parse_id()
YamlToolSource.parse_version()
YamlToolSource.parse_name()
YamlToolSource.parse_description()
YamlToolSource.parse_edam_operations()
YamlToolSource.parse_edam_topics()
YamlToolSource.parse_xrefs()
YamlToolSource.parse_sanitize()
YamlToolSource.parse_display_interface()
YamlToolSource.parse_require_login()
YamlToolSource.parse_command()
YamlToolSource.parse_expression()
YamlToolSource.parse_environment_variables()
YamlToolSource.parse_interpreter()
YamlToolSource.parse_version_command()
YamlToolSource.parse_version_command_interpreter()
YamlToolSource.parse_requirements_and_containers()
YamlToolSource.parse_input_pages()
YamlToolSource.parse_strict_shell()
YamlToolSource.parse_stdio()
YamlToolSource.parse_help()
YamlToolSource.parse_outputs()
YamlToolSource.parse_tests_to_dict()
YamlToolSource.parse_profile()
YamlToolSource.parse_license()
YamlToolSource.parse_interactivetool()
YamlToolSource.parse_python_template_version()
YamlToolSource.to_string()
to_test_assert_list()
YamlPageSource
YamlInputSource
YamlInputSource.__init__()
YamlInputSource.get()
YamlInputSource.get_bool()
YamlInputSource.parse_input_type()
YamlInputSource.parse_nested_inputs_source()
YamlInputSource.parse_test_input_source()
YamlInputSource.parse_when_input_sources()
YamlInputSource.parse_static_options()
YamlInputSource.parse_default()
- galaxy.tool_util.toolbox package
AbstractToolBox
AbstractToolBox.__init__()
AbstractToolBox.create_tool()
AbstractToolBox.create_dynamic_tool()
AbstractToolBox.can_load_config_file()
AbstractToolBox.tool_tag_manager()
AbstractToolBox.panel_views()
AbstractToolBox.panel_view_dicts()
AbstractToolBox.panel_has_tool()
AbstractToolBox.load_dynamic_tool()
AbstractToolBox.load_item()
AbstractToolBox.get_shed_config_dict_by_filename()
AbstractToolBox.update_shed_config()
AbstractToolBox.get_section()
AbstractToolBox.create_section()
AbstractToolBox.get_section_for_tool()
AbstractToolBox.add_tool_to_tool_panel_view()
AbstractToolBox.get_tool()
AbstractToolBox.has_tool()
AbstractToolBox.is_missing_shed_tool()
AbstractToolBox.get_loaded_tools_by_lineage()
AbstractToolBox.tools()
AbstractToolBox.dynamic_confs()
AbstractToolBox.default_shed_tool_conf_dict()
AbstractToolBox.dynamic_conf_filenames()
AbstractToolBox.get_tool_repository_from_xml_item()
AbstractToolBox.load_tool()
AbstractToolBox.watch_tool()
AbstractToolBox.add_tool_to_cache()
AbstractToolBox.load_tool_from_cache()
AbstractToolBox.load_hidden_lib_tool()
AbstractToolBox.load_hidden_tool()
AbstractToolBox.register_tool()
AbstractToolBox.package_tool()
AbstractToolBox.reload_tool_by_id()
AbstractToolBox.remove_tool_by_id()
AbstractToolBox.get_sections()
AbstractToolBox.find_section_id()
AbstractToolBox.tool_panel_contents()
AbstractToolBox.get_tool_to_dict()
AbstractToolBox.to_dict()
AbstractToolBox.to_panel_view()
AbstractToolTagManager
panel_item_types
ToolSection
ToolSectionLabel
- Subpackages
- Submodules
- galaxy.tool_util.toolbox.base module
ToolConfRepository
ToolBoxRegistryImpl
AbstractToolTagManager
NullToolTagManager
AbstractToolBox
AbstractToolBox.__init__()
AbstractToolBox.create_tool()
AbstractToolBox.create_dynamic_tool()
AbstractToolBox.can_load_config_file()
AbstractToolBox.tool_tag_manager()
AbstractToolBox.panel_views()
AbstractToolBox.panel_view_dicts()
AbstractToolBox.panel_has_tool()
AbstractToolBox.load_dynamic_tool()
AbstractToolBox.load_item()
AbstractToolBox.get_shed_config_dict_by_filename()
AbstractToolBox.update_shed_config()
AbstractToolBox.get_section()
AbstractToolBox.create_section()
AbstractToolBox.get_section_for_tool()
AbstractToolBox.add_tool_to_tool_panel_view()
AbstractToolBox.get_tool()
AbstractToolBox.has_tool()
AbstractToolBox.is_missing_shed_tool()
AbstractToolBox.get_loaded_tools_by_lineage()
AbstractToolBox.tools()
AbstractToolBox.dynamic_confs()
AbstractToolBox.default_shed_tool_conf_dict()
AbstractToolBox.dynamic_conf_filenames()
AbstractToolBox.get_tool_repository_from_xml_item()
AbstractToolBox.load_tool()
AbstractToolBox.watch_tool()
AbstractToolBox.add_tool_to_cache()
AbstractToolBox.load_tool_from_cache()
AbstractToolBox.load_hidden_lib_tool()
AbstractToolBox.load_hidden_tool()
AbstractToolBox.register_tool()
AbstractToolBox.package_tool()
AbstractToolBox.reload_tool_by_id()
AbstractToolBox.remove_tool_by_id()
AbstractToolBox.get_sections()
AbstractToolBox.find_section_id()
AbstractToolBox.tool_panel_contents()
AbstractToolBox.get_tool_to_dict()
AbstractToolBox.to_dict()
AbstractToolBox.to_panel_view()
- galaxy.tool_util.toolbox.integrated_panel module
- galaxy.tool_util.toolbox.panel module
panel_item_types
HasPanelItems
ToolSection
ToolSectionLabel
ToolPanelElements
ToolPanelElements.record_section_for_tool_id()
ToolPanelElements.get_section_for_tool_id()
ToolPanelElements.replace_tool_for_id()
ToolPanelElements.get_or_create_section()
ToolPanelElements.remove_tool()
ToolPanelElements.update_or_append()
ToolPanelElements.get_label()
ToolPanelElements.has_tool_with_id()
ToolPanelElements.replace_tool()
ToolPanelElements.index_of_tool_id()
ToolPanelElements.insert_tool()
ToolPanelElements.get_tool_with_id()
ToolPanelElements.append_tool()
ToolPanelElements.stub_tool()
ToolPanelElements.stub_workflow()
ToolPanelElements.stub_label()
ToolPanelElements.append_section()
ToolPanelElements.panel_items()
ToolPanelElements.walk_sections()
ToolPanelElements.closest_section()
ToolPanelElements.apply_filter()
ToolPanelElements.copy()
ToolPanelElements.has_item_recursive()
- galaxy.tool_util.toolbox.parser module
- galaxy.tool_util.toolbox.tags module
- galaxy.tool_util.toolbox.watcher module
- galaxy.tool_util.unittest_utils package
- galaxy.tool_util.verify package
verify()
make_temp_fname()
files_delta()
get_compressed_formats()
files_diff()
files_re_match()
files_re_match_multiline()
files_contains()
intersection_over_union()
get_image_metric()
files_image_diff()
- Subpackages
- galaxy.tool_util.verify.asserts package
verify_assertions()
verify_assertion()
- Submodules
- galaxy.tool_util.verify.asserts.archive module
- galaxy.tool_util.verify.asserts.hdf5 module
- galaxy.tool_util.verify.asserts.size module
- galaxy.tool_util.verify.asserts.tabular module
- galaxy.tool_util.verify.asserts.text module
- galaxy.tool_util.verify.asserts.xml module
- galaxy.tool_util.verify.asserts package
- Submodules
- galaxy.tool_util.verify.interactor module
OutputsDict
ValidToolTestDict
ValidToolTestDict.inputs
ValidToolTestDict.outputs
ValidToolTestDict.output_collections
ValidToolTestDict.stdout
ValidToolTestDict.stderr
ValidToolTestDict.expect_exit_code
ValidToolTestDict.expect_failure
ValidToolTestDict.expect_test_failure
ValidToolTestDict.maxseconds
ValidToolTestDict.num_outputs
ValidToolTestDict.command_line
ValidToolTestDict.command_version
ValidToolTestDict.required_files
ValidToolTestDict.required_data_tables
ValidToolTestDict.required_loc_files
ValidToolTestDict.error
ValidToolTestDict.tool_id
ValidToolTestDict.tool_version
ValidToolTestDict.test_index
InvalidToolTestDict
stage_data_in_history()
RunToolResponse
GalaxyInteractorApi
GalaxyInteractorApi.__init__()
GalaxyInteractorApi.cookies
GalaxyInteractorApi.api_key
GalaxyInteractorApi.keep_outputs_dir
GalaxyInteractorApi.target_galaxy_version
GalaxyInteractorApi.supports_test_data_download
GalaxyInteractorApi.get_tests_summary()
GalaxyInteractorApi.get_tool_tests()
GalaxyInteractorApi.verify_output_collection()
GalaxyInteractorApi.verify_output()
GalaxyInteractorApi.wait_for_jobs()
GalaxyInteractorApi.verify_output_dataset()
GalaxyInteractorApi.wait_for_job()
GalaxyInteractorApi.wait_for()
GalaxyInteractorApi.get_job_stdio()
GalaxyInteractorApi.get_history()
GalaxyInteractorApi.test_history()
GalaxyInteractorApi.new_history()
GalaxyInteractorApi.publish_history()
GalaxyInteractorApi.test_data_path()
GalaxyInteractorApi.test_data_download()
GalaxyInteractorApi.stage_data_async()
GalaxyInteractorApi.run_tool()
GalaxyInteractorApi.output_hid()
GalaxyInteractorApi.delete_history()
GalaxyInteractorApi.format_for_summary()
GalaxyInteractorApi.ensure_user_with_email()
GalaxyInteractorApi.api_key_header()
GalaxyInteractorApi.get_api_url()
prepare_request_params()
ensure_tool_run_response_okay()
RunToolException
verify_hid()
verify_collection()
TestConfig
NullClientTestConfig
DictClientTestConfig
verify_tool()
JobOutputsError
ToolTestDescriptionDict
ToolTestDescriptionDict.name
ToolTestDescriptionDict.inputs
ToolTestDescriptionDict.outputs
ToolTestDescriptionDict.output_collections
ToolTestDescriptionDict.stdout
ToolTestDescriptionDict.stderr
ToolTestDescriptionDict.expect_exit_code
ToolTestDescriptionDict.expect_failure
ToolTestDescriptionDict.expect_test_failure
ToolTestDescriptionDict.num_outputs
ToolTestDescriptionDict.command_line
ToolTestDescriptionDict.command_version
ToolTestDescriptionDict.required_files
ToolTestDescriptionDict.required_data_tables
ToolTestDescriptionDict.required_loc_files
ToolTestDescriptionDict.error
ToolTestDescriptionDict.tool_id
ToolTestDescriptionDict.tool_version
ToolTestDescriptionDict.test_index
ToolTestDescriptionDict.exception
ToolTestDescription
ToolTestDescription.__init__()
ToolTestDescription.name
ToolTestDescription.required_files
ToolTestDescription.required_data_tables
ToolTestDescription.required_loc_files
ToolTestDescription.num_outputs
ToolTestDescription.exception
ToolTestDescription.command_line
ToolTestDescription.command_version
ToolTestDescription.stdout
ToolTestDescription.stderr
ToolTestDescription.expect_exit_code
ToolTestDescription.expect_failure
ToolTestDescription.expect_test_failure
ToolTestDescription.test_data()
ToolTestDescription.to_dict()
test_data_iter()
- galaxy.tool_util.verify.script module
- galaxy.tool_util.verify.test_data module
- galaxy.tool_util.verify.wait module
Submodules
galaxy.tool_util.edam_util module
galaxy.tool_util.fetcher module
galaxy.tool_util.lint module
This modules contains the functions that drive the tool linting framework.
LintContext: a container for LintMessages LintMessage: the actual message and level
The idea is to define a LintContext and to apply a linting function foo
on a
target
. The level
(defined by LintLevel
) determines which linting
messages are shown:
lint_ctx = LintContext(level) # level is the reporting level
lint_ctx.lint(..., lint_func = foo, lint_target = target, ...)
The lint
function essentially calls foo(target, self)
. Hence
the function foo
must have two parameters:
the object to lint
the lint context
In foo
the lint context can be used to add LintMessages to the lint context
by using its valid
, info
, warn
, and error
functions:
lint_foo(target, lint_ctx):
lint_ctx.error("target is screwed")
Calling lint
prints out the messages emmited by the linter
function immediately. Which messages are shown can be determined with the
level
argument of the LintContext
constructor. If set to SILENT
,
no messages will be printed.
For special lint targets it might be useful to have additional information
in the lint messages. This can be achieved by subclassing LintMessage
.
See for instance XMLLintMessageLine
which has an additional argument
node
in its constructor which is used to determine the line and filename in
an XML document that caused the message.
In order to use this.
the lint context needs to be initialized with the additional parameter
lint_message_class=XMLLintMessageLine
the additional parameter needs to be added as well to calls adding messages to the lint context, e.g.
lint_ctx.error("some message", node=X)
. Note that the additional properties must be given as keyword arguments.
- class galaxy.tool_util.lint.LintLevel(value)[source]
Bases:
IntEnum
An enumeration.
- SILENT = 5
- ERROR = 4
- WARN = 3
- INFO = 2
- VALID = 1
- ALL = 0
- class galaxy.tool_util.lint.Linter[source]
Bases:
ABC
a linter. needs to define a lint method and the code property. optionally a fix method can be given
- abstract classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]
should add at most one message to the lint context
- class galaxy.tool_util.lint.LintMessage(level: str, message: str, linter: str | None = None, **kwargs)[source]
Bases:
object
a message from the linter
- class galaxy.tool_util.lint.XMLLintMessageLine(level: str, message: str, linter: str | None = None, node: Element | None = None)[source]
Bases:
LintMessage
- class galaxy.tool_util.lint.XMLLintMessageXPath(level: str, message: str, linter: str | None = None, node: Element | None = None)[source]
Bases:
LintMessage
- class galaxy.tool_util.lint.LintContext(level: ~galaxy.tool_util.lint.LintLevel | str, lint_message_class: ~typing.Type[~galaxy.tool_util.lint.LintMessage] = <class 'galaxy.tool_util.lint.LintMessage'>, skip_types: ~typing.List[str] | None = None, object_name: str | None = None)[source]
Bases:
object
- __init__(level: ~galaxy.tool_util.lint.LintLevel | str, lint_message_class: ~typing.Type[~galaxy.tool_util.lint.LintMessage] = <class 'galaxy.tool_util.lint.LintMessage'>, skip_types: ~typing.List[str] | None = None, object_name: str | None = None)[source]
- lint_message_class: Type[LintMessage]
- message_list: List[LintMessage]
- lint(name: str, lint_func: Callable[[LintTargetType, LintContext], None], lint_target: LintTargetType, module_name: str | None = None)[source]
- property valid_messages: List[LintMessage]
- property info_messages: List[LintMessage]
- property warn_messages: List[LintMessage]
- property error_messages: List[LintMessage]
- galaxy.tool_util.lint.lint_tool_source(tool_source, level=LintLevel.ALL, fail_level=LintLevel.WARN, extra_modules=None, skip_types=None, name=None) bool [source]
apply all (applicable) linters from the linters submodule and the ones in extramodules
immediately print linter messages (wrt level) and return if linting failed (wrt fail_level)
- galaxy.tool_util.lint.get_lint_context_for_tool_source(tool_source, extra_modules=None, skip_types=None, name=None) LintContext [source]
this is the silent variant of lint_tool_source it returns the LintContext from which all linter messages and the status can be obtained
- galaxy.tool_util.lint.lint_xml(tool_xml, level=LintLevel.ALL, fail_level=LintLevel.WARN, lint_message_class=<class 'galaxy.tool_util.lint.LintMessage'>, extra_modules=None, skip_types=None, name=None) bool [source]
lint an xml tool
- galaxy.tool_util.lint.lint_tool_source_with(lint_context, tool_source, extra_modules=None) LintContext [source]
- galaxy.tool_util.lint.lint_tool_source_with_modules(lint_context: LintContext, tool_source, linter_modules) LintContext [source]
- galaxy.tool_util.lint.lint_xml_with(lint_context, tool_xml, extra_modules=None) LintContext [source]
galaxy.tool_util.loader module
- galaxy.tool_util.loader.load_tool(path: str | PathLike) ElementTree
- galaxy.tool_util.loader.load_tool_with_refereces(path: str | PathLike) Tuple[ElementTree, List[str] | None]
Load XML documentation from file system and preprocesses XML macros.
Return the XML representation of the expanded tree and paths to referenced files that were imported (macros).
- galaxy.tool_util.loader.raw_tool_xml_tree(path: str | PathLike) ElementTree
Load raw (no macro expansion) tree representation of XML represented at the specified path.
galaxy.tool_util.loader_directory module
Utilities for loading and reasoning about unparsed tools in directories.
- galaxy.tool_util.loader_directory.find_possible_tools_from_path(path, recursive=False, enable_beta_formats=False)[source]
Walk a directory and find potential tool files.
- galaxy.tool_util.loader_directory.is_a_yaml_with_class(path, classes)[source]
Determine if a file is a valid YAML with a supplied
class
entry.
- galaxy.tool_util.loader_directory.is_tool_load_error(obj)[source]
Predicate to determine if object loaded for tool is a tool error.
- galaxy.tool_util.loader_directory.load_tool_elements_from_path(path, load_exception_handler=<function load_exception_handler>, recursive=False, register_load_errors=False)[source]
Walk a directory and load tool XML elements.
- galaxy.tool_util.loader_directory.load_tool_sources_from_path(path, load_exception_handler=<function load_exception_handler>, recursive=False, register_load_errors=False)[source]
Walk a directory and ToolSource objects.
- galaxy.tool_util.loader_directory.looks_like_a_cwl_artifact(path, classes=None)[source]
Quick check to see if a file looks like it may be a CWL artifact.
- galaxy.tool_util.loader_directory.looks_like_a_tool_cwl(path)[source]
Quick check to see if a file looks like it may be a CWL tool.
galaxy.tool_util.output_checker module
- class galaxy.tool_util.output_checker.DETECTED_JOB_STATE(value)[source]
-
An enumeration.
- OK = 'ok'
- OUT_OF_MEMORY_ERROR = 'oom_error'
- GENERIC_ERROR = 'generic_error'
- galaxy.tool_util.output_checker.check_output_regex(regex: ToolStdioRegex, stream: str, stream_name: str, job_messages: List[Dict[str, Any]], max_error_level: int) int [source]
check a single regex against a stream
regex the regex to check stream the stream to search in job_messages a list where the descriptions of the detected regexes can be appended max_error_level the maximum error level that has been detected so far returns the max of the error_level of the regex and the given max_error_level
- galaxy.tool_util.output_checker.check_output(stdio_regexes: List[ToolStdioRegex], stdio_exit_codes: List[ToolStdioExitCode], stdout: str, stderr: str, tool_exit_code: int) Tuple[str, str, str, List[Dict[str, Any]]] [source]
Check the output of a tool - given the stdout, stderr, and the tool’s exit code, return DETECTED_JOB_STATE.OK if the tool exited succesfully or error type otherwise. No exceptions should be thrown. If this code encounters an exception, it returns OK so that the workflow can continue; otherwise, a bug in this code could halt workflow progress.
Note that, if the tool did not define any exit code handling or any stdio/stderr handling, then it reverts back to previous behavior: if stderr contains anything, then False is returned.
galaxy.tool_util.provided_metadata module
- galaxy.tool_util.provided_metadata.parse_tool_provided_metadata(meta_file, provided_metadata_style=None, job_wrapper=None)[source]
Return a ToolProvidedMetadata object for specified file path.
If meta_file is absent, return a NullToolProvidedMetadata. If provided_metadata_style is None attempt to guess tool provided metadata type.
- class galaxy.tool_util.provided_metadata.BaseToolProvidedMetadata[source]
Bases:
object
- get_new_datasets(output_name)[source]
Find new datasets for dataset discovery for specified output.
Return a list of such datasets.
Called only in the context of discovering datasets when discover_via=”tool_provided_metadata” is defined in the tool.
- has_failed_outputs()[source]
Determine if generation of any of the outputs failed.
If True, this method should also log information about at least the first such failed output.
- get_new_dataset_meta_by_basename(output_name, basename)[source]
For a discovered dataset, get the corresponding metadata entry.
The discovery may have been from explicit listing in this file (returned from get_new_datasets) or via file regex, either way the basename of the file is used to index the fetching of the metadata entry.
- get_unnamed_outputs()[source]
Return unnamed outputs dataset introduced for upload 2.0.
Needs more formal specification but see output_collect for how destinations, types, elements, etc… are consumed.
- get_dataset_meta(output_name, dataset_id, dataset_uuid)[source]
Return primary dataset metadata for specified output.
- class galaxy.tool_util.provided_metadata.NullToolProvidedMetadata[source]
Bases:
BaseToolProvidedMetadata
- class galaxy.tool_util.provided_metadata.LegacyToolProvidedMetadata(meta_file, job_wrapper=None)[source]
Bases:
BaseToolProvidedMetadata
- get_dataset_meta(output_name, dataset_id, dataset_uuid)[source]
Return primary dataset metadata for specified output.
- get_new_dataset_meta_by_basename(output_name, basename)[source]
For a discovered dataset, get the corresponding metadata entry.
The discovery may have been from explicit listing in this file (returned from get_new_datasets) or via file regex, either way the basename of the file is used to index the fetching of the metadata entry.
- get_new_datasets(output_name)[source]
Find new datasets for dataset discovery for specified output.
Return a list of such datasets.
Called only in the context of discovering datasets when discover_via=”tool_provided_metadata” is defined in the tool.
- has_failed_outputs()[source]
Determine if generation of any of the outputs failed.
If True, this method should also log information about at least the first such failed output.
- get_unnamed_outputs()[source]
Return unnamed outputs dataset introduced for upload 2.0.
Needs more formal specification but see output_collect for how destinations, types, elements, etc… are consumed.
- class galaxy.tool_util.provided_metadata.ToolProvidedMetadata(meta_file)[source]
Bases:
BaseToolProvidedMetadata
- get_dataset_meta(output_name, dataset_id, dataset_uuid)[source]
Return primary dataset metadata for specified output.
- get_new_dataset_meta_by_basename(output_name, basename)[source]
For a discovered dataset, get the corresponding metadata entry.
The discovery may have been from explicit listing in this file (returned from get_new_datasets) or via file regex, either way the basename of the file is used to index the fetching of the metadata entry.
- get_new_datasets(output_name)[source]
Find new datasets for dataset discovery for specified output.
Return a list of such datasets.
Called only in the context of discovering datasets when discover_via=”tool_provided_metadata” is defined in the tool.
- has_failed_outputs()[source]
Determine if generation of any of the outputs failed.
If True, this method should also log information about at least the first such failed output.