Index

A

action_type (planemo.shed2tap.base.AutoconfAction attribute) (planemo.shed2tap.base.ChangeDirectoryAction attribute) (planemo.shed2tap.base.ChmodAction attribute) (planemo.shed2tap.base.DownloadBinary attribute) (planemo.shed2tap.base.DownloadByUrlAction attribute) (planemo.shed2tap.base.DownloadFileAction attribute) (planemo.shed2tap.base.MakeDirectoryAction attribute) (planemo.shed2tap.base.MakeInstallAction attribute) (planemo.shed2tap.base.MoveDirectoryFilesAction attribute) (planemo.shed2tap.base.MoveFileAction attribute) (planemo.shed2tap.base.SetEnvironmentAction attribute) (planemo.shed2tap.base.SetEnvironmentForInstallAction attribute) (planemo.shed2tap.base.SetupPerlEnvironmentAction attribute) (planemo.shed2tap.base.SetupPythonEnvironmentAction attribute) (planemo.shed2tap.base.SetupREnvironmentAction attribute) (planemo.shed2tap.base.SetupRubyEnvironmentAction attribute) (planemo.shed2tap.base.SetupVirtualenvAction attribute) (planemo.shed2tap.base.ShellCommandAction attribute) (planemo.shed2tap.base.TemplateShellCommandAction attribute)

ActionPackage (class in planemo.shed2tap.base) Actions (class in planemo.shed2tap.base) add() (in module planemo.git) add_dir_contents_to_repo() (in module planemo.github_util) alias_option() (in module planemo.options) all_tests_passed (planemo.galaxy.test.structures.GalaxyTestResults attribute) AllureListener (class in planemo.reports.allure) AllureWriter (class in planemo.reports.allure) api_exception_to_message() (in module planemo.shed) (in module planemo.shed.interface) args_to_str() (in module planemo.io) asbool() (in module planemo.shed2tap.base) AutoconfAction (class in planemo.shed2tap.base) autoupdate_tool() (in module planemo.autoupdate) autoupdate_wf() (in module planemo.autoupdate)

B

BaseAction (class in planemo.shed2tap.base) BaseEngine (class in planemo.engine.interface) BasePackage (class in planemo.shed2tap.base) best_practice_search() (in module planemo.conda) branch() (in module planemo.git) brew_dependency_resolution() (in module planemo.options) brew_option() (in module planemo.options) build() (in module planemo.tool_builder) (planemo.galaxy.test.structures.GalaxyTestCommand method)

build_conda_context() (in module planemo.conda) build_cwl_option() (in module planemo.options) build_engine() (in module planemo.engine.factory) build_involucro_context() (in module planemo.mulled) build_lint_args() (in module planemo.lint) build_mull_target_kwds() (in module planemo.mulled) build_report() (in module planemo.reports.build_report) build_tool_lint_args() (in module planemo.tool_lint)

C

cache_download() (planemo.context.PlanemoContext method) (planemo.context.PlanemoContextInterface method) calculate_summary_data() (planemo.test.results.StructuredData method) calculate_summary_data_if_needed() (planemo.test.results.StructuredData method) can_run() (planemo.engine.interface.BaseEngine method) can_write_to_path() (in module planemo.io) cancel() (planemo.galaxy.ephemeris_sleep.SleepCondition method) captured_io_for_xunit() (in module planemo.io) case_id() (in module planemo.galaxy.test.structures) cases() (in module planemo.runnable) ChangeDirectoryAction (class in planemo.shed2tap.base) check_conda() (in module planemo.autoupdate) check_output() (in module planemo.test) check_topic_init_tuto() (planemo.training.Training method) check_uploads_ok_option() (in module planemo.options) checkout() (in module planemo.git) ChmodAction (class in planemo.shed2tap.base) ci_chunk_count_option() (in module planemo.options) ci_chunk_option() (in module planemo.options) ci_find_options() (in module planemo.options) ci_group_tools_option() (in module planemo.options) ci_output_option() (in module planemo.options) cleanup() (planemo.engine.interface.BaseEngine method) (planemo.engine.interface.Engine method) clone() (in module planemo.git) clone_fork_branch() (in module planemo.github_util) clone_target_arg() (in module planemo.commands.cmd_clone) coalesce_return_codes() (in module planemo.io) collect_conda_target_lists() (in module planemo.conda) collect_conda_target_lists_and_tool_paths() (in module planemo.conda) collect_conda_targets() (in module planemo.conda) collect_mulled_target_lists() (in module planemo.mulled)

command_clone() (in module planemo.git) command_function() (in module planemo.cli) commit() (in module planemo.git) communicate() (in module planemo.io) conda_auto_init_option() (in module planemo.options) conda_auto_install_option() (in module planemo.options) conda_dependency_resolution() (in module planemo.options) conda_ensure_channels_option() (in module planemo.options) conda_exec_option() (in module planemo.options) conda_global_option() (in module planemo.options) conda_prefix_option() (in module planemo.options) conda_target_options() (in module planemo.options) conda_to_mulled_targets() (in module planemo.mulled) conda_use_local_option() (in module planemo.options) conditionally_captured_io() (in module planemo.io) configure_standard_planemo_logging() (in module planemo.context) convert() (planemo.options.ProjectOrRepositry method) (planemo.options.UriLike method) create_command() (in module planemo.virtualenv) create_database() (planemo.database.interface.DatabaseSource method) create_database_source() (in module planemo.database) (in module planemo.database.factory) create_hands_on_tutorial() (planemo.training.tutorial.Tutorial method) create_profile() (in module planemo.galaxy.profiles) create_release() (in module planemo.github_util) create_requirement_dict() (in module planemo.autoupdate) create_token_dict() (in module planemo.autoupdate) create_topic_structure() (planemo.training.topic.Topic method) create_tutorial() (planemo.training.tutorial.Tutorial method) cwl_tool (planemo.runnable.RunnableType attribute) cwl_workflow (planemo.runnable.RunnableType attribute) cwltool_no_container_option() (in module planemo.options) CwlToolEngine (class in planemo.engine.cwltool)

D

daemon_option() (in module planemo.options) data_manager_conf_path (planemo.runnable.Runnable attribute) database_connection_option() (in module planemo.options) database_identifier_argument() (in module planemo.options) database_source_options() (in module planemo.options) database_type_option() (in module planemo.options) DatabaseSource (class in planemo.database.interface) delete_database() (planemo.database.interface.DatabaseSource method) delete_profile() (in module planemo.galaxy.profiles) Dependencies (class in planemo.shed2tap.base) dependencies_script_options() (in module planemo.options) Dependency (class in planemo.shed2tap.base) dependency_resolvers_option() (in module planemo.options) describe_outputs() (in module planemo.galaxy.workflows) diff() (in module planemo.git) (in module planemo.xml.diff) diff_and_remove() (in module planemo.shed.diff) diff_repo() (in module planemo.shed) directory (planemo.runnable.RunnableType attribute)

docker_cmd_option() (in module planemo.options) docker_config_options() (in module planemo.options) docker_enable_option() (in module planemo.options) docker_extra_volume_option() (in module planemo.options) docker_galaxy_image_option() (in module planemo.options) docker_host_args() (in module planemo.docker) docker_host_option() (in module planemo.options) docker_sudo_cmd_option() (in module planemo.options) docker_sudo_option() (in module planemo.options) DockerizedManagedGalaxyEngine (class in planemo.engine.galaxy) DockerPostgresDatabaseSource (class in planemo.database.postgres_docker) download_tar() (in module planemo.shed.interface) download_tarball() (in module planemo.shed) DownloadBinary (class in planemo.shed2tap.base) DownloadByUrlAction (class in planemo.shed2tap.base) DownloadFileAction (class in planemo.shed2tap.base) downloads() (planemo.shed2tap.base.Actions method) dry_run() (in module planemo.options) dry_run_option() (in module planemo.commands.cmd_autoupdate)

E

enable_cwl_option() (in module planemo.options) enabled() (planemo.xml.validation.XsdValidator method) end_datetime (planemo.runnable.ErrorRunResponse attribute) (planemo.runnable.RunResponse attribute) Engine (class in planemo.engine.interface) engine_context() (in module planemo.engine) (in module planemo.engine.factory) engine_options() (in module planemo.options) ensure_dependency_resolvers_conf_configured() (in module planemo.deps) ensure_gh() (in module planemo.github_util) ensure_profile() (in module planemo.galaxy.profiles) ensure_runnables_served() (planemo.engine.galaxy.ExternalGalaxyEngine method) (planemo.engine.galaxy.LocalManagedGalaxyEngine method)

error() (in module planemo.io) error_message (planemo.runnable.ErrorRunResponse attribute) ErrorRunResponse (class in planemo.runnable) execute() (in module planemo.galaxy.activity) exists() (planemo.training.topic.Topic method) (planemo.training.tutorial.Tutorial method) exit() (planemo.cli.PlanemoCliContext method) exit_code (planemo.galaxy.test.structures.GalaxyTestResults attribute) ExitCodeException export_metadata_to_ordered_dict() (planemo.training.topic.Topic method) export_to_ordered_dict() (planemo.training.utils.Requirement method) export_workflow_file() (planemo.training.tutorial.Tutorial method) ExternalGalaxyEngine (class in planemo.engine.galaxy) extra_tools_option() (in module planemo.options)

F

fail_level_option() (in module planemo.options) failed_ids (planemo.test.results.StructuredData attribute) file_path_option() (in module planemo.options) fill_data_library() (planemo.training.Training method) filter_changed_in_commit_option() (in module planemo.options) filter_exclude_from_option() (in module planemo.options) filter_exclude_option() (in module planemo.options) filter_paths() (in module planemo.ci) (in module planemo.io) find_cases() (in module planemo.galaxy.test.structures) find_category_ids() (in module planemo.shed.interface) find_macros() (in module planemo.autoupdate) find_matching_directories() (in module planemo.io) find_potential_workflow_files() (in module planemo.workflow_lint) find_raw_repositories() (in module planemo.shed) find_repos_from_tool_id() (in module planemo.workflow_lint) find_repository() (in module planemo.shed.interface)

find_workflow_descriptions() (in module planemo.workflow_lint) first_download() (planemo.shed2tap.base.Actions method) fix_workflow_ga() (in module planemo.autoupdate) fix_workflow_gxformat2() (in module planemo.autoupdate) for_collections() (in module planemo.test) for_each_repository() (in module planemo.shed) for_path() (in module planemo.runnable) for_paths() (in module planemo.runnable) for_runnable_identifier() (in module planemo.runnable_resolve) for_runnable_identifiers() (in module planemo.runnable_resolve) force_option() (in module planemo.options) fork() (in module planemo.github_util) format_wf_steps() (in module planemo.training.tutorial) from_api() (planemo.shed2tap.base.Repo static method) from_elem() (planemo.shed2tap.base.BaseAction class method) from_invocation() (in module planemo.options) from_xml() (planemo.shed2tap.base.Repo static method)

G

galaxy_admin_key_option() (in module planemo.options) galaxy_branch_option() (in module planemo.options) galaxy_config() (in module planemo.galaxy) (in module planemo.galaxy.config) galaxy_config_options() (in module planemo.options) galaxy_cwl_root_option() (in module planemo.options) galaxy_datamanager (planemo.runnable.RunnableType attribute) galaxy_docker_options() (in module planemo.options) galaxy_email_option() (in module planemo.options) galaxy_host_option() (in module planemo.options) galaxy_port_option() (in module planemo.options) galaxy_profiles_directory (planemo.context.PlanemoContext attribute) (planemo.context.PlanemoContextInterface attribute) galaxy_python_version() (in module planemo.options) galaxy_root_option() (in module planemo.options) galaxy_run_options() (in module planemo.options) galaxy_serve() (in module planemo.galaxy) galaxy_serve_options() (in module planemo.options) galaxy_source_option() (in module planemo.options) galaxy_startup_timeout_option() (in module planemo.options) galaxy_target_options() (in module planemo.options) galaxy_tool (planemo.runnable.RunnableType attribute) galaxy_url_option() (in module planemo.options) galaxy_user_key_option() (in module planemo.options) galaxy_workflow (planemo.runnable.RunnableType attribute) GalaxyTestCommand (class in planemo.galaxy.test.structures) GalaxyTestResults (class in planemo.galaxy.test.structures) generate_dockstore_yaml() (in module planemo.workflow_lint) generate_tuto_from_wf() (planemo.training.Training method) get_all_actions() (planemo.shed2tap.base.BasePackage method) get_dict_value() (in module planemo.test.results) get_empty_input() (in module planemo.training.tool_input) get_empty_param() (in module planemo.training.tool_input) get_file() (planemo.shed2tap.base.Repo method) get_files_from_zenodo() (planemo.training.tutorial.Tutorial method) get_formatted_conditional_desc() (planemo.training.tool_input.ToolInput method) get_formatted_desc() (planemo.training.tool_input.ToolInput method)

get_formatted_inputs() (planemo.training.tool_input.ToolInput method) get_formatted_other_param_desc() (planemo.training.tool_input.ToolInput method) get_formatted_repeat_desc() (planemo.training.tool_input.ToolInput method) get_formatted_section_desc() (planemo.training.tool_input.ToolInput method) get_free_port() (in module planemo.network_util) get_galaxy_datatype() (in module planemo.training.tutorial) get_gh_env() (in module planemo.github_util) get_github_config() (in module planemo.github_util) get_hands_on_boxes_from_local_galaxy() (in module planemo.training.tutorial) get_hands_on_boxes_from_running_galaxy() (in module planemo.training.tutorial) get_id (planemo.runnable.RunnableOutput attribute) get_input_tool_name() (in module planemo.training.tool_input) get_lower_param_desc() (planemo.training.tool_input.ToolInput method) get_newest_tool_id() (in module planemo.autoupdate) get_option_source() (planemo.context.PlanemoContext method) (planemo.context.PlanemoContextInterface method) get_or_create_repository() (in module planemo.github_util) get_outputs() (in module planemo.runnable) get_requirements() (in module planemo.autoupdate) (planemo.training.topic.Topic method) get_shed_context() (in module planemo.shed) get_tokens() (in module planemo.autoupdate) get_tools_to_update() (in module planemo.autoupdate) get_tuto_metata() (planemo.training.tutorial.Tutorial method) get_validator() (in module planemo.xml.validation) get_wf_inputs() (in module planemo.training.tutorial) get_wf_param_values() (in module planemo.training.tutorial) get_zenodo_record() (in module planemo.training.tutorial) gi() (in module planemo.galaxy.api) git_env_for() (in module planemo.git) github_branch() (in module planemo.options) github_namespace() (in module planemo.options) glob() (in module planemo.glob) global_config (planemo.context.PlanemoContext attribute) (planemo.context.PlanemoContextInterface attribute) global_config_path() (in module planemo.config) group_paths() (in module planemo.ci)

H

handle_lint_complete() (in module planemo.lint) handle_pull_request() (planemo.commands.cmd_container_register.RegistryTarget method) handle_report_xunit_kwd() (in module planemo.reports.xunit_handler) handle_reports() (in module planemo.galaxy.test) (in module planemo.galaxy.test.actions) handle_reports_and_summary() (in module planemo.galaxy.test) (in module planemo.galaxy.test.actions) handle_tool_load_error() (in module planemo.commands.cmd_autoupdate) (in module planemo.tool_lint) handled_runnable_types (planemo.engine.cwltool.CwlToolEngine attribute) (planemo.engine.interface.BaseEngine attribute) (planemo.engine.toil.ToilEngine attribute)

has_details (planemo.galaxy.test.structures.GalaxyTestResults attribute) has_explicit_set_environments() (planemo.shed2tap.base.BasePackage method) has_multiple_set_environments() (planemo.shed2tap.base.BasePackage method) has_no_achitecture_install() (planemo.shed2tap.base.BasePackage method) has_path (planemo.runnable.Runnable attribute) has_pull_request_for() (planemo.commands.cmd_container_register.RegistryTarget method) has_tools (planemo.runnable.Runnable attribute) (planemo.runnable.RunnableType attribute) has_workflow() (planemo.training.tutorial.Tutorial method) history_name() (in module planemo.options)

I

id (planemo.galaxy.test.structures.TestId attribute) ignore_dependency_problems_option() (in module planemo.options) import_workflow() (in module planemo.galaxy.workflows) info() (in module planemo.io) init() (in module planemo.git) init_data_lib() (planemo.training.tutorial.Tutorial method) init_from_dict() (planemo.training.utils.Requirement method) init_from_existing_tutorial() (planemo.training.tutorial.Tutorial method) init_from_kwds() (planemo.training.topic.Topic method) (planemo.training.tutorial.Tutorial method) init_from_metadata() (planemo.training.topic.Topic method) init_training() (planemo.training.Training method) input_ids (planemo.runnable.TestCase attribute) install_args_list_to_runnables() (in module planemo.runnable_resolve) install_galaxy_option() (in module planemo.options)

install_repository_dependencies_option() (in module planemo.options) install_resolver_dependencies_option() (in module planemo.options) install_tool_dependencies_option() (in module planemo.options) invocation_details (planemo.runnable.ErrorRunResponse attribute) (planemo.runnable.RunResponse attribute) is_cwl_artifact (planemo.runnable.RunnableType attribute) is_galaxy_artifact (planemo.runnable.RunnableType attribute) is_galaxy_engine() (in module planemo.engine) (in module planemo.engine.factory) is_optional() (planemo.runnable.RunnableOutput method) is_remote_workflow_uri (planemo.runnable.Runnable attribute) is_rev_dirty() (in module planemo.git) is_single_artifact (planemo.runnable.Runnable attribute) (planemo.runnable.RunnableType attribute) is_tool_load_error() (in module planemo.tools)

J

job_config_option() (in module planemo.options)

job_info (planemo.runnable.ErrorRunResponse attribute) (planemo.runnable.RunResponse attribute)

K

kill_pid_file() (in module planemo.io)

kill_posix() (in module planemo.io)

L

label (planemo.galaxy.test.structures.TestId attribute) latest_installable_revision() (in module planemo.shed.interface) lint_biocontainer_registered() (in module planemo.linters.biocontainer_registered) lint_biocontainers_option() (in module planemo.options) lint_dois() (in module planemo.lint) lint_repository() (in module planemo.shed_lint) lint_requirements_in_conda() (in module planemo.linters.conda_requirements) lint_tool_dois() (in module planemo.linters.doi) lint_tool_urls() (in module planemo.linters.urls) lint_tool_xsd() (in module planemo.linters.xsd) lint_tools_on_path() (in module planemo.tool_lint) lint_urls() (in module planemo.lint) lint_workflow_artifacts_on_paths() (in module planemo.workflow_lint) lint_xsd() (in module planemo.lint)

lint_xsd_option() (in module planemo.options) list_cmds() (in module planemo.cli) list_databases() (planemo.database.interface.DatabaseSource method) list_profiles() (in module planemo.galaxy.profiles) load_tool_sources_from_path() (in module planemo.tools) load_yaml() (in module planemo.training.utils) LocalManagedGalaxyEngine (class in planemo.engine.galaxy) LocalPostgresDatabaseSource (class in planemo.database.postgres) log (planemo.runnable.ErrorRunResponse attribute) (planemo.runnable.RunResponse attribute) log() (planemo.context.PlanemoContext method) (planemo.context.PlanemoContextInterface method) looks_like_a_workflow() (in module planemo.workflow_lint) ls_remote() (in module planemo.git)

M

main() (in module planemo.galaxy.ephemeris_sleep) MakeDirectoryAction (class in planemo.shed2tap.base) MakeInstallAction (class in planemo.shed2tap.base) merge_test_json() (in module planemo.options) merge_xunit() (planemo.galaxy.test.StructuredData method) (planemo.galaxy.test.structures.StructuredData method) metadata_file_in_path() (in module planemo.ci)

MoveDirectoryFilesAction (class in planemo.shed2tap.base) MoveFileAction (class in planemo.shed2tap.base) mulled_action_option() (in module planemo.options) mulled_conda_option() (in module planemo.options) mulled_container_name() (in module planemo.linters.biocontainer_registered) mulled_containers_option() (in module planemo.options) mulled_namespace_option() (in module planemo.options) mulled_options() (in module planemo.options)

N

name (planemo.galaxy.test.structures.TestId attribute) name_to_command() (in module planemo.cli) no_cache_galaxy_option() (in module planemo.options) no_cleanup_option() (in module planemo.options) no_dependency_resolution() (in module planemo.options)

no_wait_option() (in module planemo.options) non_strict_cwl_option() (in module planemo.options) num (planemo.galaxy.test.structures.TestId attribute) num_problems (planemo.galaxy.test.structures.GalaxyTestResults attribute) num_tests (planemo.galaxy.test.structures.GalaxyTestResults attribute)

O

open_file_or_standard_output() (in module planemo.io) open_prs() (in module planemo.commands.cmd_container_register) optional_project_arg() (in module planemo.options)

optional_tools_arg() (in module planemo.options) optional_tools_or_packages_arg() (in module planemo.options) outdated_tools() (in module planemo.autoupdate) outputs_dict (planemo.runnable.SuccessfulRunResponse attribute)

P

parse_action() (planemo.shed2tap.base.BasePackage method) parse_action_package() (planemo.shed2tap.base.BasePackage method) parse_action_repo() (planemo.shed2tap.base.BaseAction method) parse_actions() (planemo.shed2tap.base.BasePackage method) parse_package_elems() (planemo.shed2tap.base.BaseAction method) parse_xunit_report() (in module planemo.galaxy.test.structures) paste_test_data_paths_option() (in module planemo.options) path (planemo.runnable.Runnable attribute) path_to_repo_name() (in module planemo.shed) perform_required_update() (in module planemo.autoupdate) pid_file_option() (in module planemo.options) planemo (module) planemo.autoupdate (module) planemo.ci (module) planemo.cli (module) planemo.commands (module) planemo.commands.cmd_autoupdate (module) planemo.commands.cmd_ci_find_repos (module) planemo.commands.cmd_ci_find_tools (module) planemo.commands.cmd_ci_setup (module) planemo.commands.cmd_clone (module) planemo.commands.cmd_conda_build (module) planemo.commands.cmd_conda_env (module) planemo.commands.cmd_conda_init (module) planemo.commands.cmd_conda_install (module) planemo.commands.cmd_conda_search (module) planemo.commands.cmd_config_init (module) planemo.commands.cmd_container_register (module) planemo.commands.cmd_create_alias (module) planemo.commands.cmd_create_gist (module) planemo.commands.cmd_database_create (module) planemo.commands.cmd_database_delete (module) planemo.commands.cmd_database_list (module) planemo.commands.cmd_delete_alias (module) planemo.commands.cmd_docker_build (module) planemo.commands.cmd_docker_shell (module) planemo.commands.cmd_dockstore_init (module) planemo.commands.cmd_docs (module) planemo.commands.cmd_lint (module) planemo.commands.cmd_list_alias (module) planemo.commands.cmd_list_invocations (module) planemo.commands.cmd_list_repos (module) planemo.commands.cmd_merge_test_reports (module) planemo.commands.cmd_mull (module) planemo.commands.cmd_mulled_init (module) planemo.commands.cmd_normalize (module) planemo.commands.cmd_open (module) planemo.commands.cmd_profile_create (module) planemo.commands.cmd_profile_delete (module) planemo.commands.cmd_profile_list (module) planemo.commands.cmd_project_init (module) planemo.commands.cmd_pull_request (module) planemo.commands.cmd_rerun (module) planemo.commands.cmd_run (module) planemo.commands.cmd_serve (module) planemo.commands.cmd_share_test (module) planemo.commands.cmd_shed_build (module) planemo.commands.cmd_shed_create (module) planemo.commands.cmd_shed_diff (module) planemo.commands.cmd_shed_download (module) planemo.commands.cmd_shed_init (module) planemo.commands.cmd_shed_lint (module) planemo.commands.cmd_shed_serve (module) planemo.commands.cmd_shed_test (module) planemo.commands.cmd_shed_update (module) planemo.commands.cmd_shed_upload (module) planemo.commands.cmd_syntax (module) planemo.commands.cmd_test (module) planemo.commands.cmd_test_reports (module) planemo.commands.cmd_tool_init (module) planemo.commands.cmd_training_fill_data_library (module) planemo.commands.cmd_training_generate_from_wf (module) planemo.commands.cmd_training_init (module) planemo.commands.cmd_upload_data (module) planemo.commands.cmd_workflow_convert (module) planemo.commands.cmd_workflow_edit (module) planemo.commands.cmd_workflow_job_init (module) planemo.commands.cmd_workflow_lint (module) planemo.commands.cmd_workflow_test_init (module) planemo.commands.cmd_workflow_upload (module) planemo.conda (module) planemo.config (module) planemo.context (module) planemo.cwl (module) planemo.cwl.run (module) planemo.cwl.toil (module) planemo.database (module)

planemo.database.factory (module) planemo.database.interface (module) planemo.database.postgres (module) planemo.database.postgres_docker (module) planemo.deps (module) planemo.docker (module) planemo.engine (module) planemo.engine.cwltool (module) planemo.engine.factory (module) planemo.engine.galaxy (module) planemo.engine.interface (module) planemo.engine.test (module) planemo.engine.toil (module) planemo.exit_codes (module) planemo.galaxy (module) planemo.galaxy.activity (module) planemo.galaxy.api (module) planemo.galaxy.config (module) planemo.galaxy.distro_tools (module) planemo.galaxy.ephemeris_sleep (module) planemo.galaxy.profiles (module) planemo.galaxy.run (module) planemo.galaxy.serve (module) planemo.galaxy.test (module) planemo.galaxy.test.actions (module) planemo.galaxy.test.structures (module) planemo.galaxy.workflows (module) planemo.git (module) planemo.github_util (module) planemo.glob (module) planemo.io (module) planemo.lint (module) planemo.linters (module) planemo.linters.biocontainer_registered (module) planemo.linters.conda_requirements (module) planemo.linters.doi (module) planemo.linters.urls (module) planemo.linters.xsd (module) planemo.mulled (module) planemo.network_util (module) planemo.options (module) planemo.reports (module) planemo.reports.allure (module) planemo.reports.build_report (module) planemo.reports.xunit_handler (module) planemo.runnable (module) planemo.runnable_resolve (module) planemo.shed (module) planemo.shed.diff (module) planemo.shed.interface (module) planemo.shed2tap (module) planemo.shed2tap.base (module) planemo.shed_lint (module) planemo.templates (module) planemo.test (module) planemo.test.data (module) planemo.test.results (module) planemo.tool_builder (module) planemo.tool_lint (module) planemo.tools (module) planemo.training (module) planemo.training.tool_input (module) planemo.training.topic (module) planemo.training.tutorial (module) planemo.training.utils (module) planemo.virtualenv (module) planemo.workflow_lint (module) planemo.xml (module) planemo.xml.diff (module) planemo.xml.validation (module) planemo_option() (in module planemo.config) PlanemoCliContext (class in planemo.cli) PlanemoContext (class in planemo.context) PlanemoContextInterface (class in planemo.context) postgres_datatype_type_option() (in module planemo.options) prepare_data_library_from_zenodo() (planemo.training.tutorial.Tutorial method) print_as_yaml() (in module planemo.ci) print_path_list() (in module planemo.ci) process() (planemo.reports.allure.AllureWriter method) process_test_case() (planemo.reports.allure.AllureWriter method) profile_database_options() (in module planemo.options) profile_name_argument() (in module planemo.options) profile_option() (in module planemo.options) ProjectOrRepositry (class in planemo.options) ps1_for_path() (in module planemo.io) publish_as_gist_file() (in module planemo.github_util) publish_dockstore_option() (in module planemo.options) push() (in module planemo.git)

R

read_global_config() (in module planemo.config) read_summary() (planemo.test.results.StructuredData method) real_io() (in module planemo.io) recipe_arg() (in module planemo.options) recipe_base_name() (planemo.shed2tap.base.Repo method) recursive_option() (in module planemo.options) recursive_shed_option() (in module planemo.options) RegistryTarget (class in planemo.commands.cmd_container_register) render() (in module planemo.templates) Repo (class in planemo.shed2tap.base) report_level_option() (in module planemo.options) report_xunit() (in module planemo.options) required_job_arg() (in module planemo.options) required_new_job_arg() (in module planemo.options) required_runnable_arg() (in module planemo.options) required_tool_arg() (in module planemo.options) required_workflow_arg() (in module planemo.options) Requirement (class in planemo.training.utils) rerun() (planemo.engine.galaxy.ExternalGalaxyEngine method)

rev() (in module planemo.git) rev_if_git() (in module planemo.git) run() (planemo.engine.interface.BaseEngine method) (planemo.engine.interface.Engine method) run_cwltool() (in module planemo.cwl) (in module planemo.cwl.run) run_download_outputs_option() (in module planemo.options) run_engine_option() (in module planemo.options) run_galaxy_command() (in module planemo.galaxy) (in module planemo.galaxy.run) run_history_tags_option() (in module planemo.options) run_output_directory_option() (in module planemo.options) run_output_json_option() (in module planemo.options) run_toil() (in module planemo.cwl) (in module planemo.cwl.toil) Runnable (class in planemo.runnable) RunnableOutput (class in planemo.runnable) RunnableType (class in planemo.runnable) RunResponse (class in planemo.runnable)

S

same_as() (planemo.shed2tap.base.BaseAction method) save_to_yaml() (in module planemo.training.utils) search_tool_path_for() (in module planemo.test.data) serve() (in module planemo.galaxy.serve) serve_daemon() (in module planemo.galaxy.serve) serve_engine_option() (in module planemo.options) set_default_requirement() (planemo.training.topic.Topic method) set_dir_name() (planemo.training.tutorial.Tutorial method) set_exit_code() (planemo.test.results.StructuredData method) set_option_source() (planemo.context.PlanemoContext method) (planemo.context.PlanemoContextInterface method) set_paths() (planemo.training.topic.Topic method) SetEnvironmentAction (class in planemo.shed2tap.base) SetEnvironmentForInstallAction (class in planemo.shed2tap.base) setup_venv() (in module planemo.galaxy) (in module planemo.galaxy.run) SetupPerlEnvironmentAction (class in planemo.shed2tap.base) SetupPythonEnvironmentAction (class in planemo.shed2tap.base) SetupREnvironmentAction (class in planemo.shed2tap.base) SetupRubyEnvironmentAction (class in planemo.shed2tap.base) SetupVirtualenvAction (class in planemo.shed2tap.base) SetVariable (class in planemo.shed2tap.base) shed_check_diff_option() (in module planemo.options) shed_dependency_resolution() (in module planemo.options) shed_email_option() (in module planemo.options) shed_fail_fast_option() (in module planemo.options) shed_force_create_option() (in module planemo.options) shed_init() (in module planemo.shed) shed_install() (planemo.engine.galaxy.LocalManagedGalaxyEngine method) shed_install_option() (in module planemo.options) shed_key_from_env_option() (in module planemo.options) shed_key_option() (in module planemo.options) shed_message_option() (in module planemo.options) shed_name_option() (in module planemo.options) shed_owner_option() (in module planemo.options) shed_password_option() (in module planemo.options) shed_project_arg() (in module planemo.options)

shed_publish_options() (in module planemo.options) shed_read_options() (in module planemo.options) shed_realization_options() (in module planemo.options) shed_repo_options() (in module planemo.options) shed_skip_metadata() (in module planemo.options) shed_skip_upload() (in module planemo.options) shed_target_option() (in module planemo.options) shed_target_options() (in module planemo.options) shed_tools_conf_option() (in module planemo.options) shed_tools_directory_option() (in module planemo.options) shed_upload_options() (in module planemo.options) shell() (in module planemo.io) shell_join() (in module planemo.io) ShellCommandAction (class in planemo.shed2tap.base) simultaneous_upload_option() (in module planemo.options) single_package() (planemo.shed2tap.base.Dependencies method) single_user_mode_option() (in module planemo.options) skip_client_build_option() (in module planemo.options) skip_install_option() (in module planemo.options) skip_option() (in module planemo.options) skip_requirements_option() (in module planemo.commands.cmd_autoupdate) skip_venv_option() (in module planemo.options) skiplist_option() (in module planemo.commands.cmd_autoupdate) sleep() (in module planemo.galaxy.ephemeris_sleep) SleepCondition (class in planemo.galaxy.ephemeris_sleep) split_job_and_test() (in module planemo.options) sqlalchemy_url() (planemo.database.interface.DatabaseSource method) (planemo.database.postgres.LocalPostgresDatabaseSource method) (planemo.database.postgres_docker.DockerPostgresDatabaseSource method) start_datetime (planemo.runnable.ErrorRunResponse attribute) (planemo.runnable.RunResponse attribute) stop_gravity() (in module planemo.io) structured_data() (planemo.runnable.RunResponse method) structured_test_data() (planemo.runnable.TestCase method) StructuredData (class in planemo.galaxy.test) (class in planemo.galaxy.test.structures) (class in planemo.test.results) SuccessfulRunResponse (class in planemo.runnable)

T

tee_captured_output() (in module planemo.io) temp_directory() (in module planemo.io) template_data() (in module planemo.reports.build_report) TemplateShellCommandAction (class in planemo.shed2tap.base) test() (planemo.engine.interface.BaseEngine method) (planemo.engine.interface.Engine method) test_data_in_parent_dir (planemo.runnable.RunnableType attribute) test_data_option() (in module planemo.options) test_data_search_path (planemo.runnable.Runnable attribute) test_option() (in module planemo.commands.cmd_autoupdate) test_options() (in module planemo.options) test_report_options() (in module planemo.options) test_runnables() (in module planemo.engine.test) TestCase (class in planemo.runnable) tested_output_ids (planemo.runnable.TestCase attribute) TestId (class in planemo.galaxy.test.structures) text_compare() (in module planemo.xml.diff) to_bash() (planemo.shed2tap.base.Actions method) (planemo.shed2tap.base.AutoconfAction method) (planemo.shed2tap.base.BaseAction method) (planemo.shed2tap.base.ChangeDirectoryAction method) (planemo.shed2tap.base.ChmodAction method) (planemo.shed2tap.base.DownloadByUrlAction method) (planemo.shed2tap.base.DownloadFileAction method) (planemo.shed2tap.base.MakeDirectoryAction method) (planemo.shed2tap.base.MakeInstallAction method) (planemo.shed2tap.base.MoveDirectoryFilesAction method) (planemo.shed2tap.base.MoveFileAction method) (planemo.shed2tap.base.SetEnvironmentAction method) (planemo.shed2tap.base.SetEnvironmentForInstallAction method) (planemo.shed2tap.base.ShellCommandAction method) to_target_str() (in module planemo.commands.cmd_container_register) ToilEngine (class in planemo.engine.toil) tool_data_path_option() (in module planemo.options) tool_data_search_path (planemo.runnable.Runnable attribute) tool_data_table_option() (in module planemo.options) tool_dependency_dir_option() (in module planemo.options) tool_init_autopygen_option() (in module planemo.options) tool_init_cite_url_option() (in module planemo.options) tool_init_command_option() (in module planemo.options) tool_init_container_option() (in module planemo.options)

tool_init_description_option() (in module planemo.options) tool_init_doi_option() (in module planemo.options) tool_init_example_command_option() (in module planemo.options) tool_init_example_input_option() (in module planemo.options) tool_init_example_output_option() (in module planemo.options) tool_init_help_from_command_option() (in module planemo.options) tool_init_help_text_option() (in module planemo.options) tool_init_id_option() (in module planemo.options) tool_init_input_option() (in module planemo.options) tool_init_macros_option() (in module planemo.options) tool_init_name_option() (in module planemo.options) tool_init_named_output_option() (in module planemo.options) tool_init_output_option() (in module planemo.options) tool_init_requirement_option() (in module planemo.options) tool_init_test_case_option() (in module planemo.options) tool_init_tool_option() (in module planemo.options) tool_init_version_command_option() (in module planemo.options) tool_init_version_option() (in module planemo.options) tool_shed_client() (in module planemo.shed) tool_shed_instance() (in module planemo.shed.interface) tool_shed_url() (in module planemo.shed) tool_source_conda_targets() (in module planemo.conda) tool_test_json() (in module planemo.options) ToolDescription (class in planemo.tool_builder) ToolInput (class in planemo.training.tool_input) Topic (class in planemo.training.topic) Training (class in planemo.training) training_datatype_option() (in module planemo.options) training_fill_data_library_options() (in module planemo.options) training_generate_tuto_from_wf_options() (in module planemo.options) training_init_options() (in module planemo.options) training_topic (planemo.workflow_lint.WorkflowLintContext attribute) training_topic_name_option() (in module planemo.options) training_topic_option() (in module planemo.options) training_tutorial_name_option() (in module planemo.options) training_tutorial_name_req_option() (in module planemo.options) training_tutorial_option() (in module planemo.options) training_tutorial_worflow_option() (in module planemo.options) training_zenodo_option() (in module planemo.options) Tutorial (class in planemo.training.tutorial) type (planemo.runnable.Runnable attribute)

U

untar_to() (in module planemo.io) update() (planemo.test.results.StructuredData method) update_xml() (in module planemo.autoupdate)

uri (planemo.runnable.Runnable attribute) UriLike (class in planemo.options) user_api_key() (in module planemo.galaxy.api) username() (in module planemo.shed.interface)

V

validate() (planemo.xml.validation.XsdValidator method) validate_shed_target_callback() (in module planemo.options)

vlog() (planemo.context.PlanemoContext method) (planemo.context.PlanemoContextInterface method)

W

wait_http_service() (in module planemo.network_util) wait_net_service() (in module planemo.network_util) wait_on() (in module planemo.io) warn() (in module planemo.io) was_successful (planemo.runnable.ErrorRunResponse attribute) (planemo.runnable.RunResponse attribute) (planemo.runnable.SuccessfulRunResponse attribute) workflow_output_artifact() (in module planemo.options)

WorkflowLintContext (class in planemo.workflow_lint) workspace (planemo.context.PlanemoContext attribute) (planemo.context.PlanemoContextInterface attribute) write_bibliography() (planemo.training.tutorial.Tutorial method) write_file() (in module planemo.io) write_hands_on_tutorial() (planemo.training.tutorial.Tutorial method) write_results() (in module planemo.reports.allure) write_targets() (planemo.commands.cmd_container_register.RegistryTarget method) write_tool_description() (in module planemo.tool_builder)

X

xml_compare() (in module planemo.xml.diff) XsdValidator (class in planemo.xml.validation)

xunit_t_elements_from_root() (in module planemo.galaxy.test.structures) xunit_testcase_elements (planemo.galaxy.test.structures.GalaxyTestResults attribute)

Y

yield_tool_sources() (in module planemo.tools)

yield_tool_sources_on_paths() (in module planemo.tools)