planemo.commands package

Submodules

planemo.commands.cmd_autoupdate module

Module describing the planemo autoupdate command.

planemo.commands.cmd_autoupdate.dry_run_option() → Callable

Perform a dry run autoupdate without modifying the XML files

planemo.commands.cmd_autoupdate.handle_tool_load_error(tool_path: str, tool_xml: galaxy.tool_util.parser.xml.XmlToolSource) → bool

Return True if tool_xml is tool load error (invalid XML), and print a helpful error message.

planemo.commands.cmd_autoupdate.skip_requirements_option() → Callable

List of requirements to skip

planemo.commands.cmd_autoupdate.skiplist_option() → Callable

List of XML files to skip

planemo.commands.cmd_autoupdate.test_option() → Callable

Test updated XML files

planemo.commands.cmd_ci_find_repos module

Module describing the planemo ci_find_repos command.

planemo.commands.cmd_ci_find_tools module

Module describing the planemo ci_find_tools command.

planemo.commands.cmd_ci_setup module

Module describing the planemo ci_setup command.

planemo.commands.cmd_clone module

Module describing the planemo clone command.

planemo.commands.cmd_clone.clone_target_arg() → Callable

Represent target to clone/branch.

planemo.commands.cmd_conda_build module

Module describing the planemo conda_build command.

planemo.commands.cmd_conda_env module

Module describing the planemo conda_env command.

planemo.commands.cmd_conda_init module

Module describing the planemo conda_init command.

planemo.commands.cmd_conda_install module

Module describing the planemo conda_install command.

planemo.commands.cmd_conda_search module

Module describing the planemo conda_search command.

planemo.commands.cmd_config_init module

Module describing the planemo config_init command.

planemo.commands.cmd_container_register module

Module describing the planemo container_register command.

class planemo.commands.cmd_container_register.RegistryTarget(ctx, **kwds)

Bases: object

Abstraction around mulled container registry (both directory and Github repo).

handle_pull_request(ctx, name, target_filename, packages_str, tools_str, base_image, **kwds)

has_pull_request_for(name)

write_targets(ctx, target_filename, mulled_targets, tag, base_image)

planemo.commands.cmd_container_register.open_prs(ctx)

planemo.commands.cmd_container_register.to_target_str(targets)

planemo.commands.cmd_create_alias module

Module describing the planemo create_alias command.

planemo.commands.cmd_create_gist module

Module describing the planemo create_gist command.

planemo.commands.cmd_database_create module

Module describing the planemo database_create command.

planemo.commands.cmd_database_delete module

Module describing the planemo database_delete command.

planemo.commands.cmd_database_list module

Module describing the planemo database_list command.

planemo.commands.cmd_delete_alias module

Module describing the planemo delete_alias command.

planemo.commands.cmd_docker_build module

Module describing the planemo docker_build command.

planemo.commands.cmd_docker_shell module

Module describing the planemo docker_shell command.

The docker_shell command takes the path to a single tool file and returns a new command to launch a new shell into the corresponding Docker container for that tool.

Galaxy will treat the identifier in the tool XML file as a published Docker image - during development such the image an image may not yet exist or may be not updated. So during development the –from_tag argument to used to treat the identifier as a locally cached tag. (Tip: Use the docker_build to populate such a tag from a Dockerfile located in the tool’s directory.

planemo.commands.cmd_dockstore_init module

Module describing the planemo dockstore_init command.

planemo.commands.cmd_docs module

Module describing the planemo docs command.

planemo.commands.cmd_lint module

Module describing the planemo lint command.

planemo.commands.cmd_list_alias module

Module describing the planemo list_alias command.

planemo.commands.cmd_list_invocations module

Module describing the planemo list_invocations command.

planemo.commands.cmd_list_repos module

Module describing the planemo list_repos command.

planemo.commands.cmd_merge_test_reports module

Module describing the planemo merge_test_reports command.

planemo.commands.cmd_mull module

Module describing the planemo mull command.

planemo.commands.cmd_mulled_init module

Module describing the planemo mulled_init command.

planemo.commands.cmd_normalize module

Module describing the planemo normalize command.

planemo.commands.cmd_open module

Module describing the planemo open command.

planemo.commands.cmd_profile_create module

Module describing the planemo profile_create command.

planemo.commands.cmd_profile_delete module

Module describing the planemo profile_delete command.

planemo.commands.cmd_profile_list module

Module describing the planemo profile_list command.

planemo.commands.cmd_project_init module

Module describing the planemo project_init command.

planemo.commands.cmd_pull_request module

Module describing the planemo pull_request command.

planemo.commands.cmd_rerun module

Module describing the planemo rerun command.

planemo.commands.cmd_run module

Module describing the planemo run command.

planemo.commands.cmd_serve module

Module describing the planemo serve command.

planemo.commands.cmd_share_test module

Module describing the planemo share_test command.

planemo.commands.cmd_shed_build module

Module describing the planemo shed_build command.

planemo.commands.cmd_shed_create module

Module describing the planemo shed_create command.

planemo.commands.cmd_shed_diff module

Module describing the planemo shed_diff command.

planemo.commands.cmd_shed_download module

Module describing the planemo shed_download command.

planemo.commands.cmd_shed_init module

Module describing the planemo shed_init command.

planemo.commands.cmd_shed_lint module

Module describing the planemo shed_lint command.

planemo.commands.cmd_shed_serve module

Module describing the planemo shed_serve command.

planemo.commands.cmd_shed_test module

Module describing the planemo shed_test command.

planemo.commands.cmd_shed_update module

Module describing the planemo shed_update command.

planemo.commands.cmd_shed_upload module

Module describing the planemo shed_upload command.

planemo.commands.cmd_syntax module

Module describing the planemo syntax command.

planemo.commands.cmd_test module

Module describing the planemo test command.

planemo.commands.cmd_test_reports module

Module describing the planemo test_reports command.

planemo.commands.cmd_tool_init module

Module describing the planemo tool_init command.

planemo.commands.cmd_training_fill_data_library module

Module describing the planemo training_fill_data_library command.

planemo.commands.cmd_training_generate_from_wf module

Module describing the planemo training_generate_from_wf command.

planemo.commands.cmd_training_init module

Module describing the planemo training_init command.

planemo.commands.cmd_upload_data module

Module describing the planemo upload_data command.

planemo.commands.cmd_workflow_convert module

Module describing the planemo workflow_convert command.

planemo.commands.cmd_workflow_edit module

Module describing the planemo workflow_edit command.

planemo.commands.cmd_workflow_job_init module

Module describing the planemo workflow_job_init command.

planemo.commands.cmd_workflow_lint module

Module describing the planemo workflow_lint command.

planemo.commands.cmd_workflow_test_init module

Module describing the planemo workflow_test_init command.

planemo.commands.cmd_workflow_upload module

Module describing the planemo workflow_upload command.

Module contents