This section is auto-generated from the help text for the planemo command
training_generate_from_wf
. This help message can be generated with planemo training_generate_from_wf
--help
.
Usage:
planemo training_generate_from_wf [OPTIONS] TOOL_PATH
Help
Create tutorial skeleton from workflow. Options:
--topic_name TEXT Name (directory name) of the topic to create or in which a tutorial should be created or updates [required] --tutorial_name TEXT Name (directory name) of the tutorial to modify [required] --workflow PATH Workflow of the tutorial (locally) --galaxy_url TEXT URL of a Galaxy instance with the workflow --galaxy_api_key TEXT API key on the Galaxy instance with the workflow --workflow_id TEXT ID of the workflow on the Galaxy instance --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. --galaxy_database_seed PATH Preseeded Galaxy sqlite database to target. --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be linted/tested/etc... but they will be available to workflows and for interactive use. --install_galaxy Download and configure a disposable copy of Galaxy from github. --galaxy_branch TEXT Branch of Galaxy to target (defaults to master) if a Galaxy root isn't specified. --galaxy_source TEXT Git source of Galaxy to target (defaults to the official galaxyproject github source if a Galaxy root isn't specified. --skip_venv Do not create or source a virtualenv environment for Galaxy, this should be used or instance to preserve an externally configured virtual environment or conda environment. --no_cache_galaxy Skip caching of Galaxy source and dependencies obtained with --install_galaxy. Not caching this results in faster downloads (no git) - so is better on throw away instances such with TravisCI. --no_cleanup Do not cleanup temp files created for and by Galaxy. --galaxy_email TEXT E-mail address to use when launching single- user Galaxy server. --docker / --no_docker Run Galaxy tools in Docker if enabled. --docker_cmd TEXT Command used to launch docker (defaults to docker). --docker_sudo / --no_docker_sudo Flag to use sudo when running docker. --docker_host TEXT Docker host to target when executing docker commands (defaults to localhost). --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). --job_config_file PATH Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. --port INTEGER Port to serve Galaxy on (default is 9090). --host TEXT Host to bind Galaxy to. Default is 127.0.0.1 that is restricted to localhost connections for security reasons set to 0.0.0.0 to bind Galaxy to all ports including potentially publicly accessible ones. --engine [galaxy|docker_galaxy|external_galaxy] Select an engine to serve aritfacts such as tools and workflows. Defaults to a local Galaxy, but running Galaxy within a Docker container. --non_strict_cwl Disable strict validation of CWL. --docker_galaxy_image TEXT Docker image identifier for docker-galaxy- flavor used if engine type is specified as ``docker-galaxy``. Defaults to quay.io/bgruening/galaxy. --docker_extra_volume PATH Extra path to mount if --engine docker. --test_data DIRECTORY test-data directory to for specified tool(s). --tool_data_table PATH tool_data_table_conf.xml file to for specified tool(s). --dependency_resolvers_config_file PATH Dependency resolver configuration for Galaxy to target. --brew_dependency_resolution Configure Galaxy to use plain brew dependency resolution. --shed_dependency_resolution Configure Galaxy to use brewed Tool Shed dependency resolution. --no_dependency_resolution Configure Galaxy with no dependency resolvers. --conda_prefix DIRECTORY Conda prefix to use for conda dependency commands. --conda_exec PATH Location of conda executable. --conda_debug Enable more verbose conda logging. --conda_channels, --conda_ensure_channels TEXT Ensure conda is configured with specified comma separated list of channels. --conda_use_local Use locally built packages while building Conda environments. --conda_dependency_resolution Configure Galaxy to use only conda for dependency resolution. --conda_copy_dependencies Conda dependency resolution for Galaxy will copy dependencies instead of attempting to link them. --conda_auto_install / --no_conda_auto_install Conda dependency resolution for Galaxy will attempt to install requested but missing packages. --conda_auto_init / --no_conda_auto_init Conda dependency resolution for Galaxy will auto install conda itself using miniconda if not availabe on conda_prefix. --profile TEXT Name of profile (created with the profile_create command) to use with this command. --postgres Use postgres database type. --database_type [postgres|postgres_docker|sqlite|auto] Type of database to use for profile - 'auto', 'sqlite', 'postgres', and 'postgres_docker' are available options. Use postgres to use an existing postgres server you user can access without a password via the psql command. Use postgres_docker to have Planemo manage a docker container running postgres. Data with postgres_docker is not yet persisted past when you restart the docker container launched by Planemo so be careful with this option. --postgres_psql_path TEXT Name or or path to postgres client binary (psql). --postgres_database_user TEXT Postgres username for managed development databases. --postgres_database_host TEXT Postgres host name for managed development databases. --postgres_database_port TEXT Postgres port for managed development databases. --file_path DIRECTORY Location for files created by Galaxy (e.g. database/files). --database_connection TEXT Database connection string to use for Galaxy. --shed_tool_conf TEXT Location of shed tools conf file for Galaxy. --shed_tool_path TEXT Location of shed tools directory for Galaxy. --galaxy_single_user / --no_galaxy_single_user By default Planemo will configure Galaxy to run in single-user mode where there is just one user and this user is automatically logged it. Use --no_galaxy_single_user to prevent Galaxy from running this way. --daemon Serve Galaxy process as a daemon. --pid_file PATH Location of pid file is executed with --daemon. --ignore_dependency_problems When installing shed repositories for workflows, ignore dependency issues. These likely indicate a problem but in some cases may not prevent a workflow from successfully executing. --shed_install / --no_shed_install By default Planemo will attempt to install repositories needed for workflow testing. This may not be appropriate for production servers and so this can disabled by calling planemo with --no_shed_install. --help Show this message and exit.