This section is auto-generated from the help text for the planemo command
test
. This help message can be generated with planemo test
--help
.
Usage:
planemo test [OPTIONS] TOOL_PATH
Help
Run specified tool's tests within Galaxy.
All referenced tools (by default all the tools in the current working directory) will be tested and the results quickly summarized.
To run these tests planemo needs a Galaxy instance to utilize, planemo
will search parent directories to see if any is a Galaxy instance
- but one can pick the Galaxy instance to use with the --galaxy_root
option or force planemo to download a disposable instance with the
--install_galaxy
flag.
In additon to to quick summary printed to the console - various detailed
output summaries can be configured. tool_test_output.html
(settable
via --test_output
) will contain a human consumable HTML report
describing the test run. A JSON file (settable via --test_output_json
and defaulting to tool_test_output.json
) will also be created. These
files can can be disabled by passing in empty arguments or globally by
setting the values default_test_output
and/or
default_test_output_json
in ~/.planemo.yml
to null
. For
continuous integration testing a xUnit-style report can be confiured using
the --test_output_xunit
.
planemo uses temporarily generated config files and environment variables to attempt to shield this execution of Galaxy from manually launched runs against that same Galaxy root - but this may not be bullet proof yet so please careful and do not try this against production Galaxy instances.
Options:
--failed Re-run only failed tests. This command will read tool_test_output.json to determine which tests failed so this file must have been produced with the same set of tool ids previously. --polling_backoff INTEGER Poll resources with an increasing interval between requests. Useful when testing against remote and/or production instances to limit generated traffic. --history_name TEXT Name for history (if a history is generated as part of testing.) --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. --galaxy_python_version [2|2.7|3|3.3|3.4|3.5|3.6|3.7] Python version to start Galaxy under --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 FILE Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. --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 FILE 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 FILE 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. --update_test_data Update test-data directory with job outputs (normally written to directory --job_output_files if specified.) --paste_test_data_paths / --no_paste_test_data_paths By default Planemo will use or not use Galaxy's path paste option to load test data into a history based on the engine type it is targeting. This can override the logic to explicitly enable or disable path pasting. --test_output PATH Output test report (HTML - for humans) defaults to tool_test_output.html. --test_output_text PATH Output test report (Basic text - for display in CI) --test_output_markdown PATH Output test report (Markdown style - for humans & computers) --test_output_xunit PATH Output test report (xunit style - for CI systems --test_output_junit PATH Output test report (jUnit style - for CI systems --test_output_json PATH Output test report (planemo json) defaults to tool_test_output.json. --job_output_files DIRECTORY Write job outputs to specified directory. --summary [none|minimal|compact] Summary style printed to planemo's standard output (see output reports for more complete summary). Set to 'none' to disable completely. --engine [galaxy|docker_galaxy|cwltool|toil|external_galaxy] Select an engine to run or test artifacts such as tools and workflows. Defaults to a local Galaxy, but running Galaxy within a Docker container or the CWL reference implementation 'cwltool' and 'toil' be selected. --non_strict_cwl Disable strict validation of CWL. --no-container, --no_container If cwltool engine is used, disable Docker container usage. --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. --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. --galaxy_url TEXT Remote Galaxy URL to use with external Galaxy engine. --galaxy_admin_key TEXT Admin key to use with external Galaxy engine. --galaxy_user_key TEXT User key to use with external Galaxy engine. --help Show this message and exit.