Commands — Planemo 0.75.31.dev0 documentation (original) (raw)

Planemo is a set of utilities for developing Galaxy tools. Each utility is implemented as a subcommand of the planemo executable. This section of the documentation describes these commands.

`autoupdate` command

This section is auto-generated from the help text for the planemo commandautoupdate. This help message can be generated with planemo autoupdate --help.

Usage:

planemo autoupdate [OPTIONS] TOOL_PATH

Help

Auto-update tool requirements by checking against Conda and updating if newer versions are available.Options:

--dry-run Perform a dry run autoupdate without modifying the XML files. -r, --recursive Recursively perform command for subdirectories. --test Test updated XML files. --skiplist TEXT Skiplist file, containing a list of tools or workflows for which autoupdate should be skipped. --skip_requirements TEXT Comma-separated list of requirements which should be not be updated. Default is python,r-base,perl. --engine [galaxy|docker_galaxy|external_galaxy] Select an engine to serve artifacts such as tools and workflows. Defaults to a local Galaxy, but running Galaxy within a Docker container. --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. --update_test_data Update test-data directory with job outputs (normally written to directory --job_output_files if specified.) --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_markdown_minimal PATH Output test report (Minimal markdown style - jost the table) --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_allure DIRECTORY Output test allure2 framework resutls --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. --test_timeout INTEGER Maximum runtime of a single test in seconds. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --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 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). --docker_run_extra_arguments TEXT Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless any conda option has been set explicitly. --galaxy_startup_timeout INTEGER RANGE Wait for galaxy to start before assuming Galaxy did not start. [x>=1] --job_config_file FILE Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. --tool_data_path DIRECTORY Directory where data used by tools is located. Required if tests are run in docker and should make use of external reference data. --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_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_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 miniforge if not availabe on conda_prefix. --simultaneous_uploads / --no_simultaneous_uploads When uploading files to Galaxy for tool or workflow tests or runs, upload multiple files simultaneously without waiting for the previous file upload to complete. --check_uploads_ok / --no_check_uploads_ok When uploading files to Galaxy for tool or workflow tests or runs, check that the history is in an 'ok' state before beginning tool or workflow execution. --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|postgres_singularity|sqlite|auto] Type of database to use for profile - 'auto', 'sqlite', 'postgres', 'postgres_docker' , and postgres_singularity 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. . Use postgres_singularity to have Planemo run postgres using singularity/apptainer. 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. --postgres-storage-location TEXT storage path for postgres database, used for local singularity postgres. --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. --report_level [all|warn|error] --report_xunit PATH Output an XUnit report, useful for CI testing --fail_level [warn|error] --galaxy_url TEXT Remote Galaxy URL to use with external Galaxy engine. --galaxy_user_key TEXT User key to use with external Galaxy engine. --galaxy_admin_key TEXT Admin key to use with external Galaxy engine. --help Show this message and exit.

`ci_find_repos` command

This section is auto-generated from the help text for the planemo commandci_find_repos. This help message can be generated with planemo ci_find_repos --help.

Usage:

planemo ci_find_repos [OPTIONS] PROJECT

Help

Find all shed repositories in one or more directories.

Currently, a repository is considered any directory with a .shed.yml or .dockstore.yml file.

Options:

--exclude PATH Paths to exclude. --exclude_from FILE File of paths to exclude. --changed_in_commit_range TEXT Exclude paths unchanged in git commit range. --chunk_count INTEGER Split output into chunks of this many item and print --chunk such group. --chunk INTEGER When output is split into --chunk_count groups, output the group 0-indexedby this option. --output TEXT File to output to, or - for standard output. --help Show this message and exit.

`ci_find_tools` command

This section is auto-generated from the help text for the planemo commandci_find_tools. This help message can be generated with planemo ci_find_tools --help.

Usage:

planemo ci_find_tools [OPTIONS] PROJECT

Help

Find all tools in one or more directories.

Tools can be chunked up, filtered, etc… to build lists of tools to perform operations over for continuous integration operations.

Options:

`ci_setup` command

This section is auto-generated from the help text for the planemo commandci_setup. This help message can be generated with planemo ci_setup --help.

Usage:

planemo ci_setup [OPTIONS]

Help

Launch Galaxy instance, then terminate instance.

Useful for populating a CI cache.

Options:

`clone` command

This section is auto-generated from the help text for the planemo commandclone. This help message can be generated with planemo clone --help.

Usage:

planemo clone [OPTIONS] TARGET PROJECT

Help

Short-cut to quickly clone, fork, and branch a relevant Github repo.

For instance, the following will clone, fork, and branch the tools-iuc repository to allow a subsequent pull request to fix a problem with bwa.

$ planemo clone –branch bwa-fix tools-iuc $ cd tools-iuc $ # Make changes. $ git add -p # Add desired changes. $ git commit -m “Fix bwa problem.” $ planemo pull_request -m “Fix bwa problem.”

These changes do require that a github access token is specified in ~/.planemo.yml. An access token can be generated by going to https://github.com/settings/tokens.

Options:

--fork / --skip_fork --branch TEXT Create a named branch on result. --help Show this message and exit.

`conda_build` command

This section is auto-generated from the help text for the planemo commandconda_build. This help message can be generated with planemo conda_build --help.

Usage:

planemo conda_build [OPTIONS] RECIPE_DIR

Help

Perform conda build with Planemo’s conda.Options:

--conda_prefix DIRECTORY Conda prefix to use for conda dependency commands. --conda_exec FILE Location of conda executable. --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. --help Show this message and exit.

`conda_env` command

This section is auto-generated from the help text for the planemo commandconda_env. This help message can be generated with planemo conda_env --help.

Usage:

planemo conda_env [OPTIONS] TOOL_PATH

Help

Activate a conda environment for tool.

Source the output of this command to activate a conda environment for this tool.

$ . <(planemo conda_env seqtk_seq.xml) Deactivate environment with conda_env_deactivate (seqtk_seq_v6) $ which seqtk /home/planemo/miniconda2/envs/jobdepsDkzcjjfecc6d406196737781ff4456ec60975c137e04884e4f4b05dc68192f7cec4656/bin/seqtk (seqtk_seq_v6) $ conda_env_deactivate $

Options:

`conda_init` command

This section is auto-generated from the help text for the planemo commandconda_init. This help message can be generated with planemo conda_init --help.

Usage:

planemo conda_init [OPTIONS]

Help

Download and install conda.

This will download conda for managing dependencies for your platform using the appropriate Miniconda installer.

By running this command, you are agreeing to the terms of the conda license a 3-clause BSD 3 license. Please review full license athttp://docs.continuum.io/anaconda/eula.

Planemo will print a warning and terminate with an exit code of 7 if Conda is already installed.

Options:

`conda_install` command

This section is auto-generated from the help text for the planemo commandconda_install. This help message can be generated with planemo conda_install --help.

Usage:

planemo conda_install [OPTIONS] TARGET

Help

Install conda packages for tool requirements.Options:

-r, --recursive Recursively perform command for subdirectories. --conda_prefix DIRECTORY Conda prefix to use for conda dependency commands. --conda_exec FILE Location of conda executable. --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. --global Install Conda dependencies globally instead of in requirement specific environments packaged for tools. If the Conda bin directory is on your PATH, tools may still use binaries but this is more designed for interactive testing and debugging. --conda_auto_init / --no_conda_auto_init Conda dependency resolution for Galaxy will auto install conda itself using miniforge if not availabe on conda_prefix. --help Show this message and exit.

`conda_search` command

This section is auto-generated from the help text for the planemo commandconda_search. This help message can be generated with planemo conda_search --help.

Usage:

planemo conda_search [OPTIONS] TERM

Help

Perform conda search with Planemo’s conda.

Implicitly adds channels Planemo is configured with.

Options:

`config_init` command

This section is auto-generated from the help text for the planemo commandconfig_init. This help message can be generated with planemo config_init --help.

Usage:

planemo config_init [OPTIONS] PROJECT

Help

Initialise global configuration for Planemo.

Helps initialize global configuration (in home directory) for Planemo.

Options:

--template TEXT --help Show this message and exit.

`container_register` command

This section is auto-generated from the help text for the planemo commandcontainer_register. This help message can be generated with planemo container_register --help.

Usage:

planemo container_register [OPTIONS] TOOL_PATH

Help

BioContainers publishes all Bioconda packages automatically as individual container images. These however are not enough for tools with multiple best-practice requirements. Such requirements should be recorded and published so that a container can be created and registered for these tools.

Options:

-r, --recursive Recursively perform command for subdirectories. --mulled_namespace TEXT Build a mulled image with the specified namespace - defaults to biocontainers. Galaxy currently only recognizes images with the namespace biocontainers. --conda_prefix DIRECTORY Conda prefix to use for conda dependency commands. --conda_exec FILE Location of conda executable. --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. --output_directory DIRECTORY Container registration directory (defaults to ~/.planemo/multi-package-containers. -m, --message TEXT Commit and pull request message template for registration interactions. --pull_request / --no_pull_request Fork and create a pull request against BioContainers/multi-package-containers for these changes. --force_push / --no_force_push Force push branch for pull request in case it already exists. --help Show this message and exit.

`create_alias` command

This section is auto-generated from the help text for the planemo commandcreate_alias. This help message can be generated with planemo create_alias --help.

Usage:

planemo create_alias [OPTIONS] OBJ

Help

Add an alias for a path or a workflow or dataset ID. Aliases are associated with a particular planemo profile.

Options:

--alias TEXT Name of an alias. --profile TEXT Name of profile (created with the profile_create command) to use with this command. [required] --help Show this message and exit.

`database_create` command

This section is auto-generated from the help text for the planemo commanddatabase_create. This help message can be generated with planemo database_create --help.

Usage:

planemo database_create [OPTIONS] IDENTIFIER

Help

Create a development database.

Currently the only implementation is postgres which will be managed withpsql.

Planemo database_ commands make it very easy to create and destroy databases, therefore it should not be used for production data - and it should not even be connnected to a production database server. Planemo is intended for development purposes only.

Planemo will assume that it can manage and access postgres databases without specifying a password. This can be accomplished by configuring postgres to not required a password for the planemo user or by specifying a password in a .pgpass file.

Planemo can be configured to not require a password for the planemo user in the postgres configuration file pg_hba.conf (on Ubuntu/Debian linux distros this file is in /etc/postgresql/<postgres_version>/main/ directory). Adding the following lines to that file will allow planemo and Galaxy to access the databases without a password.

# “local” is for Unix domain socket connections only local all all trust # IPv4 local connections: host all all 127.0.0.1/32 trust # IPv6 local connections: host all all ::1/128 trust

More information on the pg_hda.conf configuration file can be found athttp://www.postgresql.org/docs/9.3/static/auth-pg-hba-conf.html.

Information on .pgpass files can be found at at the following location:http://www.postgresql.org/docs/9.4/static/libpq-pgpass.html. In Ubuntu and Debian distros - a postgres user likely already exists and its password can be set by setting up a file ~/.pgpass file with the following contents.

_:_:*:postgres:<postgres_password>

Options:

--postgres Use postgres database type. --database_type [postgres|postgres_docker|postgres_singularity|sqlite|auto] Type of database to use for profile - 'auto', 'sqlite', 'postgres', 'postgres_docker' , and postgres_singularity 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. . Use postgres_singularity to have Planemo run postgres using singularity/apptainer. 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. --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). --docker_run_extra_arguments TEXT Extra arguments to pass to docker run. --help Show this message and exit.

`database_delete` command

This section is auto-generated from the help text for the planemo commanddatabase_delete. This help message can be generated with planemo database_delete --help.

Usage:

planemo database_delete [OPTIONS] IDENTIFIER

Help

Delete a development database.

Currently the only implementation is postgres which will be managed withpsql.

# “local” is for Unix domain socket connections only local all all trust # IPv4 local connections: host all all 127.0.0.1/32 trust # IPv6 local connections: host all all ::1/128 trust

More information on the pg_hda.conf configuration file can be found athttp://www.postgresql.org/docs/9.3/static/auth-pg-hba-conf.html.

_:_:*:postgres:<postgres_password>

Options:

`database_list` command

This section is auto-generated from the help text for the planemo commanddatabase_list. This help message can be generated with planemo database_list --help.

Usage:

planemo database_list [OPTIONS]

Help

List databases in configured database source.

Currently the only implementation is postgres which will be managed withpsql.

# “local” is for Unix domain socket connections only local all all trust # IPv4 local connections: host all all 127.0.0.1/32 trust # IPv6 local connections: host all all ::1/128 trust

More information on the pg_hda.conf configuration file can be found athttp://www.postgresql.org/docs/9.3/static/auth-pg-hba-conf.html.

_:_:*:postgres:<postgres_password>

Options:

`delete_alias` command

This section is auto-generated from the help text for the planemo commanddelete_alias. This help message can be generated with planemo delete_alias --help.

Usage:

planemo delete_alias [OPTIONS]

Help

List aliases for a path or a workflow or dataset ID. Aliases are associated with a particular planemo profile.

Options:

--alias TEXT Name of an alias. [required] --profile TEXT Name of profile (created with the profile_create command) to use with this command. [required] --help Show this message and exit.

`docker_build` command

This section is auto-generated from the help text for the planemo commanddocker_build. This help message can be generated with planemo docker_build --help.

Usage:

planemo docker_build [OPTIONS] TOOL_PATH

Help

Build (and optionally cache) Docker images.

Loads the tool or tools referenced by TOOL_PATH (by default all tools in current directory), and ensures they all reference the same Docker image and then attempts to find a Dockerfile for these tools (can be explicitly specified with --dockerfile but by default it will check the tool’s directory and the current directory as well).

This command will then build and tag the image so it is ready to be tested and published. The docker_shell command be used to test out the built image.

% planemo docker_build bowtie2.xml # asssumes Dockerfile in same dir % planemo docker_shell –from_tag bowtie2.xml

This can optionally also cache the images.

Options:

--dockerfile TEXT --docker_image_cache TEXT --docker_cmd TEXT Command used to launch docker (defaults to docker). --docker_sudo / --no_docker_sudo Flag to use sudo when running docker. --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). --docker_host TEXT Docker host to target when executing docker commands (defaults to localhost). --help Show this message and exit.

`docker_shell` command

This section is auto-generated from the help text for the planemo commanddocker_shell. This help message can be generated with planemo docker_shell --help.

Usage:

planemo docker_shell [OPTIONS] TOOL_PATH

Help

Launch shell in Docker container for a tool.

Will launch a shell in the Docker container referenced by the specified tool. Prints a command to do this the way Galaxy would in job files it generates - so be sure to wrap this in $(…) to launch the subshell.

$ $(planemo docker_shell bowtie2.xml) …root@b8754062f875:/#

Options:

--from_tag Treat the tool's Docker container identifier as a locally cached tag. --shell TEXT Shell to launch in container (defaults to /bin/bash). --docker_cmd TEXT Command used to launch docker (defaults to docker). --docker_sudo / --no_docker_sudo Flag to use sudo when running docker. --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). --docker_host TEXT Docker host to target when executing docker commands (defaults to localhost). --help Show this message and exit.

`dockstore_init` command

This section is auto-generated from the help text for the planemo commanddockstore_init. This help message can be generated with planemo dockstore_init --help.

Usage:

planemo dockstore_init [OPTIONS] PROJECT

Help

Initialize a .dockstore.yml configuration file for workflows in directory.

Walk supplied directory and find all Galaxy workflows and test configurations and create a .dockstore.yml with references to these files. Be sure to push this file to Github before registering your workflow repository with Dockstore.

Visit Dockstore at https://dockstore.org/. Find more about registering workflows with Dockstore athttps://docs.dockstore.org/en/develop/getting-started/dockstore-workflows.html.

Options:

--publish / --no_publish Set publish attribute to true in .dockstore.yml file --help Show this message and exit.

`docs` command

This section is auto-generated from the help text for the planemo commanddocs. This help message can be generated with planemo docs --help.

Usage:

Help

Open Planemo documentation in web browser.Options:

--help Show this message and exit.

`lint` command

This section is auto-generated from the help text for the planemo commandlint. This help message can be generated with planemo lint --help.

Usage:

planemo lint [OPTIONS] TOOL_PATH

Help

Check for common errors and best practices.Options:

--report_level [all|warn|error] --report_xunit PATH Output an XUnit report, useful for CI testing --fail_level [warn|error] -s, --skip TEXT Comma-separated list of lint tests to skip (e.g. passing --skip 'citations,xml_order' would skip linting of citations and best- practice XML ordering. --skip_file FILE File containing a list of lint tests to skip -r, --recursive Recursively perform command for subdirectories. --urls Check validity of URLs in XML files --doi Check validity of DOIs in XML files --conda_requirements Check tool requirements for availability in best practice Conda channels. --biocontainer, --biocontainers Check best practice BioContainer namespaces for a container definition applicable for this tool. --help Show this message and exit.

`list_alias` command

This section is auto-generated from the help text for the planemo commandlist_alias. This help message can be generated with planemo list_alias --help.

Usage:

planemo list_alias [OPTIONS]

Help

List aliases for a path or a workflow or dataset ID. Aliases are associated with a particular planemo profile.

Options:

--profile TEXT Name of profile (created with the profile_create command) to use with this command. [required] --help Show this message and exit.

`list_invocations` command

This section is auto-generated from the help text for the planemo commandlist_invocations. This help message can be generated with planemo list_invocations --help.

Usage:

planemo list_invocations [OPTIONS] WORKFLOW_IDENTIFIER

Help

Get a list of invocations for a particular workflow ID or alias.

Options:

--profile TEXT Name of profile (created with the profile_create command) to use with this command. [required] --help Show this message and exit.

`list_repos` command

This section is auto-generated from the help text for the planemo commandlist_repos. This help message can be generated with planemo list_repos --help.

Usage:

planemo list_repos [OPTIONS] PROJECT

Help

Find all shed repositories in one or more directories and output as yaml.

Currently, a shed repository is considered a directory with a .shed.yml file.

Options:

`merge_test_reports` command

This section is auto-generated from the help text for the planemo commandmerge_test_reports. This help message can be generated with planemo merge_test_reports --help.

Usage:

planemo merge_test_reports [OPTIONS] INPUT_PATHS FILE_PATH

Help

Merge tool_test_output.json files from multiple runs.Options:

--help Show this message and exit.

`mull` command

This section is auto-generated from the help text for the planemo commandmull. This help message can be generated with planemo mull --help.

Usage:

planemo mull [OPTIONS] TOOL_PATH

Help

Build containers for specified tools.

Supplied tools will be inspected for referenced requirement packages. For each combination of requirements a “mulled” container will be built. Galaxy can automatically discover this container and subsequently use it to run or test the tool.

For this to work, the tool’s requirements will need to be present in a known Conda channel such as bioconda (https://github.com/bioconda/bioconda-recipes). This can be verified by running planemo lint --conda_requirements on the target tool(s).

Options:

-r, --recursive Recursively perform command for subdirectories. --mulled_conda_version TEXT Install a specific version of Conda before running the command, by default the version that comes with the continuumio miniforge image will be used under Linux and under Mac OS X Conda will be upgraded to to work around a bug in 4.2. --mulled_namespace TEXT Build a mulled image with the specified namespace - defaults to biocontainers. Galaxy currently only recognizes images with the namespace biocontainers. --mulled_command TEXT Mulled action to perform for targets - this defaults to 'build-and-test'. --conda_channels, --conda_ensure_channels TEXT Ensure conda is configured with specified comma separated list of channels. --help Show this message and exit.

`mulled_init` command

This section is auto-generated from the help text for the planemo commandmulled_init. This help message can be generated with planemo mulled_init --help.

Usage:

planemo mulled_init [OPTIONS]

Help

Download and install involucro for mull command.

This will happen automatically when using the mull command, but this can be pre-installed in an environment using this command.

Options:

--mulled_conda_version TEXT Install a specific version of Conda before running the command, by default the version that comes with the continuumio miniforge image will be used under Linux and under Mac OS X Conda will be upgraded to to work around a bug in 4.2. --mulled_namespace TEXT Build a mulled image with the specified namespace - defaults to biocontainers. Galaxy currently only recognizes images with the namespace biocontainers. --mulled_command TEXT Mulled action to perform for targets - this defaults to 'build-and-test'. --help Show this message and exit.

`normalize` command

This section is auto-generated from the help text for the planemo commandnormalize. This help message can be generated with planemo normalize --help.

Usage:

planemo normalize [OPTIONS] TOOL_PATH

Help

Generate normalized tool XML from input.

This will break the formatting of your tool and is currently only intended for viewing macro expansions for for use with XSD validation (seehttps://github.com/JeanFred/Galaxy-XSD for instance). Please do not use the output as is - it frequently makes tool less readable not more.

The top-level blocks will be reordered and whitespace fixed according to the tool development best practices outlined on the Galaxy wiki.

% # Print normalized version of tool. % planemo normalize tool.xml … % # Print a variant of tool with all macros expanded out, useful for % # debugging complex macros. % planemo normalize –expand_macros tool.xml …

Options:

--expand_macros Expand macros while normalizing tool XML - useful to see how macros are evaluated. --skip_reorder Planemo will reorder top-level tool blocks according to tool development best practices as part of this command, this flag will disable that behavior. --skip_reindent Planemo will reindent the XML according to tool development best practices as part of this command, this flag will disable that behavior. --help Show this message and exit.

`open` command

This section is auto-generated from the help text for the planemo commandopen. This help message can be generated with planemo open --help.

Usage:

planemo open [OPTIONS] PATH

Help

Open latest Planemo test results in a web browser.Options:

--help Show this message and exit.

`profile_create` command

This section is auto-generated from the help text for the planemo commandprofile_create. This help message can be generated with planemo profile_create --help.

Usage:

planemo profile_create [OPTIONS] PROFILE_NAME

Help

Create a profile.Options:

--postgres Use postgres database type. --database_type [postgres|postgres_docker|postgres_singularity|sqlite|auto] Type of database to use for profile - 'auto', 'sqlite', 'postgres', 'postgres_docker' , and postgres_singularity 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. . Use postgres_singularity to have Planemo run postgres using singularity/apptainer. 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. --engine [galaxy|docker_galaxy|external_galaxy] Select an engine to serve artifacts such as tools and workflows. Defaults to a local Galaxy, but running Galaxy within a Docker container. --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). --docker_run_extra_arguments TEXT Extra arguments to pass to docker run. --galaxy_url TEXT Remote Galaxy URL to use with external Galaxy engine. --galaxy_user_key TEXT User key to use with external Galaxy engine. --galaxy_admin_key TEXT Admin key to use with external Galaxy engine. --help Show this message and exit.

`profile_delete` command

This section is auto-generated from the help text for the planemo commandprofile_delete. This help message can be generated with planemo profile_delete --help.

Usage:

planemo profile_delete [OPTIONS] PROFILE_NAME

Help

Delete a profile.Options:

`profile_list` command

This section is auto-generated from the help text for the planemo commandprofile_list. This help message can be generated with planemo profile_list --help.

Usage:

planemo profile_list [OPTIONS]

Help

List configured profile names.Options:

--help Show this message and exit.

`project_init` command

This section is auto-generated from the help text for the planemo commandproject_init. This help message can be generated with planemo project_init --help.

Usage:

planemo project_init [OPTIONS] PROJECT

Help

(Experimental) Initialize a new tool project.

This is only a proof-of-concept demo right now.

Options:

--template TEXT --help Show this message and exit.

`pull_request` command

This section is auto-generated from the help text for the planemo commandpull_request. This help message can be generated with planemo pull_request --help.

Usage:

planemo pull_request [OPTIONS] PROJECT

Help

Short-cut to quickly create a pull request for a relevant Github repo.

For instance, the following will clone, fork, and branch the tools-iuc repository to allow a subsequent pull request to fix a problem with bwa.

$ planemo clone –branch bwa-fix tools-iuc $ cd tools-iuc $ # Make changes. $ git add -p # Add desired changes. $ git commit -m “Fix bwa problem.” $ planemo pull_request -m “Fix bwa problem.”

These changes do require that a github access token is specified in ~/.planemo.yml. An access token can be generated by going to https://github.com/settings/tokens.

Options:

-m, --message TEXT Message describing the pull request to create. --help Show this message and exit.

`rerun` command

This section is auto-generated from the help text for the planemo commandrerun. This help message can be generated with planemo rerun --help.

Usage:

planemo rerun [OPTIONS] RERUNNABLE_IDS

Help

Planemo command for rerunning and remapping failed jobs on an external Galaxy server. Supply a list of history, invocation or job IDs, identifying the ID type using the –invocation, –history or –job flag, and all associated failed jobs will be rerun.

Please note: attempting to rerun non-remappable jobs will result in an exit code of 1. As jobs cannot be remapped more than once, running this command two or more times with the same history or job IDs will therefore return an exit code of 1. If avoiding this is important, you should specify the invocation ID instead if possible.

% planemo rerun –invocation / –history / –job RERUNNABLE_IDS

Options:

--profile TEXT Name of profile (created with the profile_create command) to use with this command. --galaxy_url TEXT Remote Galaxy URL to use with external Galaxy engine. --galaxy_user_key TEXT User key to use with external Galaxy engine. --invocation Rerun failed jobs associated by one or more invocation IDs. --history Rerun failed jobs associated by one or more history IDs. --job Rerun failed jobs specified by one or more job IDs. --help Show this message and exit.

`run` command

This section is auto-generated from the help text for the planemo commandrun. This help message can be generated with planemo run --help.

Usage:

planemo run [OPTIONS] RUNNABLE_PATH_OR_ID JOB_PATH

Help

Planemo command for running tools and jobs.

% planemo run cat1-tool.cwl cat-job.json

Options:

--galaxy_root DIRECTORY Root of development galaxy directory to execute command with. --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --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 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). --docker_run_extra_arguments TEXT Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless any conda option has been set explicitly. --galaxy_startup_timeout INTEGER RANGE Wait for galaxy to start before assuming Galaxy did not start. [x>=1] --job_config_file FILE Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. --tool_data_path DIRECTORY Directory where data used by tools is located. Required if tests are run in docker and should make use of external reference data. --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. --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_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_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 miniforge if not availabe on conda_prefix. --simultaneous_uploads / --no_simultaneous_uploads When uploading files to Galaxy for tool or workflow tests or runs, upload multiple files simultaneously without waiting for the previous file upload to complete. --check_uploads_ok / --no_check_uploads_ok When uploading files to Galaxy for tool or workflow tests or runs, check that the history is in an 'ok' state before beginning tool or workflow execution. --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|postgres_singularity|sqlite|auto] Type of database to use for profile - 'auto', 'sqlite', 'postgres', 'postgres_docker' , and postgres_singularity 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. . Use postgres_singularity to have Planemo run postgres using singularity/apptainer. 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. --postgres-storage-location TEXT storage path for postgres database, used for local singularity postgres. --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. --cwl Configure Galaxy for use with CWL tool. (this option is experimental and will be replaced when and if CWL support is merged into Galaxy). --cwl_galaxy_root DIRECTORY Root of development galaxy directory to execute command with (must be branch of Galaxy with CWL support, this option is experimental and will be replaced with --galaxy_root when and if CWL support is merged into Galaxy. --tags TEXT Comma-separated list of tags to add to the created history. --output_directory, --outdir DIRECTORY Where to store outputs of a 'run' task. --output_json FILE Where to store JSON dictionary describing outputs of a 'run' task. --download_outputs / --no_download_outputs After tool or workflow runs are complete, download the output files to the location specified by --output_directory. --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 or --biocontainers or --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. --install_tool_dependencies / --no_install_tool_dependencies Turn on installation of tool dependencies using classic toolshed packages. --install_resolver_dependencies / --no_install_resolver_dependencies Skip installing tool dependencies through resolver (e.g. conda). --install_repository_dependencies / --no_install_repository_dependencies Skip installing the repository dependencies. --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. --history_name TEXT Name to give a Galaxy history, if one is created. --history_id TEXT Send the results of the run to the history with the provided ID. A history with this ID must exist. --no_wait After invoking a job or workflow, do not wait for completion. --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. --update_test_data Update test-data directory with job outputs (normally written to directory --job_output_files if specified.) --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_markdown_minimal PATH Output test report (Minimal markdown style - jost the table) --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_allure DIRECTORY Output test allure2 framework resutls --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. --test_timeout INTEGER Maximum runtime of a single test in seconds. --no_early_termination Wait until all jobs terminate, even if some jobs have failed --help Show this message and exit.

`serve` command

This section is auto-generated from the help text for the planemo commandserve. This help message can be generated with planemo serve --help.

Usage:

planemo serve [OPTIONS] TOOL_PATH

Help

Launch Galaxy instance with specified tools.

The Galaxy tool panel will include just the referenced tool or tools (by default all the tools in the current working directory) and the upload tool.

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_rootoption or force planemo to download a disposable instance with the--install_galaxy flag.

planemo will run the Galaxy instance in an existing virtualenv if one exists in a .venv directory in the specified --galaxy_root. Otherwise, the Galaxy instance will run in a clean virtualenv created in/tmp.

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 be careful and do not try this against a production Galaxy instance.

Options:

--galaxy_root DIRECTORY Root of development galaxy directory to execute command with. --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --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 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). --docker_run_extra_arguments TEXT Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless any conda option has been set explicitly. --galaxy_startup_timeout INTEGER RANGE Wait for galaxy to start before assuming Galaxy did not start. [x>=1] --job_config_file FILE Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. --tool_data_path DIRECTORY Directory where data used by tools is located. Required if tests are run in docker and should make use of external reference data. --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 artifacts 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 or --biocontainers or --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 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_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_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 miniforge if not availabe on conda_prefix. --simultaneous_uploads / --no_simultaneous_uploads When uploading files to Galaxy for tool or workflow tests or runs, upload multiple files simultaneously without waiting for the previous file upload to complete. --check_uploads_ok / --no_check_uploads_ok When uploading files to Galaxy for tool or workflow tests or runs, check that the history is in an 'ok' state before beginning tool or workflow execution. --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|postgres_singularity|sqlite|auto] Type of database to use for profile - 'auto', 'sqlite', 'postgres', 'postgres_docker' , and postgres_singularity 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. . Use postgres_singularity to have Planemo run postgres using singularity/apptainer. 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. --postgres-storage-location TEXT storage path for postgres database, used for local singularity postgres. --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 FILE 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. --install_prebuilt_client / --no_install_prebuilt_client Install a pre-built client from npm. Turn this off you need access to visualizations. --skip_client_build Do not build Galaxy client when serving Galaxy. --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. --cwl Configure Galaxy for use with CWL tool. (this option is experimental and will be replaced when and if CWL support is merged into Galaxy). --cwl_galaxy_root DIRECTORY Root of development galaxy directory to execute command with (must be branch of Galaxy with CWL support, this option is experimental and will be replaced with --galaxy_root when and if CWL support is merged into Galaxy. --help Show this message and exit.

`share_test` command

This section is auto-generated from the help text for the planemo commandshare_test. This help message can be generated with planemo share_test --help.

Usage:

planemo share_test [OPTIONS] FILE_PATH

Help

Publish JSON test results as sharable Gist.

This will upload the JSON test results to Github as a Gist and produce sharable URL.

The sharable URL can be used to share an HTML version of the report that can be easily embedded in pull requests or commit messages.

Requires a ~/.planemo.yml with a Github access token defined in a ‘github’ section of that configuration file. An access token can be generated by going to https://github.com/settings/tokens.

Options:

--help Show this message and exit.

`shed_build` command

This section is auto-generated from the help text for the planemo commandshed_build. This help message can be generated with planemo shed_build --help.

Usage:

planemo shed_build [OPTIONS] TOOL_PATH

Help

Create a Galaxy tool tarball.

This will use the .shed.yml file to prepare a tarball (which you could upload to the Tool Shed manually).

Options:

--help Show this message and exit.

`shed_create` command

This section is auto-generated from the help text for the planemo commandshed_create. This help message can be generated with planemo shed_create --help.

Usage:

planemo shed_create [OPTIONS] PROJECT

Help

Create a repository in a Galaxy Tool Shed.

This will read the settings from the .shed.yml file.

Options:

`shed_diff` command

This section is auto-generated from the help text for the planemo commandshed_diff. This help message can be generated with planemo shed_diff --help.

Usage:

planemo shed_diff [OPTIONS] PROJECT

Help

diff between local repository and Tool Shed.

By default, this will produce a diff between this repository and what would be uploaded to the Tool Shed with the shed_upload command - but this command can be made to compare other combinations of repositories. Here are some examples

$ # diff for this repository and the main Tool Shed $ planemo shed_diff $ # diff for this repository and the test Tool Shed $ planemo shed_diff –shed_target testtoolshed $ # diff for the test Tool Shed and main Tool Shed $ planemo shed_diff –shed_target_source testtoolshed $ # diff for two an explicitly specified repositories (ignores $ # current project’s shed YAML file.) $ planemo shed_diff –owner peterjc –name blast_rbh

–shed_target_source testtoolshed

This command will return an exit code of:

0 if there are no detected differences.
1 if there are differences.
2 if the target repository doesn’t exist.
>200 if there are errors attempting to perform a diff.

Warning: shed_diff doesn’t inspect repository metadata, this difference applies only to the file contents of files that would actually be uploaded to the repository.

Options:

`shed_init` command

This section is auto-generated from the help text for the planemo commandshed_init. This help message can be generated with planemo shed_init --help.

Usage:

planemo shed_init [OPTIONS] PROJECT

Help

Bootstrap new Tool Shed .shed.yml file.

This Tool Shed configuration file is used by other planemo commands such as shed_lint, shed_create, shed_upload, and shed_diffto manage repositories in a Galaxy Tool Shed.

Options:

`shed_lint` command

This section is auto-generated from the help text for the planemo commandshed_lint. This help message can be generated with planemo shed_lint --help.

Usage:

planemo shed_lint [OPTIONS] PROJECT

Help

Check Tool Shed repository for common issues.

With the --tools flag, this command lints actual Galaxy tools in addition to tool shed artifacts.

With the --urls flag, this command searches for<package>$URL</package> and download actions which specify URLs. Each of those are accessed individually. By default, this tool requests the first hundred or so bytes of each listed URL and validates that a 200 OK was received. In tool XML files, the --urls option checks through the help text for mentioned URLs and checks those.

Options:

-r, --recursive Recursively perform command for nested repository directories. --fail_fast If multiple repositories are specified and an error occurs stop immediately instead of processing remaining repositories. --report_level [all|warn|error] --fail_level [warn|error] -s, --skip TEXT Comma-separated list of lint tests to skip (e.g. passing --skip 'citations,xml_order' would skip linting of citations and best- practice XML ordering. --skip_file FILE File containing a list of lint tests to skip --tools Lint tools discovered in the process of linting repositories. --ensure_metadata Ensure .shed.yml files contain enough metadata for each repository to allow automated creation and/or updates. --urls Check validity of URLs in XML files --biocontainer, --biocontainers Check best practice BioContainer namespaces for a container definition applicable for this tool. --help Show this message and exit.

`shed_serve` command

This section is auto-generated from the help text for the planemo commandshed_serve. This help message can be generated with planemo shed_serve --help.

Usage:

planemo shed_serve [OPTIONS] PROJECT

Help

Launch Galaxy with Tool Shed dependencies.

This command will start a Galaxy instance configured to target the specified shed, find published artifacts (tools and dependencies) corresponding to command-line arguments and .shed.yml file(s), install these artifacts, and serve a Galaxy instances that can be logged into and explored interactively.

Options:

-r, --recursive Recursively perform command for nested repository directories. --fail_fast If multiple repositories are specified and an error occurs stop immediately instead of processing remaining repositories. --owner TEXT Tool Shed repository owner (username). --name TEXT Tool Shed repository name (defaults to the inferred tool directory name). --shed_email TEXT E-mail for Tool Shed auth (required unless shed_key is specified). --shed_key TEXT API key for Tool Shed access. An API key is required unless e-mail and password is specified. This key can be specified with either --shed_key or --shed_key_from_env. --shed_key_from_env TEXT Environment variable to read API key for Tool Shed access from. --shed_password TEXT Password for Tool Shed auth (required unless shed_key is specified). -t, --shed_target TEXT Tool Shed to target (this can be 'toolshed', 'testtoolshed', 'local' (alias for http://localhost:9009/), an arbitrary url or mappings defined ~/.planemo.yml. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --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 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). --docker_run_extra_arguments TEXT Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless any conda option has been set explicitly. --galaxy_startup_timeout INTEGER RANGE Wait for galaxy to start before assuming Galaxy did not start. [x>=1] --job_config_file FILE Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. --tool_data_path DIRECTORY Directory where data used by tools is located. Required if tests are run in docker and should make use of external reference data. --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 artifacts 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 or --biocontainers or --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 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_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_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 miniforge if not availabe on conda_prefix. --simultaneous_uploads / --no_simultaneous_uploads When uploading files to Galaxy for tool or workflow tests or runs, upload multiple files simultaneously without waiting for the previous file upload to complete. --check_uploads_ok / --no_check_uploads_ok When uploading files to Galaxy for tool or workflow tests or runs, check that the history is in an 'ok' state before beginning tool or workflow execution. --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|postgres_singularity|sqlite|auto] Type of database to use for profile - 'auto', 'sqlite', 'postgres', 'postgres_docker' , and postgres_singularity 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. . Use postgres_singularity to have Planemo run postgres using singularity/apptainer. 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. --postgres-storage-location TEXT storage path for postgres database, used for local singularity postgres. --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 FILE 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. --install_prebuilt_client / --no_install_prebuilt_client Install a pre-built client from npm. Turn this off you need access to visualizations. --skip_client_build Do not build Galaxy client when serving Galaxy. --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. --skip_dependencies Do not install shed dependencies as part of repository installation. --help Show this message and exit.

`shed_test` command

This section is auto-generated from the help text for the planemo commandshed_test. This help message can be generated with planemo shed_test --help.

Usage:

planemo shed_test [OPTIONS] PROJECT

Help

Run tests of published shed artifacts.

Options:

-r, --recursive Recursively perform command for nested repository directories. --fail_fast If multiple repositories are specified and an error occurs stop immediately instead of processing remaining repositories. --owner TEXT Tool Shed repository owner (username). --name TEXT Tool Shed repository name (defaults to the inferred tool directory name). --shed_email TEXT E-mail for Tool Shed auth (required unless shed_key is specified). --shed_key TEXT API key for Tool Shed access. An API key is required unless e-mail and password is specified. This key can be specified with either --shed_key or --shed_key_from_env. --shed_key_from_env TEXT Environment variable to read API key for Tool Shed access from. --shed_password TEXT Password for Tool Shed auth (required unless shed_key is specified). -t, --shed_target TEXT Tool Shed to target (this can be 'toolshed', 'testtoolshed', 'local' (alias for http://localhost:9009/), an arbitrary url or mappings defined ~/.planemo.yml. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --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 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). --docker_run_extra_arguments TEXT Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless any conda option has been set explicitly. --galaxy_startup_timeout INTEGER RANGE Wait for galaxy to start before assuming Galaxy did not start. [x>=1] --job_config_file FILE Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. --tool_data_path DIRECTORY Directory where data used by tools is located. Required if tests are run in docker and should make use of external reference data. --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_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_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 miniforge if not availabe on conda_prefix. --simultaneous_uploads / --no_simultaneous_uploads When uploading files to Galaxy for tool or workflow tests or runs, upload multiple files simultaneously without waiting for the previous file upload to complete. --check_uploads_ok / --no_check_uploads_ok When uploading files to Galaxy for tool or workflow tests or runs, check that the history is in an 'ok' state before beginning tool or workflow execution. --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|postgres_singularity|sqlite|auto] Type of database to use for profile - 'auto', 'sqlite', 'postgres', 'postgres_docker' , and postgres_singularity 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. . Use postgres_singularity to have Planemo run postgres using singularity/apptainer. 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. --postgres-storage-location TEXT storage path for postgres database, used for local singularity postgres. --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. --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. --update_test_data Update test-data directory with job outputs (normally written to directory --job_output_files if specified.) --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_markdown_minimal PATH Output test report (Minimal markdown style - jost the table) --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_allure DIRECTORY Output test allure2 framework resutls --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. --test_timeout INTEGER Maximum runtime of a single test in seconds. --skip_dependencies Do not install shed dependencies as part of repository installation. --help Show this message and exit.

`shed_update` command

This section is auto-generated from the help text for the planemo commandshed_update. This help message can be generated with planemo shed_update --help.

Usage:

planemo shed_update [OPTIONS] PROJECT

Help

Update Tool Shed repository.

By default this command will update both repository metadata from .shed.yml and upload new contents from the repository directory.

% planemo shed_update

This will update the main tool shed with the repository defined by a .shed.yml file in the current working directory. Both the location of the .shed.yml and the tool shed to upload to can be easily configured. For instance, the following command can be used if .shed.yml if contained in path/to/repo and the desire is to update the test tool shed.

% planemo shed_update –shed_target testtoolshed path/to/repo

Another important option is --check_diff - this doesn’t affect the updating of shed metadata but it will check for differences before uploading new contents to the tool shed. This may important because the tool shed will automatically populate certain attributes in tool shed artifact files (such as tool_dependencies.xml) and this may cause unwanted installable revisions to be created when there are no important changes.

The lower-level shed_upload command should be used instead if the repository doesn’t define complete metadata in a .shed.yml.

Options:

--report_xunit PATH Output an XUnit report, useful for CI testing -r, --recursive Recursively perform command for nested repository directories. --fail_fast If multiple repositories are specified and an error occurs stop immediately instead of processing remaining repositories. --owner TEXT Tool Shed repository owner (username). --name TEXT Tool Shed repository name (defaults to the inferred tool directory name). --shed_email TEXT E-mail for Tool Shed auth (required unless shed_key is specified). --shed_key TEXT API key for Tool Shed access. An API key is required unless e-mail and password is specified. This key can be specified with either --shed_key or --shed_key_from_env. --shed_key_from_env TEXT Environment variable to read API key for Tool Shed access from. --shed_password TEXT Password for Tool Shed auth (required unless shed_key is specified). -t, --shed_target TEXT Tool Shed to target (this can be 'toolshed', 'testtoolshed', 'local' (alias for http://localhost:9009/), an arbitrary url or mappings defined ~/.planemo.yml. -m, --message TEXT Commit message for tool shed upload. --force_repository_creation If a repository cannot be found for the specified user/repo name pair, then automatically create the repository in the toolshed. --check_diff Skip uploading if the shed_diff detects there would be no 'difference' (only attributes populated by the shed would be updated.) --skip_upload Skip upload contents as part of operation, only update metadata. --skip_metadata Skip metadata update as part of operation, only upload new contents. --help Show this message and exit.

`shed_upload` command

This section is auto-generated from the help text for the planemo commandshed_upload. This help message can be generated with planemo shed_upload --help.

Usage:

planemo shed_upload [OPTIONS] PROJECT

Help

Low-level command to upload tarballs.

Generally, shed_update should be used instead since it also updates both tool shed contents (via tar ball generation and upload) as well as metadata (to handle metadata changes in .shed.yml files).

% planemo shed_upload –tar_only ~/ % tar -tzf shed_upload.tar.gz test-data/blastdb.loc … tools/ncbi_blast_plus/tool_dependencies.xml % tar -tzf shed_upload.tar.gz | wc -l 117

Options:

`syntax` command

This section is auto-generated from the help text for the planemo commandsyntax. This help message can be generated with planemo syntax --help.

Usage:

Help

Open tool config syntax page in web browser.Options:

--help Show this message and exit.

`test` command

This section is auto-generated from the help text for the planemo commandtest. This help message can be generated with planemo test --help.

Usage:

planemo test [OPTIONS] TOOL_PATH

Help

Run specified tool or workflow 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 addition 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_jsonand 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/ordefault_test_output_json in ~/.planemo.yml to null. For continuous integration testing a xUnit-style report can be configured 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. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --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 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). --docker_run_extra_arguments TEXT Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless any conda option has been set explicitly. --galaxy_startup_timeout INTEGER RANGE Wait for galaxy to start before assuming Galaxy did not start. [x>=1] --job_config_file FILE Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. --tool_data_path DIRECTORY Directory where data used by tools is located. Required if tests are run in docker and should make use of external reference data. --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_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_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 miniforge if not availabe on conda_prefix. --simultaneous_uploads / --no_simultaneous_uploads When uploading files to Galaxy for tool or workflow tests or runs, upload multiple files simultaneously without waiting for the previous file upload to complete. --check_uploads_ok / --no_check_uploads_ok When uploading files to Galaxy for tool or workflow tests or runs, check that the history is in an 'ok' state before beginning tool or workflow execution. --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|postgres_singularity|sqlite|auto] Type of database to use for profile - 'auto', 'sqlite', 'postgres', 'postgres_docker' , and postgres_singularity 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. . Use postgres_singularity to have Planemo run postgres using singularity/apptainer. 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. --postgres-storage-location TEXT storage path for postgres database, used for local singularity postgres. --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. --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. --update_test_data Update test-data directory with job outputs (normally written to directory --job_output_files if specified.) --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_markdown_minimal PATH Output test report (Minimal markdown style - jost the table) --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_allure DIRECTORY Output test allure2 framework resutls --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. --test_timeout INTEGER Maximum runtime of a single test in seconds. --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 or --biocontainers or --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. --install_tool_dependencies / --no_install_tool_dependencies Turn on installation of tool dependencies using classic toolshed packages. --install_resolver_dependencies / --no_install_resolver_dependencies Skip installing tool dependencies through resolver (e.g. conda). --install_repository_dependencies / --no_install_repository_dependencies Skip installing the repository dependencies. --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. --history_name TEXT Name to give a Galaxy history, if one is created. --history_id TEXT Send the results of the run to the history with the provided ID. A history with this ID must exist. --no_wait After invoking a job or workflow, do not wait for completion. --help Show this message and exit.

`test_reports` command

This section is auto-generated from the help text for the planemo commandtest_reports. This help message can be generated with planemo test_reports --help.

Usage:

planemo test_reports [OPTIONS] FILE_PATH

Help

Generate human readable tool test reports.

Creates reports in various formats (HTML, text, markdown) from the structured test output (tool_test_output.json).

Options:

--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_markdown_minimal PATH Output test report (Minimal markdown style - jost the table) --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_allure DIRECTORY Output test allure2 framework resutls --help Show this message and exit.

`tool_init` command

This section is auto-generated from the help text for the planemo commandtool_init. This help message can be generated with planemo tool_init --help.

Usage:

planemo tool_init [OPTIONS]

Help

Generate tool outline from given arguments.Options:

-i, --id TEXT Short identifier for new tool (no whitespace) -f, --force Overwrite existing tool if present. -t, --tool FILE Output path for new tool (default is .xml) -n, --name TEXT Name for new tool (user facing) --version TEXT Tool XML version. -d, --description TEXT Short description for new tool (user facing) -c, --command TEXT Command potentially including cheetah variables ()(e.g. 'seqtk seq -A input>input > input>output') --example_command TEXT Example to command with paths to build Cheetah template from (e.g. 'seqtk seq -A 2.fastq > 2.fasta'). Option cannot be used with --command, should be used --example_input and --example_output. --example_input TEXT For use with --example_command, replace input file (e.g. 2.fastq with a data input parameter). --example_output TEXT For use with --example_command, replace input file (e.g. 2.fastq with a tool output). --named_output TEXT Create a named output for use with command block for example specify --named_output=output1.bam and then use '-o $output1' in your command block. --input TEXT An input description (e.g. input.fasta) --output TEXT An output location (e.g. output.bam), the Galaxy datatype is inferred from the extension. --help_text TEXT Help text (reStructuredText) --help_from_command TEXT Auto populate help from supplied command. --doi TEXT Supply a DOI (http://www.doi.org/) easing citation of the tool for Galxy users (e.g. 10.1101/014043). --cite_url TEXT Supply a URL for citation. --test_case For use with --example_commmand, generate a tool test case from the supplied example. --macros Generate a macros.xml for reuse across many tools. --version_command TEXT Command to print version (e.g. 'seqtk --version') --requirement TEXT Add a tool requirement package (e.g. 'seqtk' or 'seqtk@1.68'). --container TEXT Add a Docker image identifier for this tool. --cwl Build a CWL tool instead of a Galaxy tool. --autopygen TEXT Option for automatic generation of tool file, from python source code that uses argparse. Parameter is a path to source file containing definition of the parser --help Show this message and exit.

`training_fill_data_library` command

This section is auto-generated from the help text for the planemo commandtraining_fill_data_library. This help message can be generated with planemo training_fill_data_library --help.

Usage:

planemo training_fill_data_library [OPTIONS] TOOL_PATH

Help

Build training template from workflow.Options:

`training_generate_from_wf` command

This section is auto-generated from the help text for the planemo commandtraining_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_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --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 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). --docker_run_extra_arguments TEXT Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless any conda option has been set explicitly. --galaxy_startup_timeout INTEGER RANGE Wait for galaxy to start before assuming Galaxy did not start. [x>=1] --job_config_file FILE Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. --tool_data_path DIRECTORY Directory where data used by tools is located. Required if tests are run in docker and should make use of external reference data. --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 artifacts 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 or --biocontainers or --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 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_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_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 miniforge if not availabe on conda_prefix. --simultaneous_uploads / --no_simultaneous_uploads When uploading files to Galaxy for tool or workflow tests or runs, upload multiple files simultaneously without waiting for the previous file upload to complete. --check_uploads_ok / --no_check_uploads_ok When uploading files to Galaxy for tool or workflow tests or runs, check that the history is in an 'ok' state before beginning tool or workflow execution. --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|postgres_singularity|sqlite|auto] Type of database to use for profile - 'auto', 'sqlite', 'postgres', 'postgres_docker' , and postgres_singularity 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. . Use postgres_singularity to have Planemo run postgres using singularity/apptainer. 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. --postgres-storage-location TEXT storage path for postgres database, used for local singularity postgres. --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 FILE 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. --install_prebuilt_client / --no_install_prebuilt_client Install a pre-built client from npm. Turn this off you need access to visualizations. --skip_client_build Do not build Galaxy client when serving Galaxy. --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.

`training_init` command

This section is auto-generated from the help text for the planemo commandtraining_init. This help message can be generated with planemo training_init --help.

Usage:

planemo training_init [OPTIONS] TOOL_PATH

Help

Build training template 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] --topic_title TEXT Title of the topic to create --topic_summary TEXT Summary of the topic --topic_target [use|admin-dev|instructors] Target audience for the topic --tutorial_name TEXT Name (directory name) of the tutorial to create or to modify --tutorial_title TEXT Title of the tutorial --hands_on Add hands-on for the new tutorial --slides Add slides for the new tutorial --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 --zenodo_link TEXT Zenodo URL with the input data --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --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 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). --docker_run_extra_arguments TEXT Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless any conda option has been set explicitly. --galaxy_startup_timeout INTEGER RANGE Wait for galaxy to start before assuming Galaxy did not start. [x>=1] --job_config_file FILE Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. --tool_data_path DIRECTORY Directory where data used by tools is located. Required if tests are run in docker and should make use of external reference data. --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 artifacts 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 or --biocontainers or --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 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_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_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 miniforge if not availabe on conda_prefix. --simultaneous_uploads / --no_simultaneous_uploads When uploading files to Galaxy for tool or workflow tests or runs, upload multiple files simultaneously without waiting for the previous file upload to complete. --check_uploads_ok / --no_check_uploads_ok When uploading files to Galaxy for tool or workflow tests or runs, check that the history is in an 'ok' state before beginning tool or workflow execution. --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|postgres_singularity|sqlite|auto] Type of database to use for profile - 'auto', 'sqlite', 'postgres', 'postgres_docker' , and postgres_singularity 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. . Use postgres_singularity to have Planemo run postgres using singularity/apptainer. 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. --postgres-storage-location TEXT storage path for postgres database, used for local singularity postgres. --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 FILE 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. --install_prebuilt_client / --no_install_prebuilt_client Install a pre-built client from npm. Turn this off you need access to visualizations. --skip_client_build Do not build Galaxy client when serving Galaxy. --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.

`upload_data` command

This section is auto-generated from the help text for the planemo commandupload_data. This help message can be generated with planemo upload_data --help.

Usage:

planemo upload_data [OPTIONS] RUNNABLE_PATH_OR_ID JOB_PATH NEW_JOB_PATH

Help

Planemo command for uploading data to an external Galaxy server.

% planemo upload_data wf.ga wf-job.yml new-wf-job.yml –profile profile

Running this subcommand requires a workflow file or identifier and a job file, just as for planemo run. In addition, a third argument is required, for the location of a new job file which Planemo will write. The data will be uploaded to the specified external Galaxy server and the job file will be recreated at the specified location, with all instances of path or locationfor input datasets and collections replaced by galaxy_id. The new job file can then be used to run the workflow separately from the already completed data upload.

Options:

`workflow_convert` command

This section is auto-generated from the help text for the planemo commandworkflow_convert. This help message can be generated with planemo workflow_convert --help.

Usage:

planemo workflow_convert [OPTIONS] WORKFLOW_PATH_OR_ID

Help

Convert Format 2 workflows to native Galaxy workflows, and vice-versa.Options:

-f, --force Overwrite existing files if present. -o, --output FILE --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --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 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). --docker_run_extra_arguments TEXT Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless any conda option has been set explicitly. --galaxy_startup_timeout INTEGER RANGE Wait for galaxy to start before assuming Galaxy did not start. [x>=1] --job_config_file FILE Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. --tool_data_path DIRECTORY Directory where data used by tools is located. Required if tests are run in docker and should make use of external reference data. --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 artifacts 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 or --biocontainers or --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 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_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_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 miniforge if not availabe on conda_prefix. --simultaneous_uploads / --no_simultaneous_uploads When uploading files to Galaxy for tool or workflow tests or runs, upload multiple files simultaneously without waiting for the previous file upload to complete. --check_uploads_ok / --no_check_uploads_ok When uploading files to Galaxy for tool or workflow tests or runs, check that the history is in an 'ok' state before beginning tool or workflow execution. --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|postgres_singularity|sqlite|auto] Type of database to use for profile - 'auto', 'sqlite', 'postgres', 'postgres_docker' , and postgres_singularity 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. . Use postgres_singularity to have Planemo run postgres using singularity/apptainer. 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. --postgres-storage-location TEXT storage path for postgres database, used for local singularity postgres. --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 FILE 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. --install_prebuilt_client / --no_install_prebuilt_client Install a pre-built client from npm. Turn this off you need access to visualizations. --skip_client_build Do not build Galaxy client when serving Galaxy. --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.

`workflow_edit` command

This section is auto-generated from the help text for the planemo commandworkflow_edit. This help message can be generated with planemo workflow_edit --help.

Usage:

planemo workflow_edit [OPTIONS] WORKFLOW_PATH_OR_ID

Help

Open a synchronized Galaxy workflow editor.Options:

--galaxy_root DIRECTORY Root of development galaxy directory to execute command with. --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --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 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). --docker_run_extra_arguments TEXT Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless any conda option has been set explicitly. --galaxy_startup_timeout INTEGER RANGE Wait for galaxy to start before assuming Galaxy did not start. [x>=1] --job_config_file FILE Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. --tool_data_path DIRECTORY Directory where data used by tools is located. Required if tests are run in docker and should make use of external reference data. --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 artifacts 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 or --biocontainers or --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 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_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_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 miniforge if not availabe on conda_prefix. --simultaneous_uploads / --no_simultaneous_uploads When uploading files to Galaxy for tool or workflow tests or runs, upload multiple files simultaneously without waiting for the previous file upload to complete. --check_uploads_ok / --no_check_uploads_ok When uploading files to Galaxy for tool or workflow tests or runs, check that the history is in an 'ok' state before beginning tool or workflow execution. --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|postgres_singularity|sqlite|auto] Type of database to use for profile - 'auto', 'sqlite', 'postgres', 'postgres_docker' , and postgres_singularity 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. . Use postgres_singularity to have Planemo run postgres using singularity/apptainer. 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. --postgres-storage-location TEXT storage path for postgres database, used for local singularity postgres. --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 FILE 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. --install_prebuilt_client / --no_install_prebuilt_client Install a pre-built client from npm. Turn this off you need access to visualizations. --skip_client_build Do not build Galaxy client when serving Galaxy. --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.

`workflow_job_init` command

This section is auto-generated from the help text for the planemo commandworkflow_job_init. This help message can be generated with planemo workflow_job_init --help.

Usage:

planemo workflow_job_init [OPTIONS] WORKFLOW_PATH_OR_ID

Help

Initialize a Galaxy workflow job description for supplied workflow.

Be sure to your lint your workflow with workflow_lint before calling this to ensure inputs and outputs comply with best practices that make workflow testing easier.

Jobs can be run with the planemo run command (planemo run workflow.ga job.yml). Planemo run works with Galaxy tools and CWL artifacts (both tools and workflows) as well so this command may be renamed to to job_init at something along those lines at some point.

Options:

-f, --force Overwrite existing files if present. -o, --output FILE --galaxy_url TEXT Remote Galaxy URL to use with external Galaxy engine. --galaxy_user_key TEXT User key to use with external Galaxy engine. --from_invocation / --from_uri Build a workflow test or job description from an invocation ID run on an external Galaxy.A Galaxy URL and API key must also be specified. This allows test data to be downloadedand inputs and parameters defined automatically. Alternatively, the default is to build thedescriptions from a provided workflow URI. --profile TEXT Name of profile (created with the profile_create command) to use with this command. --help Show this message and exit.

`workflow_lint` command

This section is auto-generated from the help text for the planemo commandworkflow_lint. This help message can be generated with planemo workflow_lint --help.

Usage:

planemo workflow_lint [OPTIONS] TARGET

Help

Check workflows for syntax errors and best practices.Options:

`workflow_test_init` command

This section is auto-generated from the help text for the planemo commandworkflow_test_init. This help message can be generated with planemo workflow_test_init --help.

Usage:

planemo workflow_test_init [OPTIONS] WORKFLOW_PATH_OR_ID

Help

Initialize a Galaxy workflow test description for supplied workflow.

Be sure to lint your workflow with workflow_lint before calling this to ensure inputs and outputs comply with best practices that make workflow testing easier.

Options:

-f, --force Overwrite existing files if present. -o, --output FILE --split_test / --no_split_test Write workflow job and test definitions to separate files. --galaxy_url TEXT Remote Galaxy URL to use with external Galaxy engine. --galaxy_user_key TEXT User key to use with external Galaxy engine. --from_invocation / --from_uri Build a workflow test or job description from an invocation ID run on an external Galaxy.A Galaxy URL and API key must also be specified. This allows test data to be downloadedand inputs and parameters defined automatically. Alternatively, the default is to build thedescriptions from a provided workflow URI. --profile TEXT Name of profile (created with the profile_create command) to use with this command. --help Show this message and exit.

`workflow_test_on_invocation` command

This section is auto-generated from the help text for the planemo commandworkflow_test_on_invocation. This help message can be generated with planemo workflow_test_on_invocation --help.

Usage:

planemo workflow_test_on_invocation [OPTIONS] TEST.YML INVOCATION_ID

Help

Run defined tests against existing workflow invocation.Options:

--galaxy_url TEXT Remote Galaxy URL to use with external Galaxy engine. [required] --galaxy_user_key TEXT User key to use with external Galaxy engine. [required] --test_index INTEGER Select which test to check. Counting starts at 1 --update_test_data Update test-data directory with job outputs (normally written to directory --job_output_files if specified.) --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_markdown_minimal PATH Output test report (Minimal markdown style - jost the table) --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_allure DIRECTORY Output test allure2 framework resutls --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. --test_timeout INTEGER Maximum runtime of a single test in seconds. --help Show this message and exit.

`workflow_upload` command

This section is auto-generated from the help text for the planemo commandworkflow_upload. This help message can be generated with planemo workflow_upload --help.

Usage:

planemo workflow_upload [OPTIONS] TARGET

Help

Upload workflows to github organization.Options:

--namespace TEXT Organization or username under which to create or update workflow repository. Must be a valid github username or organization --github_branch TEXT GitHub branch to use for the action. Default is main. --dry_run Don't execute action, show preview of action. --help Show this message and exit.

Commands — Planemo 0.75.31.dev0 documentation (original) (raw)

autoupdate command

ci_find_repos command

ci_find_tools command

ci_setup command

clone command

conda_build command

conda_env command

conda_init command

conda_install command

conda_search command

config_init command

container_register command

create_alias command

database_create command

database_delete command

database_list command

delete_alias command

docker_build command

docker_shell command

dockstore_init command

docs command

lint command

list_alias command

list_invocations command

list_repos command

merge_test_reports command

mull command

mulled_init command

normalize command

open command

profile_create command

profile_delete command

profile_list command

project_init command

pull_request command

rerun command

run command

serve command

share_test command

shed_build command

shed_create command

shed_diff command

shed_init command

shed_lint command

shed_serve command

shed_test command

shed_update command

shed_upload command

syntax command

test command

test_reports command

tool_init command

training_fill_data_library command

training_generate_from_wf command

training_init command

upload_data command

workflow_convert command

workflow_edit command

workflow_job_init command

workflow_lint command

workflow_test_init command

workflow_test_on_invocation command

workflow_upload command

`autoupdate` command

`ci_find_repos` command

`ci_find_tools` command

`ci_setup` command

`clone` command

`conda_build` command

`conda_env` command

`conda_init` command

`conda_install` command

`conda_search` command

`config_init` command

`container_register` command

`create_alias` command

`database_create` command

`database_delete` command

`database_list` command

`delete_alias` command

`docker_build` command

`docker_shell` command

`dockstore_init` command

`docs` command

`lint` command

`list_alias` command

`list_invocations` command

`list_repos` command

`merge_test_reports` command

`mull` command

`mulled_init` command

`normalize` command

`open` command

`profile_create` command

`profile_delete` command

`profile_list` command

`project_init` command

`pull_request` command

`rerun` command

`run` command

`serve` command

`share_test` command

`shed_build` command

`shed_create` command

`shed_diff` command

`shed_init` command

`shed_lint` command

`shed_serve` command

`shed_test` command

`shed_update` command

`shed_upload` command

`syntax` command

`test` command

`test_reports` command

`tool_init` command

`training_fill_data_library` command

`training_generate_from_wf` command

`training_init` command

`upload_data` command

`workflow_convert` command

`workflow_edit` command

`workflow_job_init` command

`workflow_lint` command

`workflow_test_init` command

`workflow_test_on_invocation` command

`workflow_upload` command