Commands

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.

bioc_conda_recipe_init command

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

Usage:

planemo bioc_conda_recipe_init [OPTIONS]

Help

Make a bioconda recipe, given a R or bioconductor package name.

package_name = motifbreakR

bioconda_dir = ‘/Users/nturaga/Documents/workspace’.

Options:

-u, --update / --no_update    Update an existing bioconda recipe
-b, --bioconda_dir_path TEXT  Give the path to folder containing bioconda
                              repository
-c, --clone / --no_clone      Clone bioconda repository from github or not?
-p, --package_name TEXT       Give the name of a Bioconductor package to
                              create a new bioconda recipe
--help                        Show this message and exit.

bioc_tool_init command

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

Usage:

planemo bioc_tool_init [OPTIONS]

Help

Generate a bioconductor tool outline from supplied arguments. Options:

-i, --id TEXT             Short identifier for new tool (no whitespace)
-f, --force               Overwrite existing tool if present.
-t, --tool PATH           Output path for new tool (default is <id>.xml)
-n, --name TEXT           Name for new R/Bioconductor tool (user facing).
-d, --description TEXT    Short description for new tool (user facing)
-c, --command TEXT        Command potentially including cheetah variables
                          ()(e.g. 'seqtk seq -a $input > $output')
--rscript PATH            Name of an R script from which to create a Tool
                          definition file. Requires use of --input and
                          --output arguments. (e.g. --rscript 'file.R')
--rversion TEXT           R version this tool requries, if not given, the tool
                          defaults to R 3.2.1, (eg: --rversion 'R 3.2.1').
                          This option adds the R dependency in the tool
                          requirements.
--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.
--requirement TEXT        Name of the R/Bioconductor package. Requirements
                          will be set using Bioconda. (e.g. --requirement
                          'affy')
--help_text TEXT          Help text (reStructuredText)
--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.
--version TEXT            Tool XML version.
--help_from_command TEXT  Auto populate help from supplied command.
--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.
--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.
--bioconda_path TEXT      Path to bioconda repository. If left empty, path
                          will be made in home directory.
--help                    Show this message and exit.

brew command

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

Usage:

planemo brew [OPTIONS] TOOL_PATH

Help

Install tool requirements using brew.

An experimental approach to versioning brew recipes will be used. See full discussion on the homebrew-science issues page here - https://github.com/Homebrew/homebrew-science/issues/1191. Information on the implementation can be found at https://github.com/jmchilton/platform-brew until a more permanent project home is setup.

Options:

--brew PATH  Homebrew 'brew' executable to use.
--help       Show this message and exit.

brew_env command

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

Usage:

planemo brew_env [OPTIONS] TOOL_PATH

Help

List commands to inject brew dependencies.

Display commands used to modify environment to inject tool’s brew dependencies.

% . <(planemo brew_env bowtie2.xml)
% which bowtie2
/home/john/.linuxbrew/Cellar/bowtie2/2.1.0/bin/bowtie2

By default this will attempt to attempt to install these recipes as needed. This automatic installation can be skipped with the --skip_install flag.

Intead of injecting the enviornment into your current shell using the above idiom, the --shell flag can be sent to launch a new subshell when sourced.

% . <(planemo brew_env --skip_install --shell bowtie2.xml)
(bowtie2) % which bowtie2
/home/john/.linuxbrew/Cellar/bowtie2/2.1.0/bin/bowtie2

Options:

--brew PATH     Homebrew 'brew' executable to use.
--skip_install  Skip installation - only source requirements already
                available.
--shell
--help          Show this message and exit.

brew_init command

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

Usage:

planemo brew_init [OPTIONS]

Help

Download linuxbrew install & run it in ruby.

Linuxbrew is a fork of Homebrew (http://brew.sh/linuxbrew/).

For more information on installing linuxbrew and pre-requisites see https://github.com/Homebrew/linuxbrew#installation.

Homebrew or linuxbrew are required in order to use the other commands brew and brew_shell.

Options:

--help  Show this message and exit.

ci_find_repos command

This section is auto-generated from the help text for the planemo command ci_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 shed repository is considered a directory with a .shed.yml file.

Options:

--exclude PATH                  Paths to exclude.
--exclude_from PATH             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 command ci_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:

--exclude PATH                  Paths to exclude.
--exclude_from PATH             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.

clone command

This section is auto-generated from the help text for the planemo command clone. 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 username and password are specified in ~/.planemo.yml.

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 command conda_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 PATH               Location of conda executable.
--conda_debug                   Enable more verbose conda logging.
--conda_channels, --conda_ensure_channels TEXT
                                Ensure conda is configured with specified
                                comma separated list of channels.
--conda_use_local               Use locally built packages while building
                                Conda environments.
--help                          Show this message and exit.

conda_env command

This section is auto-generated from the help text for the planemo command conda_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_prefix DIRECTORY        Conda prefix to use for conda dependency
                                commands.
--conda_exec PATH               Location of conda executable.
--conda_debug                   Enable more verbose conda logging.
--conda_channels, --conda_ensure_channels TEXT
                                Ensure conda is configured with specified
                                comma separated list of channels.
--conda_use_local               Use locally built packages while building
                                Conda environments.
--help                          Show this message and exit.

conda_init command

This section is auto-generated from the help text for the planemo command conda_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 at http://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_prefix DIRECTORY        Conda prefix to use for conda dependency
                                commands.
--conda_exec PATH               Location of conda executable.
--conda_debug                   Enable more verbose conda logging.
--conda_channels, --conda_ensure_channels TEXT
                                Ensure conda is configured with specified
                                comma separated list of channels.
--conda_use_local               Use locally built packages while building
                                Conda environments.
--help                          Show this message and exit.

conda_install command

This section is auto-generated from the help text for the planemo command conda_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 PATH               Location of conda executable.
--conda_debug                   Enable more verbose conda logging.
--conda_channels, --conda_ensure_channels TEXT
                                Ensure conda is configured with specified
                                comma separated list of channels.
--conda_use_local               Use locally built packages while building
                                Conda environments.
--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 miniconda if
                                not availabe on conda_prefix.
--help                          Show this message and exit.

conda_lint command

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

Usage:

planemo conda_lint [OPTIONS] RECIPE_DIR

Help

Check conda recipe for common issues.

Built in large part on the work from the BSD licensed anaconda-verify project. For more information on anacoda-verify see: https://github.com/ContinuumIO/anaconda-verify.

Options:

--report_level [all|warn|error]
--fail_level [warn|error]
-r, --recursive                 Recursively perform command for nested conda
                                directories.
--help                          Show this message and exit.

conda_search command

This section is auto-generated from the help text for the planemo command conda_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:

--conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                commands.
--conda_exec PATH               Location of conda executable.
--conda_debug                   Enable more verbose conda logging.
--conda_channels, --conda_ensure_channels TEXT
                                Ensure conda is configured with specified
                                comma separated list of channels.
--conda_use_local               Use locally built packages while building
                                Conda environments.
--help                          Show this message and exit.

config_init command

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

Usage:

planemo container_register [OPTIONS] TOOL_PATH

Help

Register multi-requirement containers as needed.

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 PATH               Location of conda executable.
--conda_debug                   Enable more verbose conda logging.
--conda_channels, --conda_ensure_channels TEXT
                                Ensure conda is configured with specified
                                comma separated list of channels.
--conda_use_local               Use locally built packages while building
                                Conda environments.
--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.

cwl_script command

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

Usage:

planemo cwl_script [OPTIONS] TOOL_PATH JOB_PATH

Help

Compile simple CWL workflows to shell script.

Compiles simple common workflow language (CWL) workflows to a shell script.

Options:

--no_container
--output_dir PATH
--base_dir PATH
--help             Show this message and exit.

database_create command

This section is auto-generated from the help text for the planemo command database_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 with psql.

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 at http://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_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.
--help                         Show this message and exit.

database_delete command

This section is auto-generated from the help text for the planemo command database_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 with psql.

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 at http://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_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.
--help                         Show this message and exit.

database_list command

This section is auto-generated from the help text for the planemo command database_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 with psql.

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 at http://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_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.
--help                         Show this message and exit.

dependency_script command

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

Usage:

planemo dependency_script [OPTIONS] PROJECT

Help

Compile tool_dependencies.xml to bash script.

An experimental approach parsing tool_dependencies.xml files into bash shell scripts, intended initially for use within Continuous Integration testing setups like TravisCI.

Parses the tool_dependencies.xml files from the specified projects, and converts them into an installation bash script (dep_install.sh), and a shell script (env.sh) defining any new/edited environment variables.

These are intended to be used via bash dep_install.sh (once), and as source env.sh prior to running any of the dependencies to set the environment variable within the current shell session.

Both dep_install.sh and env.sh require $INSTALL_DIR be defined before running them, set to an existing directory with write permissions. Beware than if run on multiple tools, they can over-write each other (for example if you have packages for different versions of the same tool). In this case make separate calls to planemo dependency_script and call the scripts with different installation directories.

This command will download (and cache) any URLs specified via Galaxy download actions. This is in order to decompress them and determine the relevant sub-folder to change into as per the Tool Shed install mechanism, so that this can be recorded as a cd comand in the bash script.

The download cache used by planemo dependency_script and the resulting output script dep_install.sh defaults to ./download_cache (under the current working directory), and can be set with $DOWNLOAD_CACHE.

If the tool_dependencies.xml file includes SHA256 checksums for downloads, these will be verified after downloading to the cache (by either planemo dependency_script or bash dep_install.sh).

This is experimental, and is initially intended for use within continuous integration testing setups like TravisCI to both verify the dependency installation receipe works, and to use this to run functional tests.

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.
--download_cache DIRECTORY  Directory to cache downloaded files, default is
                            $DOWNLOAD_CACHE
--help                      Show this message and exit.

docker_build command

This section is auto-generated from the help text for the planemo command docker_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 command docker_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.

docs command

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

Usage:

planemo docs [OPTIONS]

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 command lint. 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.
--xsd / --no_xsd                Include tool XSD validation in linting
                                process.
-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.

mull command

This section is auto-generated from the help text for the planemo command mull. 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 miniconda3
                                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 command mulled_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 miniconda3 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 command normalize. 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 (see https://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
<tool>
...
% # Print a variant of tool with all macros expanded out, useful for
% # debugging complex macros.
% planemo normalize --expand_macros tool.xml
<tool>
...

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 command open. 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 command profile_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|sqlite]
                                Type of database to use for profile -
                                currently only 'postgres' is available.
--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]
                                Select an engine to serve aritfacts such as
                                tools and workflows. Defaults to a local
                                Galaxy, but running Galaxy within a Docker
                                container.
--help                          Show this message and exit.

profile_delete command

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

Usage:

planemo profile_delete [OPTIONS] PROFILE_NAME

Help

Delete a profile. Options:

--postgres                      Use postgres database type.
--database_type [postgres|sqlite]
                                Type of database to use for profile -
                                currently only 'postgres' is available.
--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.
--help                          Show this message and exit.

profile_list command

This section is auto-generated from the help text for the planemo command profile_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 command project_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 command pull_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 username and password are specified in ~/.planemo.yml.

Options:

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

run command

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

Usage:

planemo run [OPTIONS] TOOL_URI 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_database_seed PATH     Preseeded Galaxy sqlite database to target.
--extra_tools PATH              Extra tool sources to include in Galaxy's tool
                                panel (file or directory). These will not be
                                linted/tested/etc... but they will be
                                available to workflows and for interactive
                                use.
--install_galaxy                Download and configure a disposable copy of
                                Galaxy from github.
--galaxy_branch TEXT            Branch of Galaxy to target (defaults to
                                master) if a Galaxy root isn't specified.
--galaxy_source TEXT            Git source of Galaxy to target (defaults to
                                the official galaxyproject github source if a
                                Galaxy root isn't specified.
--skip_venv                     Do not create or source a virtualenv
                                environment for Galaxy, this should be used or
                                instance to preserve an externally configured
                                virtual environment or conda environment.
--no_cache_galaxy               Skip caching of Galaxy source and dependencies
                                obtained with --install_galaxy. Not caching
                                this results in faster downloads (no git) - so
                                is better on throw away instances such with
                                TravisCI.
--no_cleanup                    Do not cleanup temp files created for and by
                                Galaxy.
--galaxy_email TEXT             E-mail address to use when launching single-
                                user Galaxy server.
--docker / --no_docker          Run Galaxy tools in Docker if enabled.
--docker_cmd TEXT               Command used to launch docker (defaults to
                                docker).
--docker_sudo / --no_docker_sudo
                                Flag to use sudo when running docker.
--docker_host TEXT              Docker host to target when executing docker
                                commands (defaults to localhost).
--docker_sudo_cmd TEXT          sudo command to use when --docker_sudo is
                                enabled (defaults to sudo).
--mulled_containers, --biocontainers
                                Test tools against mulled containers (forces
                                --docker).
--job_config_file PATH          Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
                                Tool dependency dir for Galaxy to target.
--port INTEGER                  Port to serve Galaxy on (default is 9090).
--host TEXT                     Host to bind Galaxy to. Default is 127.0.0.1
                                that is restricted to localhost connections
                                for security reasons set to 0.0.0.0 to bind
                                Galaxy to all ports including potentially
                                publicly accessible ones.
--test_data DIRECTORY           test-data directory to for specified tool(s).
--tool_data_table PATH          tool_data_table_conf.xml file to for specified
                                tool(s).
--dependency_resolvers_config_file PATH
                                Dependency resolver configuration for Galaxy
                                to target.
--brew_dependency_resolution    Configure Galaxy to use plain brew dependency
                                resolution.
--shed_dependency_resolution    Configure Galaxy to use brewed Tool Shed
                                dependency resolution.
--no_dependency_resolution      Configure Galaxy with no dependency resolvers.
--conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                commands.
--conda_exec PATH               Location of conda executable.
--conda_debug                   Enable more verbose conda logging.
--conda_channels, --conda_ensure_channels TEXT
                                Ensure conda is configured with specified
                                comma separated list of channels.
--conda_use_local               Use locally built packages while building
                                Conda environments.
--conda_dependency_resolution   Configure Galaxy to use only conda for
                                dependency resolution.
--conda_copy_dependencies       Conda dependency resolution for Galaxy will
                                copy dependencies instead of attempting to
                                link them.
--conda_auto_install / --no_conda_auto_install
                                Conda dependency resolution for Galaxy will
                                attempt to install requested but missing
                                packages.
--conda_auto_init / --no_conda_auto_init
                                Conda dependency resolution for Galaxy will
                                auto install conda itself using miniconda if
                                not availabe on conda_prefix.
--profile TEXT                  Location of pid file is executed with
                                --daemon.
--postgres                      Use postgres database type.
--database_type [postgres|sqlite]
                                Type of database to use for profile -
                                currently only 'postgres' is available.
--postgres_psql_path TEXT       Name or or path to postgres client binary
                                (psql).
--postgres_database_user TEXT   Postgres username for managed development
                                databases.
--postgres_database_host TEXT   Postgres host name for managed development
                                databases.
--postgres_database_port TEXT   Postgres port for managed development
                                databases.
--file_path DIRECTORY           Location for files created by Galaxy (e.g.
                                database/files).
--database_connection TEXT      Database connection string to use for Galaxy.
--shed_tool_conf TEXT           Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT           Location of shed tools directory for Galaxy.
--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.
--output_directory, --outdir DIRECTORY
                                Where to store outputs of a 'run' task.
--output_json PATH              Where to store JSON dictionary describing
                                outputs of a 'run' task.
--engine [galaxy|docker_galaxy|cwltool]
                                Select an engine to run or test aritfacts such
                                as tools and workflows. Defaults to a local
                                Galaxy, but running Galaxy within a Docker
                                container or the CWL reference implementation
                                'cwltool' and 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 to bgruening
                                /galaxy-stable.
--help                          Show this message and exit.

serve command

This section is auto-generated from the help text for the planemo command serve. 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_root option 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_database_seed PATH     Preseeded Galaxy sqlite database to target.
--extra_tools PATH              Extra tool sources to include in Galaxy's tool
                                panel (file or directory). These will not be
                                linted/tested/etc... but they will be
                                available to workflows and for interactive
                                use.
--install_galaxy                Download and configure a disposable copy of
                                Galaxy from github.
--galaxy_branch TEXT            Branch of Galaxy to target (defaults to
                                master) if a Galaxy root isn't specified.
--galaxy_source TEXT            Git source of Galaxy to target (defaults to
                                the official galaxyproject github source if a
                                Galaxy root isn't specified.
--skip_venv                     Do not create or source a virtualenv
                                environment for Galaxy, this should be used or
                                instance to preserve an externally configured
                                virtual environment or conda environment.
--no_cache_galaxy               Skip caching of Galaxy source and dependencies
                                obtained with --install_galaxy. Not caching
                                this results in faster downloads (no git) - so
                                is better on throw away instances such with
                                TravisCI.
--no_cleanup                    Do not cleanup temp files created for and by
                                Galaxy.
--galaxy_email TEXT             E-mail address to use when launching single-
                                user Galaxy server.
--docker / --no_docker          Run Galaxy tools in Docker if enabled.
--docker_cmd TEXT               Command used to launch docker (defaults to
                                docker).
--docker_sudo / --no_docker_sudo
                                Flag to use sudo when running docker.
--docker_host TEXT              Docker host to target when executing docker
                                commands (defaults to localhost).
--docker_sudo_cmd TEXT          sudo command to use when --docker_sudo is
                                enabled (defaults to sudo).
--mulled_containers, --biocontainers
                                Test tools against mulled containers (forces
                                --docker).
--job_config_file PATH          Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
                                Tool dependency dir for Galaxy to target.
--port INTEGER                  Port to serve Galaxy on (default is 9090).
--host TEXT                     Host to bind Galaxy to. Default is 127.0.0.1
                                that is restricted to localhost connections
                                for security reasons set to 0.0.0.0 to bind
                                Galaxy to all ports including potentially
                                publicly accessible ones.
--engine [galaxy|docker_galaxy]
                                Select an engine to serve aritfacts such as
                                tools and workflows. Defaults to a local
                                Galaxy, but running Galaxy within a Docker
                                container.
--non_strict_cwl                Disable strict validation of CWL.
--docker_galaxy_image TEXT      Docker image identifier for docker-galaxy-
                                flavor used if engine type is specified as
                                ``docker-galaxy``. Defaults to to bgruening
                                /galaxy-stable.
--test_data DIRECTORY           test-data directory to for specified tool(s).
--tool_data_table PATH          tool_data_table_conf.xml file to for specified
                                tool(s).
--dependency_resolvers_config_file PATH
                                Dependency resolver configuration for Galaxy
                                to target.
--brew_dependency_resolution    Configure Galaxy to use plain brew dependency
                                resolution.
--shed_dependency_resolution    Configure Galaxy to use brewed Tool Shed
                                dependency resolution.
--no_dependency_resolution      Configure Galaxy with no dependency resolvers.
--conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                commands.
--conda_exec PATH               Location of conda executable.
--conda_debug                   Enable more verbose conda logging.
--conda_channels, --conda_ensure_channels TEXT
                                Ensure conda is configured with specified
                                comma separated list of channels.
--conda_use_local               Use locally built packages while building
                                Conda environments.
--conda_dependency_resolution   Configure Galaxy to use only conda for
                                dependency resolution.
--conda_copy_dependencies       Conda dependency resolution for Galaxy will
                                copy dependencies instead of attempting to
                                link them.
--conda_auto_install / --no_conda_auto_install
                                Conda dependency resolution for Galaxy will
                                attempt to install requested but missing
                                packages.
--conda_auto_init / --no_conda_auto_init
                                Conda dependency resolution for Galaxy will
                                auto install conda itself using miniconda if
                                not availabe on conda_prefix.
--profile TEXT                  Location of pid file is executed with
                                --daemon.
--postgres                      Use postgres database type.
--database_type [postgres|sqlite]
                                Type of database to use for profile -
                                currently only 'postgres' is available.
--postgres_psql_path TEXT       Name or or path to postgres client binary
                                (psql).
--postgres_database_user TEXT   Postgres username for managed development
                                databases.
--postgres_database_host TEXT   Postgres host name for managed development
                                databases.
--postgres_database_port TEXT   Postgres port for managed development
                                databases.
--file_path DIRECTORY           Location for files created by Galaxy (e.g.
                                database/files).
--database_connection TEXT      Database connection string to use for Galaxy.
--shed_tool_conf TEXT           Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT           Location of shed tools directory for Galaxy.
--daemon                        Serve Galaxy process as a daemon.
--pid_file TEXT                 Location of pid file is executed with
                                --daemon.
--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 command share_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 Github ‘username’ and ‘password’ defined in a ‘github’ section of that configuration file.

Options:

--help  Show this message and exit.

shed_build command

This section is auto-generated from the help text for the planemo command shed_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 command shed_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:

-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.
--skip_upload             Skip upload contents as part of operation, only
                          update metadata.
--help                    Show this message and exit.

shed_diff command

This section is auto-generated from the help text for the planemo command shed_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:

-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.
-o, --output PATH          Send diff output to specified file.
--shed_target_source TEXT  Source Tool Shed to diff against (will ignore local
                           project info specified). To compare the main Tool
                           Shed against the test, set this to testtoolshed.
--raw                      Do not attempt smart diff of XML to filter out
                           attributes populated by the Tool Shed.
--report_xunit PATH        Output an XUnit report, useful for CI testing
--help                     Show this message and exit.

shed_init command

This section is auto-generated from the help text for the planemo command shed_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_diff to manage repositories in a Galaxy Tool Shed.

Options:

--from_workflow PATH            Attempt to generate repository dependencies
                                from specified workflow.
--description TEXT              Specify repository description for .shed.yml.
--long_description TEXT         Specify repository long_description for
                                .shed.yml.
--remote_repository_url TEXT    Specify repository remote_repository_url for
                                .shed.yml.
--homepage_url TEXT             Specify repository homepage_url for .shed.yml.
--category [Assembly|ChIP-seq|Combinatorial Selections|Computational chemistry|Constructive Solid Geometry|Convert Formats|Epigenetics|Data Export|Data Managers|Data Source|Fasta Manipulation|Fastq Manipulation|Flow Cytometry Analysis|Genome-Wide Association Study|Genomic Interval Operations|Graphics|Imaging|Metabolomics|Metagenomics|Micro-array Analysis|Next Gen Mappers|NLP|Ontology Manipulation|Phylogenetics|Proteomics|RNA|SAM|Sequence Analysis|Statistics|Systems Biology|Text Manipulation|Tool Dependency Packages|Tool Generators|Transcriptomics|Variant Analysis|Visualization|Web Services]
                                Specify repository category for .shed.yml (may
                                specify multiple).
--owner TEXT                    Tool Shed repository owner (username).
--name TEXT                     Tool Shed repository name (defaults to the
                                inferred tool directory name).
-f, --force                     Overwrite existing files if present.
--help                          Show this message and exit.

shed_lint command

This section is auto-generated from the help text for the planemo command shed_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]
--tools                         Lint tools discovered in the process of
                                linting repositories.
--xsd / --no_xsd                Include tool XSD validation in linting
                                process.
--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
--help                          Show this message and exit.

shed_serve command

This section is auto-generated from the help text for the planemo command shed_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_database_seed PATH     Preseeded Galaxy sqlite database to target.
--extra_tools PATH              Extra tool sources to include in Galaxy's tool
                                panel (file or directory). These will not be
                                linted/tested/etc... but they will be
                                available to workflows and for interactive
                                use.
--install_galaxy                Download and configure a disposable copy of
                                Galaxy from github.
--galaxy_branch TEXT            Branch of Galaxy to target (defaults to
                                master) if a Galaxy root isn't specified.
--galaxy_source TEXT            Git source of Galaxy to target (defaults to
                                the official galaxyproject github source if a
                                Galaxy root isn't specified.
--skip_venv                     Do not create or source a virtualenv
                                environment for Galaxy, this should be used or
                                instance to preserve an externally configured
                                virtual environment or conda environment.
--no_cache_galaxy               Skip caching of Galaxy source and dependencies
                                obtained with --install_galaxy. Not caching
                                this results in faster downloads (no git) - so
                                is better on throw away instances such with
                                TravisCI.
--no_cleanup                    Do not cleanup temp files created for and by
                                Galaxy.
--galaxy_email TEXT             E-mail address to use when launching single-
                                user Galaxy server.
--docker / --no_docker          Run Galaxy tools in Docker if enabled.
--docker_cmd TEXT               Command used to launch docker (defaults to
                                docker).
--docker_sudo / --no_docker_sudo
                                Flag to use sudo when running docker.
--docker_host TEXT              Docker host to target when executing docker
                                commands (defaults to localhost).
--docker_sudo_cmd TEXT          sudo command to use when --docker_sudo is
                                enabled (defaults to sudo).
--mulled_containers, --biocontainers
                                Test tools against mulled containers (forces
                                --docker).
--job_config_file PATH          Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
                                Tool dependency dir for Galaxy to target.
--port INTEGER                  Port to serve Galaxy on (default is 9090).
--host TEXT                     Host to bind Galaxy to. Default is 127.0.0.1
                                that is restricted to localhost connections
                                for security reasons set to 0.0.0.0 to bind
                                Galaxy to all ports including potentially
                                publicly accessible ones.
--test_data DIRECTORY           test-data directory to for specified tool(s).
--tool_data_table PATH          tool_data_table_conf.xml file to for specified
                                tool(s).
--dependency_resolvers_config_file PATH
                                Dependency resolver configuration for Galaxy
                                to target.
--brew_dependency_resolution    Configure Galaxy to use plain brew dependency
                                resolution.
--shed_dependency_resolution    Configure Galaxy to use brewed Tool Shed
                                dependency resolution.
--no_dependency_resolution      Configure Galaxy with no dependency resolvers.
--conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                commands.
--conda_exec PATH               Location of conda executable.
--conda_debug                   Enable more verbose conda logging.
--conda_channels, --conda_ensure_channels TEXT
                                Ensure conda is configured with specified
                                comma separated list of channels.
--conda_use_local               Use locally built packages while building
                                Conda environments.
--conda_dependency_resolution   Configure Galaxy to use only conda for
                                dependency resolution.
--conda_copy_dependencies       Conda dependency resolution for Galaxy will
                                copy dependencies instead of attempting to
                                link them.
--conda_auto_install / --no_conda_auto_install
                                Conda dependency resolution for Galaxy will
                                attempt to install requested but missing
                                packages.
--conda_auto_init / --no_conda_auto_init
                                Conda dependency resolution for Galaxy will
                                auto install conda itself using miniconda if
                                not availabe on conda_prefix.
--profile TEXT                  Location of pid file is executed with
                                --daemon.
--postgres                      Use postgres database type.
--database_type [postgres|sqlite]
                                Type of database to use for profile -
                                currently only 'postgres' is available.
--postgres_psql_path TEXT       Name or or path to postgres client binary
                                (psql).
--postgres_database_user TEXT   Postgres username for managed development
                                databases.
--postgres_database_host TEXT   Postgres host name for managed development
                                databases.
--postgres_database_port TEXT   Postgres port for managed development
                                databases.
--file_path DIRECTORY           Location for files created by Galaxy (e.g.
                                database/files).
--database_connection TEXT      Database connection string to use for Galaxy.
--shed_tool_conf TEXT           Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT           Location of shed tools directory for Galaxy.
--pid_file TEXT                 Location of pid file is executed with
                                --daemon.
--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 command shed_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.

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 run the tool tests for these commands.

This command requires the target to be version 15.07 or newer.

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_database_seed PATH     Preseeded Galaxy sqlite database to target.
--extra_tools PATH              Extra tool sources to include in Galaxy's tool
                                panel (file or directory). These will not be
                                linted/tested/etc... but they will be
                                available to workflows and for interactive
                                use.
--install_galaxy                Download and configure a disposable copy of
                                Galaxy from github.
--galaxy_branch TEXT            Branch of Galaxy to target (defaults to
                                master) if a Galaxy root isn't specified.
--galaxy_source TEXT            Git source of Galaxy to target (defaults to
                                the official galaxyproject github source if a
                                Galaxy root isn't specified.
--skip_venv                     Do not create or source a virtualenv
                                environment for Galaxy, this should be used or
                                instance to preserve an externally configured
                                virtual environment or conda environment.
--no_cache_galaxy               Skip caching of Galaxy source and dependencies
                                obtained with --install_galaxy. Not caching
                                this results in faster downloads (no git) - so
                                is better on throw away instances such with
                                TravisCI.
--no_cleanup                    Do not cleanup temp files created for and by
                                Galaxy.
--galaxy_email TEXT             E-mail address to use when launching single-
                                user Galaxy server.
--docker / --no_docker          Run Galaxy tools in Docker if enabled.
--docker_cmd TEXT               Command used to launch docker (defaults to
                                docker).
--docker_sudo / --no_docker_sudo
                                Flag to use sudo when running docker.
--docker_host TEXT              Docker host to target when executing docker
                                commands (defaults to localhost).
--docker_sudo_cmd TEXT          sudo command to use when --docker_sudo is
                                enabled (defaults to sudo).
--mulled_containers, --biocontainers
                                Test tools against mulled containers (forces
                                --docker).
--job_config_file PATH          Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
                                Tool dependency dir for Galaxy to target.
--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_xunit PATH        Output test report (xUnit style - for
                                computers).
--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.
--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 command shed_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 command shed_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:

-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.)
--tar_only                   Produce tar file for upload but do not publish to
                             a tool shed.
--tar PATH                   Specify a pre-existing tar file instead of
                             automatically building one as part of this
                             command.
--help                       Show this message and exit.

syntax command

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

Usage:

planemo syntax [OPTIONS]

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 command test. This help message can be generated with planemo test --help.

Usage:

planemo test [OPTIONS] TOOL_PATH

Help

Run specified tool’s tests within Galaxy.

All referenced tools (by default all the tools in the current working directory) will be tested and the results quickly summarized.

To run these tests planemo needs a Galaxy instance to utilize, planemo will search parent directories to see if any is a Galaxy instance - but one can pick the Galaxy instance to use with the –galaxy_root option or force planemo to download a disposable instance with the --install_galaxy flag.

In additon to to quick summary printed to the console - various detailed output summaries can be configured. tool_test_output.html (settable via --test_output) will contain a human consumable HTML report describing the test run. A JSON file (settable via --test_output_json and defaulting to tool_test_output.json) will also be created. These files can can be disabled by passing in empty arguments or globally by setting the values default_test_output and/or default_test_output_json in ~/.planemo.yml to null. For continuous integration testing a xUnit-style report can be confiured using the --test_output_xunit.

planemo uses temporarily generated config files and environment variables to attempt to shield this execution of Galaxy from manually launched runs against that same Galaxy root - but this may not be bullet proof yet so please careful and do not try this against production Galaxy instances.

Options:

--failed                        Re-run only failed tests. This command will
                                read tool_test_output.json to determine which
                                tests failed so this file must have been
                                produced with the same set of tool ids
                                previously.
--galaxy_root DIRECTORY         Root of development galaxy directory to
                                execute command with.
--galaxy_database_seed PATH     Preseeded Galaxy sqlite database to target.
--extra_tools PATH              Extra tool sources to include in Galaxy's tool
                                panel (file or directory). These will not be
                                linted/tested/etc... but they will be
                                available to workflows and for interactive
                                use.
--install_galaxy                Download and configure a disposable copy of
                                Galaxy from github.
--galaxy_branch TEXT            Branch of Galaxy to target (defaults to
                                master) if a Galaxy root isn't specified.
--galaxy_source TEXT            Git source of Galaxy to target (defaults to
                                the official galaxyproject github source if a
                                Galaxy root isn't specified.
--skip_venv                     Do not create or source a virtualenv
                                environment for Galaxy, this should be used or
                                instance to preserve an externally configured
                                virtual environment or conda environment.
--no_cache_galaxy               Skip caching of Galaxy source and dependencies
                                obtained with --install_galaxy. Not caching
                                this results in faster downloads (no git) - so
                                is better on throw away instances such with
                                TravisCI.
--no_cleanup                    Do not cleanup temp files created for and by
                                Galaxy.
--galaxy_email TEXT             E-mail address to use when launching single-
                                user Galaxy server.
--docker / --no_docker          Run Galaxy tools in Docker if enabled.
--docker_cmd TEXT               Command used to launch docker (defaults to
                                docker).
--docker_sudo / --no_docker_sudo
                                Flag to use sudo when running docker.
--docker_host TEXT              Docker host to target when executing docker
                                commands (defaults to localhost).
--docker_sudo_cmd TEXT          sudo command to use when --docker_sudo is
                                enabled (defaults to sudo).
--mulled_containers, --biocontainers
                                Test tools against mulled containers (forces
                                --docker).
--job_config_file PATH          Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
                                Tool dependency dir for Galaxy to target.
--test_data DIRECTORY           test-data directory to for specified tool(s).
--tool_data_table PATH          tool_data_table_conf.xml file to for specified
                                tool(s).
--dependency_resolvers_config_file PATH
                                Dependency resolver configuration for Galaxy
                                to target.
--brew_dependency_resolution    Configure Galaxy to use plain brew dependency
                                resolution.
--shed_dependency_resolution    Configure Galaxy to use brewed Tool Shed
                                dependency resolution.
--no_dependency_resolution      Configure Galaxy with no dependency resolvers.
--conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                commands.
--conda_exec PATH               Location of conda executable.
--conda_debug                   Enable more verbose conda logging.
--conda_channels, --conda_ensure_channels TEXT
                                Ensure conda is configured with specified
                                comma separated list of channels.
--conda_use_local               Use locally built packages while building
                                Conda environments.
--conda_dependency_resolution   Configure Galaxy to use only conda for
                                dependency resolution.
--conda_copy_dependencies       Conda dependency resolution for Galaxy will
                                copy dependencies instead of attempting to
                                link them.
--conda_auto_install / --no_conda_auto_install
                                Conda dependency resolution for Galaxy will
                                attempt to install requested but missing
                                packages.
--conda_auto_init / --no_conda_auto_init
                                Conda dependency resolution for Galaxy will
                                auto install conda itself using miniconda if
                                not availabe on conda_prefix.
--profile TEXT                  Location of pid file is executed with
                                --daemon.
--postgres                      Use postgres database type.
--database_type [postgres|sqlite]
                                Type of database to use for profile -
                                currently only 'postgres' is available.
--postgres_psql_path TEXT       Name or or path to postgres client binary
                                (psql).
--postgres_database_user TEXT   Postgres username for managed development
                                databases.
--postgres_database_host TEXT   Postgres host name for managed development
                                databases.
--postgres_database_port TEXT   Postgres port for managed development
                                databases.
--file_path DIRECTORY           Location for files created by Galaxy (e.g.
                                database/files).
--database_connection TEXT      Database connection string to use for Galaxy.
--shed_tool_conf TEXT           Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT           Location of shed tools directory for Galaxy.
--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_xunit PATH        Output test report (xUnit style - for
                                computers).
--test_output_json PATH         Output test report (planemo json) defaults to
                                tool_test_output.json.
--job_output_files DIRECTORY    Write job outputs to specified directory.
--summary [none|minimal|compact]
                                Summary style printed to planemo's standard
                                output (see output reports for more complete
                                summary). Set to 'none' to disable completely.
--engine [galaxy|docker_galaxy|cwltool]
                                Select an engine to run or test aritfacts such
                                as tools and workflows. Defaults to a local
                                Galaxy, but running Galaxy within a Docker
                                container or the CWL reference implementation
                                'cwltool' and 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 to bgruening
                                /galaxy-stable.
--help                          Show this message and exit.

test_reports command

This section is auto-generated from the help text for the planemo command test_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)
--help                       Show this message and exit.

tool_factory command

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

Usage:

planemo tool_factory [OPTIONS]

Help

(Experimental) Launch Galaxy with Tool Factory 2.

For more information about the Galaxy Tool Factory see the publication Creating reusable tools from scripts: the Galaxy Tool Factory by Lazarus et. al. (10.1093/bioinformatics/bts573). Available at http://www.ncbi.nlm.nih.gov/pubmed/23024011.

Options:

--galaxy_root DIRECTORY         Root of development galaxy directory to
                                execute command with.
--galaxy_database_seed PATH     Preseeded Galaxy sqlite database to target.
--extra_tools PATH              Extra tool sources to include in Galaxy's tool
                                panel (file or directory). These will not be
                                linted/tested/etc... but they will be
                                available to workflows and for interactive
                                use.
--install_galaxy                Download and configure a disposable copy of
                                Galaxy from github.
--galaxy_branch TEXT            Branch of Galaxy to target (defaults to
                                master) if a Galaxy root isn't specified.
--galaxy_source TEXT            Git source of Galaxy to target (defaults to
                                the official galaxyproject github source if a
                                Galaxy root isn't specified.
--skip_venv                     Do not create or source a virtualenv
                                environment for Galaxy, this should be used or
                                instance to preserve an externally configured
                                virtual environment or conda environment.
--no_cache_galaxy               Skip caching of Galaxy source and dependencies
                                obtained with --install_galaxy. Not caching
                                this results in faster downloads (no git) - so
                                is better on throw away instances such with
                                TravisCI.
--no_cleanup                    Do not cleanup temp files created for and by
                                Galaxy.
--galaxy_email TEXT             E-mail address to use when launching single-
                                user Galaxy server.
--docker / --no_docker          Run Galaxy tools in Docker if enabled.
--docker_cmd TEXT               Command used to launch docker (defaults to
                                docker).
--docker_sudo / --no_docker_sudo
                                Flag to use sudo when running docker.
--docker_host TEXT              Docker host to target when executing docker
                                commands (defaults to localhost).
--docker_sudo_cmd TEXT          sudo command to use when --docker_sudo is
                                enabled (defaults to sudo).
--mulled_containers, --biocontainers
                                Test tools against mulled containers (forces
                                --docker).
--job_config_file PATH          Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
                                Tool dependency dir for Galaxy to target.
--port INTEGER                  Port to serve Galaxy on (default is 9090).
--host TEXT                     Host to bind Galaxy to. Default is 127.0.0.1
                                that is restricted to localhost connections
                                for security reasons set to 0.0.0.0 to bind
                                Galaxy to all ports including potentially
                                publicly accessible ones.
--engine [galaxy|docker_galaxy]
                                Select an engine to serve aritfacts such as
                                tools and workflows. Defaults to a local
                                Galaxy, but running Galaxy within a Docker
                                container.
--non_strict_cwl                Disable strict validation of CWL.
--docker_galaxy_image TEXT      Docker image identifier for docker-galaxy-
                                flavor used if engine type is specified as
                                ``docker-galaxy``. Defaults to to bgruening
                                /galaxy-stable.
--test_data DIRECTORY           test-data directory to for specified tool(s).
--tool_data_table PATH          tool_data_table_conf.xml file to for specified
                                tool(s).
--dependency_resolvers_config_file PATH
                                Dependency resolver configuration for Galaxy
                                to target.
--brew_dependency_resolution    Configure Galaxy to use plain brew dependency
                                resolution.
--shed_dependency_resolution    Configure Galaxy to use brewed Tool Shed
                                dependency resolution.
--no_dependency_resolution      Configure Galaxy with no dependency resolvers.
--conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                commands.
--conda_exec PATH               Location of conda executable.
--conda_debug                   Enable more verbose conda logging.
--conda_channels, --conda_ensure_channels TEXT
                                Ensure conda is configured with specified
                                comma separated list of channels.
--conda_use_local               Use locally built packages while building
                                Conda environments.
--conda_dependency_resolution   Configure Galaxy to use only conda for
                                dependency resolution.
--conda_copy_dependencies       Conda dependency resolution for Galaxy will
                                copy dependencies instead of attempting to
                                link them.
--conda_auto_install / --no_conda_auto_install
                                Conda dependency resolution for Galaxy will
                                attempt to install requested but missing
                                packages.
--conda_auto_init / --no_conda_auto_init
                                Conda dependency resolution for Galaxy will
                                auto install conda itself using miniconda if
                                not availabe on conda_prefix.
--profile TEXT                  Location of pid file is executed with
                                --daemon.
--postgres                      Use postgres database type.
--database_type [postgres|sqlite]
                                Type of database to use for profile -
                                currently only 'postgres' is available.
--postgres_psql_path TEXT       Name or or path to postgres client binary
                                (psql).
--postgres_database_user TEXT   Postgres username for managed development
                                databases.
--postgres_database_host TEXT   Postgres host name for managed development
                                databases.
--postgres_database_port TEXT   Postgres port for managed development
                                databases.
--file_path DIRECTORY           Location for files created by Galaxy (e.g.
                                database/files).
--database_connection TEXT      Database connection string to use for Galaxy.
--shed_tool_conf TEXT           Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT           Location of shed tools directory for Galaxy.
--daemon                        Serve Galaxy process as a daemon.
--pid_file TEXT                 Location of pid file is executed with
                                --daemon.
--help                          Show this message and exit.

tool_init command

This section is auto-generated from the help text for the planemo command tool_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 PATH           Output path for new tool (default is <id>.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 > $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.
--help                    Show this message and exit.

travis_init command

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

Usage:

planemo travis_init [OPTIONS] PROJECT

Help

Create files to use GitHub/TravisCI testing.

Setup files in a github tool repository to enable continuous integration testing.

% planemo travis_init .
% # setup Ubuntu 12.04 w/ dependencies in
% vim .travis/setup_custom_dependencies.bash
% git add .travis.yml .travis
% git commit -m "Add Travis CI testing infrastructure for tools."
% git push # and register repository @ http://travis-ci.org/

These tests were inspired by work original done and documented by Peter Cock here http://bit.ly/gxtravisci.

Options:

--help  Show this message and exit.

virtualenv command

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

Usage:

planemo virtualenv [OPTIONS] VIRTUALENV_PATH

Help

Create a virtualenv.

Use virtualenv as library to create a virtualenv for Galaxy if virtualenv is not available on the PATH.

Options:

-p, --python PYTHON_EXE
--help                   Show this message and exit.