Provided by: cwltool_1.0.20180302231433-1_all 
NAME
cwltool - Refefence executor for Common Workflow Language
DESCRIPTION
usage: __main__.py [-h] [--basedir BASEDIR] [--outdir OUTDIR] [--parallel]
[--preserve-environment ENVVAR | --preserve-entire-environment] [--rm-container |
--leave-container] [--record-container-id] [--cidfile-dir CIDFILE_DIR]
[--cidfile-prefix CIDFILE_PREFIX] [--tmpdir-prefix TMPDIR_PREFIX]
[--tmp-outdir-prefix TMP_OUTDIR_PREFIX | --cachedir CACHEDIR] [--rm-tmpdir |
--leave-tmpdir] [--move-outputs | --leave-outputs | --copy-outputs] [--enable-pull
| --disable-pull] [--rdf-serializer RDF_SERIALIZER] [--eval-timeout EVAL_TIMEOUT]
[--print-rdf | --print-dot | --print-pre | --print-deps | --print-input-deps |
--pack | --version | --validate | --print-supported-versions] [--strict |
--non-strict] [--skip-schemas] [--verbose | --quiet | --debug] [--timestamps]
[--js-console] [--user-space-docker-cmd CMD | --singularity | --no-container]
[--tool-help] [--relative-deps {primary,cwd}] [--enable-dev] [--enable-ext]
[--default-container DEFAULT_CONTAINER] [--no-match-user] [--disable-net]
[--custom-net CUSTOM_NET] [--enable-ga4gh-tool-registry |
--disable-ga4gh-tool-registry] [--add-ga4gh-tool-registry GA4GH_TOOL_REGISTRIES]
[--on-error {stop,continue}] [--compute-checksum] [--no-compute-checksum]
[--relax-path-checks] [--make-template] [--force-docker-pull] [--no-read-only]
[--overrides OVERRIDES] [cwl_document] ...
Reference executor for Common Workflow Language standards.
positional arguments:
cwl_document
path or URL to a CWL Workflow, CommandLineTool, or ExpressionTool. If the
`inputs_object` has a `cwl:tool` field indicating the path or URL to the
cwl_document, then the `workflow` argument is optional.
inputs_object
path or URL to a YAML or JSON formatted description of the required input values
for the given `cwl_document`.
optional arguments:
-h, --help
show this help message and exit
--basedir BASEDIR
--outdir OUTDIR
Output directory, default current directory
--parallel
[experimental] Run jobs in parallel. Does not currently keep track of
ResourceRequirements like the number of coresor memory and can overload this system
--preserve-environment ENVVAR
Preserve specific environment variable when running CommandLineTools. May be
provided multiple times.
--preserve-entire-environment
Preserve all environment variable when running CommandLineTools.
--rm-container
Delete Docker container used by jobs after they exit (default)
--leave-container
Do not delete Docker container used by jobs after they exit
--tmpdir-prefix TMPDIR_PREFIX
Path prefix for temporary directories
--tmp-outdir-prefix TMP_OUTDIR_PREFIX
Path prefix for intermediate output directories
--cachedir CACHEDIR
Directory to cache intermediate workflow outputs to avoid recomputing steps.
--rm-tmpdir
Delete intermediate temporary directories (default)
--leave-tmpdir
Do not delete intermediate temporary directories
--move-outputs
Move output files to the workflow output directory and delete intermediate output
directories (default).
--leave-outputs
Leave output files in intermediate output directories.
--copy-outputs
Copy output files to the workflow output directory, don't delete intermediate
output directories.
--enable-pull
Try to pull Docker images
--disable-pull
Do not try to pull Docker images
--rdf-serializer RDF_SERIALIZER
Output RDF serialization format used by --print-rdf (one of turtle (default), n3,
nt, xml)
--eval-timeout EVAL_TIMEOUT
Time to wait for a Javascript expression to evaluate before giving an error,
default 20s.
--print-rdf
Print corresponding RDF graph for workflow and exit
--print-dot
Print workflow visualization in graphviz format and exit
--print-pre
Print CWL document after preprocessing.
--print-deps
Print CWL document dependencies.
--print-input-deps
Print input object document dependencies.
--pack Combine components into single document and print.
--version
Print version and exit
--validate
Validate CWL document only.
--print-supported-versions
Print supported CWL specs.
--strict
Strict validation (unrecognized or out of place fields are error)
--non-strict
Lenient validation (ignore unrecognized fields)
--skip-schemas
Skip loading of schemas
--verbose
Default logging
--quiet
Only print warnings and errors.
--debug
Print even more logging
--timestamps
Add timestamps to the errors, warnings, and notifications.
--js-console
Enable javascript console output
--user-space-docker-cmd CMD
(Linux/OS X only) Specify a user space docker command (like udocker or dx-docker)
that will be used to call 'pull' and 'run'
--singularity
[experimental] Use Singularity runtime for running containers. Requires Singularity
v2.3.2+ and Linux with kernel version v3.18+ or with overlayfs support backported.
--no-container
Do not execute jobs in a Docker container, even when `DockerRequirement` is
specified under `hints`.
--tool-help
Print command line help for tool
--relative-deps {primary,cwd}
When using --print-deps, print paths relative to primary file or current working
directory.
--enable-dev
Enable loading and running development versions of CWL spec.
--enable-ext
Enable loading and running cwltool extensions to CWL spec.
--default-container DEFAULT_CONTAINER
Specify a default docker container that will be used if the workflow fails to
specify one.
--no-match-user
Disable passing the current uid to `docker run --user`
--disable-net
Use docker's default networking for containers; the default is to enable
networking.
--custom-net CUSTOM_NET
Will be passed to `docker run` as the '--net' parameter. Implies '--enable-net'.
--enable-ga4gh-tool-registry
Enable resolution using GA4GH tool registry API
--disable-ga4gh-tool-registry
Disable resolution using GA4GH tool registry API
--add-ga4gh-tool-registry GA4GH_TOOL_REGISTRIES
Add a GA4GH tool registry endpoint to use for resolution, default
['https://dockstore.org:8443']
--on-error {stop,continue}
Desired workflow behavior when a step fails. One of 'stop' or 'continue'. Default
is 'stop'.
--compute-checksum
Compute checksum of contents while collecting outputs
--no-compute-checksum
Do not compute checksum of contents while collecting outputs
--relax-path-checks
Relax requirements on path names to permit spaces and hash characters.
--make-template
Generate a template input object
--force-docker-pull
Pull latest docker image even if it is locally present
--no-read-only
Do not set root directory in the container as readonly
--overrides OVERRIDES
Read process requirement overrides from file.
Options for recording the Docker container identifier into a file:
--record-container-id
If enabled, store the Docker container ID into a file. See --cidfile-dir to
specify the directory.
--cidfile-dir CIDFILE_DIR
Directory for storing the Docker container ID file. The default is the current
directory
--cidfile-prefix CIDFILE_PREFIX
Specify a prefix to the container ID filename. Final file name will be followed by
a timestamp. The default is no prefix.
SEE ALSO
http://commonwl.org
http://wiki.debian.org/CommonWorkflowLanguage