cwltest

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########################################## Common Workflow Language testing framework ##########################################

|Linux Build Status| |Code coverage|

PyPI: |PyPI Version| |PyPI Downloads Month| |Total PyPI Downloads|

Conda: |Conda Version| |Conda Installs|

.. |Linux Build Status| image:: https://github.com/common-workflow-language/cwltest/actions/workflows/ci-tests.yml/badge.svg?branch=main :target: https://github.com/common-workflow-language/cwltest/actions/workflows/ci-tests.yml .. |Code coverage| image:: https://codecov.io/gh/common-workflow-language/cwltest/branch/master/graph/badge.svg :target: https://codecov.io/gh/common-workflow-language/cwltest

.. |PyPI Version| image:: https://badge.fury.io/py/cwltest.svg :target: https://badge.fury.io/py/cwltest

.. |PyPI Downloads Month| image:: https://pepy.tech/badge/cwltest/month :target: https://pepy.tech/project/cwltest

.. |Total PyPI Downloads| image:: https://static.pepy.tech/personalized-badge/cwltest?period=total&units=international_system&left_color=black&right_color=orange&left_text=Total%20PyPI%20Downloads :target: https://pepy.tech/project/cwltest

.. |Conda Version| image:: https://anaconda.org/bioconda/cwltest/badges/version.svg :target: https://anaconda.org/bioconda/cwltest

.. |Conda Installs| image:: https://anaconda.org/bioconda/cwltest/badges/downloads.svg :target: https://anaconda.org/bioconda/cwltest

This is a testing tool for checking the output of Tools and Workflows described with the Common Workflow Language. Among other uses, it is used to run the CWL conformance tests.

This is written and tested for Python 3.8, 3.9, 3.10, 3.11, and 3.12.

.. contents:: Table of Contents :local:

Install

Installing the official package from PyPi

.. code:: bash

pip install cwltest

Or from bioconda

.. code:: bash

conda install -c bioconda cwltest

Or from source

.. code:: bash

git clone https://github.com/common-workflow-language/cwltest.git cd cwltest && pip install .

Run on the command line

Simple command::

cwltest --test test-descriptions.yml --tool cwl-runner

Generate conformance badges using cwltest

To make badges that show the results of the conformance test, you can generate JSON files for https://badgen.net by using --badgedir option

To generate JSON files::

cwltest --test test-descriptions.yml --tool cwl-runner --badgedir badges ... $ cat badges/command_line_tool.json | jq . { "subject": "command_line_tool", "status": "100%", "color": "green" }

Once you upload JSON file to a server, you make a badge by using a link like https://badgen.net/https/path/to/generated/json or https://flat.badgen.net/https/path/to/generated/json (for flat badges).

Here is an example of markdown to add a badge::