wft4galaxy:
Workflow Tester for Galaxy

Description

wft4galaxy is a Python module which allows to automate the running of Galaxy workflow tests. It can be used either as local Python library or a Docker image running inside a Docker container.

Installation

Basically, to install wft4galaxy as a local Python library, you need to follow the two speps below:

1. clone the github repository:

     git clone https://github.com/phnmnl/wft4galaxy

2. install the module using the usual setup script:

    cd wft4galaxy
    python setup.py install

Notice. If you are using a Linux based system, like Ubuntu, you probably need to install the two libraries python-lxml and libyaml-dev as a further prerequisite.

Alternatively, you can use wft4galaxy with Docker (see Docker-based Installation).

Usage Instructions

If you have installed wft4galaxy as native Python library, you can launch it from your terminal:

wft4galaxy [options]

The the main available options are:

usage: wft4galaxy [-h] [--server GALAXY_URL] [--api-key GALAXY_API_KEY]
                  [-f FILE] [--enable-logger] [--debug] [--disable-cleanup]
                  [--output-format {text,xunit}] [--xunit-file FILE_PATH] [-o PATH]
                  [test [test ...]]

positional arguments:
  test                      Workflow Test Name

optional arguments:
  -h, --help                    show this help message and exit
  --server GALAXY_URL           Galaxy server URL
  --api-key GALAXY_API_KEY      Galaxy server API KEY
  -f FILE, --file FILE          YAML configuration file of workflow tests (default is workflow-test-suite.yml)
  --enable-logger               Enable log messages
  --debug                       Enable debug mode
  --disable-cleanup             Disable cleanup
  --output-format {text,xunit}  Choose output type
  --xunit-file FILE_PATH        Set the path of the xUnit report file (absolute or relative to the output folder)
  -o PATH, --output PATH        Path of the output folder

As an example, you can run tests defined in your workflow-test-suite.yml definition file by typing:

wft4galaxy

Alternatively, you can run one or more tests (e.g., change_case) in your definition file specifying their names:

 wft4galaxy change_case

See documentation for more details.