run_galaxy_function

This function executes the provided function as a galaxy processing
This provided function is expected to take two parameters:<ul>
<li>args, a list of command line parameters</li>
<li>logger, the logger created for the tool</li>
</ul>

Provides a set of utility function to prevent the spread of
utility scripts in W4M (Workflow4Metabolomics) tools, and centralize
them in a single package.
To note, some are meant to be replaced by the use of dedicated packages in the future, like
the parse_args() function: it is here only to prepare the ground for
more global changes in W4M scripts and tools.
This package is used by part of the W4M Galaxy modules, some of them
being available on the community-maintained GitHub repository for
Metabolomics' Galaxy tools <https://github.com/workflow4metabolomics/tools-metabolomics>.
See Delporte et al (2025) <doi:10.1002/cpz1.70095> for more details.

Melanie Petera

W4MRUtils

Useful Functions for Harmonized W4M Tool Development

Lain Pavot

Helge Hecht

run_galaxy_function function

<dl><dt>tool_name</dt>
<dd><ul>
<li>The name of the tool</li>
</ul></dd>
<dt>func</dt>
<dd><ul>
<li>The function to be run, after galaxy header is displayed</li>
</ul></dd>
<dt>...</dt>
<dd><ul>
<li>Parameters propagated to run_galaxy_processing</li>
</ul></dd></dl>

Arguments

Author

run_galaxy_function - automate running functions in galaxy — run_galaxy_function

<dl>

<dt>tool_name</dt>
<dd><ul>
<li>The name of the tool</li>
</ul></dd>


<dt>func</dt>
<dd><ul>
<li>The function to be run, after galaxy header is displayed</li>
</ul></dd>


<dt>...</dt>
<dd><ul>
<li>Parameters propagated to run_galaxy_processing</li>
</ul></dd>

</dl>

run_galaxy_function: run_galaxy_function - automate running functions in galaxy

Description

Usage

Value

Arguments

Author

See Also