Summary

• Tool: parsec
• Link to external repository containing the wrapper XML: https://unh-pfem-gitlab.ara.inrae.fr/parsec/parsec-galaxy-250102588

Steps

Setup

• Copy the code from the other repository into a sub-folder under tools/
• Check planemo lint . and planemo test .

Make planemo lint . and planemo test . pass

• Check and/or update dependencies
• Update the Galaxy profile version
• Update the tool wrapper to recent standards
• Add citations -> default should be latest W4M publication
• Update tool wrapper version

Improvements

This is an example of a recent tool wrapper that complies with recent best practices.

• Make the tool work with Pulsar (see including required files
• Add EDAM topics and operations (see here)
• Add creator tag (see here)

<organization
  url="https://workflow4metabolomics.org/"
  email="workflow4metabolomics@proton.me"
  name="Workflow4Metabolomics" />

• Update help text and parameter documentation
• Code seems unfunctionnal: fix it
• Tests expected output files missing: add it

Cleanup

• Archive the other repository and update the README.md file there