[MIGRATION]: isa2w4m

[melpetera]

Summary

• Tool: isa2w4m
• Link to external repository containing the wrapper XML: https://github.com/workflow4metabolomics/isa2w4m
• Link to the toolshed repository (if there is no shed.yml file) https://toolshed.g2.bx.psu.edu/repository/view_repository?f-free-text-search=w4m&sort=name&operation=view_or_manage_repository&id=2e211bb07b58bd13

Steps

These are the default steps to be completed - if something is not applicable, please remove it or mark it as completed.

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

Cleanup

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