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Add ENA Webin cli as a Galaxy tool #6807

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@bedroesb bedroesb commented Feb 27, 2025

FOR CONTRIBUTOR:

  • I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • License permits unrestricted use (educational + commercial)
  • This PR adds a new tool or tool collection
  • This PR updates an existing tool or tool collection
  • This PR does something else (explain below)

This work is done in collaboration with ENA to make bring submission/validation functionalities of ENA to Galaxy. This tool will live next to the ena_upload Galaxy tool which is focused on RAW read submissions. This tool will be focused on Assemblies and other types of analysis submissions. The goal is to make it work well in combination with the ena_upload Galaxy tool.

To Do's

  • Fetch credentials from User settings
  • Interactive way of filling in metadata for submission
  • Have main cli on BioConda
  • Test with latest version Webin CLI
  • Agree on a tool name
  • Update README
  • Add test files that are also used on ENAs side
  • Write more tests
  • Align this work with the ena_upload Galaxy tool
    • Initial POC with receipt coming from ena_upload
  • Check if current form is still compliant valid for assembly submissions
  • Add the option to submit metadata through uploading a manifest file

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