Metaphlan issue with --unknown estimation parameter

Hello! I am trying to run the most recent version of Metaphlan (4.0.6+galaxy2) with the --unknown_estimation parameter, but am receiving an error (photo attached).

Is it possible that the commandline needs to be updated to “–unclassified_estimation” rather than “–unknown_estimation”?

Hi @bethp

Two options from here:

Issue Ticket

  1. Starting at the tool form, go to the Options menu and click into the See in Tool Shed link.
  2. Let that completely load, then click into the Development Repository.
  3. Start up an Issue ticket to report the problem to the developer. If you can include a very small shared history with an example that will help the author to reproduce the original problem, and to test the correction.

Galaxy Help

  1. Provide the small example here with a shared history.
  2. A moderator will create the Issue ticket instead based on that example.

Thanks! :slight_smile:

Thanks! Below is a link to a history I created with two sample files (forward and reverse reads) and my attempt at using the unknown_estimation option in Metaphlan.

Let me know if anything else is needed

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Hi @bethp

Great! Thanks so much for sharing the history. You can unshare it now.

The issue is with the tool wrapper. Please follow this ticket for updates → Wrapper bug: metaphlan 4.0.6+galaxy2 · Issue #5958 · galaxyproject/tools-iuc · GitHub

Hi @bethp,

Thanks for pointing out the bug in the MetaPhlAn tool. We have now fixed the bug and you should now be able to use the unclassified_estimation parameter in Galaxy

Cheers,
Saim

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