galaxyproject / galaxyproject/tools-iuc

Mother update request

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Description

Dear Galaxy maintainers,

I would like to ask for an update of the Mothur version on the usegalaxy server.
Currently the installed version is 1.39.5.0, whereas the latest version is 1.46.1 (on mothur.org).

The more recent version allows for converting DADA2 count table output to shared data format using the command "make.shared" with count and label=asv parameters as input.
The ancient Mothur version doesn't permit this conversion.

The shared format would be very useful allowing make.biom to output biom format files in a second step.

So thanks to this update, both Mothur and DADA2 analysis methods would be capable to output biom format files.

Thanks in advance and best greetings,
Laurent

Contributor guide

Open the contributing guide

Research direction

No files, tests, or entry points are named. Start by locating the Mothur wrapper and its tool definition in this repository, then check how version 1.39.5.0 is configured. Done means Mothur is updated to 1.46.1 and the make.shared count/label=asv workflow can feed make.biom.

Written by the indexing model from the issue text.

Assessment

Domain
bioinformatics
Issue type
Feature
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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