STRY0020017 - Update Galaxy tool wrapper for StarAMR to version 0.12.1

[emarinier]

Description

As a data analyst, I would like the Galaxy tool wrapper for StarAMR to be updated to use the latest version (0.12.1), so that I can work with the updated StarAMR in Galaxy.

Acceptance Criteria

• Update Galaxy StarAMR wrapper to use StarAMR 0.12.1 (latest release)

[apetkau]

This looks amazing Eric. Thanks so much for your great work 😄

One request I do have, can you change the list of selectable mlst schemes that are in the wrapper to match the most recent list from the updated mlst software?

galaxy_tools/tools/staramr/staramr_search.xml

Lines 142 to 145 in 9276325

	<option value="auto" selected="true">Automatic</option>
	<option value="aactinomycetemcomitans">aactinomycetemcomitans</option>
	<option value="abaumannii">abaumannii</option>
	<option value="abaumannii_2">abaumannii_2</option>

You can view the list by running:

mlst --list

On previous updates, I took this list of schemes from the mlst software and transformed into the XML format needed in the tool wrapper and copy/pasted those entries in.

[emarinier]

Updated MLST options in c682d3a

[apetkau]

Thanks so much for making all these changes Eric. I've approved this for whenever tests succeed.

[emarinier]

Tests are failing because http://www.genomicepidemiology.org/services/ is down and has been down for at least a few days now.