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phac-nml / irida-plugin-amr-detection

IRIDA Plugin for AMR Detection
Apache License 2.0
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Move selection of PointFinder organism to a required parameter in IRIDA #19

Closed apetkau closed 1 year ago

apetkau commented 1 year ago

Right now, the parameter used to enable the use of the PointFinder database and select an organism is hidden among all the other parameters that can be adjusted and so is not as obvious that it needs to be configured:

image

I believe we should move this parameter to the front of the parameters list that gets displayed to users in IRIDA so that it's more obvious it needs to be set, similar to selecting an RGI database:

image

The way this can be accomplished is to update the use_pointfinder parameter setting:

https://github.com/phac-nml/irida-plugin-amr-detection/blob/52e3ec2f1e086d48e7d19325a503df4fc319a42d/src/main/resources/workflows/0.3.0/irida_workflow.xml#L42-L44

such that you add required="true" and then add multiple sub <choice>salmonella</choice> entries (one for every validated organism in staramr: campylobacter, enterococcus_faecalis, enterococcus_faecium, escherichia_coli, helicobacter_pylori, salmonella, and disabled).

For example:

<parameter name="staramr-2-use_pointfinder" defaultValue="disabled" required="true">
  <choices>
    <choice>disabled</choice>
    <choice>salmonella</choice>
    <choice>campylobacter</choice>
  </choices>
  <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.9.1+galaxy0" parameterName="use_pointfinder"/>
</parameter>

This is how the biohansel pipeline in IRIDA operates:

image

Code for BioHansel: https://github.com/phac-nml/irida/blob/edf0556af75021c309b1f3fe5328a1a28a1e1137/src/main/resources/ca/corefacility/bioinformatics/irida/model/workflow/analysis/type/workflows/BioHansel/2.0.0/irida_workflow.xml#L12-L18