All tool that allow user section of a built-in genome index should have variant build help included again

[jennaj]

See discussion here with an example of an older tool wrapper that includes the info.

https://help.galaxyproject.org/t/does-default-hg38-build-version-contain-alt-contigs-a-note-on-built-in-reference-genomes/1408

Mimimum set of wrappers to update:

• RNA STAR
• HISAT2
• BWA
• BWA Mem

[bernt-matthias]

I guess this is not a Galaxy/Tool issue, but rather an issue of the names given in the loc files on the specific Galaxy instance.

Or maybe the issue is more that its complicated/impossible to find out about the origin of the reference data that is available on the Galaxy instances. Currently in the best case only the admins can find this out.

[jennaj]

hi @bernt-matthias

The idea was to just add in that help text to the other tool wrappers. Example in the GHelp post, here again:

Screenshot of the older wrapper for Map with Bowtie for Illumina (Galaxy Version 1.1.2) tool form help section. This is the info that I think should be added again to the help section, across mapping tools. Seems like it got dropped in the updated/new wrappers.

What "help" text to display on any given tool form is not dependent on whatever genomes happen to be in any tools loc file/available as an indexed genome as far as I know, or that would have triggered the help showing up already for the tools above (have variant genomes indexed for the tools at Galaxy Main, and probably other servers (public or not).

It is supplemental help, and wouldn't harm to include it, even if a particular server doesn't have any variant genomes indexed.

Thoughts? I think what I was asking for was maybe misunderstood? The GHelp post covers more details to help that specific user. And their point is a good one -- adding in the help text above would have probably aided them to solve the question about which genome to use, on their own.

Is there an option to use only toplevel sequence? And if there is no mention of the type of build used as default (I didn’t find any), it’s probably a good idea to include it.