RNA STARsolo UI Mislabelling in Galaxy

[quacksawbones]

Hi folks,

I've found what appears to be a misconfigured parameter in RNA STARsolo in the Galaxy implementation.

When selecting the input parameters, under "Reference genome with or without an annotation", when "use genome reference without builtin gene model" is selected, the form displays "Gene model (gff3,gtf) file for splice junctions" with an input for a gene model file (see RNA_STARsolo_UI_issue_1a.png and RNA_STARsolo_UI_issue_1b.png). Similarly, when "use genome reference with builtin gene model" is selected, there is no way to enter a gene model file, as the option is not present (RNA_STARsolo_UI_issue_2a.png and RNA_STARsolo_UI_issue_2b.png).

The tool will not allow you to advance without a gene model being selected.

Unsure if it should be it's own issue or rolled into this one: #3540

Thanks,

Darren

[bernt-matthias]

For the gene model input: Do you have a gff3/gtf dataset in your history?

For the builtin reference genome selector the admin of the Galaxy instance probably has to setup the rnastar_index2x_versioned data table.

[quacksawbones]

Apologies, I don't think I was accurate in my explanation/issue title. The issue is not that I don't have a gene annotation file, but that the UI is labelled incorrectly. I have revised the issue title to better describe the issue.

I believe the Galaxy XML file (rg_rnaStarSolo.xml) needs to be modified such that when "use genome reference without builtin gene model" is selected under "Reference genome with or without an annotation", the input box for gene models (gff3/gtf) is not present, and vice versa.

I think it is a simple matter of relabelling the dropdown box somewhere between lines 160 and 176 (the underlying functionality should be unaffected), but I do not have the experience/confidence with Git to make the changes myself.

[bernt-matthias]

I think its correct the way it is, but its confusing.

If you select a reference genome with buildin model this means that the annotation is already present and the user does not need to provide one.

If you select a reference genome without buildin model this means that the user needs to provide one.

The trick in the implementation is here:

tools-iuc/tools/rgrnastar/macros.xml

Line 42 in 5161812

<filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />

I will leave this open, maybe someone has a good idea how to improve docs here.

[pavanvidem]

@quacksawbones StarSolo must use an annotation file to generate a count matrix. There is no option to run StarSolo without a GTF file. Hence, now the label changed from "Reference genome with or without an annotation" to "Reference genome with an annotation". Hope this clears the confusion with the label now.

[bgruening]

Please reopen if this is not clear.