Question: Extract identifiers from collection in tool XML
gravatar for mtn14
4 months ago by
mtn140 wrote:

If I have a collection of files, how would I extract the identifiers in an XML to pass it into an in-house tool.

Example: I have this collection and want to pass in the identifiers (SRR*.fastq) to a tool, how would I do it?


This is how I'm passing in the files: <inputs> <param name="reports" type="data" format="txt" label="Qualimap Genome Report" help="" optional="false" multiple="True" /> </inputs>

If I try to pass in ${} for $reports, I just get the location of the .dat file.

ADD COMMENTlink modified 4 months ago by Jennifer Hillman Jackson25k • written 4 months ago by mtn140


I asked the developers for some feedback at the Galaxy Gitter channel:

Please feel free to join in on the conversation and/or add more details.

Planemo is the recommended way to troubleshoot tool development issues, but the developers will have more input if that is not working for you, or the resolution is not covered in the current documentation (or I couldn't find it), or the functionality to do this is in progress and/or yet to be ticketed.

Thanks! Jen, Galaxy team

ADD REPLYlink modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The developers recognized the issue and replied at Gitter.

Quoted reply from at

.element_identifier instead of .name

There's a section on that in the planemo docs:

Hope that helps! Jen, Galaxy team

ADD COMMENTlink written 4 months ago by Jennifer Hillman Jackson25k
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