Question: Extract identifiers from collection in tool XML
0
gravatar for mtn14
20 days ago by
mtn140
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?

Example

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 ${report.name} for $reports, I just get the location of the .dat file.

ADD COMMENTlink modified 19 days ago by Jennifer Hillman Jackson25k • written 20 days ago by mtn140

Hello,

I asked the developers for some feedback at the Galaxy Gitter channel: https://gitter.im/galaxyproject/Lobby?at=5b60dd0dac380e3f3a10f30c

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 19 days ago • written 19 days ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
19 days ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The developers recognized the issue and replied at Gitter.

Quoted reply from https://github.com/mvdbeek at https://gitter.im/galaxyproject/Lobby?at=5b60dd4ffe0be93f3b242d6a


.element_identifier instead of .name

There's a section on that in the planemo docs: https://planemo.readthedocs.io/en/latest/writing_advanced.html?highlight=element_identifier#processing-identifiers


Hope that helps! Jen, Galaxy team

ADD COMMENTlink written 19 days ago by Jennifer Hillman Jackson25k
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