Question: Galaxy tool config for paired collection (list:paired) output?
gravatar for mrals89
3.4 years ago by
United States
mrals8950 wrote:

Hello everyone!

My question today is the proper way to produce a list of paired outputs (e.g. subsampling fastq files). I have been experimenting with different combinations of tags, ordering, filtering. The following is very close (creates a list of paired outputs), but fails to collapse the single datasets into the list of pairs after completion. Instead they are listed underneath "10: subsampled collection 3"

"9: random subsample on data 4, data 3 and others"

"8: random subsample on data 4, data 3, and others" etc. Closer inspection of the command lines of dataset 8, 9, and the second pair of collection 10 shows that the files are indeed the same, they are just not collapsing.

    <collection name="out_paired" type="paired" label="Subsampled ${on_string}" >
      <data name="forward" type="data" format="fastq"/>
      <data name="reverse" type="data" format="fastq"/>



I imagine it has something to do with the "collection" tag and the "data" tags. What would a proper XML configuration look like (bonus points for how the separate pieces are referenced in the "command" tags)? Thank you

ADD COMMENTlink written 3.4 years ago by mrals8950

Related C: Documentation for <collection> tag?

ADD REPLYlink written 3.4 years ago by mrals8950
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