> I’m good with everything except the <output dir>. I can’t figure out how to
> pass that directory information from Galaxy to the RUM_runner.pl in such a
> way that Galaxy will be able to subsequently capture the data. Does anybody
> have any advice, or can someone point me towards an existing wrapper that
> does something similar?
You have two options:
(a) you can set up the tool to report only a subset of outputs from the tool;
(b) you can use a composite datatype to store the complete directory:
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