> 
> 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;

or

(b) you can use a composite datatype to store the complete directory:

http://wiki.g2.bx.psu.edu/Admin/Datatypes/Composite%20Datatypes

Best,
J.
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