I'm currently writing a Galaxy wrapper for RUM (RNA-seq Unified Mapper). RUM is 
a tool that generates many output files. It is run from the command line using 
the following syntax:

RUM_runner.pl <config file> <reads file(s)> <output dir> <num chunks> <name> 

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?


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