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> [options]

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?

Thanks!

Dan