On Mon, Jun 3, 2013 at 11:53 AM, Saket Choudhary <sake...@gmail.com> wrote: > As part of a warmup, I added a tool for perming eQTL analysis using > PANAMA(http://ml.sheffield.ac.uk/qtl/panama/). > > > By default PANAMA writes to stderr and creates a PANAM_results.csv file in > the same directory as the input files. > > I wrote ... XML : https://gist.github.com/saketkc/5697388 > > Apparently the above XML runs too, but I dont get back a CSV. Essentially I > need to move the PANAMA_results.csv file to output1. Can this be done > without using a wrapper at all , just using the XML files ? > > Is there a way to nest the commands in the XML so that I could do a > <move command> after <panama command> , but how would the paths be specified > ?
Hi Saket, You could try this (two commands in one shell line), but catching error conditions would be a problem: <command>panama $expression_data $snp_data; mv PANAMA_results.csv $output1</command> In cases like this where the underlying tool is too inflexible to accept an output filename, I would personally use a wrapper script which can handle moving things to the desired location, and raising a clear error if the file was not created. Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/