Hi Saket If you want to redirect the executable's stdout to a new Galaxy dataset you've defined as $output, something like: > '$output' is a workable idiom for a command line AFAIK - you need to escape the redirection '>' character or you'll confuse the xml parser. It's often possible to hack a complex command line (or use configfile to write a script!) but as Peter says, it all boils down to personal preference - they all work. Use whatever you find most convenient but remember you may need to maintain it :)
On Mon, Jun 3, 2013 at 9:05 PM, Peter Cock <[email protected]>wrote: > On Mon, Jun 3, 2013 at 11:53 AM, Saket Choudhary <[email protected]> > 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/
