On Mon, Jun 3, 2013 at 11:53 AM, Saket Choudhary <saketkc@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