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 a python wrapper https://bitbucket.org/saketkc/galaxy-central/src/3eb26205af5a0b77fa6177d5ecd...
for this.
I however also came across how stderr text can be handled in Galaxy : http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cstdio.3E.2C_....
and thus wrote a new 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 ?
Saket