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/3eb26205af5a0b77fa6177d5ecd1413ffd4d7a87/tools/eqtl_tools/panama_run.py?at=gsoc2013

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_.3Cregex.3E.2C_and_.3Cexit_code.3E_tag_sets

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
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