Ok, Now I can answer myself Instead of running: * * * mytool inputfile -outputname=result -outputformat=zzz* now I run a script I created *mytool.sh $input $output * And the script is: *mytool $1 -outputformat=zzz -outputname=$2 * *mv ${2%.dat}.zzz $3* * * I hope it helps, Andreu * * On Wed, Sep 22, 2010 at 12:44 PM, Peter <peter@maubp.freeserve.co.uk> wrote:
On Wed, Sep 22, 2010 at 10:56 AM, Andreu Alibés <aalibes@gmail.com> wrote:
Hi,
I'm trying to add to Galaxy a tool that, basically, it runs this way
mytool inputfile -outputname=result -outputformat=zzz
This would output a file called result.zzz
How do I catch the result.zzz file? Because
<outputs> <data format="zzz" name="output" /> </outputs>
will look for a file called output, but not a file called output.zzz
Thanks,
Andreu
I'd be interested to know if you can solve this within Galaxy as I can think of situations where it would be handy.
If not, you could write your own wrapper script which renames the output file to something consistent.
Peter
-- -------------------------------------------- *Andreu Alibés, PhD **Bioinformatics Core & EMBL-CRG Systems Biology Unit Center for Genomic Regulation* C/ Dr. Aiguader 88, 08003 Barcelona, Spain Phone: +34 93 316 0202 http://sites.google.com/site/aalibes