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