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