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(a)maubp.freeserve.co.uk> wrote:
On Wed, Sep 22, 2010 at 10:56 AM, Andreu Alibés
<aalibes(a)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