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
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
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
galaxy-dev@lists.galaxyproject.org