Just to add to what Peter said - you definitely don't want to use
from_work_dir and reference the outputs ($output1) in the same
command. If you know where the file is going to be relative to your
working directory there should be no reason to pass it to your script.
Also I think you want format instead of format_source as the attribute
on output.

On Mon, Apr 7, 2014 at 8:49 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Sat, Apr 5, 2014 at 8:07 AM, ANGELICA GOMEZ ROIG
> <nirvanargr2...@gmail.com> wrote:
>> Hi Jen,
>> I tried what you explain, but still doens't work.
>> I did create a new datatype, gem.  And I modified my code as you suggested.
>> The tool i'm using always generates by default two archives . gem and .log.
>> Those are the ones that I can't show in the galaxy interface, the output I
>> get is empty, the dataset_54.dat and the dataset_55.dat.  I can't handle to
>> show me the .dat.gem and .dat.log ones.
>>
>>
>>
>> dataset_54.dat   (my first declared output that it's empty)
>> dataset_54.dat.gem (the output that throws the tool)
>> dataset_54.dat.log (the other output file that throws the tool)
>> dataset_55.dat (my second declared output that it's empty)
>>
>> Here it is the gem_indexer.xml
>>
>> <tool id="GEM Index" name="create GEM Indexer">
>>   <command interpreter="python"> gem_indexer.py  $input $output1
>> $output2</command>
>> <inputs>
>> <param name="input" type="data" format="fasta" label="Fichero de
>> entrada(formato .fas)" />
>> </inputs>
>> <stdio>
>>     <exit_code range="1:"   level="fatal"   description="Bad input dataset"
>> />
>> </stdio>
>> <outputs>
>> <data format_source="gem" name="output1" label="${tool.name} on
>> ${on_string}: salida" from_work_dir="gem_tools/salida.gem" />
>> <data format_source="tab" name="output2" label="${tool.name} on
>> ${on_string}: salida" from_work_dir="gem_tools/salida.log" />
>> </outputs>
>> </tool>
>>
>> And the gem_indexer.py
>>
>> import sys,os
>>
>> def __main__():
>>
>>
>>
>> # Command to run GEM tool. Here the Gem indexer is getting invoked along
>> with arguments to be passed.
>>
>>     cmd="gem-indexer -i "+sys.argv[1]+" -o salida"
>>     os.system(cmd)
>>
>>
>> if __name__ == "__main__" : __main__()
>>
>
> Since you are using a wrapper script already, I would add
> lines to rename the generated files (based on sys.argv[1]
> plus the extensions) to the filename Galaxy is providing
> (here sys.argv[2] and sys.argv[3]).
>
> Peter
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