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__()


2014-04-04 6:05 GMT+02:00 Jennifer Jackson <j...@bx.psu.edu>:

 Reply posted:
>
> http://dev.list.galaxyproject.org/known-name-outputs-shown-in-database-files-but-not-in-galaxy-windows-tt4664079.html
>
> Angelica,
> Next time it would be great to post to only a single list. The
> galaxy-...@bx.psu.edu list is best for this type of question.
> Take care,
> Jen
> Galaxy team
>
>
> On 4/3/14 12:13 AM, ANGELICA GOMEZ ROIG wrote:
>
>  I have made a wrapper that has a tool that giving it an input file,
> gives you two output files with known extension: .gem and .log
> I call the tool with a python file, and I pass it the input file and the
> two output file names for galaxy to show them, but when I look into de
> database/files/000/ i get four files:
>
> 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)
>
> So,what I'm getting in the galaxy interface is  _54.dat and _55.dat, both
> empty, instead of _54.dat.gem and _54.dat.log that are the good ones.  How
> can I fix these?
> Thanks
>
>
> ___________________________________________________________
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> --
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>
>
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