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 <jen@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-dev@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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