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]).

Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

To search Galaxy mailing lists use the unified search at:

Reply via email to