Thanks. Finally it worked!! I pass the solution:
My python file:
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 "+sys.argv[2]
os.system(cmd)
name_gem=sys.argv[2]+".gem"
os.rename(name_gem,sys.argv[2])
if __name__ == "__main__" : __main__()
Take care!!!!
2014-04-07 15:51 GMT+02:00 John Chilton <jmchil...@gmail.com>:
> 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
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
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> >
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>
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