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.cock@googlemail.com> wrote:
On Sat, Apr 5, 2014 at 8:07 AM, ANGELICA GOMEZ ROIG <nirvanargr2012@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" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/