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...
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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