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)
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,
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.
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
