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?