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?
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