I'm trying to use the bowtie2 wrapper but it generates and empty output with the "no peek" sign. I have sucesfully recreated the analysis with the same datatsets on the shell, so it must be something to do with Galaxy, but I don't know where to look at. Any clues? Thanks

I'm using bowtie2-2.1.0 and Galaxy: 

changeset:   10421:a477486bf18e
branch:      stable
tag:         tip
user:        Nate Coraor <nate@bx.psu.edu>
date:        Thu Sep 26 11:02:58 2013 -0400
summary:     Bugfix for tool-to-destination mapping, tool ids are lowercased but the mapping id was not lowercased

Mikel Egaņa Aranguren, Ph.D.