[galaxy-user] Empty bowtie2 output

Hi; 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(a)bx.psu.edu&gt; 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 Egaña Aranguren, Ph.D. http://mikeleganaaranguren.com