Thanks Jennifer, that exactly how we solved it using a bash wrapper wunning the actual tool and then rename it to something known by galaxy. Thanks for the reply. Alex ________________________________________ Van: Jennifer Jackson [jen@bx.psu.edu] Verzonden: woensdag 20 oktober 2010 16:26 Aan: Bossers, Alex CC: galaxy-user@lists.bx.psu.edu Onderwerp: Re: [galaxy-user] tool config and fixed output file names Hello Alex, File extensions are an unchangeable function of many of the 3rd party tools wrapped in Galaxy. The best work-around advice is to just rename the output as a post-processing step. Thanks! Jen Galaxy team On 10/3/10 11:29 PM, Bossers, Alex wrote:

Hi all, I am probably missing something very obvious. I am struggling to make a tool config file (and/or perl/bash wrapper) that runs some tools that have several input files (no problem) but also several FIXED name output files. I am able to give it some prefix but the extensions (if any) cannot be changed. Any help appreciated how to link/get this in $output. Alex

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