Hi Peter, thanks for the link. Searching efficiently the archives of posts is cumbersome :( I was thinking along the lines suggested. Prefered langue is perl and tried having `mv from to` but somehow got stuck and thought it might have something to do with local working directories.... But I will try again using bash. Indeed a pity galaxy is not offering such things straight from the tool_config and that we need work arounds for that including an extra layer of maintenance. Keep you posted on success. Alex ________________________________________ Van: p.j.a.cock@googlemail.com [p.j.a.cock@googlemail.com] namens Peter [peter@maubp.freeserve.co.uk] Verzonden: woensdag 6 oktober 2010 12:21 Aan: Bossers, Alex CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] tool config and fixed output file names On Mon, Oct 4, 2010 at 7:36 AM, Bossers, Alex <Alex.Bossers@wur.nl> 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
PS: sorry for cross posting users and dev. Not sure where the tool stuff belongs.
Hi Alex, Andreu asked a similar question last month where the tool picked the output filename extension based on the format requested: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-September/003348.html The same basic work around should work in your example too: have a wrapper script (perl/bash/python) which knows about the fixed output names, and renames them to a filename passed from Galaxy. (As I wrote in the referenced thread, I'm curious if there is a nicer solution within the Galaxy XML wrapper itself.) Peter