On Thu, Apr 11, 2013 at 7:54 AM, Holtgrewe, Manuel <manuel.holtgrewe@fu-berlin.de> wrote:

Dear all,

is it possible to make Galaxy use a specific extension for a given data type without a wrapper?

I.e. can I make Galaxy use the extension .bam, .sam, .fasta etc. internally instead of .dat?

Thanks, Manuel

I think you must use a wrapper for dealing with inflexible tools with hard coded filename/extension assumptions. If you are wrapping a tool which insists on a particular input filename or extension, you can try creating a symlink to the Galaxy *.dat file in a tool wrapper script. Or if that fails, make a copy of the file. Similarly, you can rename hard coded output filenames to the Galaxy assigned *.dat filename once the tool has run using a wrapper script. Peter