On Thu, Apr 11, 2013 at 7:54 AM, Holtgrewe, Manuel
<manuel.holtgr...@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.

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