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. Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
