On Mon, Mar 2, 2015 at 4:08 PM, Roberto Alonso CIPF ralonso@cipf.es wrote:
Hello,
I would like to add a very simple GATK wrapper to galaxy, but I am facing one problem. When you want to use UnifiedGenotyper tool, the extension of the bam file must be .bam, and when you upload something to galaxy it changes its extension,is there any way to change this extension? or is it anyway of solving this issue?
The most common solution to inflexible tools which insist on a specific file extension on inputs is to create a symlink with the right extension. e.g.
https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/...
Similarly where a tool does not give you full control of the output filenames, you must often move/copy the file to the filename which Galaxy has assigned.
Peter