On Mon, Mar 2, 2015 at 4:08 PM, Roberto Alonso CIPF <ralo...@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/samtools/samtools_idxstats/samtools_idxstats.xml

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
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