You might be able to do this by accepting a collection of
SAM/BAM files as input instead. This is a quite new feature
in Galaxy, see:

https://wiki.galaxyproject.org/News/2014_06_02_Galaxy_Distribution

Peter

On Wed, Sep 3, 2014 at 10:00 AM, Philippe Moncuquet
<philippe.m...@gmail.com> wrote:
> Hi,
>
> I am trying to write a wrapper for a tool that take a directory containing
> SAM/BAM files as an input. I am not sure how to do that, is there another
> tool that implements this and that I can have a look at ? Any suggestions
> would be greatly appreciated.
>
> Regards,
> Philip
>
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