Hi Ryan -

I have done similar things with our tools as well.  For now I have edited
the xml file to include the following option in the <command> section that
would get passed into the picard script wrapper:


I considered exposing this out in the UI, but have teetered on whether to
expose the complexity out to the end user.



>Message: 8
>Date: Thu, 12 Jan 2012 11:37:23 -0500
>From: Ryan Golhar <ngsbioinformat...@gmail.com>
>To: galaxy-dev@lists.bx.psu.edu
>Subject: [galaxy-dev] Picard MarkDups
>       <cafbjochhoioiw7a8t4p0gvs8zaywux82gv4bjv1rnuzjxc0...@mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>I'm trying to run Picard MarkDups through Galaxy.  Picard is using the
>standard 4g for the java max heap size.  I need to increase this. Is it
>possible to offer this as an option to the user?  If not, where do I
>this?  I see the entry in picard_wrapper.py.  Do I change it here or in
>XML file for MarkDups?
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