First off thank you heartily for pointing me in the right direction here.

It SEEMS like i have managed to accomplish this.  Meaning: i finally got the
run to get past the parsing of the config file and now have a process
running on the cpu and the server log shows a command line string that
matches what I was trying to get.  However I am VERY new at the whole
Cheetah craziness, so I DEF want you folks to double check my work.

I would LOVE to contribute a patch but have these questions and concerns:

   1. I cloned the 'dist' branch not the 'central' branch originally and am
   not sure if my tophat_wrapper.xml version will clash with any that have been
   included in the central branch, I would assume that the system's diff
   capabilities SHOULD be able to sort this out but I am WAY more familiar with
   git than hg.
   2. I have created a bitbucket account and supplied my pubkey, but I dont
   see anything on the wiki that describes how a person gets "push" or similar
   permissions on the galaxy project what is the procedure for correctly
   submitting these types of piecemeal single file changes?

Thanks again for your help and I am very excited to have a chance to give


On Mon, Jul 11, 2011 at 8:51 AM, Jeremy Goecks <>wrote:

> > I recommend to use the repeat tag (see
> around the
> existing parameter to make it possible to select multiple files.
> Sarah's suggestion is spot on. See the Cuffcompare wrapper for an example
> of how to use this tag.
> Gus, if you end up modifying the Tophat wrapper to support multiple input
> datasets, please submit a patch or fork galaxy-central via bitbucket and
> I'll integrate these enhancements into the Galaxy code base as this would be
> nice functionality to have.
> Best,
> J.

In science, "fact" can only mean "confirmed to such a degree that it would
be perverse to withhold provisional assent." I suppose that apples might
start to rise tomorrow, but the possibility does not merit equal time in
physics classrooms.
*-Stephen Jay Gould*
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