Good to hear about your progress. Please send me a patch of your changes and 
I'll take a look. You can create a patch using Mercurial from the command line 
as follows.

% hg diff > tophat.patch


On Jul 13, 2011, at 7:37 PM, W. Augustine Dunn III wrote:

> 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:
> 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.
> 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 
> back!
> Gus
> 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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