I just remembered what I did for the tophat wrapper. All I did was change the 
default behavior  of the use coverage search option. I believe no is the 
default behavior and you have it as yes.

From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
Sent: Thursday, August 11, 2011 7:22 AM
To: Chorny, Ilya
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: Updated Cufflinks Wrapper

Hi Ilya,

Thanks for the contribution; most of it has been committed in changeset 

A couple notes:

*I couldn't transplant your changes because your commit did not include recent 
changes to the Cufflinks wrapper. It appears you didn't merge correctly with 
the main repository at some point; please try to merge correctly as it speeds 
up the inclusion process significantly on our end.

*I didn't include your changes to the Tophat wrapper because merging was 
incorrect and I couldn't figure out what you were trying to do.

Let us know if you have any questions.


On Jul 27, 2011, at 7:26 PM, Chorny, Ilya wrote:

I  made some changes to the cufflinks wrapper.  I added the -g/--GTF-guide use 
reference transcript annotation to guide assembly as an option. The version 
number needs to still be updated in my commit.


Ilya Chorny Ph.D.
Bioinformatics - Intern

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