Hi Ilya,

Thanks for the contribution; most of it has been committed in changeset 
0ef81af1de09

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.

Best,
J.

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.
>  
>  
> https://bitbucket.org/ichorny/galaxy-central/changeset/fc5e24d453e5
>  
> Ilya Chorny Ph.D.
> Bioinformatics – Intern
> icho...@illumina.com
> 858-202-4582
>  

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