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,

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
ichorny@illumina.com
858-202-4582