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.goecks@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 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 ichorny@illumina.com<mailto:ichorny@illumina.com> 858-202-4582