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.commailto:ichorny@illumina.com 858-202-4582