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
858-202-4582