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