If you are running Cuffdiff outside of Galaxy, the Galaxy Cummerbund wrapper wouldn't be an appropriate choice. It expects output from the Galaxy Cuffdiff wrapper.
Run the Cuffdiff analysis in Galaxy and output the SQLite database. Do this by setting the option "Generate SQLite" to "yes" on the Cuffdiff tool form.
Use Cummerbund outside of Galaxy.
Thanks! Jen, Galaxy team