I'm very surprised to see that the only available output for cuffdiff is now in the cummerbund compatible rsqlite db. I can't see any way to actually analyze that data in galaxy. Although I'm competent with bash, not as much w/ R. It seems to me now that there is no way to actually analyze your RNA-seq using cuffdiff in Galaxy. The only way is to download the Rsqllite db output and analzye it there. Isn't this contrary to the entire purpose of galaxy? Its a bit frustrating that the older version of Cuffdiff, which output tab-delimited text files was much easier to interface with other datasets either on the command line or in galaxy. Am I missing something here?
you need to have this tool available: https://toolshed.g2.bx.psu.edu/view/devteam/cummerbund_to_tabular
It will extract you all needed information as before. See also this discussion here: https://github.com/galaxyproject/tools-devteam/pull/138.
If you have cummerbund around (https://toolshed.g2.bx.psu.edu/view/devteam/cummerbund) you can also produce a lot of pictures from your sqlite storage.