[galaxy-dev] cufflinks in the main galaxy instance is not able to produce compatible FPKM score

Hi, Most people using the RNA-Seq toolkit use a combination of Tophat/Cufflinks/Cuffdiff. A known issue is that cufflinks and cuffdiff use different normalisation schemes ( http://seqanswers.com/forums/archive/index.php/t-26041.html). Users overcome this problem by running cufflinks with the following flags: --compatible-hits-norm --max-frag-multihits 1 However, in galaxy it is not possible to run cufflinks with these flags. Can you, perhaps, add support for them? many thanks, Nikolay