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,
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