Overall Problem:
Given sample names are not carried through Cufflinks pipeline. Instead, they are referenced with a number and in final Cuffdiff output are referred to as Sample 1/Q1, Sample 2/Q2 etc., instead of given name which requires tedious re-labeling.

Is there a way to implement -L function in Galaxy so that sample names are carried through from Cufflinks to Cuffdiff?

Originally posted in Seqanswers: http://seqanswers.com/forums/showthread.php?t=20338, where commenter suggested using -L as a fix but I don't see this option in Galaxy.

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