Assuming cuffcompare generates a TMAP and REFMAP file for each input file, does this mean the wrapper tool retrieves only the first and second input files' TMAP and REFMAP files ?

Yes, this is the way it works currently. This is clearly problematic, but it meets most users' needs as it enables them to generate a file of combined transcripts--which is needed for Cuffdiff--from many sets of Cufflinks' transcripts. Currently, the Galaxy framework isn't set up to generate multiple outputs for each input; I'm not sure how difficult it will be make these extensions, and it hasn't been a priority as users haven't voiced a need for these files.

Of course, contributions are always welcome if you put something together.


and others are ignored ? Or is there some galaxy black magic python code that iterates multiple inputs and imports them all ?

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