Assaf,

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.

Best,
J.

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





___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/

Reply via email to