It seems like tophat2 does not support  "--transcriptome-mismatches" option
but Galaxy is still configured to call tophat2 with this option when run
with "Full parameter setting" option within Galaxy. Is there new wrapper
with this fix? If not, how to remove this option from Galaxy so that
tophat2 is not call with this option. I am assuming that this is specified
somewhere in the wrapper.

Thanks,

Sachit
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