This thread addresses your issue:
http://dev.list.galaxyproject.org/tophat-option-transcriptome-mismatches-not-recognized-td4657568.html
In the future, please use the mailing list search before posting your question.
You'll save time for both yourself and others.
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
