This thread addresses your issue:
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On Dec 20, 2012, at 2:03 AM, Sachit Adhikari wrote:
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.
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