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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