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.

http://galaxyproject.org/search/mailinglists/

Best,
J.


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. 
> 
> Thanks,
> 
> Sachit
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