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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