This thread addresses your issue:

http://dev.list.galaxyproject.org/tophat-option-transcriptome-mismatches-not...

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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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