Al, We agree that this is a good parameter to have available, and are going to be adding this in the near future. Regards, Kelly On Oct 19, 2010, at 2:11 PM, Al Simons wrote:

I'm a new Galaxy tool integrator. I'm integrating a tool that requires the secondary Bowtie output file of the reads it couldn't map due to there being too many matching locations (greater than the value specified by the -m option). This file is specified in Bowtie with the --max <filename> option.

I don't see a way to request this additional output with the current Bowtie jacket and xml. Has anyone already modified the jacket to do this?

I'm about to start delving into the Bowtie jacket and xml.

Thanks for any pointers -Al _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev