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