One of our users has requested to see if we could add specifying an alignment search option to Bowtie2 (-k and -a option http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#default-mode-search-f... )
Is this something anyone else has added to their galaxy installs? If so, how?
I was looking at galaxy/dist/tools/sr_mapping/bowtie2_wrapper.* and it does not seem to challenging to add another field where a user could specify some integer value that we simply pass to the the <command> tag in the xml file.
Would this be the correct way to go about this?
Thanks in advanced! -Adam
-- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences
Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/
University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne@uci.edu