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