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-for-multiple-alignments-report-the-best-one
)

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/
aebre...@uci.edu
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