One of our users has requested to see if we could add specifying an
alignment search option to Bowtie2 (-k and -a option

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 Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

Research Computing Support
Office of Information Technology

University of California, Irvine
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