Re: [galaxy-dev] Bowtie2 Specifying -k value (Alignment Search)
> 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 > tag in the xml file. > > Would this be the correct way to go about this? Yes, this is correct; the -X or -I option are good examples of using integer parameters. The Bowtie2 wrapper has never been fleshed out; if you do decided to add options, please consider submitting a pull request so that others can benefit from your work as well. Best, J. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Bowtie2 Specifying -k value (Alignment Search)
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 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 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
