26 Jun
2013
26 Jun
'13
8:42 p.m.
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?
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.