Integrated JS and variable split ids for dbOTUs

[spacocha]

Also added mothur to the user.cfg.template

[swo]

A couple fixes...

• i can't merge this request because there has been some new changes. you'll have to pull and integrate those changes first.
• JS should be dbotu_js
• JS_cutoff should be dbotu_js_cutoff. I'm trying to keep all the dbotu flags with some common prefix. And none of the other ones have capital letters.
• in lines 624 and 630, there is no need to use str. the execute routine does that itself.
• in lines 626/627 and 629/630 and 636/637, don't call x.append(y); x.append(z). instead do x += [y, z].

[swo]

also, the user config file shouldn't have any personal info. follow the example of the previous lines for path/to/ and user.