refactor core_qiime_analyses.py to perform only downstream processing

[gregcaporaso]

This script isn't widely used, and would likely be more generally useful if it started with an OTU table, tree, mapping file, and optional list of categories of interest and wrapped the most common downstream processes (alpha_rarefaction, beta_diversity_through_plots, summarize_taxa_through_plots, et al).

• [x] remove upstream processing steps so input is tree, otu table, mapping file, and categories
• [x] add compare_alpha_diversities.py if categories is passed
• [x] add make_distance_boxplots.py if categories is passed, and remove make_distance_histograms.py
• [x] update tests to use data set defined in #582

[gregcaporaso]

I think this would save a lot of time so am going to work on this.

[gregcaporaso]

This is mostly done, and I think it will be really useful. Still working on some tests, but here's some example output.

I'm thinking of changing the name of this script to something like summarize_diversity.py or something along those lines. I'd also like to work on the top-level index page a little bit to add some information about QIIME and BIOM at the very bottom, and also some links into the documentation. I could see this evolving into a first pass set of diversity analyses that we would do from any BIOM table, so it'd be really nice to have some text in there that links to tutorials illustrating where to go from here (e.g., if you're interested in the taxa results and PCoA plot, then see this tutorial on biplots, ...).

Also note that we'd clean up the html to be nicer - the current page is just an attempt to get all of the information in the right places.

[wasade]

+1

[wasade]

Possible to check BIOM table type? Tree and unifrac don't make sense for a gene table, for instance