first pass addition of boxplots

works at the script level, needs testing and documentation
added test
expanded test
expanded test
added test
updated change log to describe differences in compare_alpha_diversity.py interface
Solving 3 first issues from #750
Changing default on functions to True, this will make all the test fall on the defaults
added missing code
getting close to having this hooked up to core_diversity_analyses.py, but either i'm insane or @antgonza and i have had a little too much to drink in mx city tonight... coming back to this one in the morning
Fixing last bugs and adding tests
Do not need 2 HTML templates, removing 1
Merge branch 'issue-750' of https://github.com/antgonza/qiime into issue-750

Conflicts:
	ChangeLog.md
fixed issue where file was being passed around where object should have been passed
prepping for new output
updated script usage examples and qiime_test_data output files
updated to delete intermediate files
prep for new qiime_test_data
added new qiime_test_data output
prep for new qiime_test_data output