BUG: Update summarize_otu_by_cat.py to BIOM 2.x

This one slipped through the cracks, I have added an extra script usage
case to test for this.

Fixes #1713
DOC: Fix documentation problems
BUG: 'observation' -> 'sample'
Merge pull request #1730 from ElDeveloper/issue-1713

BUG: Update summarize_otu_by_cat.py to use biom 2.x