partially addresses #688

This addresses a few of the points in #688. I'd like to get this merged now and will continue adding new features in another pull request as I might not have time to work on this over the next few days, and the new features here are pretty stand-alone. 

Specific things addressed here:
- Added output of print_biom_table_summary.py.
- Improved formatting of index.html, but there is still a lot more to be done. 
- Added filtering of low sequence count samples as an initial step, and added the filtered, gzipped biom table as an additional link in index.html.