Update scripts/collate_alpha.py

Update the collate alpha script to ignore directories. Empty directories can be left over from previous (interrupted) alpha_diversity.py run 
Update scripts/collate_alpha.py

Updates as per Greg's suggestion
now runs print_biom_table_summary.py

and links output from index.html
added information on QIIME to index page
added ability to sort results in index
added prefiltering of biom table

Now removes samples with fewer than sampling_depth sequences before running any analyses. Previously samples with very few sequences (e.g., 1) were included in the rarefaction plots and taxa summaries, which was misleading (for the taxa summaries) and inconvenient (for the rarefaction plots, as some lines would end before others). This additionally ensures that the same samples are compared in all of the core diversity analyses. A link to this gzipped biom table is included in the index.html.
update comments
updated unit tests to test existance of output biom table
fixed typos
updates to allow core_diversity_analyses to run in 'print only' mode

'print only' mode allows the user to generate the list of commands that would be run by the workflow, without actually running them. this is really useful for recovering from failed runs.

- added parameter ``suppress_md5`` which allows the caller to turn off computation of md5 sums when generating the log file. this is redundant when these functions are called from core_diversity_analyses as core_diversity_analyses itself computes and logs the input md5sums. this additionally caused an issue because the low-sequence-count sample filtering step, which creates the otu table that gets passed to the individual workflows, isn't created when these functions are called in 'print only' mode. trying to compute the md5 of that file would therefore fail. we don't really need the md5 of that file however as the file itself is included in the output (and linked from the index.html page).
- removed some checking for the the existence of the input otu table. this was inconsistently done through the different workflows, but isn't really necessary as it now always happens during parsing of the command line parameters.
added support for running core_diversity_analyses in 'print only' mode

this allows users to print the list of commands to be run, but not actually run them.
all links now open in new tab/window
added suppress_md5 option to these workflow functions

for consistency with the 'downstream' workflows
udpated index headers to be read from a dict

rather than repeated many times through-out the code
Fixed issues 611 and 622.
Merge pull request #730 from gregcaporaso/issue-688

partially addresses #688
Change read mode for parameter files

Parameter files in these scripts were previously open without using the
'U' mode.

This should fix #727
Added support for empty distribution boxplots.

Support added at lower level distribution_plots.py code. Need to add tests and then work on make_distance_boxplots.py code to make sure that it will support empty distributions as well.
Updated existing distribution_plots.py tests.
Added tests for empty distributions and coloring.