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
Fixed issues 611 and 622.
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.
Updated pairwise tests text to be clearer.
Fixes issue #711

Modifies the defaults as @gregcaporaso suggested so that if a depth is not passed it will use the deepest available. Updated the documentation in the script and library and added a test.
Updated to address initial problems.
Merge pull request #741 from wdwvt1/issue_711

Fixes issue #711
Added name to credits
Checking in tests fix for te 1.0
Solves issue #758
Merge pull request #759 from wdwvt1/tiny_doc_fix

Solves issue #758 -- a truly monumental commit
Merge pull request #753 from meganap/te_1.0

Checking in tests fix for te 1.0
Merge pull request #733 from kpatnode/master

Quick fixes
Removed make_cluster_jobs.py test.

Discussed with @gregcaporaso and we decided that this test should be removed since it is essentially testing that qsub runs correctly with the generated jobs file. This means that in order to get all QIIME tests to pass on a system, a queueing system has to be correctly set up, which is a pain.
Merge pull request #761 from jrrideout/denoiser_test_fix

Removed make_cluster_jobs.py test.
added suppress_taxa_summary option

to function and script interface
add suppress_beta_diversity option

to function and script. also fixed bug where category labels could be wrong in index.html