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
Use 'choice' option type for --binning_method

This addition is in favor of Galaxy integration as described in item one
of #632.
Added test.py to pycogent_backports.

Needed fix for mc_t_two_sample as we sometimes get failures in core_diversity_analyses.py unit tests.
Merge pull request #715 from ElDeveloper/add_alpha_options

Use 'choice' option type for --binning_method
Merge branch 'master' into mc_t_two_sample_fix
Copied over latest version of test.py.
Fixed import in test_test.py
Fixing the option types for ampliconnoise.py
Forgot to modify the credits of the script
Merge pull request #720 from jrrideout/mc_t_two_sample_fix

Ported mc_t_two_sample fix from PyCogent.
Merge pull request #721 from josenavas/opt_ampliconnoise

Fixing the option types for ampliconnoise.py
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.