Add descriptive error to add_alpha_to_mapping_file

The library function was changed to check for the existance of the
specified rarefaction depth; it will now raise an exception if a
non-existant depth is passed. This exception is now catched from the
script interface and displayed using option_parser.error.

The test suite was updated accordingly for this module.

An unnecessary type cast was also removed from the script interface.

This should fix #827
Add available depths to the exception message
Add default depth as the highest

Mean alpha is now retrieve the highest available rarefaction depth when
None is specified. Script usage and unit tests were updated accordingly.

A new option was added to the script interface to indicate when the user
is trying to pass collated data as the input, since --depth is no longer
required to determine whether or not the execution will be over collated
or non-collated data, there was a redundancy that this option resolves.
Adds library and script files for make_bipartite_network

This functionality is being built to replace make_otu_network.py because that script has become nearly non-functional given changes to Cytoscape and Qiime including the biom format.
Fixed typos

Thanks @jrrideout
Updated script and added library rewrites as well as tests.
Added test data and outputs.

Verified that it works with %prog command in help documentation.
Addressed comments by @lkursell and @ElDeveloper
Addressed changes suggested by @ElDeveloper and @josenavas
Change redundant if else statement

Thanks @gregcaporaso!
Significant changes to script interface

Changes mades to the script interface so that the --md_fields option would be required. This, coupled with a change to the library, allows an individual to passbiom files which have jagged metadata (if metadata is list or string). Laura pointed out that this was likely the most common use case, and so it needed to be supported.
Merge pull request #840 from ElDeveloper/issue_827

Add descriptive error to add_alpha_to_mapping_file
Added a space in doc string to resolve positional argument failure.
Modified so resolve jenkins failures

added script_usage_output_to_remove directories to the script.
Change -o option type for cluster_quality.py

new_path -> new_filepath
added function write small test data set files to output_dir

This function is convenient for interactive testing. If you need
some test files to work with, you can just run:

python -c "from qiime.test import write_test_data; write_test_data('.')"
Merge pull request #890 from gregcaporaso/get-test-data

added function write small test data set files to output_dir
Merge pull request #882 from ElDeveloper/cluster_quality_option

Change -o option type for cluster_quality.py
updated to officially replace per_library_stats.py with print_biom_table_summary.py

fixes #592
removing script documentation