Made modifications to scripts, merged library functions into single workflow file per discussion with Greg C. Should cover automation of commands for multiple input fastq files for join_paired_ends.py, extract_barcodes.py, and split_libraries_fastq.py. Putting all of these under #1715 as they are related code/functionality.
new differential_abundance, now written with Rscript instead of rpy2.  tests also added.
Initial commit

Provides baseline functionality without tests.
Updated function names/calls.
small update

removed a useless function, renamed a function, figured out which tests were missing.
Add script usage tests + modifications

This commit adds script usage tests and modifies the help text as well as minor tweaks to functionality for correlations.py
add changes to ChangeLog and /doc/install/install.rst
Merge branch 'master' into correlations
Addressed formatting comments
Updated Changlog message
Merge branch 'master' into correlations
MAINT: more specific name for compute_index.py
Updates after review

Updates the name of the script and adds tests to several untested functions. Add's to help documentation. Removes the paired t functionality.
changelog update
Merge branch 'master' into correlations
documentation addition

added a lot of help documentation to mimic group_significance.py.
Merge branch 'master' into correlations
Merge branch 'master' of github.com:qiime/qiime into index_name_change
Renaming teh things
Merge branch 'master' into correlations