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.
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
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
Standardize option longnames on underscores

Fix #1786
Update changelog with dash to underscore changes

Conflicts:
	ChangeLog.md
Remove option-label entry from script_info

Was used by n3phele, not needed any more
Renaming teh things