sortmerna + sumaclust added to the open refernce OTU picking pipeline
Fixing documentation
Merge branch 'master' of git://github.com/qiime/qiime into new-software-otu-picking
Solving PEP8 issues on the test file
Adding tests for sortmerna+sumaclust
Fixing merge conflicts
Merge pull request #1 from josenavas/new-software-otu-picking

Tests for new open ref workflow
added suma
Merge branch 'new-software-otu-picking' of https://github.com/ekopylova/qiime into new-software-otu-picking

pulled API updates
tests finished for pick_open_reference_otus using sortmerna and sumaclust, sortmerna_otu_id_prefix option removed - now reference sequence ID is the OTU id to be consistent with other methods
pep8
Merge branch 'master' of https://github.com/biocore/qiime into new-software-otu-picking

pull changes from upstream
removed conditional statement to allow other tools (apart from uclust,sumaclust) to be used in de novo picking
all tests passed local system
otu id changed to reference id in sortmerna_otumap_fp, tests for test_pick_otus.py all pass locally
modified default value and argument check for --sortmerna_best_N_alignments
added script usage for sortmerna/sumaclust, updated ChangeLog.md and fixed minor errors from code review
BUG/DOC: Remove reference to make_emperor.py

If the script name is written as make_emperor.py, the autogenerated
documentation will create a dead link as there's no script named
make_emperor.py in QIIME.

Removing the extension fixes this problem.
Merge pull request #1629 from ElDeveloper/make-emperor-py

BUG/DOC: Remove reference to make_emperor.py
Merge pull request #1604 from ekopylova/new-software-otu-picking

sortmerna + sumaclust added to the open reference OTU picking pipeline