Merge branch 'fix_issue_685' of https://github.com/antgonza/qiime into fix_issue_685
Added a SourceTracker tutorial rst file and image related to that tutorial
updated to use open-reference otu picking and core_diversity_analyses.py

need to make an udpate to qiime to use change from #741.
updated to use open reference otu picking and core_diversity_analyses.py
added check_id_map.py step
changed {} to None as default function parameters and more

It is advised not to use mutable object (such as {} and []) as default
parameters to avoid possible bugs. See
http://satyajit.ranjeev.in/2012/01/12/python--dangerous-default-value-as-argument.html
for details.

Also fixed a typo
Merge branch 'master' of github.com:qiime/qiime into sourcetracker_tutorial
Removed example output from help command in order to avoid confilicts with changes to the option list in future releases.
added text to clarify the description of the filter_otus_from_otu_table.py
Improved the description of adding columns to the mapping file.
made a few minor changes to clarify descriptions and fix grammer.
Fixing --input_fps option for count_seqs.py. Not finished (currently does not support filepath pattern expansions)
Now requires minimum version of R instead of exact match, see issue #624
added the print_qiime_config.py command to the tutorial.
Fixing ci_type and metrics option type of conditional_uncovered_probability.py
Fixing test_alpha_diversity.py in test_pycogent_backports
closed reference otu picking works in serial mode
added usearch_ref usage example
fixed test failure
modified so otu_table.biom is created in top-level output dir

previously was created under the otu picking output directory which was inconsistent with other upstream workflows, and annoying.