Fixing option types and example definition
Fixing --metrics option type for beta_diversity.py
Fixing scaling_method and vectors_algorithm option types for make_3d_plots.py
Fixing metrics option type of parallel_alpha_diversity.py
Merge branch 'master' of github.com:qiime/qiime into par_alpha_div
Fixing the way params is passed in parallel_alpha_diversity.py
Merge branch 'master' of github.com:qiime/qiime into make_3d_plots
Adding eldeveloper's comments
updated to address #831
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.
added note on new placement of otu_table.biom
fixed bug where params file could be ignored
Merge pull request #832 from gregcaporaso/issue-831

updated to address #831
Merge branch 'master' of github.com:qiime/qiime into make_bootstrapped_tree
Avoid appending .pdf to the file name and fix documentation
Merge branch 'master' of github.com:qiime/qiime into beta_diversity
Changing metric_list to metrics and adding tests for string and list cases