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
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
Merge branch 'master' of github.com:qiime/qiime into make_3d_plots
Changing import from pycogent_backports.option_parsing to import from qiime.util
Merge branch 'master' of github.com:qiime/qiime into par_alpha_div
Changing import from pycogent_backports.option_parsing to import from qiime.util
Fixing metrics option of parallel_beta_diversity.py