initial commit
first check in, ported from QiimeUtils
moved core functionality to its own function to prepare for port to QIIME.
ported the core functionality to qiime.
updates to code to reflect changes in the run_script_usage_tests function.
added test input and output
added test input and output for parallel_assign_taxonomy_blast
added test input and output for parallel_assign_taxonomy_rdp
added test input and output for parallel_blast
added test input and output for parallel_identify_chimeric_seqs
added test input and output for parallel_pick_otus_blast
added test input and output for parallel_pick_otus_uclust_ref
bug fix.
added test input and output
added script input/output for compute_core_microbiome.py
remove output files corresponding to old interface
added output corresponding to new interface
fixed a few issues with parameter help text and default value
print output only when the user specifies verbose to adhere to qiime coding standards
added tests of new functional_assignment.py script