fix issue #1695

Edited files,

1. /qiime/scripts/pick_closed_reference_otus.py
   + added the option "--assign_taxonomy" to allow taxonomy assignation using a classifier, rather than copying original strings from the taxonomy map

2. /qiime/qiime/workflow/upstream.py
   + added code to run_pick_closed_reference_otus() to support taxonomy assignation using assign_taxonomy.py (almost identical from function run_pick_de_novo_otus())

3. /qiime/tests/test_workflow/test_upstream.py
  + added two tests test_run_pick_closed_reference_otus_tax_assign() and test_run_pick_closed_reference_otus_rdp_tax_assign() for assigning taxonomy using the default classifier and a custom one

4. ChangeLog

5. Additional modifications to other lines of code for pep8 compatibility 
Change to:

Added --assign_taxonomy option to pick_closed_reference_otus.py to allow taxonomy assignment using a classifier, rather than the default of using the taxonomic assignment of the cluster centroid.