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
Fixing --input_fps option for count_seqs.py. Not finished (currently does not support filepath pattern expansions)
Merge branch 'make_bipartite_network.py' of git://github.com/wdwvt1/qiime
Update denoise_wrapper.py

Fixed filepaths-problem when using multiple flowgram-files in the commandline. 
Lines 47,99-113
Merge branch 'master' into illumina-tutorial-updates

Conflicts:
	examples/ipynb/illumina_overview_tutorial.ipynb
more updates to the tutorial following re-organization of data in the tutorial tgz
fixed typos
Merge branch 'master' of git://github.com/qiime/qiime
updated to fix some bugs in the commands
removed output from each command
includes output for a full successful run
Merge branch 'master' of git://github.com/qiime/qiime
Add check where all samples are filtered out

Add a test to the test suite with this case.
Add try except block for --valid_states input

Fixes #779
fix issue 705 by moving where consensus tree is placed
Updating blast_db option type in all needed scripts
Fixing a small bug in blast_db option type
Clarified error message.