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)
Fixing ci_type and metrics option type of conditional_uncovered_probability.py
Fixing test_alpha_diversity.py in test_pycogent_backports
Merge branch 'master' of github.com:qiime/qiime into conditional_uncovered_prob
Changing import from pycogent_backports.option_parsis to qiime.util
Merge branch 'master' of github.com:qiime/qiime into conditional_uncovered_prob
Merge branch 'master' of github.com:qiime/qiime into conditional_uncovered_prob
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' of github.com:qiime/qiime into conditional_uncovered_prob
Changing metrics_list to metrics
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
Adding new option 'blast_db' and fixing parallel_blast.py
updated to fix some bugs in the commands