Merge branch 'fix_issue_685' of https://github.com/antgonza/qiime into fix_issue_685
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
Modified compare_alpha_diversity.py

This commit modifies compare_alpha_diversity.py so that it will output the average alpha diversity of the compared categories. I find myself wanting this information frequently when doing tests and it wasn't available. These changes modify the output of the script so that you pass a directory to be created and it puts two files in that directory. One specifying the comparisons and their values, and one specifying the averages and std's of the averages for each treatment group. I have updated the script usage tests and verified that they work so that jenkins should be happy.

In addition, I needed to modify core_diversity_analysis.py because it depended on the output. I only had to modify several lines in the workflow/core_diversity_analysis.py code to alter the way it was handling the output directories.
Removed old test files which have been migrated.
Modified tests

Tests now use assertFloatEqual where appropriate which will hopefully resolve the failures with the latest jenkins build for compare_alpha_diversity.py. Also changed some locations in test_workflow/test_core_diversity_analysis.py to reflect changes in output structure of compare_alpha_diversity.py
Modifies test_downstream.py to account for alpha div changes.
Update denoise_wrapper.py

Fixed filepaths-problem when using multiple flowgram-files in the commandline. 
Lines 47,99-113
Modifies to address comments.
Forgot a documentation change.
Modified documentation in script and Changelog.md
Commiting modified test_downstream.py

Avoids automerge conflict resulting from simultaneous edits.
Merge branch 'master' of https://github.com/qiime/qiime into compare_alpha_div_improvement

Conflicts:
	tests/test_workflow/test_downstream.py
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