New output looks like:

```
$ python tests/all_tests.py --suppress_unit_tests --script_usage_tests add_alpha_to_mapping_file,filter_fasta,make_distance_boxplots
Scripts to test:
 add_alpha_to_mapping_file filter_fasta make_distance_boxplots


Testing 3 usage examples from: /home/jrideout/.virtualenvs/qiime/qiime/scripts/add_alpha_to_mapping_file.py
Running tests in: /tmp/script_usage_tests/add_alpha_to_mapping_file
Tests:
add_alpha_to_mapping_file usage examples do not all use %prog to represent the command name. You may not be running the version of the command that you think you are!
add_alpha_to_mapping_file.py -i adiv_pd.txt -m mapping.txt -b 4 -o alpha_mapping.txt : Pass
/home/jrideout/.virtualenvs/qiime/qiime/scripts/add_alpha_to_mapping_file.py -i adiv_pd.txt -m mapping.txt -b 4 -o alpha_mapping_quantile.txt --binning_method=quantile : Pass
/home/jrideout/.virtualenvs/qiime/qiime/scripts/add_alpha_to_mapping_file.py -i 'shannon.txt,chao1.txt' -m mapping.txt -b 4 -o collated_alpha_mapping.txt --depth=49 --collated_input : Pass

Could not import the script filter_fasta.py. Original error message:

Traceback (most recent call last):
  File "/home/jrideout/.virtualenvs/qiime/qiime/qiime/test.py", line 883, in _load_usage_examples
    script = __import__(script_name)
  File "/home/jrideout/.virtualenvs/qiime/qiime/scripts/filter_fasta.py", line 24, in <module>
    import baz
ImportError: No module named baz

Could not import the script make_distance_boxplots.py. Original error message:

Traceback (most recent call last):
  File "/home/jrideout/.virtualenvs/qiime/qiime/qiime/test.py", line 883, in _load_usage_examples
    script = __import__(script_name)
  File "/home/jrideout/.virtualenvs/qiime/qiime/scripts/make_distance_boxplots.py", line 19, in <module>
    import bleh
ImportError: No module named bleh

==============
Result summary
==============

Script usage test result summary
--------------------------------

Ran 3 commands to test 3 scripts. 0 of these commands failed and 2 scripts could not be tested due to errors.
2 scripts could not be imported. Scripts were: filter_fasta.py make_distance_boxplots.py
Warnings:
 add_alpha_to_mapping_file usage examples do not all use %prog to represent the command name. You may not be running the version of the command that you think you are!

```

@gregcaporaso are you okay with this?