Add jackknifing script interface infrastructure

Add the multiple checks for things that can go wrong when passing in
multiple files.
Merge branch 'light_fixes' into issue_11
Merge branch 'light_fixes' into issue_11
Change format_pcoa data to write ellipses data

This is a change that will only happen if ellipses data is available,
else no ellipses data will be written to the output.
Add option to perform jackknifing on the pcoa data

Test suite was updated accordingly.
Add jackknifing option to the script interface

The script interface is now capable of producing jackknifed plots, an
option to select what method you want to use for this calculation was
added as well.

The main input option, no longer takes a single file only, now it is
capable of taking a directory with multiple files in it. Several
different checks are being performed from the script interface.

This should fix #11
Merge branch 'light_fixes' into issue_11
Change preprocess_coords to be --master_pcoa aware

This function will now consider the first element of the coords
attributes the master pcoa i. e. the coordinates that serve as the
center for the ellipsoides.
Add option --master_pcoa (-s) to the interface

Passing a file with this optional option will serve to indicate the
center of the ellipsoides, passing nothing will randomly select one as
the center.
Add script_usage entries for jackknifing
Merge branch 'master' of git://github.com/qiime/emperor into issue_11
Add check to prevent custom_axes and jackknifing

This feature was originally avoided from make_3d_plots.py to support
this, the functionality would have to be changed in the
qiime.util.summarize_pcoa function.
Add ability to use a custom axis with jackknifing

A custom axis can now be added to jackknifed plots,
preprocess_coords_file is now updated to handle this type of data
requests. The test suite was updated accordingly.

The script interface will no longer disallow a custom axis and
jackknifed plots. However no more than one custom axis can be used and
that's still forbidden by the script interface.
Fix script interface for jackknifing

Checking the number of custom_axes was failing when None was specified,
this has been fixed in this commit.

Thanks for catching this one @antgonza.
Merge pull request #39 from ElDeveloper/issue_11

Add jackknifing functionality -- fixes issue 11
Change output filename: emperor.html -> index.html

This fixes #43
Merge pull request #46 from ElDeveloper/issue_43

Change output filename: emperor.html -> index.html