Rename script interface arguments

The naming is more standard now
Fix different aspects of the documentation

Mainly:
    - Made all lines fewer than 80 columns.
    - Change strings in the documentation to reflect the actual
      filenames that these are processing (it seems that it was still
      pointing to .txt contingency tables)

Fixes #304
Add note about the interface change.
Fixes issue with emtpy tables if data points are missing. Fixes #1197
Test catches raised error when data points are missing. Fixes #1197.
Modifications and test additions to resolve issue #1160
Fixed script usage test
Fixed contrib
Modified test and function.

There is an untested function in this code that makes boxplots. The build failed because that function called the modified function from the previous commit.
Stylistic fix
Merge branch 'master' into issue_1160
Merge branch 'master' into issue_1160
addresses #1247
Fixed script usage strings
Merge branch 'master' into issue_1160
Resolved @wasade's comments.
parse_coords is now more flexible on input type
improved parsing of taxonomy files
updated test
modified test to confirm that spaces are stripped