BUG/DOC: Remove reference to make_emperor.py

If the script name is written as make_emperor.py, the autogenerated
documentation will create a dead link as there's no script named
make_emperor.py in QIIME.

Removing the extension fixes this problem.
Merge pull request #1629 from ElDeveloper/make-emperor-py

BUG/DOC: Remove reference to make_emperor.py