Fixing option types and example definition

This pull request solves item `make_bootstrapped_tree.py` of #632

On the other hand, I think this script won't work in Galaxy because it automatically appends `.pdf` to the output file if it is not defined. This functionality is implemented in `cogent` and that's why I haven't make any change to solve that.

On the other hand, how much important is this script and how many people are still using it?