added tool dependencies and new functions

Hi Aaron,

this PR adds tool-dependencies to the bedtools Galaxy wrappers. It will automatically download and compile version 2.18.2 of bedtools.
Furthermore, <version_command> was added, tool-versions are increased and some code cleanup. The intersect tool is rewritten to offer new features.

You can test the latest wrapper under my test repository under:
http://testtoolshed.g2.bx.psu.edu/view/bgruening/bedtools_test_bag

Thanks!
Bjoern