Allow tophat2 to consume paired collections.

w/new test to verify collection functionality.

Also bump verion.

[View Tool Test Results](http://galaxyproject.github.io/planemo/tool_test_viewer.html?test_data_url=https://gist.githubusercontent.com/jmchilton/9d4351c9545d34209904/raw/9ed285d3cf98e435fc4a743320363275949ad63c/index)