Param tuning code integration:no param tuning

[ntalluri]

No description provided.

[ntalluri]

@agitter Do this PR third (then follow up with the pull requests #209 after this one is merged)

Will need to merge with updated master after #193 and #207 is merged. (hopefully this will remove the repeated files through out the PRs)

• there will be merge conflicts with the Snakefile, evaluation.py and the test suite.

Included in this PR:

1. update to evaluation.py that updates the code to include precision_and_recall per pathway
2. a new test suite evaluate for only no parameter tuning idea
3. updates to Snakemake file that will run evaluation per dataset and per algortihm-dataset pair for no parameter tuning idea