Update Tophat2 tests.

 - There was an ambigious parameter read_mismatches when full parameters were specified that was specified twice, so I broke all the test parameters out into conditional blocks to disambiguate.
 - Added library test data so the two parameters depending on indices work with stand-alone and/or planemo testing.
 - Last test seemed to cause tophat2 to fail with message "the read mismatches (5) and the read gap length (2) should be less than or equal to the read edit dist (2)" - so I set the edit distance parameter to 5 to match read mismatches.
 - Updated test data to reflect these changes.