Fix cuffmerge bug.

Was being passed a new parameter (min_isoform_fraction) but it is still using a wrapper so the parameter was undefined.
Fix cuffquant test case.
Fix test data for cufflinks test?
Fix incorrect test parameter in cufflinks test.
Fix cuffcompare output.

Looks a lot more like it did prior to 15de3e17b7d255011775834a258cffe05e4b7c49.
Reduce lines of diff need in cuffcompare test case.
Add run.info output file.  This is needed by cummeRbund, which requires all 21 outputs for full functionality.
Fix commented out cuffdiff test case.

Test framework now supports arbitrary and unambigious conditions, repeats, etc....

Updated with fix from @nsoranzo.
Merge pull request #12 from jmchilton/cuffdiff_test

Try fixing commented out cuffdiff test case.
Merge pull request #13 from jmchilton/cufflinks_test

Fix cufflinks test case and test-data
Merge pull request #14 from jmchilton/cuffcompare_test

Fixes for cuffcompare test.
Setup cufflinks macros.
Move cuff* versions into macros.
More use of macros to reduce condition related dup in cuffdiff and cuffnorm.
Macros for consuming cufflinks GTS in cuffcompare and merge.
Use multi-data input to make cuffmerge and cuffcompare collection-compatible.

Should also make it easier to specify many traditional datasets to these tools as well outside of collections.
Allow sending multiple collections to cuffmerge/cuffcompare.

This is kind of a hack I will admit - Trello card that would allow eliminating this here https://trello.com/c/opwaxldT.
WIP: Collection aware cuffnorm/cuffdiff.