add gitignore file
Add wrapper updates from Geert Vandeweyer. For more information please see: https://trello.com/c/bfr0jKut. Added small enhancements and the new citation tag.
Remove yield statement from citation tag. I'm so used to macros, Oo.
Specify output ftype="bam" on bowtie2 wrapper get sam output for failing test.
Merge pull request #5 from nsoranzo/master

Fixes for various tools and remove revision and toolshed tag from package definitions ...
Merge pull request #6 from jmchilton/bowtie2_output_type

Specify output ftype="bam" on bowtie2 wrapper get sam output for failing test.
mgere latest commit
fix a copy and paste error spotted by @nsoranzo
Merge pull request #7 from bgruening/master

Update cufflinks wrappers.
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.