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.
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.
Added new Package for new FastQC version
This commit implements some major changes over the last version that
come from an internal project. It mostly implements version 0.11.2 of
FastQC but also covers some bug-fixes and error handling, adds better
code documentation and implements another input parameter that was
introduced in the new version of FastQC: a limit.txt file that allows
to excluded modules from the output and setting of threshold for the
warning parameters.
Includes the fastqc_data.txt as output file.
Updated the integrated test. The check for the html file is
reluctant as it only contains a single line with all the
output but as the text outout file contain very similar data
this should not change much. If an error occurs in the html
file it will almost certainly also occur in the text file.