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.
Now also with fastqc_data.txt
Added second test with custom limits file
Implemeted changes/bug fixes from Github discussion
Now with correct usage of shutil.copyfileobj
adjust the test for bowtie2, one line is always different (bowtie2 version and local env paths)
Merge pull request #17 from aerval/fastqc0_11_2

Fastqc 0.11.2
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.
Collection aware cuffnorm/cuffdiff.

Allow specifying a condition's bam/sam/qxb files via a multiple select. Also allow the list itself to specify conditions - probably need more sanitiziation of condition sample names coming off the collection before deploying on a real server.