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.
Merge pull request #20 from jmchilton/cuff_collections

Enhance cufflinks for Dataset Collections
Merge branch 'master' of https://github.com/galaxyproject/tools-devteam
Fix issues in mpileup wrapper, update citation syntax.