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 #23 from bgruening/fix-samtools-filter2

Fix https://trello.com/c/wJNnl2Dp
Add citations to a few more tools.
Update README.md

added link to ENCODE tools repo
Add bx-python dependency for fasta_concatenate_by_species.
Update links to Tophat manual.
Remove trailing whitespaces.
Add params for --nofw and --norc options also for single-end reads.
Add <conditional> to specify -k only when not using -a .

When specifying both options, bowtie discards -k .
Also add min value for -k .
Show fields for --pairtries and --maxbts options only when noTryHard.

Bowtie discards these 2 options when -y is also specified.
Also add min value for both options.
Fix ftype typos.
Remove basic <parallelism> tag, which does not work with multiple inputs.

Fix testing with planemo.
Merge pull request #24 from bgruening/citations

Add citations to a few more tools.
Update bowtie2 in help citation per @nsoranzo suggestion.
Add citation to bowtie wrapper - per @nsoranzo's suggestion.
Merge pull request #27 from jmchilton/pr24followup

Follow up suggestions on Pull Request 24
Merge pull request #20 from jmchilton/cuff_collections

Enhance cufflinks for Dataset Collections
new package for cufflinks 2.2.1