Add .shed.yml file to each repository.

PRO: keeps track of which directories map to which repositories.
PRO: simple uploads with planemo
  - Configure global tool shed credentials in ~/.planemo.yml
  - Upload a directory to either shed with `planemo shed_upload --shed_target [testtoolshed|toolshed]`
CON: Kind of makes it harder to upload these repositories to the tool shed without planemo (got to make sure to exclude .shed.yml from tar if tarring outside planemo).
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.
Add citations to a few more tools.
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
Update samtools to 1.1
Also update mpileup and rmdup.
Fix tool data table definition for samtools calmd.
Remove file that doesn't belong in test-data.
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.
new package for cufflinks 2.2.1
Merge pull request #25 from nsoranzo/master

Various fixes for bowtie_wrapper.
major update to bowtie2. no tests yet
add new tools and remove revison and toolshed attributes