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).
>dd stdio tags and a few style changes.
Get rid of the out-prefix name.
Add colon after {on_string}. Thanks Nicola!
move bamtools into tool_collections folder and split into three folders with one wrapper each
change version number back to old version schema
remove unused dependencies for bamtools_split and bamtools_filter
rename the freebayses package to adhere to standards
fix left-align XML wrapper citation
fix for freebayes and leftalign tool dependency package naming
Merge pull request #35 from bgruening/fastqc

Fastqc update
Add samtools_idxstats.
Add citation for Peter Cock as the original author of the samtools idxstats wrapper.
Citation update, change help text to CDATA.
correct bwa package definition, remove changeset_revision
rename bwa_mem folder to bwa, fix versions and ids of both wrappers inside
Merge pull request #9 from jmchilton/shed_yml

Add .shed.yml file to each repository.
Allow tophat2 to consume paired collections.

w/new test to verify collection functionality.

Also bump verion.

[View Tool Test Results](http://galaxyproject.github.io/planemo/tool_test_viewer.html?test_data_url=https://gist.githubusercontent.com/jmchilton/9d4351c9545d34209904/raw/9ed285d3cf98e435fc4a743320363275949ad63c/index)