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).
Dependency definition for picard1.126
Committing picard 126 tools. All updated to comply with new picard command line usage (introduced at 1.124).
Update tool_dependencies.xml
Replaced test files with much smaller ones. Thanks Martin for noticing this.
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)
Merge pull request #40 from jmchilton/tophat2_collection

Allow tophat2 to consume paired collections.
correct the name of freebayes package 0.9.18
remove wrong version prefix for freebayes 0.9.18 package
Update tool_dependencies.xml

fix incomplete destination directory
remove invalid .shed file and create it in correct folder with correct contents
Merge pull request #34 from nekrut/picard_update

Picard update
rename package picard folder to reflect the repo name
fix invalid XML in picard wrapper
link to correctly named package with picard 1.126.0