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 branch 'master' of https://github.com/galaxyproject/tools-devteam
Fix issues in mpileup wrapper, update citation syntax.
major update to bowtie2. no tests yet
add new tools and remove revison and toolshed attributes
Merge branch 'master' of https://github.com/galaxyproject/tools-devteam into fix-samtools-filter2
Merge pull request #29 from bgruening/fix-samtools-filter2

Update the cuff-tools suite definition file.
Merge pull request #30 from bgruening/master

Remove revision and tool_shed tag from repository_dependencies file.
added test and test files
modified bowtie wrapper per bgruening and jmchilton suggestions
added package_bowtie2_2_4
new version string for bowtie2
added bwa and bwa-mem after removing command line options. planemo tests are passed. i will close my own bwa-mem github repo and will only maintain these under tools-devteam github repo after this PR is accepted
Merge pull request #28 from InitHello/master

Update SAMtools wrappers to use version 1.1
Moved bwa_7_10 package to packages dir
changed version string of bowtie2 per Marten's request
Merge branch 'master' of https://github.com/nekrut/tools-devteam into nekrut-master

Resolved Conflicts in :
	tools/bowtie2/bowtie2_wrapper.xml