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.
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
Merge branch 'master' of https://github.com/galaxyproject/tools-devteam into fix-samtools-filter2
Remove revision and tool_shed tag from repository_dependencies file.
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