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.
Merge pull request #25 from nsoranzo/master

Various fixes for bowtie_wrapper.