Merge pull request #8 from pavanvidem/deseq2

Added new option and improved some texts.
add tool dependency definition for Aragorn, as requested by Nicola Soranzo
Merge branch 'master' of https://github.com/bgruening/galaxytools
add cmstat wrapper
first version for cmbuild, added datatypes for STOCKHOLM and CM
add remove ending tool
add a bunch of test files from Assafs original collection
add two new tools
include Assafs License conditions
style fixes
add tRNAscan tool dependency definition and update the trna_prediction wrappers
update readme files
add repository for Multiple Sequence Alignment file formats
add readme file and stockholm example file
move the definition of MSA datatypes to an own repository and depend on it
add str() to conditionals
change default amount of used cpu to 4
add safeguard
add obsolete but still in use uniq tools
deprecate the biopython tool definition, it now hosted under the biopython umbrella