new features & bug fixes

- using conditionals
- using macros for stdio, requirements, references ...
- fixing boolean parameters in commandline (using truevalue)
- concatenating nested parameters via ':' to make it work with FileFilter
- moved all input files to the top of the wrapper

I tested it with FileFilter, a more complex tool and it nearly works. There is still one bug when if the param.name is the same for different params (they are nested in CDT, but not in Galaxy) and the concatenation for nested parameters via ':' is probably only valid for OpenMS tools.