modified to define default moltype for functions used in QIIME

fixes #17

@josenavas, do you have a system with all of the applications installed? I'm not able to confirm that all tests pass with this PR because I don't have a system with all of the wrapped applications installed. If you have this, can you pull this branch and test? If you don't I can work on it, but won't be able to get to it right away.