working on making the API convenient to work with

currently modified the option lists to be converted to a dict for convenient overwriting of defaults
added function to support calling a QiimeCommand via an API
modified call_qiime_command so paramters can be passed in multiple ways

for convenience, users can now pass short-form parameter names (-i), long-form parameter names (--input_fp), or the name without preceeding dashes (input_fp or i).
updated to make passing of lists more convenient

previously could only pass as a comma-separated string