common command-line interface for Pacific Biosciences analysis modules

 To integrate with the pbsmrtpipe workflow engine, one must to be able to
 generate a Tool Contract and to be able to run from a Resolved Tool Contract.
 A Tool Contract contains the metadata of the exe, such as the file types of
 inputs, outputs and options.
 There are two principal use cases, first wrapping/calling Python functions that
 have been defined in external Python packages, or scripts. Second, creating a
 CLI tool that supports emitting tool contracts, running resolved tool contracts
 and complete argparse-style CLI.