common command-line interface for Pacific Biosciences analysis modules
DescriptionTo 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.
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