It'd be good to have a section at the beginning here that briefly summarizes the conceptual idea of a Command is (even though this is covered on another page). You should highlight that a Command accepts input and produces output, and that it is (ideally) not tied to the filesystem, i.e., no filepaths, I/O, etc.. Give some examples of why this is desirable (parallel processing, unit testing, etc.). Make it very clear that at the Command (API) level, inputs and outputs are structured, e.g., the input is a list of tuples, or a ```biom.table.Table```, etc., **not** a file that needs to be parsed.