I don't think it would work because from the user's standpoint, they are only providing a single input table via --input_fp or something. This table simultaneously needs to be parsed into a biom.Table and passed to the Command, and also tied to a separate option (with no parameter) that opens the file and computes the MD5. And somewhere in there the --suppress_md5_sum option needs to be respected, and the MD5 (if it was computed) need to be added to the output summary.