niu-lab/msisensor2 ? reverse-engineered prompt

Build me a simple command line tool for MSI detection from tumor only sequencing data, like the one described here. I want to be able to give it a tumor BAM file and a model directory, then get back an MSI score, a distribution file, and a list of somatic microsatellite sites. It should work with hg38, hg19 or GRCh37, and b37 or HumanG1Kv37 models, and it should handle common tumor only use cases like WES, WGS, panels, FFPE, and cfDNA.

Please also include a small R plotting script or example so I can visualize the MSI score output after running it. Make the usage easy to follow from the terminal, with a clear help message and an example command. If you need to look up current docs online for anything unclear, go ahead.