Shntool is a multi-purpose WAVE data processing and reporting utility. File formats are abstracted from its core, so it can process any file that contains WAVE data, compressed or not - provided there exists a format module to handle that particular file type.
shntool has native support for .wav files. If you want it to work with other formats, you must have the appropriate helper program installed. Some of these helper programs - notably for Monkey's Audio, LPAC, OptimFROG - are not (yet) available in Debian.
With the helper programs mentioned above, shntool is able to convert files between all supported formats.