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 lossless audio formats, you must have the appropriate helper program installed. The "Helper programs" section below contains links to helper programs for each format that shntool supports.