I am making an application in PHP that hides a string in audio file. I have seen several command line tools like SoX, AC3, ffmpeg, but they don't seem to support the functionality of adding text. Below are some links to their command line interface descriptions:
I am looking for a tool that allows me to hide text within the MP3 or .wav
audio files.
Unless you want to simply put data in the headers (eg, the MP3 ID3 tags), then you are interested in audio watermarking. The wikipedia entry isn't particularly useful:
http://en.wikipedia.org/wiki/Audio_watermark
This answer gives some clues:
Audio watermarking open source projects
Commercial watermarking systems exist that are extremely robust, and can survive even when audio is converted between formats, D/A/D'ed, band-limited, eq'ed and so on. I'm not aware of an open source project that comes anywhere close to this, but I haven't researched it recently.
For uncompressed formats, you can use LSB stenography:
http://www.jsums.edu/cms/tues/docs/Steganography/LSB-Steganography.pdf