Decoding software works with .wav files
While that is true, just the audio from the headphone port will not work for that purpose. Any audio that comes out of the speakers or earphones of your scanner has been run through filters that actually will clip or distort the digital data, and it will not decode properly.
To capture the data stream, you will need to modify your scanner to add a "
discriminator tap" which will pull off the unfiltered audio, which you could then use for that purpose. The project is not for the faint of heart (opening the case, thus voiding any warranty, soldering components and wires onto the board, etc.)
You're better off getting an
SDR radio (around $25-30) and plugging it straight into the computer. There's a number of software applications that will record/decode the audio properly using the SDR.