I will answer myself, in case someone is having the same kind of problem: I got what I wanted from the signal using a different software, which converted the pulse signal to angular speed (deg/s) signal. By taking the fft of this angular speed signal I got a nice graph showing the frequency content which I was looking for.
I do not know exactly what kind of operation the software did, but apparently it is about frequency to voltage conversion. All I had to tell the program was the number of teeth on the gearwheel. I can find plenty of information about this conversion in Google, but almost all of it is about electronics, I guess it is a pretty popular thing to do in that domain.
I will maybe try to do the conversion sometime on my own using Matlab, I can post the solution here if I manage to come up with a solution.