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It looks like https://github.com/ros-drivers/audio_common/blob/hydro-devel/audio_capture/src/audio_capture.cpp is a thin wrapper around GStreamer, which is very flexible, but the wrapper itself is mostly hardcoded. The source is set to alsasrc (when you would want it to be filesrc, unless you can play your file into alsasrc), and the only parameter is for bitrate, but that is mp3 bitrate.

The encoder is set to lame, which I think means only mp3:

    _encode = gst_element_factory_make("lame", "encoder");

It might be a learning curve to use the gstreamer api but maybe not too hard to hack the existing audio_capture to do what you want (and maybe there are gstreamer experts on stackoverflow)- or even better extend it and push the changes back into the public repo.