Did you try java -jar %XUGGLE_HOME%\share\java\jars\xuggle-xuggler.jar in.mov out.mp4
And to use a user-supplied (rather than guessed) video codec, pass "--vcodec libx264" for H264 video, or "--acodec libfaac" for AAC audio.
- Art
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http://www.xuggle.com/xu‧ggle (zŭ' gl) v. To freely encode, decode, and experience audio and video.
Use Xuggle to get the power of FFMPEG in Java.