Transcoding MKV w/ subtitle and multiple audio tracks

[abraun]

Good morning, everybody!
I've used VLC for some time now as a GUI tool for viewing and transcoding files with much success, but I find myself in a position now where the GUI does not provide me the kind of control I need and I'd like to use the command line to get things done. Unfortunately, my experience with VLC from the command line is rather limited and insufficient to this current task. I was hoping that somebody out there might be able to help me out

In short, I have some .mkv files which have two audio tracks (English and Japanese) and a subtitle track. I'd like to be able to convert this file for use on my AppleTV - which basically means something that'll work in iTunes... which itself means QuickTime. QT itself, iTunes and the ATV will handle a media file with these characteristics, but I'm unsure as to how to actually get the conversion done. The best possible solution would be to preserve both language tracks and the subtitle track so that I can use the display software to pick which one(s) I want to use at viewing time. If that's not possible, I guess that dropping the primary (Japanese) audio track in favor of the secondary (English) audio track and dropping the subtitles altogether would be a workable (though inferior) alternate solution.

So... Does anybody have any suggestions as to what that command might look like? I'm using OS X and the most recent VLC if that makes any difference.

Thanks in advance!