Convert videos with all contained subtitles and audio into mp4 via commandline using handbrake

I'd like to convert my videos with Handbrake from mkv to mp4. But I want all audio files and subtitles contained in the mkv into the new mp4 container!

I use Handbrake 0.9.9 GUI because in this version you can predefine the amount of audio tracks and subtitles per default under preferences ('Add all remaining' / 'Add all'. Now i'd like to achive the same via HandBrakeCLI.