You can do it easily using ffmpeg
.
If it is not already installed, install it using apt
:
sudo apt-get install ffmpeg
To convert and rotate the file:
clockwise by 90 degrees:
ffmpeg -i input.mov -vf transpose=1 output.wmv
counter-clockwise by 90 degrees:
ffmpeg -i input.mov -vf transpose=2 output.wmv
By 180 degrees:
ffmpeg -i input.mov -vf transpose=1,transpose=1 output.wmv
There are plethora of other options to configure. You can look and tweak them according to your needs, some options to consider closely would be the following video and audio options:
-c:v wmv2 -q:v 4 -c:a wmav2 -b:a 128k
This will give quite reasonable video quality with reasonable audio quality in a relatively small file size...