If you can't do muscle-ups, work on basics and parts of the movement. For example false grip work:
http://gymnasticswod.com/content/false-grip-progressions-pt1
http://gymnasticswod.com/content/false-grip-progressions-pt2
http://gymnasticswod.com/content/false-grip-progressions-pt3

and/or transition progressions:
http://gymnasticswod.com/content/muscle-transition-progression-pt1
http://gymnasticswod.com/content/muscle-transition-progression-pt2
http://gymnasticswod.com/content/muscle-transition-progression-pt3

Or ring pull-ups.

If you can do muscle-ups, do strict or kipping muscle-ups using the 5x10 reps table:

• 3 x 2
• 5 x 2
• 3 x 4
• 4 x 4
• 4 x 6
• 5 x 6
• 4 x 8
• 4 x 10
• 5 x 10