Even though dodge technically reduces the auto-attack damage you take on Malphite by a higher amount than armor. I'd still recommend getting armor runes instead because it improves the damage on groundslam. Frozen Heart is also a must because Malphite's cooldowns are really long.

Never take Ninja tabi on malphite! I know it provides armor, its cheap and it provides dodge, but in most games you need merc treads to deal with cc and get extra magic resist. The other good boot option for malphite is Ionian boots: Almost as cheap, 15% cooldown for faster shards and groundslams (more survivability), and a shorter ult cd to allow you to use it in fights more.

Ap seems popular for malphite in guides, but the truth is that in most games Groundslam can do a much higher percentage of your magic damage than shard and Ult combined. Malphite does great building armor for damage, and a little physical damage on him can go a long way. (AOE auto-attacksdamage buff).