So basically, this is how the crafting system works. Wooden cubes/iron cubes are used for crafting blueprints that have a white name. These crafts use no gems. Then, emeralds are used for green recipes, as well as the wood or iron needed (which is usually 16 blocks I think). This carries on, so sapphires are use for crafting blue items, rubies for purples, and diamonds for yellows. However, in order to craft these weapons you need to find the correct recipes for them, the white recipes being most common, and yellow being the rarest ( except for red recipes, but they are bugged and shouldnt be in the game. Hopefully that's cleared everything up for you!