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Google Webmaster Tool shows traffic for each keyword separately, it gives more information about website performance according to Google search query. This tool does not cover search query result from others search engines, such as Bing, Yahoo, or Baidu.
Google Analytics shows total traffic of a website such as clicks to your site regardless of where they came from and what search terms were used. It shows whatever search terms brought up your site in the listings. While your keywords might be there too, many will probably be specific terms or long-tail search terms. There are probably even search terms where Google offered your site even though they don't see a perfect match. If Google thinks the searcher meant something else, maybe they displayed your site for that word or term as a suitable match even though that word is not listed in Webmaster Tools as even being on your site.