You should go with Mechanical Engineering for GATE because Tool Engineering is a branch of a Mechanical Engineering. Its function is to plan the process of manufacture, develop various tools and machines and integrate facilities required for producing particular products with minimal expenditure of time, labour and material. Tool engineering is based on the use and application of various industrial tools within a manufacturing set-up.

In Your engineering courses what You studied will be in many aspects similar to Mechanical Engineering, so You should go for Mechanical, once have a look at the syllabus of Mechanical and if you see similarities go with it otherwise compare syllabus and go with something you like, But not this year as GATE application is already over.