can someone help me add a cooldown on this animation script?

Using debounce would be a good idea when making cooldowns:

local Tool = script.Parent
local Animation = Tool.Animation
local debounce = false

Tool.Activated:Connect(function()
    if not debounce then
        debounce = true
            local Character = Tool.Parent
            local Humanoid = Character.Humanoid

            local AnimationTrack = Humanoid:LoadAnimation(Animation)
            AnimationTrack:Play()

        wait(5) -- change cooldown time
        debounce = false
    end
end)

In this script, a variable debounce was added (you can change the variable name if you want to). It was false at first. When you activated the tool, it will check if debounce is false. If yes, if will turn debounce to true and run the animation. Then it will wait until it finished cooling down and turn it to false again.

To cooldown use a debounce, Debounce is used as a bool value variable, You can change the name to cooldown or something, It's your choice, If you need a example try this

local Tool = script.Parent
local Animation = Tool.Animation
local deboune = false

Tool.Activated:Connect(function()
    if debounce == false the

         local Character = Tool.Parent
         local Humanoid = Character.Humanoid

         local AnimationTrack = Humanoid:LoadAnimation(Animation)
         AnimationTrack:Play()

        wait(3) -- Colodwn time
        debounce = false
    end
end)