How do I stop a looping animation when the player clicks?

You can make a value checking if it's on or off

it's better just to show you myself

Tool = script.parent
local player = game.Players.LocalPlayer
repeat wait() until player.Character ~= nil
local hum = player.Character:WaitForChild("Humanoid")

local animation = Tool.Animation
local AnimTrack = hum:LoadAnimation(animation)

local On = false -- On value (if tool is on)

Tool.Selected:connect(function(mouse)
     mouse.Button1Down:connect(function()
    if not On then -- Checking if it's not on
          AnimTrack:Play()
      On = true -- turning value to true because it is on now
    else
      AnimTrack:Stop()
      On = false -- turning value to true because it's off now
    end
    end)
end)

Add a toggle variable. This would allow it to be clicked to start and stop over again.

Tool = script.parent
local toggle = false -- add a variable to toggle
local player = game.Players.LocalPlayer
repeat wait() until player.Character ~= nil
local hum = player.Character:WaitForChild("Humanoid")

local animation = Tool.Animation
local AnimTrack = hum:LoadAnimation(animation)

Tool.Selected:connect(function(mouse)
    if toggle == false then -- checks for the state
     mouse.Button1Down:connect(function()
        AnimTrack:Play()
    toggle = true --changes the state
    end)
  end
    if toggle == true then --changes the state
    AnimTrack:Stop()
    toggle = false -- changes the state
end
end)