User Input Service script not working properly?

Ok, I think you got a bit mixed up with UIS.

1. Make sure you're using a localscript! Very important as UIS only runs on the client

2. The InputBegan event gives two parameters, the input and the game processed event, not the player. Just get the player through game.Players.LocalPlayer

3. UserInputType detects what type of input the player is using, such as keyboard, mouse, touchscreen, etc. To sense if the user is pressing a specific key, change the UserInputType you're checking for to keyboard, then add the following code inside:

if input.KeyCode == Enum.KeyCode.E then
    --E is pressed
end

This should work:

local UIS = game:GetService("UserInputService")
local tool = script.Parent

local function OnInputBegan(input, GPE)
    if input.UserInputType == Enum.UserInputType.Keyboard then
        if input.KeyCode == Enum.KeyCode.E then
            tool:Clone().Parent = player.Backpack
            print("E was pressed")
        end
    end
end

UIS.InputBegan:Connect(OnInputBegan)

Hopefully this helps