Tools are a hybrid between a setting and a custom scenario. They are like a setting because you can turn them on once for the Job Flow and then never have to touch it again. They are like a custom scenario because they will check every message to see if they should be triggered or not.
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You can access the Tools menu by clicking on the tool icon within the Job Flow on the right side.

You will be able to easily view which tools you have enabled for your Job Flow by looking at the right side of the screen and seeing the icons.