Note: This article is obsolete. As of JAMS V5.0, auto reset triggers are reset when the job(s) that the trigger submitted complete. So, as long as your triggered job actually processes the file that fired the trigger, you won't generate a loop. If your job doesn't process the file and JAMS detects a trigger loop, it will disable the trigger.
In the definition of a JAMS trigger the "Status" tab has an option to reset the trigger after it fires:

This option does not apply to triggers that have any "File" events because the Trigger would continuously fire multiple times as the file would still be present. The simplest way to reset a trigger that relies on "File" events is to run a PowerShell Job afterwards that resets the trigger using the "Reset-JAMSTrigger" cmdlet. This could be done by creating a new Job with PowerShell as it's execution method. The source for this job would be:
Reset-JAMSTrigger -Name YourTriggerName
After running this job your trigger would then be active.