Whether a ticket is started when a customer sends an email or I generate a ticket with API, the customer get the template "New ticket auto-reply"I'd like to be able to have another template for API generated messages, so the user gets an email with the text I send from the APII have created a copy of " osTicket Default Template (HTML)  (System Default)", 

Can I use that for responses from API? I have set up a filter which catches messages from the API, but I can't see how to proceed from here,

I feel like you are making this more difficult than you need to.If your using the API, you can assign the ticket to a custom department.At that level shut off the auto response.Use your script to send them an auto reply saying whatever you want.

Does the api give me the info I need to make a link for the customer to log into the ticket?

No.  You would have to craft your own URLs.

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