Third-Party Software Fees

I'm a doctor in a solo private practice. I use third-party practice management software for billing and payments. The system keeps my patients' credit cards on file electronically. After a visit, I charge the card on file for the respective client directly through my practice management software. My question is, what are the Square fees for such a transaction? Would this be considered a swipe transaction or a manually-entered transaction? Also, would Square consider a custom transaction fee to match or beat the rate of my current credit card processor?

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