Create order and collect payment through API

Shopify Partner
5 1 2

Hello, we are wondering if it is possible to create an order for a customer and perform a transaction for that order automatically through Shopify API. We have the customer's payment information stored from past purchases so there is no need for the customer to provide the payment method again. From what is documented here it seems like performing a transaction is impossible. Wondering what should be the recommended solution to do this? 

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