This paper demonstrates how argumentation schemes can be used in decision support systems that help clinicians in making treatment decisions. The work builds on the use of computational argumentation, a rigorous approach to reasoning with complex data that places strong emphasis on being able to justify and explain the decisions that are recommended. The main contribution of the paper is to present a novel set of specialised argumentation schemes that can be used in the context of a clinical decision support system to assist in reasoning about what treatments to offer. These schemes provide a mechanism for capturing clinical reasoning in such a way that it can be handled by the formal reasoning mechanisms of formal argumentation. The paper describes how the integration between argumentation schemes and formal argumentation may be carried out, sketches how this is achieved by an implementation that we have created and illustrates the overall process on a small set of case studies.