Certain aspects relate to systems and techniques for aligning inputs on medical instruments. In one aspect, the method includes receiving, at a data reader of the instrument drive mechanism, alignment data from the tool when the tool is positioned within a threshold distance of the data reader. The tool include one or more inputs and one or more pull wires configured to be actuated by output shafts of the instrument drive mechanism via the one or more inputs. The method also includes receiving, at a processor, the alignment data from the data reader, and rotating, via the processor, the one or more output shafts of the instrument drive mechanism into alignment with the one or more inputs of the tool based on the alignment data. Each of the output shafts is configured to mechanically couple with a corresponding one of the inputs of the tool.