The ATLAS Transformation Language (ATL) is a well-known hybrid model transformation language that allows both declarative and imperative constructs to be used in the definition of model transformations. In this paper, we present ATL transformations providing an integrated structural description of the source and target metamodels and the transformation between them. More specifically, the paper presents translation rules of Systems Modeling Language (SysML) state machines models into a class of non-autonomous Petri net models using ATL. The target formalism for the translation is the class of Input-Output Place Transition Nets (IOPT), which extends the well-known low-level Petri net class of Place/Transition Petri nets with input and output signals and events dependencies. Based on this Petri net class, a set of tools have been developed and integrated on a framework for the project of embedded systems using co-design techniques. The main goal is to benefit from the model-based attitude while allowing the integration of development flows based on SysML state machines with the ones based on Petri nets.