Cyber-physical systems are vulnerable to Advanced Persistent Threats (APTs), which exploit system vulnerabilities using stealthy, long-term attacks. Anomaly-based intrusion detection systems are a promising means to protect against APTs. Still, they depend on high-quality datasets, which often fail to represent APT complexity and the evolution of the attacker strategies through time. This paper proposes a methodology to create semi-synthetic, labeled datasets that represent the complex attack graphs of APTs in cyber-physical systems. To demonstrate our approach, we replicate publish/subscribe network traffic from a real testbed with realistic noise and multi-step APT attacks based on the MITRE ATT&CK framework. The dataset captures detailed APT stages and enables the evaluation of the intrusion detection systems that revolve around false positives and the time to detection.