Different hypotheses about a quantum system such as the logical state of a qubit or the value of physical interaction parameters can be investigated by the interaction with a probe field. Such fields may be prepared in particularly sensitive quantum states and we demonstrate here the use of quantum trajectories to model the stochastic measurement record and conditional evolution of the state of the quantum system subject to its interaction with a traveling pulse of radiation. Our analysis applies to different measurement strategies and to arbitrary input quantum states of the probe field pulse and it thus permits direct comparison of their metrological advantages. A theoretical lower limit to the mean discrimination error can be calculated in a deterministic manner and we verify that it lies below the average inference error in all our examples.