We study the transport properties of a Bose-Einstein condensate formed by an ultracold gas of bosonic atoms that is coupled from a magnetic trap into a one-dimensional waveguide. Our theoretical approach to tackling this problem is based on the truncated Wigner method for which we assume the system to consist of two semi-infinite noninteracting leads and a finite interacting scattering region with two constrictions modeling an atomic quantum dot. The transmission is computed in the steady-state regime and we find a good agreement between truncated Wigner and matrix-product state calculations. We also identify clear signatures of inelastic resonant scattering by analyzing the distribution of energy in the transmitted atomic-matter wave beam.