The effect of electron-phonon interactions in the conductance through metallic atomic wires is theoretically analyzed. The proposed model allows to consider an atomic size region electrically and mechanically coupled to bulk electrodes. We show that under rather general conditions the features due to electron-phonon coupling are described by universal functions of the system transmission coefficients. It is predicted that the reduction of the conductance due to electron-phonon coupling which is observed close to perfect transmission should evolve into an enhancement at low transmission. This crossover can be understood in a transparent way as arising from the competition between elastic and inelastic processes.