The measured fluxes of secondary particles produced by the interactions of Cosmic Rays (CRs) with the astronomical environment play a crucial role in understanding the physics of CR transport. In this work we present a comprehensive calculation of the secondary hadron, lepton, gamma-ray and neutrino yields produced by the inelastic interactions between several species of stable or long-lived cosmic rays projectiles (p, D, T, 3He, 4He, 6Li, 7Li, 9Be, 10Be, 10B, 11B, 12C, 13C, 14C, 14N, 15N, 16O, 17O, 18O, 20Ne, 24Mg and 28Si) and different target gas nuclei (p, 4He, 12C, 14N, 16O, 20Ne, 24Mg, 28Si and 40Ar). The yields are calculated using FLUKA, a simulation package designed to compute the energy distributions of secondary products with large accuracy in a wide energy range. The present results provide, for the first time, a complete and self-consistent set of all the relevant inclusive cross sections regarding the whole spectrum of secondary products in nuclear collisions. We cover, for the projectiles, a kinetic energy range extending from $0.1 GeV/n$ up to $100 TeV/n$ in the lab frame. In order to show the importance of our results for multi-messenger studies about the physics of CR propagation, we evaluate the propagated spectra of Galactic secondary nuclei, leptons, and gamma rays produced by the interactions of CRs with the insterstellar gas, exploiting the numerical codes DRAGON and GammaSky. We show that, adopting our cross section database, we are able to provide a good fit of a complete sample of CR observables, including: leptonic and hadronic spectra measured at Earth, the local interstellar spectra measured by Voyager, and the gamma-ray emissivities from Fermi-LAT collaboration. We also show a set of gamma-ray and neutrino full-sky maps and spectra.