S-type asymptotic giant branch (AGB) stars are thought to be intermediates in the evolution of oxygen- to carbon-rich AGB stars. The chemical compositions of their circumstellar envelopes are also intermediate, but have not been studied in as much detail as their carbon- and oxygen-rich counterparts. We aim to determine the abundances of AlCl and AlF from rotational lines, which have been observed for the first time towards an S-type AGB star, W Aql. In combination with models based on PACS observations, we aim to update our chemical kinetics network based on these results. We analyse ALMA observations towards W Aql of AlCl in the ground and first two vibrationally excited states and AlF in the ground vibrational state. Using radiative transfer models, we determine the abundances and spatial abundance distributions of Al$^{35}$Cl, Al$^{37}$Cl, and AlF. We also model HCl and HF emission and compare these models to PACS spectra to constrain the abundances of these species. AlCl is found in clumps very close to the star, with emission confined within 0.1$^{primeprime}$ of the star. AlF emission is more extended, with faint emission extending 0.2$^{primeprime}$ to 0.6$^{primeprime}$ from the continuum peak. We find peak abundances, relative to H$_2$, of $1.7times 10^{-7}$ for Al$^{35}$Cl, $7times 10^{-8}$ for Al$^{37}$Cl and $1times 10^{-7}$ for AlF. From the PACS spectra, we find abundances of $9.7times 10^{-8}$ and $leq 10^{-8}$, relative to H$_2$, for HCl and HF, respectively. The AlF abundance exceeds the solar F abundance, indicating that fluorine synthesised in the AGB star has already been dredged up to the surface of the star and ejected into the circumstellar envelope. From our analysis of chemical reactions in the wind, we conclude that AlF may participate in the dust formation process, but we cannot fully explain the rapid depletion of AlCl seen in the wind.
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