there is no "official" API for the OWL2SHACL converter, but you can invoke the same web service that also the manual feature is using from ADS scripts:
graph.swp('ontologyprojects:OWL2SHACLPage', {
projectGraph: graph.namedNode('urn:x-evn-master:aaaaa'),
graphs: 'urn:x-evn-master:aaaaa',
replace: false,
})
(Replace the aaaaa with the Ontology that contains the OWL triples after RDF file import).
To fully automate this, you could probably wrap this into a dash:Service including the file upload, but this depends on your use case.
If I may ask, how many files do you need to convert and does this happen repeatedly?
HTH
Holger