My ex-wife , children and I live in Israel. She has run off to France with them. Does the fact that I only have visitation rights, while she has custody, stop me from bringing child abduction proceedings to get my children back to Israel?

No, not at all. Do not be confused by terminology. You have to prove that under Israeli law you have what is termed 'rights of custody' in terms of the 1980 Hague Convention on the Civil Aspects of Child Abduction. Visitation rights in Israel count as 'rights of custody' in Hague Convention child abduction proceedings. Thus you are able to initiate Hague proceedings for the return of your abducted children to Israel, even though  you are not the custodian.  Failure to give non-custodial parents this right to get their abducted minors back would make a mockery of the convention as a custodial parent would have the green light to abduct from Israel , under cover of a custody order !