I don't know of any tool that will convert stored procedures from Microsoft SQL Server to MySQL. Even if one existed, I'd be unlikely to trust it.
MySQL and SQL Server are similar pieces of software, but there are so many important differences that automated translation is impossible. MySQL treats as suggestions some of the SQL features that I think of as critical, and will implement those features (transactions, referential integrity, etc) some times but not always.
I would re-write the stored procedures, and either be VERY specific about how MySQL should be configured or re-write the application and the stored procedures so that they can tolerate the issues that can arise from not being able to depend on those features.