What you do is to
a) take a mysqldump of your database:
mysqldump --user my_user --password=<pass> --host=my_db schema_name > my_schema.sql
b) then use a tool such as sed to substitute MyISAM for InnoDB:
sed -i 's/ENGINE=MyISAM/ENGINE=InnoDB/g' my_schema.sql
c) restore the dump on your 5.6 instance:
mysql --user=my_user --password=<pass> my_schema < my_schema.sql
If you're on Windows, you can use vim for Windows or the editing tool of your choice.
You might be better off using a command like
sed 's/ENGINE=MyISAM/ENGINE=InnoDB/g' my_schema.sql > my_schema2.sql
or take a backup of your .sql file - with 260 GB, you never know what can go wrong - from the sed manpage
when in-place editing files, as you risk corruption or partial content
in situ- ations where disk space is exhausted, etc.