<?php
    // connect your database here first 
    //

    // Actual code starts here

    $sql = "SELECT TABLE_NAME FROM INFORMATION_SCHEMA.TABLES
        WHERE TABLE_SCHEMA = 'your_database_name' 
        AND ENGINE = 'MyISAM'";

    $rs = mysql_query($sql);

    while($row = mysql_fetch_array($rs))
    {
        $tbl = $row[0];
        $sql = "ALTER TABLE `$tbl` ENGINE=INNODB";
        mysql_query($sql);
    }
?>