You can use this:

Process p = Runtime.getRuntime().exec( "su" );
DataOutputStream os = new DataOutputStream(p.getOutputStream());
os.writeBytes(command1 + "\n");
os.writeBytes(command2 + "\n");
os.writeBytes("exit\n");
os.flush();

As your device is rooted you must use su command to use commands for rooted devices. I used this solution for restarting our rooted devices from our app and it worked. You can add multiple commands as you see in the code. Hope it works.

You can use this:

Process p = Runtime.getRuntime().exec( "su" );
DataOutputStream os = new DataOutputStream(p.getOutputStream());
os.writeBytes(command1 + "\n");
os.writeBytes(command2 + "\n");
os.writeBytes("exit\n");
os.flush();

As your device is rooted you must use su command to use commands for rooted devices. I used this solution for restarting our rooted devices from our app and it worked. You can add multiple commands as you see in the code. Hope it works.

Update:

You can use array of commands too. Like this:

Process proc = Runtime.getRuntime()
              .exec(new String[] { "su", "-c", command1,command2,"exit" });
proc.waitFor();

or you can use extra exec commands if you need it:

Runtime runtime = Runtime.getRuntime();
runtime.exec("su");
runtime.exec("export LD_LIBRARY_PATH=/vendor/lib:/system");
runtime.exec("pm clear "+PACKAGE_NAME);

This samples will work too, I used them before.

You can use this:

Process p = Runtime.getRuntime().exec( "su" );
DataOutputStream os = new DataOutputStream(p.getOutputStream());
os.writeBytes(command + "\n");
os.writeBytes("exit\n");
os.flush();

You can use this:

Process p = Runtime.getRuntime().exec( "su" );
DataOutputStream os = new DataOutputStream(p.getOutputStream());
os.writeBytes(command1 + "\n");
os.writeBytes(command2 + "\n");
os.writeBytes("exit\n");
os.flush();

As your device is rooted you must use su command to use commands for rooted devices. I used this solution for restarting our rooted devices from our app and it worked. You can add multiple commands as you see in the code. Hope it works.