I dont know which game. I think your talking about the spirit tracks.
Hold the stylus on it and move it down to pull the cord.
u pull that rope and use the stylus
The whistle is in the top right hand corner, in case you haven't noticed. To blow it touch the whistle with your stylus and pull it down.
The clues are stone fishes with orbs in their mouth. You have to pull your trains whistle till the orb in their mouth turns blue do this to all of them and the entrance will be activated.
If you mean when you are in the train it is simple; you just pull down on the rope hanging down from the top of your screen. This does these things: Frighten some animals off the tracks, disturbs some monsters, opens portals and more.
you have to get the tears of light with out being killed by the phantom and then you hit the phantom in the back with your sword. then princess Zelda should be inside the phantoms body. then you guide her to the door and yu both pull the door open.
If there is a flaming torch near, pull out your boomrang, and create a track with it that hits the flaming torch, then hits both of the not flaming torches. They will catch on fire.
simple. while you are driving your train you will see a rope in the corner. tap it with your pen, and......
Pull it apart, but do not pull too hard.
Its easier not to use L + R. Pull the golden circle with ur whip to let the spinner out. touch the whip button and touch the circle on the spinner. u cannot let ur stylus off the touch screen, u must hold it on, or else u'll fall!
There is a little rope at the top right hand corner of the touch screen while you are riding the train. If you pull on it the whistle will blow.