Custom Pane (minimizes itself) http://stackoverflow.com/questions/24756285/javafx-how-to-make-a-netbeans-like-tool-window

customPane.fxml

<?xml version="1.0" encoding="UTF-8"?>

<?import java.lang.*?>
<?import javafx.scene.control.*?>
<?import javafx.scene.layout.*?>
<?import javafx.scene.shape.*?>

<fx:root prefHeight="400.0" prefWidth="400.0"
	type="javafx.scene.layout.AnchorPane" xmlns="http://javafx.com/javafx/8"
	xmlns:fx="http://javafx.com/fxml/1">
	<children>
		<Rectangle fx:id="separator" arcHeight="5.0" arcWidth="5.0" fill="WHITE"
			height="33.0" layoutY="1.0" stroke="BLACK" strokeType="INSIDE" width="600.0" />
		<Button fx:id="closePane" layoutX="573.0" layoutY="6.0"
			mnemonicParsing="false" text="X" />
		<Button fx:id="minPane" layoutX="545.0" layoutY="6.0"
			mnemonicParsing="false" text="__" />
		<Label fx:id="title" layoutX="14.0" layoutY="12.0" text="Title" />
		<Pane fx:id="contentPane" layoutY="34.0" prefHeight="366.0"
			prefWidth="600.0" />
	</children>
</fx:root>

CustomPane.java

import java.net.URL;
import java.util.ResourceBundle;

import javafx.collections.ObservableList;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.fxml.FXML;
import javafx.fxml.FXMLLoader;
import javafx.fxml.Initializable;
import javafx.scene.Node;
import javafx.scene.control.Button;
import javafx.scene.control.Label;
import javafx.scene.layout.AnchorPane;
import javafx.scene.layout.Pane;
import javafx.scene.shape.Rectangle;


public class CustomPane extends AnchorPane implements Initializable {
    @FXML Button closePane;
    @FXML Button minPane;
    @FXML Label title;
    @FXML Pane contentPane;
    @FXML Rectangle  separator;
    private boolean restoreFlag = false;
    private double prefX;
    private double prefY;
    public CustomPane(String title){
        FXMLLoader fxmlLoader = new FXMLLoader(getClass().getResource(
"CustomPane.fxml"));
        fxmlLoader.setRoot(this);
        fxmlLoader.setController(this);
        try {
            fxmlLoader.load();
        } catch (Exception exception) {
            throw new RuntimeException(exception);
        }
        this.title.setText(title);
        setButtonsLayout();
        setStandardLayout();
    }
    public CustomPane(String title, double y, double x){
        FXMLLoader fxmlLoader = new FXMLLoader(getClass().getResource(
"CustomPane.fxml"));
        fxmlLoader.setRoot(this);
        fxmlLoader.setController(this);
        try {
            fxmlLoader.load();
        } catch (Exception exception) {
            throw new RuntimeException(exception);
        }
        this.title.setText(title);
        this.setPrefSize(x, y);
        setButtonsLayout();
        setStandardLayout();
        restoreRoot();
    }
    @Override
    public void initialize(URL location, ResourceBundle resources) {
        closePane.setOnAction(new EventHandler<ActionEvent>(){
            @Override
            public void handle(ActionEvent event) {
                setInvisible();
            }
        });
        minPane.setOnAction(new EventHandler<ActionEvent>(){
            @Override
            public void handle(ActionEvent event) {
                if(restoreFlag){
                    restoreFlag = false;
                    minPane.setText("_");
                    restoreRoot();
                }
                else{
                    restoreFlag = true;
                    minPane.setText("▭");
                    minimizeRoot();
                }
            }
        });
        
    }
    protected void minimizeRoot() {
        this.setPrefSize(prefX/2, title.getPrefHeight() + 5.0);
        separator.setWidth(prefX/2 + 5);
        this.setLayoutX(0);
        this.setLayoutY(prefY-40);
        setButtonsLayout();
        contentPane.setVisible(false);
    }
    protected void restoreRoot() {
        this.setPrefSize(prefX, prefY);
        separator.setWidth(prefX);
        contentPane.setVisible(true);
        this.setLayoutX(0);
        this.setLayoutY(0);
        setButtonsLayout();
    }
    private void setStandardLayout() {
        prefX = this.getPrefHeight();
        prefY = this.getPrefWidth()-50;
    }
    public void setButtonsLayout(){
        closePane.setLayoutX(this.getPrefWidth()-30);
        minPane.setLayoutX(this.getPrefWidth()-55);
    }
    public void setInvisible(){
        this.setVisible(false);
    }
    public ObservableList<Node> getContent(){
        return contentPane.getChildren();
    }
}

CustomTest.java

import javafx.application.Application;
import javafx.scene.Scene;
import javafx.scene.control.TreeItem;
import javafx.scene.control.TreeView;
import javafx.scene.layout.Pane;
import javafx.stage.Stage;


public class CustomTest extends Application{

    @Override
    public void start(Stage primaryStage) throws Exception {
       Pane p = new Pane();
       CustomPane cp = new CustomPane("Costumer Window",400,500);
       TreeItem<String> rootItem = new TreeItem<String> ("Inbox");
       rootItem.setExpanded(true);
       for (int i = 1; i < 6; i++) {
           TreeItem<String> item = new TreeItem<String> ("Message" + i);            
           rootItem.getChildren().add(item);
       }        
       TreeView<String> tree = new TreeView<String> (rootItem); 
       tree.setPrefSize(400,500);
       cp.getContent().add(tree);
       p.getChildren().add(cp);
       Scene scene = new Scene(p);
       primaryStage.setScene(scene);
       primaryStage.show();
    }
    public static void main(String[] args){
        launch(args);
    }
        
}