Basic YUI Widget Structure, commented up to work with yuidocs.

yui-widget-structure.js

/* global YUI */

/**
 * My Module's purpose
 * @module my-module
 * @requires base-build, widget
*/ 
YUI.add("my-module", function (Y) {
  "use strict";  

  /**
   * @class Y.MyWidget
   * @extends Y.Widget
   * @constructor
   **/
  Y.MyWidget = Y.Base.create("my-module", Y.Widget, [], {
    /**
     * Publishing events and running 
     * instantiations that doesn't require DOM.
     * @method initializer
     */    
    initializer: function () {
      // publish any events
      // do any instantiation that doesn't require DOM
    },
    /**
     * The renderUI method creates the following {Y.Node}s and appends them to the {contentBox}:
     * <ol>
     *  <li>Title Node</li>
     *  <li>Button Node</li>
     * </ol>
     * @method renderUI
     */    
    renderUI: function () {
      // create all DOM nodes
      var title = Y.Node.create("<div></div>"),
          button = Y.Node.create("<div>Click Me!</div>");
      
      // use this.getClassName(arg1s...) to create unque classes
      title.addClass(this.getClassName("title"));
      button.addClass(this.getClassName("button"));
      
      // add nodes to the page all at once
      this.get("contentBox").append(Y.all([title, button]));
      
      // store shortcuts for DOM you'll need to reference
      this._titleNode = title;
      this._buttonNode = button;
    },
    /**
     * Bind events listeners in widget.
     * @method bindUI
     */    
    bindUI: function () {
      // store references to event handlers you set on other
      // objects for clean up later
      this._buttonClickHandler = this._buttonNode.on("click", function (event) {
        Y.log("you clicked the button!");
        event.halt();
      }, this);
      // assign listeners to events on the instance directly
      // they're cleaned up automatically
      this.after("titleChange", this._afterTitleChange, this);
    },
    /**
     * The change event handler for the title attribute.
     * @private
     * @method _afterTitleChange
     * @param {Object} event Title Change Event
     */        
    _afterTitleChange: function (event) {
      this._titleNode.setContent(event.newVal);
    },
    /**
     * Method's purpose
     * @method syncUI
     */
    syncUI: function () {
      // now that the DOM is created, syncUI sets it up
      // given the current state of our ATTRS
      this._afterTitleChange({
        newVal: this.get("title")
      });
    },
    /**
     * Detaching event handlers and nulling node references.
     * @method destructor
     */
    destructor: function () {
      if (this.get("rendered")) {
        // bindUI was called, clean up events
        this._buttonClickHandler.detach();
        this._buttonClickHandler = null;
        // renderUI was called, clean up shortcuts
        this._titleNode = this._buttonNode = null;
      }
    }
  }, {
    // Public attributes that broadcast change events
    ATTRS: {
      /**
       * The title attribute of the widget.
       *
       * @attribute title
       * @type String
       * @default "No one gave me a title :("
       */      
      title: {
        value: "No one gave me a title :("
      }
    },
    // Attributes whose default values can be scraped from HTML
    HTML_PARSER: {
      title: function (srcNode) {
        return srcNode.getAttribute("title");
      }
    }
  });
  
}, "3.3.0", {
  requires: [
    "base-build", // provides Y.Base.create
    "widget"      // provides Y.Widget
  ],
  group: "nfl",     // declares the nfl group (important for skins)
  skinnable: true   // declares that your module is skinned
});

yuidoc.json

{
    "name": "YUI Doc Test",
    "description": "YUIDoc documentation tool written in Javascript",
    "version": "Version 0.0.1",
    "url": "",
    "options": {
        "linkNatives": "true",
        "attributesEmit": "true",
        "outdir": "out/"
    }
}

You'll need npm (node package manager) installed in your system before yuidoc can be installed.

Clone and install yuidoc from: https://github.com/davglass/yuidocjs. Follow the steps in the project's home page.

Put the two files above into a directory and invoke "yuidoc ." and check out the "out" directory for the output.