The following code allows me to print the secondary menu.
<?php print theme('links__system_secondary_menu', array('links' => $secondary_menu, 'attributes' => array('id' => 'secondary-menu', 'class' => 'menu nav navbar-nav secondary hidden-xs'))); ?>
I get the following output.
<ul id="secondary-menu" class="menu nav navbar-nav secondary hidden-xs">
<li class="menu-6734 first"><a href="/" title="">link 1</a></li>
<li class="menu-6735 first"><a href="/" title="">link 2</a></li>
<li class="menu-6736 first"><a href="/" title="">link 3</a></li>
</ul>
Now, I need to add dropdown to the last menu item but I have no idea how to do it. Any guidance much appreciated!