<!--
  ~ Copyright (c) 2012, The Broad Institute
  ~
  ~ Permission is hereby granted, free of charge, to any person
  ~ obtaining a copy of this software and associated documentation
  ~ files (the "Software"), to deal in the Software without
  ~ restriction, including without limitation the rights to use,
  ~ copy, modify, merge, publish, distribute, sublicense, and/or sell
  ~ copies of the Software, and to permit persons to whom the
  ~ Software is furnished to do so, subject to the following
  ~ conditions:
  ~
  ~ The above copyright notice and this permission notice shall be
  ~ included in all copies or substantial portions of the Software.
  ~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
  ~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
  ~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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  ~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
  ~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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<#--
        This file contains all the theming neccesary to present GATKDocs on the GATK website
        Included are the paths to our bootstrap assets as well as helper functions to generate relevant links

        -->

    <#global siteRoot = "http://www.broadinstitute.org/gatk/" />
    <#global guideIndex = "http://www.broadinstitute.org/gatk/guide/" />
    <#global forum = "http://gatkforums.broadinstitute.org/" />

    <#macro footerInfo>
        <hr>
        <p><a href='#top'><i class='fa fa-chevron-up'></i> Return to top</a></p>
        <hr>
        <p class="see-also">See also 
        	<a href="${guideIndex}">Guide Index</a> | 
        	<a href="index">Tool Documentation Index</a> |
        	<a href="${forum}">Support Forum</a>
        </p>

        <p class="version">GATK version ${version} built at ${timestamp}.
        <#-- closing P tag in next macro -->
    </#macro>
    
    <#macro footerClose>
    	<#-- ugly little hack to enable adding tool-specific info inline -->
        </p>
    </#macro>

    <#macro getCategories groups>
        <style>
            #sidenav .accordion-body a {
                color : gray;
            }

            .accordion-body li {
                list-style : none;
            }
        </style>
        <ul class="nav nav-pills nav-stacked" id="sidenav">
        	<#assign seq = ["engine", "tools", "utilities", "other"]>
        	<#list seq as supercat>
        		<hr>
        		<#list groups?sort_by("name") as group>
        			<#if group.supercat == supercat>
						<li><a data-toggle="collapse" data-parent="#sidenav" href="#${group.id}">${group.name}</a>
							<div id="${group.id}"
								<?php echo ($group == '${group.name}')? 'class="accordion-body collapse in"'.chr(62) : 'class="accordion-body collapse"'.chr(62);?>
								<ul>
									<#list data as datum>
										<#if datum.group == group.name>
											<li>
												<a href="${datum.filename}">${datum.name}</a>
											</li>
										</#if>
									</#list>
								</ul>
							</div>
						</li>
        			</#if>
        		</#list>
        	</#list>
        </ul>
    </#macro>