gatk-3.8/settings/helpTemplates/generic.template.html

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<#include "common.html"/>

<#macro argumentlist name myargs>
    <#if myargs?size != 0>
        <tr>
            <th colspan="4" id="row-divider">${name}</th>
        </tr>
        <#list myargs as arg>
            <tr>
                <td><a href="#${arg.name}">${arg.name}</a></td>
                <td>${arg.type}</td>
                <td>${arg.defaultValue!"NA"}</td>
                <td>${arg.summary}</td>
            </tr>
            <#--
            <
            td>${arg.required}</td>
            -->
        </#list>
    </#if>
</#macro>

<#macro argumentDetails arg>
    <h3><a name="${arg.name}">${arg.name}
        <#if arg.synonyms??> / ${arg.synonyms}</#if>
    </a>
        (
        <#if arg.attributes??>${arg.attributes}</#if>
        ${arg.type}
        <#if arg.defaultValue??> with default value ${arg.defaultValue}</#if>
        )
    </h3>
    <p class="args">
        ${arg.summary}. ${arg.fulltext}
        <#if arg.rodTypes??>${arg.name} binds reference ordered data. This argument supports ROD files of the
            following types: ${arg.rodTypes}
        </#if>
        <#if arg.options??>
            <br>
            The ${arg.name} argument is an enumerated type (${arg.type}), which can have one of the following values:
            <dl class="enum">
                <#list arg.options as option>
                    <dt class="enum">${option.name}</dt>
                    <dd class="enum">${option.summary}</dd>
                </#list>
            </dl>
        </#if>
    </p>
</#macro>
<#macro relatedByType name type>
    <#list relatedDocs as relatedDoc>
        <#if relatedDoc.relation == type>
            <h3>${name}</h3>
            <ul>
                <#list relatedDocs as relatedDoc>
                    <#if relatedDoc.relation == type>
                        <li><a href="${relatedDoc.filename}">${relatedDoc.name}</a> is a ${relatedDoc.relation}</li>
                    </#if>
                </#list>
            </ul>
            <#break>
        </#if>
    </#list>
</#macro>

<?php $group = '${group}'; ?>
<@makeHeader title="${name} documentation" isIndex=false />
<section class="span4">
    <aside class="well">
        <h2>Categories</h2>
        <@getCategories groups=groups />
    </aside>
    <?php getForumPosts( '${name}' ) ?>

</section>

<div class="span8">

    <h1>${name}</h1>

    <p class="lead">${summary}</p>
    <#if author??>
        <h3>Author
            <small> ${author}</small>
        </h3>
    </#if>
    <#if group?? >
        <h3>Category
            <small> ${group}</small>
        </h3>
    </#if>
    <br/>

    <h2>Introduction</h2>
    ${description}

    <#-- Create the argument summary -->
        <#if arguments.all?size != 0>
            <hr>
            <h3>${name} specific arguments</h3>
            <table class="table table-striped table-bordered table-condensed">
                <thead>
                <tr>
                    <th>Name</th>
                    <th>Type</th>
                    <th>Default value</th>
                    <th>Summary</th>
                </tr>
                </thead>
                <tbody>
                <@argumentlist name="Required" myargs=arguments.required/>
                <@argumentlist name="Optional" myargs=arguments.optional/>
                <@argumentlist name="Advanced" myargs=arguments.advanced/>
                <@argumentlist name="Hidden" myargs=arguments.hidden/>
                <@argumentlist name="Depreciated" myargs=arguments.depreciated/>
                </tbody>
            </table>
        </#if>

        <#-- Create references to additional capabilities if appropriate -->
        	<#if readfilters?size != 0>
        		<hr>
        		<h3>Read Filters</h3>
        		<#if readfilters?size = 1>
        			<p>This Read Filter is automatically applied to the data by the Engine before processing by ${name}.</p>
        		</#if>
        		<#if (readfilters?size > 1) >
        			<p>These Read Filters are automatically applied to the data by the Engine before processing by ${name}.</p>
        		</#if>
        		<ul>
					<#list readfilters as filter>
						<li><a href="${filter.filename}">${filter.name}</a></li>	
					</#list>
        		</ul>
        	</#if>
            <#if extradocs?size != 0>
                <hr>
                <h2>Additional capabilities</h2>
                <p>The arguments described in the entries below can be supplied to this tool to modify
                its behavior. For example, the -L argument directs the GATK engine restricts processing
                to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).</p>
                <ul>
                    <#list extradocs as extradoc>
                        <li><a href="${extradoc.filename}">${extradoc.name}</a></li>
                    </#list>
                </ul>
            </#if>

            <#-- This class is related to other documented classes via sub/super relationships -->
                <#if relatedDocs?? && relatedDocs?size != 0>
                    <hr>
                    <h2>Related capabilities</h2>
                    <@relatedByType name="Superclasses" type="superclass"/>
                    <@relatedByType name="Subclasses" type="subclass"/>
                </#if>

                <#-- List all of the -->
                    <#if arguments.all?size != 0>
                        <hr>
                        <#-- Create the argument details -->
                            <h2>Argument details</h2>
                            <#list arguments.all as arg>
                                <@argumentDetails arg=arg/>
                            </#list>
                    </#if>

                    <@footerInfo />
                    <@pageFooter />