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

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  ~
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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> ${group}</small>
        </h3>
    </#if>
	<#if walkertype != "">
		<h3>Traversal
			<small>${walkertype}</small>
		</h3>
	</#if>
	<#if walkertype != "">
		<h3>PartitionBy
			<small>${partitiontype}</small>
		</h3>
	</#if>
	<#if annotfield != "" >
		<h3>VCF Field
			<small>${annotfield}</small>
		</h3>
	</#if>
	<#if annotinfo != "" >
		<h3>Type
			<small>${annotinfo}</small>
		</h3>
	</#if>

	<hr>
    <h2>Overview</h2>
    ${description}
    
	<#-- Create references to additional capabilities if appropriate -->
		<#if readfilters?size != 0 || parallel?size != 0>
			<hr>
			<h2>Additional Information</h2>
			<p></p>
		</#if>
		<#if readfilters?size != 0>
			<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}">${filter.name}</a></li>	
				</#list>
			</ul>
		</#if>
		<#if parallel?size != 0>
			<h3>Parallelism options</h3>
			<#if parallel?size == 1>
				<p>This tool can be run in multi-threaded mode using this option.</p>
			</#if>
			<#if (parallel?size > 1)>
				<p>This tool can be run in multi-threaded mode using these options.</p>
			</#if>
			<ul>
				<#list parallel as option>
					<li><a href="${option.link}">${option.name} (${option.arg})</a></li>
				</#list>
			</ul>
		</#if>
		<#if downsampling?size != 0>
			<h3>Downsampling settings</h3>
			<#if downsampling.by == "NONE">
				<p>This tool does not apply any downsampling by default.</p>
			</#if>
			<#if downsampling.by != "NONE">
				<p>This tool applies the following downsampling settings by default.</p>
				<ul>
					<li>Mode: <b>${downsampling.by}</b></li>
					<li>To coverage: <b>${downsampling.to_cov}</b></li>
				</ul>
			</#if>
		</#if>
		<#if refwindow?size != 0>
			<h3>Window size</h3>
			<p>This tool uses a sliding window on the reference.</p>
			<ul>
				<li>Window start: <b>${refwindow.start}</b> bp before the locus</li>
				<li>Window stop: <b>${refwindow.stop}</b> bp after the locus</li>
			</ul> 
		</#if>
		<#if activeregion?size != 0>
			<h3>ActiveRegion settings</h3>
			<p>This tool uses ActiveRegions on the reference.</p>
			<ul>
				<li>Minimum region size: <b>${activeregion.min}</b> bp</li>
				<li>Maximum region size: <b>${activeregion.max}</b> bp</li>
				<li>Extension increments: <b>${activeregion.ext}</b> bp</li>
			</ul> 
		</#if>
		<#if extradocs?size != 0 || arguments.all?size != 0>
			<hr>
			<h2>Command-line Arguments</h2>
			<p></p>
		</#if>
		<#if extradocs?size != 0>
			<h3>Inherited arguments</h3>
			<p>The arguments described in the entries below can be supplied to this tool to modify
			its behavior. For example, the -L argument directs the GATK engine restricts processing
			to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).</p>
			<ul>
				<#list extradocs as extradoc>
					<li><a href="${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>
				<h3>Related capabilities</h3>
				<@relatedByType name="Superclasses" type="superclass"/>
				<@relatedByType name="Subclasses" type="subclass"/>
			</#if>
		
		<#-- Create the argument summary -->
			<#if arguments.all?size != 0>
				<h3>${name} specific arguments</h3>
				<p>This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.</p>
				<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 Inputs" myargs=arguments.required_in/>
					<@argumentlist name="Required Outputs" myargs=arguments.required_out/>
					<@argumentlist name="Required Parameters" myargs=arguments.required_param/>
					<@argumentlist name="Required Flags" myargs=arguments.required_flag/>
					<@argumentlist name="Optional Inputs" myargs=arguments.optional_in/>
					<@argumentlist name="Optional Outputs" myargs=arguments.optional_out/>
					<@argumentlist name="Optional Parameters" myargs=arguments.optional_param/>
					<@argumentlist name="Optional Flags" myargs=arguments.optional_flag/>
					<@argumentlist name="Advanced Inputs" myargs=arguments.advanced_in/>
					<@argumentlist name="Advanced Outputs" myargs=arguments.advanced_out/>
					<@argumentlist name="Advanced Parameters" myargs=arguments.advanced_param/>
					<@argumentlist name="Advanced Flags" myargs=arguments.advanced_flag/>
					<@argumentlist name="Hidden" myargs=arguments.hidden/>
					<@argumentlist name="Deprecated" myargs=arguments.deprecated/>
					</tbody>
				</table>
			</#if>
	
		<#-- List all of the -->
				<#if arguments.all?size != 0>
					<#-- Create the argument details -->
						<h3>Argument details</h3>
						<p>Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.</p>
						<#list arguments.all as arg>
							<@argumentDetails arg=arg/>
						</#list>
				</#if>

			<@footerInfo />
			<@pageFooter />