121 lines
3.6 KiB
HTML
121 lines
3.6 KiB
HTML
<#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>
|
|
${arg.summary}. ${arg.fulltext}<br>
|
|
<#if arg.options??>
|
|
<p>The ${arg.name} argument is an enumerated type (${arg.type}), which can have one of the following values:</p>
|
|
<dl class="enum">
|
|
<#list arg.options as option>
|
|
<dt>${option.name}
|
|
<dd>${option.summary}
|
|
</#list>
|
|
</dl>
|
|
</#if>
|
|
</#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 ${relatedDoc.relation}</li>
|
|
</#if>
|
|
</#list>
|
|
</ul>
|
|
<#break>
|
|
</#if>
|
|
</#list>
|
|
</#macro>
|
|
|
|
<html>
|
|
<@makeHeader title="${name} documentation"/>
|
|
<body>
|
|
<h1>${name}</h1>
|
|
<@headerInfo />
|
|
<p class="summary">${summary}</p>
|
|
<#if author??>
|
|
<h2>Author</h2>
|
|
${author}
|
|
</#if>
|
|
<h2>Introduction</h2>
|
|
${description}
|
|
|
|
<#-- Create the argument summary -->
|
|
<#if arguments.all?size != 0>
|
|
<hr>
|
|
<h2>${name} specific arguments</h2>
|
|
<table id="hor-minimalist-b">
|
|
<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="Hidden" myargs=arguments.hidden/>
|
|
<@argumentlist name="Depreciated" myargs=arguments.depreciated/>
|
|
</tbody>
|
|
</table>
|
|
</#if>
|
|
|
|
<#-- Create references to additional capabilities if appropriate -->
|
|
<#if extradocs?size != 0>
|
|
<hr>
|
|
<h2>Additional capabilities</h2>
|
|
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 capability is available to all GATK walkers.
|
|
<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?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 />
|
|
</body>
|
|
</html>
|