121 lines
3.6 KiB
HTML
121 lines
3.6 KiB
HTML
<#include "common.html"/>
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<#macro argumentlist name myargs>
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<#if myargs?size != 0>
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<tr><th colspan="4" id="row-divider">${name}</th></tr>
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<#list myargs as arg>
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<tr>
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<td><a href="#${arg.name}">${arg.name}</a></td>
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<td>${arg.type}</td>
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<td>${arg.defaultValue!"NA"}</td>
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<td>${arg.summary}</td>
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</tr>
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<#--
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<td>${arg.required}</td>
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-->
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</#list>
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</#if>
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</#macro>
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<#macro argumentDetails arg>
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<h3><a name="${arg.name}">${arg.name}<#if arg.synonyms??> / ${arg.synonyms}</#if></a>
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(<#if arg.attributes??>${arg.attributes} </#if>${arg.type}<#if arg.defaultValue??> with default value ${arg.defaultValue}</#if>)</h3>
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${arg.summary}. ${arg.fulltext}<br>
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<#if arg.options??>
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<p>The ${arg.name} argument is an enumerated type (${arg.type}), which can have one of the following values:</p>
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<dl class="enum">
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<#list arg.options as option>
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<dt>${option.name}
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<dd>${option.summary}
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</#list>
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</dl>
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</#if>
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</#macro>
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<#macro relatedByType name type>
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<#list relatedDocs as relatedDoc>
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<#if relatedDoc.relation == type>
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<h3>${name}</h3>
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<ul>
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<#list relatedDocs as relatedDoc>
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<#if relatedDoc.relation == type>
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<li><a href="${relatedDoc.filename}">${relatedDoc.name}</a> is a ${relatedDoc.relation}</li>
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</#if>
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</#list>
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</ul>
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<#break>
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</#if>
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</#list>
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</#macro>
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<html>
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<@makeHeader title="${name} documentation"/>
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<body>
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<h1>${name}</h1>
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<@headerInfo />
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<p class="summary">${summary}</p>
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<#if author??>
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<h2>Author</h2>
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${author}
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</#if>
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<h2>Introduction</h2>
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${description}
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<#-- Create the argument summary -->
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<#if arguments.all?size != 0>
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<hr>
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<h2>${name} specific arguments</h2>
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<table id="hor-minimalist-b">
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<thead>
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<tr>
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<th>Name</th>
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<th>Type</th>
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<th>Default value</th>
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<th>Summary</th>
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</tr>
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</thead>
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<tbody>
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<@argumentlist name="Required" myargs=arguments.required/>
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<@argumentlist name="Optional" myargs=arguments.optional/>
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<@argumentlist name="Hidden" myargs=arguments.hidden/>
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<@argumentlist name="Depreciated" myargs=arguments.depreciated/>
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</tbody>
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</table>
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</#if>
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<#-- Create references to additional capabilities if appropriate -->
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<#if extradocs?size != 0>
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<hr>
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<h2>Additional capabilities</h2>
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The arguments described in the entries below can be supplied to this tool to modify
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its behavior. For example, the -L argument directs the GATK engine restricts processing
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to specific genomic intervals. This capability is available to all GATK walkers.
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<ul>
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<#list extradocs as extradoc>
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<li><a href="${extradoc.filename}">${extradoc.name}</a></li>
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</#list>
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</ul>
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</#if>
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<#-- This class is related to other documented classes via sub/super relationships -->
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<#if relatedDocs?? && relatedDocs?size != 0>
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<hr>
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<h2>Related capabilities</h2>
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<@relatedByType name="Superclasses" type="superclass"/>
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<@relatedByType name="Subclasses" type="subclass"/>
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</#if>
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<#-- List all of the -->
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<#if arguments.all?size != 0>
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<hr>
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<#-- Create the argument details -->
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<h2>Argument details</h2>
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<#list arguments.all as arg>
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<@argumentDetails arg=arg/>
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</#list>
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</#if>
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<@footerInfo />
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</body>
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</html>
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