#include "common.html"/>
<#macro argumentlist name myargs>
<#if myargs?size != 0>
${name} |
<#list myargs as arg>
${arg.name} |
${arg.type} |
${arg.defaultValue!"NA"} |
${arg.summary} |
<#--
${arg.required} |
-->
#list>
#if>
#macro>
<#macro argumentDetails arg>
${arg.name}<#if arg.synonyms??> / ${arg.synonyms}#if>
(<#if arg.attributes??>${arg.attributes} #if>${arg.type}<#if arg.defaultValue??> with default value ${arg.defaultValue}#if>)
${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??>
The ${arg.name} argument is an enumerated type (${arg.type}), which can have one of the following values:
<#list arg.options as option>
- ${option.name}
- ${option.summary}
#list>
#if>
#macro>
<#macro relatedByType name type>
<#list relatedDocs as relatedDoc>
<#if relatedDoc.relation == type>
${name}
<#list relatedDocs as relatedDoc>
<#if relatedDoc.relation == type>
- ${relatedDoc.name} is a ${relatedDoc.relation}
#if>
#list>
<#break>
#if>
#list>
#macro>
<@makeHeader title="${name} documentation"/>
${name}
<@headerInfo />
${summary}
<#if author??>
Author
${author}
#if>
Introduction
${description}
<#-- Create the argument summary -->
<#if arguments.all?size != 0>
${name} specific arguments
Name |
Type |
Default value |
Summary |
<@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/>
#if>
<#-- Create references to additional capabilities if appropriate -->
<#if extradocs?size != 0>
Additional capabilities
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.
#if>
<#-- This class is related to other documented classes via sub/super relationships -->
<#if relatedDocs?? && relatedDocs?size != 0>
Related capabilities
<@relatedByType name="Superclasses" type="superclass"/>
<@relatedByType name="Subclasses" type="subclass"/>
#if>
<#-- List all of the -->
<#if arguments.all?size != 0>
<#-- Create the argument details -->
Argument details
<#list arguments.all as arg>
<@argumentDetails arg=arg/>
#list>
#if>
<@footerInfo />