<#macro argumentlist name myargs> <#if myargs?size != 0> ${name} <#list myargs as arg> ${arg.name} ${arg.synonyms} ${arg.type} ${arg.summary} <#-- ${arg.required} --> <#macro argumentDetails arg>

${arg.name} / ${arg.synonyms}

Summary: ${arg.summary}
Attributes: ${arg.attributes}
Type: ${arg.type}
Options: ${arg.options}
Details: ${arg.fulltext}
<#macro relatedByType name type> <#list relatedDocs as relatedDoc> <#if relatedDoc.relation == type>

${name}

${relatedDoc.name} is a ${relatedDoc.relation}

<#break> ${name} documentation

${name}

Brief summary

${summary} <#if author??>

Author

${author}

Detailed description

${description} <#-- Create the argument summary --> <#if arguments.all?size != 0>

Feature specific arguments

<@argumentlist name="Required" myargs=arguments.required/> <@argumentlist name="Optional" myargs=arguments.optional/> <@argumentlist name="Hidden" myargs=arguments.hidden/> <@argumentlist name="Depreciated" myargs=arguments.depreciated/>

Name	Synonyms	Type	Summary

<#-- 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.

${extradoc.name}

<#-- This class is related to other documented classes via sub/super relationships --> <#if relatedDocs?size != 0>

Related capabilities

<@relatedByType name="Superclasses" type="superclass"/> <@relatedByType name="Subclasses" type="subclass"/>

<#-- List all of the --> <#if arguments.all?size != 0>

<#-- Create the argument details -->

Argument details

<#list arguments.all as arg> <@argumentDetails arg=arg/>