<#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} --> <#macro argumentDetails arg>

### ${arg.name}<#if arg.synonyms??> / ${arg.synonyms} (<#if arg.attributes??>${arg.attributes} ${arg.type}<#if arg.defaultValue??> with default value ${arg.defaultValue})

${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 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}

<#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}

<#break>
<@makeHeader title="${name} documentation"/>

# ${name}

<@headerInfo />

${summary}

<#if author??>

## Author

${author}

## 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/>

<#-- 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.

<#list extradocs as extradoc>
- ${extradoc.name}

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

<#-- Create the argument details -->

## Argument details

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