<#include "common.html"/> <#macro argumentlist name myargs> <#if myargs?size != 0>
${name}
<#list myargs as arg>
${arg.name} ${arg.type} ${arg.defaultValue!"NA"} ${arg.summary}
<#-- < td>${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" isIndex=false />

## Categories

<@getCategories groups=groups />

# ${name}

${summary}

<#if author??>

### Author ${author}

<#if group?? >

### Category ${group}

<#if walkertype != "">

### Traversal ${walkertype}

<#if walkertype != "">

### PartitionBy ${partitiontype}

<#if annotfield != "" >

### VCF Field ${annotfield}

<#if annotinfo != "" >

### Type ${annotinfo}

## Overview

${description} <#-- Create references to additional capabilities if appropriate --> <#if readfilters?size != 0 || parallel?size != 0>

## Additional Information

<#if readfilters?size != 0>

### Read filters

<#if readfilters?size = 1>

This Read Filter is automatically applied to the data by the Engine before processing by ${name}.

<#if (readfilters?size > 1) >

These Read Filters are automatically applied to the data by the Engine before processing by ${name}.

<#list readfilters as filter>
- ${filter.name}

<#if parallel?size != 0>

### Parallelism options

<#if parallel?size == 1>

This tool can be run in multi-threaded mode using this option.

<#if (parallel?size > 1)>

This tool can be run in multi-threaded mode using these options.

<#list parallel as option>
- ${option.name} (${option.arg})

<#if downsampling?size != 0>

### Downsampling settings

<#if downsampling.by == "NONE">

This tool does not apply any downsampling by default.

<#if downsampling.by != "NONE">

This tool applies the following downsampling settings by default.

- Mode: ${downsampling.by}
- To coverage: ${downsampling.to_cov}

<#if refwindow?size != 0>

### Window size

This tool uses a sliding window on the reference.

- Window start: ${refwindow.start} bp before the locus
- Window stop: ${refwindow.stop} bp after the locus

<#if activeregion?size != 0>

### ActiveRegion settings

This tool uses ActiveRegions on the reference.

- Minimum region size: ${activeregion.min} bp
- Maximum region size: ${activeregion.max} bp
- Extension increments: ${activeregion.ext} bp

<#if extradocs?size != 0 || arguments.all?size != 0>

## Command-line Arguments

<#if extradocs?size != 0>

### Inherited arguments

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 is an Engine capability and is therefore 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"/> <#-- Create the argument summary --> <#if arguments.all?size != 0>

### ${name} specific arguments

This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.

Name | Type | Default value | Summary
--- | --- | --- | ---
<@argumentlist name="Required Inputs" myargs=arguments.required_in/> <@argumentlist name="Required Outputs" myargs=arguments.required_out/> <@argumentlist name="Required Parameters" myargs=arguments.required_param/> <@argumentlist name="Required Flags" myargs=arguments.required_flag/> <@argumentlist name="Optional Inputs" myargs=arguments.optional_in/> <@argumentlist name="Optional Outputs" myargs=arguments.optional_out/> <@argumentlist name="Optional Parameters" myargs=arguments.optional_param/> <@argumentlist name="Optional Flags" myargs=arguments.optional_flag/> <@argumentlist name="Advanced Inputs" myargs=arguments.advanced_in/> <@argumentlist name="Advanced Outputs" myargs=arguments.advanced_out/> <@argumentlist name="Advanced Parameters" myargs=arguments.advanced_param/> <@argumentlist name="Advanced Flags" myargs=arguments.advanced_flag/> <@argumentlist name="Hidden" myargs=arguments.hidden/> <@argumentlist name="Deprecated" myargs=arguments.deprecated/>

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

### Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.

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