<#include "common.html"/> <#macro argumentlist name myargs> <#if myargs?size != 0>
${name}
<#list myargs as arg>
${arg.name}
<#if arg.synonyms??> <#if arg.name[2..] != arg.synonyms[1..]> ${arg.synonyms} ${arg.defaultValue!"NA"} ${arg.summary}
<#macro argumentDetails arg>

### ${arg.name} <#if arg.synonyms??> / ${arg.synonyms}

${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}

<#if arg.required??> <#if arg.required == "yes"> R ${arg.type} <#if arg.defaultValue??> ${arg.defaultValue} <#if arg.minValue??> [ [ ${arg.minValue} <#if arg.minRecValue??> [ ${arg.minRecValue} <#if arg.maxRecValue??> ${arg.maxRecValue} ] <#if arg.maxValue??> ${arg.maxValue} ] ]

<#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="GATK | ${name} documentation" isIndex=false />

## Categories

<@getCategories groups=groups />

# ${name}

${summary}

<#-- using goto dev annotation instead, see above footer <#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 more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s) | 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 /> <#-- Specify go-to developer (for internal use) --> <#if gotoDev??> GTD: ${gotoDev} <@footerClose /> <@pageFooter />