<#include "common.html"/> <#macro argumentlist name myargs> <#if myargs?size != 0> ${name} <#list myargs as arg> ${arg.name}
<#if arg.synonyms != "NA"> <#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.otherArgumentRequired != "NA">

Dependency: This argument requires that you also specify ${arg.otherArgumentRequired}.

<#if arg.exclusiveOf != "NA">

Exclusion: This argument cannot be used at the same time as ${arg.exclusiveOf}.

<#if arg.options?has_content>

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

${name}

${summary}

<#if group?? >

Category ${group}

<#if walkertype?? && walkertype != "">

Traversal ${walkertype}


Overview

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

Additional Information

<#if readFilter?? && readFilter?size != 0>

Read filters

<#if readFilter?size = 1>

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

<#if (readFilter?size > 1) >

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

<#if extradocs?size != 0>

Additional references

See these additional references.

<#-- 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.

<@argumentlist name="Positional Arguments" myargs=arguments.positional/> <@argumentlist name="Required Arguments" myargs=arguments.required/> <@argumentlist name="Optional Tool Arguments" myargs=arguments.optional/> <@argumentlist name="Optional Common Arguments" myargs=arguments.common/> <@argumentlist name="Advanced Arguments" myargs=arguments.advanced/> <@argumentlist name="Hidden Arguments" myargs=arguments.hidden/> <@argumentlist name="Deprecated Arguments" myargs=arguments.deprecated/>
Argument name(s) Default value Summary
<#-- List all of the things --> <#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 /> <@footerClose />