#include "common.html"/>
<#macro argumentlist name myargs>
<#if myargs?size != 0>
${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>
<#if arg.options??>
The ${arg.name} argument is an enumerated type (${arg.type}), which can have one of the following values:
${name}
${summary}
<#if author??>
Author
${author}
#if>
<#if group?? >
Category
${group}
#if>
<#if walkertype != "">
Traversal
${walkertype}
#if>
<#if walkertype != "">
PartitionBy
${partitiontype}
#if>
<#if annotinfo != "" >
Annotation type
${annotinfo}
#if>
Introduction
${description}
<#-- Create references to additional capabilities if appropriate -->
<#if readfilters?size != 0 || parallel?size != 0>
Additional Information
#if>
<#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>
<#if (readfilters?size > 1) >
These Read Filters are automatically applied to the data by the Engine before processing by ${name}.
#if>
#if>
<#if parallel?size != 0>
Parallelism options
<#if parallel?size == 1>
This tool can be run in multi-threaded mode using this option.
#if>
<#if (parallel?size > 1)>
This tool can be run in multi-threaded mode using these options.
#if>
#if>
<#if downsampling?size != 0>
Downsampling settings
This tool overrides the engine's default downsampling settings.
- Mode: ${downsampling.by}
- To coverage: ${downsampling.to_cov}
#if>
<#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>
<#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>
<#if extradocs?size != 0 || arguments.all?size != 0>
Command-line Arguments
#if>
<#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).
#if>
<#-- 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"/>
#if>
<#-- 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" 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/>
#if>
<#-- 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/>
#list>
#if>
<@footerInfo />
<@pageFooter />