272 lines
9.1 KiB
HTML
272 lines
9.1 KiB
HTML
<!--
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~ Copyright (c) 2012, The Broad Institute
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~
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~ Permission is hereby granted, free of charge, to any person
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~ obtaining a copy of this software and associated documentation
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~ files (the "Software"), to deal in the Software without
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~ restriction, including without limitation the rights to use,
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~ copy, modify, merge, publish, distribute, sublicense, and/or sell
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~ copies of the Software, and to permit persons to whom the
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~ Software is furnished to do so, subject to the following
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~ conditions:
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~
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~ The above copyright notice and this permission notice shall be
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~ included in all copies or substantial portions of the Software.
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~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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~ OTHER DEALINGS IN THE SOFTWARE.
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-->
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<#include "common.html"/>
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<#macro argumentlist name myargs>
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<#if myargs?size != 0>
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<tr>
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<th colspan="4" id="row-divider">${name}</th>
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</tr>
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<#list myargs as arg>
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<tr>
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<td><a href="#${arg.name}">${arg.name}</a></td>
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<td>${arg.type}</td>
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<td>${arg.defaultValue!"NA"}</td>
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<td>${arg.summary}</td>
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</tr>
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<#--
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<
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td>${arg.required}</td>
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-->
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</#list>
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</#if>
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</#macro>
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<#macro argumentDetails arg>
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<h3><a name="${arg.name}">${arg.name}
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<#if arg.synonyms??> / ${arg.synonyms}</#if>
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</a>
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(
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<#if arg.attributes??>${arg.attributes}</#if>
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${arg.type}
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<#if arg.defaultValue??> with default value ${arg.defaultValue}</#if>
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)
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</h3>
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<p class="args">
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${arg.summary}. ${arg.fulltext}
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<#if arg.rodTypes??>${arg.name} binds reference ordered data. This argument supports ROD files of the
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following types: ${arg.rodTypes}
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</#if>
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<#if arg.options??>
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<br>
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The ${arg.name} argument is an enumerated type (${arg.type}), which can have one of the following values:
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<dl class="enum">
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<#list arg.options as option>
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<dt class="enum">${option.name}</dt>
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<dd class="enum">${option.summary}</dd>
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</#list>
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</dl>
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</#if>
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</p>
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</#macro>
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<#macro relatedByType name type>
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<#list relatedDocs as relatedDoc>
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<#if relatedDoc.relation == type>
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<h3>${name}</h3>
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<ul>
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<#list relatedDocs as relatedDoc>
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<#if relatedDoc.relation == type>
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<li><a href="${relatedDoc.filename}">${relatedDoc.name}</a> is a ${relatedDoc.relation}</li>
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</#if>
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</#list>
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</ul>
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<#break>
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</#if>
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</#list>
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</#macro>
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<?php $group = '${group}'; ?>
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<@makeHeader title="${name} documentation" isIndex=false />
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<section class="span4">
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<aside class="well">
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<h2>Categories</h2>
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<@getCategories groups=groups />
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</aside>
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<?php getForumPosts( '${name}' ) ?>
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</section>
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<div class="span8">
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<h1>${name}</h1>
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<p class="lead">${summary}</p>
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<#if author??>
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<h3>Author
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<small> ${author}</small>
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</h3>
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</#if>
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<#if group?? >
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<h3>Category
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<small> ${group}</small>
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</h3>
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</#if>
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<#if walkertype != "">
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<h3>Traversal
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<small>${walkertype}</small>
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</h3>
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</#if>
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<#if walkertype != "">
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<h3>PartitionBy
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<small>${partitiontype}</small>
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</h3>
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</#if>
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<#if annotfield != "" >
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<h3>VCF Field
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<small>${annotfield}</small>
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</h3>
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</#if>
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<#if annotinfo != "" >
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<h3>Type
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<small>${annotinfo}</small>
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</h3>
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</#if>
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<hr>
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<h2>Overview</h2>
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${description}
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<#-- Create references to additional capabilities if appropriate -->
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<#if readfilters?size != 0 || parallel?size != 0>
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<hr>
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<h2>Additional Information</h2>
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<p></p>
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</#if>
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<#if readfilters?size != 0>
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<h3>Read filters</h3>
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<#if readfilters?size = 1>
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<p>This Read Filter is automatically applied to the data by the Engine before processing by ${name}.</p>
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</#if>
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<#if (readfilters?size > 1) >
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<p>These Read Filters are automatically applied to the data by the Engine before processing by ${name}.</p>
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</#if>
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<ul>
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<#list readfilters as filter>
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<li><a href="${filter.filename}">${filter.name}</a></li>
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</#list>
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</ul>
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</#if>
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<#if parallel?size != 0>
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<h3>Parallelism options</h3>
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<#if parallel?size == 1>
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<p>This tool can be run in multi-threaded mode using this option.</p>
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</#if>
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<#if (parallel?size > 1)>
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<p>This tool can be run in multi-threaded mode using these options.</p>
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</#if>
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<ul>
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<#list parallel as option>
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<li><a href="${option.link}">${option.name} (${option.arg})</a></li>
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</#list>
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</ul>
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</#if>
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<#if downsampling?size != 0>
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<h3>Downsampling settings</h3>
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<#if downsampling.by == "NONE">
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<p>This tool does not apply any downsampling by default.</p>
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</#if>
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<#if downsampling.by != "NONE">
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<p>This tool applies the following downsampling settings by default.</p>
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<ul>
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<li>Mode: <b>${downsampling.by}</b></li>
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<li>To coverage: <b>${downsampling.to_cov}</b></li>
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</ul>
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</#if>
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</#if>
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<#if refwindow?size != 0>
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<h3>Window size</h3>
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<p>This tool uses a sliding window on the reference.</p>
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<ul>
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<li>Window start: <b>${refwindow.start}</b> bp before the locus</li>
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<li>Window stop: <b>${refwindow.stop}</b> bp after the locus</li>
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</ul>
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</#if>
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<#if activeregion?size != 0>
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<h3>ActiveRegion settings</h3>
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<p>This tool uses ActiveRegions on the reference.</p>
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<ul>
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<li>Minimum region size: <b>${activeregion.min}</b> bp</li>
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<li>Maximum region size: <b>${activeregion.max}</b> bp</li>
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<li>Extension increments: <b>${activeregion.ext}</b> bp</li>
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</ul>
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</#if>
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<#if extradocs?size != 0 || arguments.all?size != 0>
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<hr>
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<h2>Command-line Arguments</h2>
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<p></p>
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</#if>
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<#if extradocs?size != 0>
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<h3>Inherited arguments</h3>
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<p>The arguments described in the entries below can be supplied to this tool to modify
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its behavior. For example, the -L argument directs the GATK engine restricts processing
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to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).</p>
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<ul>
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<#list extradocs as extradoc>
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<li><a href="${extradoc.filename}">${extradoc.name}</a></li>
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</#list>
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</ul>
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</#if>
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<#-- This class is related to other documented classes via sub/super relationships -->
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<#if relatedDocs?? && relatedDocs?size != 0>
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<h3>Related capabilities</h3>
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<@relatedByType name="Superclasses" type="superclass"/>
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<@relatedByType name="Subclasses" type="subclass"/>
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</#if>
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<#-- Create the argument summary -->
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<#if arguments.all?size != 0>
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<h3>${name} specific arguments</h3>
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<p>This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.</p>
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<table class="table table-striped table-bordered table-condensed">
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<thead>
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<tr>
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<th>Name</th>
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<th>Type</th>
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<th>Default value</th>
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<th>Summary</th>
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</tr>
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</thead>
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<tbody>
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<@argumentlist name="Required Inputs" myargs=arguments.required_in/>
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<@argumentlist name="Required Outputs" myargs=arguments.required_out/>
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<@argumentlist name="Required Parameters" myargs=arguments.required_param/>
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<@argumentlist name="Required Flags" myargs=arguments.required_flag/>
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<@argumentlist name="Optional Inputs" myargs=arguments.optional_in/>
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<@argumentlist name="Optional Outputs" myargs=arguments.optional_out/>
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<@argumentlist name="Optional Parameters" myargs=arguments.optional_param/>
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<@argumentlist name="Optional Flags" myargs=arguments.optional_flag/>
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<@argumentlist name="Advanced Inputs" myargs=arguments.advanced_in/>
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<@argumentlist name="Advanced Outputs" myargs=arguments.advanced_out/>
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<@argumentlist name="Advanced Parameters" myargs=arguments.advanced_param/>
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<@argumentlist name="Advanced Flags" myargs=arguments.advanced_flag/>
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<@argumentlist name="Hidden" myargs=arguments.hidden/>
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<@argumentlist name="Deprecated" myargs=arguments.deprecated/>
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</tbody>
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</table>
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</#if>
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<#-- List all of the -->
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<#if arguments.all?size != 0>
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<#-- Create the argument details -->
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<h3>Argument details</h3>
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<p>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.</p>
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<#list arguments.all as arg>
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<@argumentDetails arg=arg/>
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</#list>
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</#if>
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<@footerInfo />
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<@pageFooter /> |