<tool id="mergemutectstats" name="gatk4 MergeMutectStats" version="@WRAPPER_VERSION@" profile="21.01">
    <description>Merge the stats output by scatters of a single Mutect2 job</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_cmd"/>
    <command detect_errors="exit_code">
        <![CDATA[
        gatk MergeMutectStats
        #for $file in $inputs:
            --stats $file
        #end for
            --output $merge_stats
        ]]>
    </command>
    <inputs>
        <param name="inputs" type="data" format="tabular" label="stats files" multiple="true"
               help="merge the stats files from multiple Mutect2 jobs"/>
    </inputs>
    <outputs>
        <data format="tabular" name="merge_stats" label="Merged Mutect2 callable statistics" />
    </outputs>
    <tests>
        <test>
            <param name="inputs" value="chr1_stats.tsv,chr2_stats.tsv,chrM_stats.tsv" ftype="tabular" />
            <output name="merge_stats" file="merged_Mutect2_stats.tsv" />
        </test>
    </tests>
    <help><![CDATA[
Usage examples
~~~~~~~~~~~~~~


::

    gatk MergeMutectStats \
    
        -stats unfiltered1.vcf.stats \
    
        -stats unfiltered2.vcf.stats \
    
        -O merged.stats


Mutect2 creates unfiltered.vcf.stats and FilterMutectCalls knows to look for it. However,
if you are scattering Mutect2 over multiple jobs you must merge the stats files with MergeMutectStats:

Usage
~~~~~


::

    USAGE: MergeMutectStats [arguments]
    
    Merge the stats output by scatters of a single Mutect2 job
    Version:4.1.7.0
    
    
    Required Arguments:
    
    --output,-O:File              Output stats  Required.
    
    --stats:File                  Stats from Mutect2 scatters of a single tumor or tumor-normal pair  This argument must be
                                  specified at least once. Required.
    
    
    Optional Arguments:
    
    --arguments_file:File         read one or more arguments files and add them to the command line  This argument may be
                                  specified 0 or more times. Default value: null.
    
    --gatk-config-file:String     A configuration file to use with the GATK.  Default value: null.
    
    --gcs-max-retries,-gcs-retries:Integer
                                  If the GCS bucket channel errors out, how many times it will attempt to re-initiate the
                                  connection  Default value: 20.
    
    --gcs-project-for-requester-pays:String
                                  Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be
                                  accessed.  Default value: .
    
    --help,-h:Boolean             display the help message  Default value: false. Possible values: {true, false}
    
    --QUIET:Boolean               Whether to suppress job-summary info on System.err.  Default value: false. Possible
                                  values: {true, false}
    
    --tmp-dir:GATKPathSpecifier   Temp directory to use.  Default value: null.
    
    --use-jdk-deflater,-jdk-deflater:Boolean
                                  Whether to use the JdkDeflater (as opposed to IntelDeflater)  Default value: false.
                                  Possible values: {true, false}
    
    --use-jdk-inflater,-jdk-inflater:Boolean
                                  Whether to use the JdkInflater (as opposed to IntelInflater)  Default value: false.
                                  Possible values: {true, false}
    
    --verbosity,-verbosity:LogLevel
                                  Control verbosity of logging.  Default value: INFO. Possible values: {ERROR, WARNING,
                                  INFO, DEBUG}
    
    --version:Boolean             display the version number for this tool  Default value: false. Possible values: {true,
                                  false}
    
    
    Advanced Arguments:
    
    --showHidden,-showHidden:Boolean
                                  display hidden arguments  Default value: false. Possible values: {true, false}

]]></help>
    <citations>
        <expand macro="citations"/>
    </citations>
</tool>