<tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>compute metrics for evaluating of whole genome sequencing experiments</description>
    <macros>
        <import>picard_macros.xml</import>
        <token name="@WRAPPER_VERSION@">0</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
    @java_options@
    @symlink_element_identifier@
    ##set up input files

    #set $reference_fasta_filename = "localref.fa"

    @handle_reference_source@

    picard
    CollectWgsMetrics
    --INPUT '$escaped_element_identifier'
    --OUTPUT '${outFile}'
    --REFERENCE_SEQUENCE '${reference_fasta_filename}'
    --MINIMUM_MAPPING_QUALITY '${minimum_mapping_quality}'
    --MINIMUM_BASE_QUALITY '${minimum_base_quality}'
    --COVERAGE_CAP '${coverage_cap}'

    --VALIDATION_STRINGENCY '${validation_stringency}'
    --QUIET true
    --VERBOSITY ERROR

  ]]></command>
    <inputs>
        <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Load reference genome from">
                <option value="cached">Local cache</option>
                <option value="history">History</option>
            </param>
            <when value="cached">
                <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
                    <options from_data_table="all_fasta">
          </options>
                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                </param>
            </when>
            <when value="history">
                <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference"/>
            </when>
        </conditional>
        <param name="minimum_mapping_quality" type="integer" value="20" label="Minimum mapping quality for a read to contribute coverage" help="MINIMUM_MAPPING_QUALITY; default=20"/>
        <param name="minimum_base_quality" type="integer" value="20" label="Minimum base quality for a base to contribute coverage" help="MINIMUM_BASE_QUALITY; default=20"/>
        <param name="coverage_cap" type="integer" value="250" label="Treat bases with coverage exceeding this value as if they had coverage at this value" help="COVERAGE_CAP; default=250"/>
        <expand macro="VS"/>
    </inputs>
    <outputs>
        <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
    </outputs>
    <tests>
        <test>
            <param name="reference_source_selector" value="history"/>
            <param name="minimum_mapping_quality" value="20"/>
            <param name="minimum_base_quality" value="20"/>
            <param name="coverage_cap" value="250"/>
            <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa"/>
            <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam"/>
            <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
        </test>
    </tests>
    <help>

.. class:: infomark

**Purpose**

Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.

@dataset_collections@

@description@

  MINIMUM_MAPPING_QUALITY=Integer
  MQ=Integer                    Minimum mapping quality for a read to contribute coverage.  Default value: 20.

  MINIMUM_BASE_QUALITY=Integer
  Q=Integer                     Minimum base quality for a base to contribute coverage.  Default value: 20.

  COVERAGE_CAP=Integer
  CAP=Integer                   Treat bases with coverage exceeding this value as if they had coverage at this value.
                                Default value: 250.

@more_info@

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