<tool name="QualityScoreDistribution" id="picard_QualityScoreDistribution" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>chart quality score distribution</description>
    <macros>
        <import>picard_macros.xml</import>
        <token name="@WRAPPER_VERSION@">0</token>
    </macros>
    <expand macro="requirements">
  </expand>
    <command detect_errors="exit_code"><![CDATA[
    @java_options@
    ##set up input files
    @symlink_element_identifier@
    #set $reference_fasta_filename = "localref.fa"

    @handle_reference_source@

    picard QualityScoreDistribution
    --INPUT '$escaped_element_identifier'
    --OUTPUT '${outFile}'
    --CHART_OUTPUT '${pdfFile}'
    --REFERENCE_SEQUENCE '${reference_fasta_filename}'
    --ALIGNED_READS_ONLY '${aligned_reads_only}'
    --PF_READS_ONLY '${pf_reads_only}'
    --INCLUDE_NO_CALLS '${include_no_calls}'

    --ASSUME_SORTED '${assume_sorted}'

    --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="aligned_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true, calculate mean quality over aligned reads only" help="ALIGNED_READS_ONLY; default=False"/>
        <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/>
        <param name="include_no_calls" type="boolean" label="If set to true, include quality for no-call bases in the distribution" help="INCLUDE_NO_CALLS; default=False"/>
        <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED; default=True"/>
        <expand macro="VS"/>
    </inputs>
    <outputs>
        <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
        <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
    </outputs>
    <tests>
        <test>
            <param name="assume_sorted" value="true"/>
            <param name="aligned_reads_only" value="false"/>
            <param name="pf_reads_only" value="false"/>
            <param name="include_no_calls" value="false"/>
            <param name="reference_source_selector" value="history"/>
            <param name="ref_file" value="picard_QualityScoreDistribution_ref.fa"/>
            <param name="inputFile" value="picard_QualityScoreDistribution.bam" ftype="bam"/>
            <output name="outFile" file="picard_QualityScoreDistribution_test1.tab" ftype="tabular" lines_diff="4"/>
        </test>
    </tests>
    <help>

.. class:: infomark

**Purpose**

Program to chart quality score distributions in a SAM or BAM dataset.

@dataset_collections@

@description@

  ALIGNED_READS_ONLY=Boolean    If set to true, calculate the base distribution over aligned reads only.  Default value:
                                false. Possible values: {true, false}

  PF_READS_ONLY=Boolean         If set to true calculate the base distribution over PF reads only.  Default value: false.
                                Possible values: {true, false}

  INCLUDE_NO_CALLS=Boolean      If set to true, include quality for no-call bases in the distribution.  Default value:
                                false. Possible values: {true, false}

  ASSUME_SORTED=Boolean
  AS=Boolean                    If true (default), then the sort order in the header file will be ignored.  Default: True

@more_info@

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