<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>writes a file containing summary alignment metrics</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 CollectAlignmentSummaryMetrics
    --INPUT '$escaped_element_identifier'
    --OUTPUT '${outFile}'
    --MAX_INSERT_SIZE ${maxinsert}
    #for $sequence in $adapters:
        --ADAPTER_SEQUENCE '${sequence.adapter}'
    #end for
    #for $level in str($metric_accumulation_level).split(','):
        --METRIC_ACCUMULATION_LEVEL '${level}'
    #end for
    --IS_BISULFITE_SEQUENCED '${bisulphite}'

    --REFERENCE_SEQUENCE '${reference_fasta_filename}'

    --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 following 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="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL">
            <option value="ALL_READS" selected="True">All reads</option>
            <option value="SAMPLE">Sample</option>
            <option value="LIBRARY">Library</option>
            <option value="READ_GROUP">Read group</option>
        </param>
        <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
        <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/>
        <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences">
            <param name="adapter" type="text" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/>
        </repeat>
        <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" help="MAX_INSERT_SIZE"/>
        <expand macro="VS"/>
    </inputs>
    <outputs>
        <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
    </outputs>
    <tests>
        <test>
            <param name="bisulphite" value="false"/>
            <param name="assume_sorted" value="true"/>
            <repeat name="adapters">
                <param name="adapter" value=""/>
            </repeat>
            <param name="maxinsert" value="100000"/>
            <param name="reference_source_selector" value="history"/>
            <param name="ref_file" value="picard_CASM_ref.fa"/>
            <param name="inputFile" value="picard_CASM.bam" ftype="bam"/>
            <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/>
        </test>
    </tests>
    <help>

.. class:: infomark

**Purpose**

Reads a SAM or BAM file and writes a file containing summary alignment metrics.

@dataset_collections@

@description@

  MAX_INSERT_SIZE=Integer       Paired end reads above this insert size will be considered chimeric along with
                                inter-chromosomal pairs.  Default value: 100000.

  ADAPTER_SEQUENCE=String       List of adapter sequences to use when processing the alignment metrics  This option may
                                be specified 0 or more times.

  METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
  LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics.    Possible values: {ALL_READS, SAMPLE,
                                LIBRARY, READ_GROUP} This option may be specified 0 or more times.

  IS_BISULFITE_SEQUENCED=Boolean
  BS=Boolean                    Whether the SAM or BAM file consists of bisulfite sequenced reads.


  REFERENCE_SEQUENCE=File
  R=File                        Reference sequence fasta  Default value: null.

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

@more_info@

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