<tool name="FixMateInformation" id="picard_FixMateInformation" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>ensure that all mate-pair information is in sync between each read and it's mate pair</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@
    picard FixMateInformation
    --INPUT '${inputFile}'
    --OUTPUT '${outFile}'
    --ASSUME_SORTED ${assume_sorted}
    --ADD_MATE_CIGAR ${add_mate_cigar}

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

  ]]></command>
    <inputs>
        <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
        <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
        <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/>
        <expand macro="VS"/>
    </inputs>
    <outputs>
        <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/>
    </outputs>
    <tests>
        <test>
            <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/>
            <param name="add_mate_cigar" value="True"/>
            <param name="assume_sorted" value="False"/>
            <param name="validation_stringency" value="LENIENT"/>
            <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="4"/>
        </test>
    </tests>
    <help>

**Purpose**

Ensure that all mate-pair information is in sync between each read and it's mate pair. Reads marked with the secondary alignment flag are written to the output file unchanged.

------

.. class:: warningmark

**Warning on using ASSUME_SORTED option**

Datasets imported into Galaxy are automatically coordinate sorted. So use this option (set it to True) only if you are sure that this is necessary. If you are not sure - a good rule of thumb
is to assume that the BAM you are working with is coordinate sorted.

@dataset_collections@

@description@

  ASSUME_SORTED=Boolean
  AS=Boolean                    If true, assume that the input file is queryname sorted, even if the header says
                                otherwise.  Default value: false.

  ADD_MATE_CIGAR=Boolean
  MC=Boolean                    Adds the mate CIGAR tag (MC) if true, does not if false.  Default value: true.

@more_info@

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