<tool name="RevertOriginalBaseQualitiesAndAddMateCigar" id="picard_RevertOriginalBaseQualitiesAndAddMateCigar" version="1.126.0">
  <description>revert the original base qualities and add the mate cigar tag</description>
  <requirements>
    <requirement type="package" version="1.126.0">picard</requirement>
  </requirements>
  
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  
  <command>
    @java_options@
    
    java -jar \$JAVA_JAR_PATH/picard.jar
    RevertOriginalBaseQualitiesAndAddMateCigar
    
    INPUT="${inputFile}"
    OUTPUT="${outFile}"
    
    RESTORE_ORIGINAL_QUALITIES="${restore_original_qualities}"
    MAX_RECORDS_TO_EXAMINE="${max_records_to_examine}"
    
    SORT_ORDER=coordinate
    VALIDATION_STRINGENCY="${validation_stringency}"
    QUIET=true
    VERBOSITY=ERROR
  
  </command>
  <inputs>
    <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
    <param name="restore_original_qualities" type="boolean" checked="True" label="Restore original qualities from the OQ field to the QUAL field if available" help="RESTORE_ORIGINAL_QUALITIES; default=True"/>
    <param name="max_records_to_examine" type="integer" value="10000" min="0" label="The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the dataset" help="MAX_RECORDS_TO_EXAMINE; default=10,000"/>

    <expand macro="VS" />
    
  </inputs> 
  
  <outputs>
    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Reverted BAM dataset"/>
  </outputs>
  
  <tests>
    <test>
      <param name="inputFile" value="picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam" ftype="bam"/>
      <param name="restore_original_qualities" value="True"/>
      <param name="max_records_to_examine" value="10000"/>
      <param name="validation_stringency" value="LENIENT"/>
      <output name="outFile" file="picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam" ftype="bam" lines_diff="2"/>
    </test>
  </tests>
  
  <stdio>
    <exit_code range="1:"  level="fatal"/>
  </stdio>
  
  <help>

**Purpose**

Reverts the original base qualities and adds the mate cigar tag to SAM or BAMs.

@dataset_collections@

@description@

  RESTORE_ORIGINAL_QUALITIES=Boolean
  OQ=Boolean                    True to restore original qualities from the OQ field to the QUAL field if available.  
                                Default value: true. Possible values: {true, false} 
  
  MAX_RECORDS_TO_EXAMINE=IntegerThe maximum number of records to examine to determine if we can exit early and not 
                                output, given that there are a no original base qualities (if we are to restore) and mate 
                                cigars exist. Set to 0 to never skip the file.  Default value: 10000.

@more_info@

  </help>
</tool>