<tool id="picard_CleanSam" name="CleanSam" version="1.135">
  <description>perform SAM/BAM grooming</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>
    @java_options@
    java -jar \$JAVA_JAR_PATH/picard.jar
    CleanSam
    INPUT="${inputFile}"
    OUTPUT="${outFile}"
    QUIET=true
    VERBOSITY=ERROR
    VALIDATION_STRINGENCY=${validation_stringency}
  </command>
  
  <inputs>
    <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
    
    <expand macro="VS" />
    
  </inputs>
  
  <outputs>
    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: cleaned BAM dataset">
    </data>
  </outputs>
  
  <stdio>
    <exit_code range="1:"  level="fatal"/>
  </stdio>
  
  <tests>
    <test>
      <param name="inputFile" ftype="bam" value="picard_CleanSam.bam" />
      <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" />
    </test>
  </tests>
  
  <help>

.. class:: infomark

**Purpose**

Read SAM/BAM and perform various fix-ups. Currently, the only fix-ups are:

 1. to soft-clip an alignment that hangs off the end of its reference sequence.
 2. to set MAPQ to 0 if a read is unmapped.
 
@dataset_collections@
 
@more_info@

  </help>
</tool>