<tool id="picard_cleansam" name="CleanSam" version="1.106.0">
    <!-- Documentation: http://picard.sourceforge.net/command-line-overview.shtml#CleanSam
Read SAM 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; and 2: to set MAPQ to 0 if a read is unmapped.
-->
  <description>Read SAM and perform various fix-ups.</description>
  
  <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
  
  <command interpreter="bash">
    cleansamwrapper.sh $input1 $output1
  </command>
  
  <inputs>
    <param name="input1" type="data" format="sam" label="SAM File to clean" />
  </inputs>
  
  <outputs>
    <data name="output1" format_source="input1" label="${tool.name} on ${on_string}: ${input1.datatype.file_ext}">
    </data>
  </outputs>
  
  <tests>
    <test>
      <param name="input1" value="cleansamtestinput.sam" />
      <output name="output1" file="cleansamtestoutput.sam" ftype="sam" />
    </test>
  </tests>
  
  <help>

**What it does**

Read SAM and perform various fix-ups. Currently, the only fix-up it to soft-clip an alignment that hangs off the end of its reference sequence.

  </help>
</tool>