<tool id="picard_CleanSam" name="CleanSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
  <description>perform SAM/BAM grooming</description>
  <macros>
    <import>picard_macros.xml</import>
    <token name="@WRAPPER_VERSION@">1</token>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    @symlink_element_identifier@
    picard
    CleanSam
    INPUT='$escaped_element_identifier'
    OUTPUT="${outFile}"
    QUIET=true
    VERBOSITY=ERROR
    @TMPDIR_OPTION@
    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>


  <tests>
    <test>
      <param name="inputFile" ftype="bam" value="picard_CleanSam.bam" />
      <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" lines_diff="4"/>
    </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>
  <expand macro="citations" />
</tool>
