<tool id="picard_CleanSam" name="CleanSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>perform SAM/BAM grooming</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@
    @symlink_element_identifier@
    picard CleanSam
    --INPUT '$escaped_element_identifier'
    --OUTPUT '${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>
    <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>