<tool id="picard_SortSam" name="SortSam" version="@TOOL_VERSION@.1">
  <description>sort SAM/BAM dataset</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>
    @java_options@
    java -jar \$JAVA_JAR_PATH/picard.jar
    SortSam
    INPUT="${inputFile}"
    OUTPUT="${outFile}"
    SORT_ORDER="${sort_order}"
    QUIET=true
    VERBOSITY=ERROR
    VALIDATION_STRINGENCY=${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"/>
    <param name="sort_order" type="select" display="radio" label="Sort order" help="SORT_ORDER; default=coordinate">
      <option value="coordinate" selected="True">Coordinate</option>
      <option value="queryname">Queryname</option>
    </param>
    <expand macro="VS" />
  </inputs>
  
  <outputs>
    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM sorted in ${sort_order} order">
    </data>
  </outputs>
  
  <stdio>
    <exit_code range="1:"  level="fatal"/>
  </stdio>
  
  <tests>
    <test>
      <param name="inputFile" ftype="bam" value="picard_SortSam.bam" />
      <param name="sort_order" value="queryname"/>
      <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="2"/>
    </test>
  </tests>
  
  <help>

.. class:: infomark

**Purpose**

Sorts the input SAM or BAM.

@dataset_collections@

@description@

  SORT_ORDER=SortOrder
  SO=SortOrder          Sort order of output file. You can either sort by queryname or by coordinate.
 
 @more_info@

  </help>
</tool>