<tool name="Sort Sam" id="picard_SortSam" version="1.106.0">
<!-- adapted from https://github.com/najoshi/ucd-biocore-galaxy/blob/master/tools/picard/picard_SortSam.xml -->
  <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
  <command interpreter="python">
    picard_wrapper.py
      --input "$inputFile"
      -s "$sort_order"
      -o "$outFile"
      --output-format $outputFormat
      -j "\$JAVA_JAR_PATH/SortSam.jar"
  </command>
  <inputs>
    <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be sorted"
      help="If empty, upload or import a SAM/BAM dataset." />
    <param name="sort_order" type="select" label="Sort order">
      <option value="coordinate" selected="True">coordinate</option>
      <option value="queryname">queryname</option>
      <option value="unsorted">unsorted</option>
    </param>
    <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
  </inputs>
  <outputs>
    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: ${outputFormat}" />
      <change_format>
        <when input="outputFormat" value="sam" format="sam" />
      </change_format>
  </outputs>
 <help>

SortSam

USAGE: SortSam [options]

Documentation: http://picard.sourceforge.net/command-line-overview.shtml#SortSam

Sorts the input SAM or BAM.

Input and output formats are determined by file extension.
Option	Description
INPUT=File	The BAM or SAM file to sort. Required.
OUTPUT=File	The sorted BAM or SAM output file. Required.
SORT_ORDER=SortOrder	Sort order of output file Required. Possible values: {unsorted, queryname, coordinate} 
  </help>
</tool>




