<tool id="rtg_cgmap" name="CG map">
  <description>reads with rtg cg map</description>
  <command interpreter="bash">galaxy-rtg-map-wrapper.sh paired $output1 $output2 $__new_file_path__ 
cgmap -t ${template.extra_files_path} 
--repeat-freq ${repeat}
-i ${reads.extra_files_path}
--min-insert-size $minlength --max-insert-size $maxlength
--max-mated-score $maxscore --max-unmated-score $maxuscore
</command>
  <inputs>
    <param name="template" type="data" format="rtg_sdf" label="Reference SDF"/>
    <param name="reads" type="data" format="rtg_sdf" label="Reads SDF"/>
    <param name="repeat" type="text" value="90%" label="Repeat frequency">
      <sanitizer sanitize="False"/>
    </param>

	<param name="maxscore" type="text" value="10%" label="Maximum alignment score for mated reads">
	  <sanitizer sanitize="False"/>
	</param>
        <param name="maxuscore" type="text" value="10%" label="Maximum alignment score for umated reads">
	  <sanitizer sanitize="False"/>
	</param>
        <param name="minlength" type="integer" value="0" label="Minimum insert size"/>
	<param name="maxlength" type="integer" value="1000" label="Maximum insert size"/>

  </inputs>
  <outputs>
    <data name="output1" format="samix" label="Cgmap mated on reads data ${reads.hid} and template data ${template.hid}"/>
    <data name="output2" format="samix" label="Cgmap unmated on reads data ${reads.hid} and template data ${template.hid}"/>
  </outputs>

  <help>
This tool performs a NGS read mapping using rtg cgmap
  </help>

</tool>