<tool id="rtg_mapx" name="MapX">
  <description>protein reads with rtg mapx</description>
  <command interpreter="bash">galaxy-rtg-mapx-wrapper.sh $output1 $__new_file_path__ 
mapx -t ${template.extra_files_path} 
--repeat-freq ${repeat}
-i ${reads.extra_files_path}
--max-alignment-score $maxscore
</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 reads (percentages do not work ATM)">
	  <sanitizer sanitize="False"/>
	</param>

  </inputs>
  <outputs>
    <data name="output1" format="tabular" />
  </outputs>

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

</tool>