<tool id="rtg_mapf" name="Mapf">
  <description>reads with rtg mapf</description>
  <command interpreter="bash">galaxy-rtg-map-wrapper.sh $paired.sPaired $output1 $output2 $__new_file_path__ 
mapf -t ${template.extra_files_path} 
--repeat-freq ${repeat}
-i ${reads.extra_files_path}
#if $paired.sPaired == "paired":
--min-insert-size $paired.minlength --max-insert-size $paired.maxlength
--max-mated-score $paired.maxscore --max-unmated-score $paired.maxuscore
#else:
--max-alignment-score $paired.maxscore
#end if
--sam
</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>

    <conditional name="paired">
      <param name="sPaired" type="select" label="Are you mapping paired-end reads?">
        <option value="paired">Paired-end</option>
        <option value="single">Single-end</option>
      </param>
      <when value="single">
	<param name="maxscore" type="text" value="10%" label="Maximum alignment score for reads (percentages do not work ATM)">
	  <sanitizer sanitize="False"/>
	</param>
      </when>
      <when value="paired">
	<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="200" label="Minimum insert size"/>
	<param name="maxlength" type="integer" value="400" label="Maximum insert size"/>
      </when>
    </conditional>	

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

  <help>
This tool filters reads for contaminant sequences by mapping them against the contaminant template using rtg mapf
  </help>

</tool>