<tool id="rtg_coverage" name="Coverage">
  <description>coverage</description>
  <command interpreter="bash">galaxy-rtg-singleoutput-wrapper.sh $output $output.id $__new_file_path__ coverage.bed
coverage -t ${template.extra_files_path} 
$input1
#for $i in $inputs
  ${i.input}
#end for
-Z
</command>
  <inputs>
    <param name="template" type="data" format="rtg_sdf" label="Reference SDF"/>
    <param name="input1" label="First SAM file" type="data" format="sam,samix" />
    <repeat name="inputs" title="Input SAM Files">
      <param name="input" label="Add file" type="data" format="sam,samix" />
    </repeat>
  </inputs>
  <outputs>
    <data name="output" format="bed"/>
  </outputs>

  <help>
This tool calculates coverage using rtg coverage 
  </help>

</tool>