<tool id="rtg_snp" name="Call SNPs">
  <description>from SAM files with rtg snp</description>
  <command interpreter="bash">galaxy-rtg-singleoutput-wrapper.sh $output $output.id $__new_file_path__ snps.vcf
snp -t ${template.extra_files_path} 
--max-as-mated $maxscore
--max-as-unmated $maxuscore
--machine-errors $machine
$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="maxscore" type="integer" value="3" label="Maximum alignment score for mated reads"/>
    <param name="maxuscore" type="integer" value="1" label="Maximum alignment score for umated reads"/>
    <param name="machine" type="select" label="Select machine type">
      <option value="illumina">Illumina</option>
      <option value="cg">Complete Genomics</option>
      <option value="454_se">454 single-end</option>
      <option value="454_pe">454 paired-end</option>
    </param>
    <param name="input1" label="First tabix-ed SAM file" type="data" format="samix" />
    <repeat name="inputs" title="Input tabix-ed SAM Files">
      <param name="input" label="Add file" type="data" format="samix" />
    </repeat>
  </inputs>
  <outputs>
    <data name="output" format="vcf" />
  </outputs>

  <help>
This tool calls snps from SAM files
  </help>

</tool>