<tool id="rtg_snpintersection" name="SNP intersection">
  <description>with RTG SNP intersection</description>
  <command interpreter="bash">galaxy-rtg-snpintersect-wrapper.sh 
-Z -i ${input}
-I ${input2}
-o ${output.extra_files_path} >$output</command>
  <inputs>
    <param name="input" type="data" format="vcf" label="first SNPs input file"/>
    <param name="input2" type="data" format="vcf" label="second SNPs input file" />
  </inputs>
  <outputs>
    <data format="vcf" name="output" />
  </outputs>

  <help>
This tool creates an SNP intersection.
  </help>

</tool>