<tool id="rtg_snpsim" name="Simulate SNPs">
  <description>with rtg snpsim</description>
  <command interpreter="bash">galaxy-rtg-snpsim-wrapper.sh ${output3} ${output3.extra_files_path} snpsim
 --seed $seed -i ${input.extra_files_path} 
-o ${output.extra_files_path}
#if $str($diploid) == "true":
-O ${output2.extra_files_path}
#end if
>$output</command>
  <inputs>
    <param name="input" type="data" format="rtg_sdf" label="SDF containing input genome"/>
    <param name="diploid" type="select" label="Generate diploid mutations">
      <option value="true">Yes</option>
      <option value="false" selected="true">No</option>
    </param>
    <param name="seed" type="integer" value="42" label="Seed" help="Seed for the random number generator"/>
  </inputs>
  <outputs>
    <data format="rtg_sdf" name="output" label="Mutated genome on data ${input.hid}"/>
    <data format="rtg_sdf" name="output2" label="Second mutated genome on data ${input.hid}">
      <filter>diploid == "true"</filter>
    </data>
    <data format="vcf" name="output3" label="SNPs file generated on data ${input.hid}" />
  </outputs>

  <help>
This tool creates a simulated mutation of a reference genome. Can generate either haploid or diploid mutations.
  </help>

</tool>