<tool id="rtg_cgsim" name="Simulate CG reads">
  <description>with RTG cgsim</description>
  <command interpreter="bash">galaxy-rtg-wrapper.sh cgsim
-t ${input.extra_files_path}
#if $limit.sType == "numreads":
-n $limit.n
#else
-c $limit.c
#end if
-m $m
-M $M
--seed $seed
-o ${output.extra_files_path} >$output</command>
  <inputs>

    <param name="input" type="data" format="rtg_sdf" label="Source SDF"/>
    <param name="m" type="integer" value="350" label="Minimum fragment length" help=""/>
    <param name="M" type="integer" value="500" label="Maximum fragment length" help=""/>

    <conditional name="limit">
      <param name="sType" type="select" label="Select read limit">
        <option value="numreads">Fixed number of reads</option>
        <option value="coverage">Fixed coverage</option>
      </param>
      <when value="numreads">
        <param name="n" type="integer" value="1000" label="Number of reads" help="Total number of reads"/>
      </when>
      <when value="coverage">
        <param name="c" type="float" value="1" label="Coverage" help="Total coverage"/>
      </when>
    </conditional>	

    <param name="seed" type="integer" label="Seed" value="42" help="Seed for the random number generator"/>
  </inputs>
  <outputs>
    <data format="rtg_sdf" name="output" />
  </outputs>

  <help>
This tool creates an SDF containing randomly generated CG reads.
  </help>

</tool>