<tool id="rtg_readsim" name="Simulate reads">
  <description>with RTG readsim</description>
  <command interpreter="bash">galaxy-rtg-wrapper.sh readsim
-t ${input.extra_files_path}
#if str($input2) != "None":
-T ${input2.extra_files_path}
#end if
#if $limit.sType == "numreads":
-n $limit.n
#else
-c $limit.c
#end if
-m $m
-M $M
--machine $machine.sMachine
#if $machine.sMachine == "illumina_se":
-r $machine.r
#else if $machine.sMachine == "illumina_pe":
-L $machine.L
-R $machine.R
#else if $machine.sMachine == "454_pe":
--454-min-total-size $machine.454-min
--454-max-total-size $machine.454-max
#end if
--seed $seed
-o ${output.extra_files_path} >$output</command>
  <inputs>

    <param name="input" type="data" format="rtg_sdf" label="SDF containing input genome"/>
    <param name="input2" type="data" format="rtg_sdf" label="SDF with second genome for simulating diploid genomes" optional="true" />
    <param name="m" type="integer" value="200" label="Minimum fragment length" help="Total number of reads"/>
    <param name="M" type="integer" value="400" label="Minimum fragment length" help="Total number of reads"/>

    <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>	

    <conditional name="machine">
      <param name="sMachine" type="select" label="Select machine type">
        <option value="illumina_pe">Illumina paired-end</option>
        <option value="illumina_se">Illumina single-end</option>
        <option value="454_pe">454 paired-end</option>
      </param>
      <when value="illumina_se">
        <param name="r" type="integer" value="100" label="Read length" help="Target read length on left side"/>
      </when>
      <when value="illumina_pe">
        <param name="L" type="integer" value="100" label="Left read length" help="Target read length on left side"/>
        <param name="R" type="integer" value="100" label="Right read length" help="Target read length on right side"/>
      </when>
      <when value="454_pe">
        <param name="454-min" type="integer" value="500" label="Minimum total length" help="Minimum sum of left and right read lengths"/>
        <param name="454-max" type="integer" value="300" label="Maximum total length" help="Maximum sum of left and right read lengths"/>
      </when>
    </conditional>	
    <param name="seed" type="integer" value="42" label="Seed" 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 reads.
  </help>

</tool>