<tool id="soap_denovo" name="SOAPdenovo" version="1.0.0">
  <description>Short-read de novo assembly</description>
  <!--
      # SOAPdenovo-127mer all -s ${soap_config} -o assembly -K ${k} -p 8 -d -D
      # cat ${soap_config} > ${output1}
      # cp ${soap_config} ${output1} &amp;&amp;
  -->
  <command>
      SOAPdenovo-127mer all -s ${soap_config} -o assembly -K ${k} -p 24 -d -D -R
  </command>
  <inputs>
    <conditional name="inputs">
      <param name="read_type" type="select" label="Illumina read type">
        <option value="single">Single fragment</option>
        <option value="paired">Paired-end</option>
      </param>
      <when value="single">
        <param name="input1" format="fastq" type="data" label="FASTQ file for reads"/>
      </when>
      <when value="paired">
        <param name="input1" format="fastq" type="data" label="FASTQ file for forward reads"/>
        <param name="input2" format="fastq" type="data" label="FASTQ file for reverse reads"/>
        <param name="d" type="integer" value="500" label="Estimated insert size for paired-end reads" />
      </when>
    </conditional>
    <param name="k" type="integer" value="23" label="Size of k for forming the de Bruijn overlap graph" />
  </inputs>
  <configfiles>
    <configfile name="soap_config">max_rd_len=105
[LIB]
#if $inputs.read_type == "single"
q=${inputs.input1.file_name}
#else
avg_ins=${inputs.d}
asm_flags=3
reverse_seq=0
q1=${inputs.input1.file_name}
q2=${inputs.input2.file_name}
#end if
    </configfile>
  </configfiles>
  <outputs>
    <data name="assembled_contigs" format="fasta" from_work_dir="assembly.scafSeq" label="Assembled contigs from ${on_string}" />
  </outputs>
  <help>

**What it does**

Runs SOAPdenovo_ to generate a genome assembly
using single-fragment or paired-end short reads.

Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J.
"De novo assembly of human genomes with massively parallel short read sequencing."
*Genome Res.* 2010 Feb;20(2):265-72.

.. _SOAPdenovo: http://soap.genomics.org.cn/soapdenovo.html

**Parameter list**

k
    k-mer size for constructing the de Bruijn graph.  The appropriate size of k is genome and data set dependent, but a good starting choice might be 75% of the read length.

Insert size
    For paired-end libraries, the expected insert size.

**Output**

assembly

  </help>
</tool>