/tools/ilmn_pacbio/soap_denovo.xml

 1<tool id="soap_denovo" name="SOAPdenovo" version="1.0.0">
 2  <description>Short-read de novo assembly</description>
 3  <!--
 4      # SOAPdenovo-127mer all -s ${soap_config} -o assembly -K ${k} -p 8 -d -D
 5      # cat ${soap_config} > ${output1}
 6      # cp ${soap_config} ${output1} &amp;&amp;
 7  -->
 8  <command>
 9      SOAPdenovo-127mer all -s ${soap_config} -o assembly -K ${k} -p 24 -d -D -R
10  </command>
11  <inputs>
12    <conditional name="inputs">
13      <param name="read_type" type="select" label="Illumina read type">
14        <option value="single">Single fragment</option>
15        <option value="paired">Paired-end</option>
16      </param>
17      <when value="single">
18        <param name="input1" format="fastq" type="data" label="FASTQ file for reads"/>
19      </when>
20      <when value="paired">
21        <param name="input1" format="fastq" type="data" label="FASTQ file for forward reads"/>
22        <param name="input2" format="fastq" type="data" label="FASTQ file for reverse reads"/>
23        <param name="d" type="integer" value="500" label="Estimated insert size for paired-end reads" />
24      </when>
25    </conditional>
26    <param name="k" type="integer" value="23" label="Size of k for forming the de Bruijn overlap graph" />
27  </inputs>
28  <configfiles>
29    <configfile name="soap_config">max_rd_len=105
30[LIB]
31#if $inputs.read_type == "single"
32q=${inputs.input1.file_name}
33#else
34avg_ins=${inputs.d}
35asm_flags=3
36reverse_seq=0
37q1=${inputs.input1.file_name}
38q2=${inputs.input2.file_name}
39#end if
40    </configfile>
41  </configfiles>
42  <outputs>
43    <data name="assembled_contigs" format="fasta" from_work_dir="assembly.scafSeq" label="Assembled contigs from ${on_string}" />
44  </outputs>
45  <help>
46
47**What it does**
48
49Runs SOAPdenovo_ to generate a genome assembly
50using single-fragment or paired-end short reads.
51
52Li 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.
53"De novo assembly of human genomes with massively parallel short read sequencing."
54*Genome Res.* 2010 Feb;20(2):265-72.
55
56.. _SOAPdenovo: http://soap.genomics.org.cn/soapdenovo.html
57
58**Parameter list**
59
60k
61    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.
62
63Insert size
64    For paired-end libraries, the expected insert size.
65
66**Output**
67
68assembly
69
70  </help>
71</tool>
72
73