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comparison tools/ilmn_pacbio/soap_denovo.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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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 $inputs.read_type == "single"
32 q=${inputs.input1.file_name}
33 #else
34 avg_ins=${inputs.d}
35 asm_flags=3
36 reverse_seq=0
37 q1=${inputs.input1.file_name}
38 q2=${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
49 Runs SOAPdenovo_ to generate a genome assembly
50 using single-fragment or paired-end short reads.
51
52 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.
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
60 k
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
63 Insert size
64 For paired-end libraries, the expected insert size.
65
66 **Output**
67
68 assembly
69
70 </help>
71 </tool>
72
73