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