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1 <tool id="dwgsim" name="Generate simulated reads" version="1.0.0">
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2 <description>from a fasta sequence using dwgsim</description>
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3 <command interpreter="python">dwgsim_wrapper.py \
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4 -e $eRateFirstread \
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5 -E $eRateSecondread \
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6 -d $innerDist \
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7 -s $stDev \
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8 -N $noReadpairs \
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9 -1 $loFirstread \
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10 -2 $loSecondread \
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11 -r $rateOfMut \
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12 -R $rateOfIndels \
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13 -X $probExtRead \
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14 -y $probRandRead \
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15 -n $maxAllowN \
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16 -S $strandDirection \
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17 $colorSpace \
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18 $haploMode \
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19 -f $input \
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20 -3 $outputSingleReads \
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21 -4 $outputPEFirst \
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22 -5 $outputPESecond \
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23 -6 $outputMutations
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24 </command>
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25 <inputs>
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26 <param format="fasta" name="input" type="data" label="Select fasta file to generate reads from"/>
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27 <param name="eRateFirstread" size="4" type="text" value="0.020">
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28 <label>base/color error rate of the first read</label>
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29 </param>
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30 <param name="eRateSecondread" size="4" type="text" value="0.020">
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31 <label>base/color error rate of the second read</label>
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32 </param>
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33 <param name="innerDist" size="4" type="text" value="500">
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34 <label>inner distance between the two ends</label>
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35 </param>
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36 <param name="stDev" size="4" type="text" value="50">
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37 <label>Standard deviation</label>
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38 </param>
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39 <param name="noReadpairs" size="12" type="text" value="1000000">
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40 <label>number of read pairs</label>
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41 </param>
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42 <param name="loFirstread" size="4" type="text" value="70">
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43 <label>length of the first read </label>
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44 </param>
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45 <param name="loSecondread" size="4" type="text" value="70">
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46 <label>length of the second read </label>
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47 </param>
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48 <param name="rateOfMut" size="4" type="text" value="0.0010">
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49 <label>rate of mutations</label>
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50 </param>
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51 <param name="rateOfIndels" size="4" type="text" value="0.10">
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52 <label>fraction of indels </label>
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53 </param>
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54 <param name="probExtRead" size="4" type="text" value="0.30">
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55 <label>probability an indel is extended</label>
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56 </param>
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57 <param name="probRandRead" size="4" type="text" value="0.10">
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58 <label>probability of a random DNA read</label>
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59 </param>
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60 <param name="maxAllowN" size="4" type="text" value="0">
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61 <label>maximum number of Ns allowed in a given read</label>
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62 </param>
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63 <param name="colorSpace" type="boolean" truevalue="-c" falsevalue="" checked="False" label="generate reads in color space (SOLiD reads)"/>
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64 <param name="strandDirection" type="select" label="Direction of strand (default: opposite strand for Illumina, same for SOLiD)">
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65 <option value="0" selected="True">Default</option>
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66 <option value="1">Same strand (mate pair)</option>
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67 <option value="2">Opposite strand (paired end)</option>
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68 </param>
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69 <param name="haploMode" type="boolean" truevalue="-H" falsevalue="" checked="False" label="Haplotype mode"/>
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70 </inputs>
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71
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72 <outputs>
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73 <data format="fastqsanger" name="outputSingleReads"/>
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74 <data format="fastqsanger" name="outputPEFirst"/>
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75 <data format="fastqsanger" name="outputPESecond"/>
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76 <data format="text" name="outputMutations"/>
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77 </outputs>
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78
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79 <help>
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80 This tools simulate reads from a given fasta file.
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81 For more information, please see https://sourceforge.net/apps/mediawiki/dnaa/index.php?title=Whole_Genome_Simulation
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82 </help>
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83
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84 </tool>
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