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comparison dwgsim_wrapper.xml @ 1:512671604bab default tip

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author nilshomer
date Sun, 14 Aug 2011 20:08:09 -0400
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0:1f7032731f66 1:512671604bab
1 <tool id="dwgsim" name="Generate simulated reads" version="1.0.0">
2 <description>from a fasta sequence using dwgsim</description>
3 <command interpreter="python">dwgsim_wrapper.py \
4 -e $eRateFirstread \
5 -E $eRateSecondread \
6 -d $innerDist \
7 -s $stDev \
8 -N $noReadpairs \
9 -1 $loFirstread \
10 -2 $loSecondread \
11 -r $rateOfMut \
12 -R $rateOfIndels \
13 -X $probExtRead \
14 -y $probRandRead \
15 -n $maxAllowN \
16 -S $strandDirection \
17 $colorSpace \
18 $haploMode \
19 -f $input \
20 -3 $outputSingleReads \
21 -4 $outputPEFirst \
22 -5 $outputPESecond \
23 -6 $outputMutations
24 </command>
25 <inputs>
26 <param format="fasta" name="input" type="data" label="Select fasta file to generate reads from"/>
27 <param name="eRateFirstread" size="4" type="text" value="0.020">
28 <label>base/color error rate of the first read</label>
29 </param>
30 <param name="eRateSecondread" size="4" type="text" value="0.020">
31 <label>base/color error rate of the second read</label>
32 </param>
33 <param name="innerDist" size="4" type="text" value="500">
34 <label>inner distance between the two ends</label>
35 </param>
36 <param name="stDev" size="4" type="text" value="50">
37 <label>Standard deviation</label>
38 </param>
39 <param name="noReadpairs" size="12" type="text" value="1000000">
40 <label>number of read pairs</label>
41 </param>
42 <param name="loFirstread" size="4" type="text" value="70">
43 <label>length of the first read </label>
44 </param>
45 <param name="loSecondread" size="4" type="text" value="70">
46 <label>length of the second read </label>
47 </param>
48 <param name="rateOfMut" size="4" type="text" value="0.0010">
49 <label>rate of mutations</label>
50 </param>
51 <param name="rateOfIndels" size="4" type="text" value="0.10">
52 <label>fraction of indels </label>
53 </param>
54 <param name="probExtRead" size="4" type="text" value="0.30">
55 <label>probability an indel is extended</label>
56 </param>
57 <param name="probRandRead" size="4" type="text" value="0.10">
58 <label>probability of a random DNA read</label>
59 </param>
60 <param name="maxAllowN" size="4" type="text" value="0">
61 <label>maximum number of Ns allowed in a given read</label>
62 </param>
63 <param name="colorSpace" type="boolean" truevalue="-c" falsevalue="" checked="False" label="generate reads in color space (SOLiD reads)"/>
64 <param name="strandDirection" type="select" label="Direction of strand (default: opposite strand for Illumina, same for SOLiD)">
65 <option value="0" selected="True">Default</option>
66 <option value="1">Same strand (mate pair)</option>
67 <option value="2">Opposite strand (paired end)</option>
68 </param>
69 <param name="haploMode" type="boolean" truevalue="-H" falsevalue="" checked="False" label="Haplotype mode"/>
70 </inputs>
71
72 <outputs>
73 <data format="fastqsanger" name="outputSingleReads"/>
74 <data format="fastqsanger" name="outputPEFirst"/>
75 <data format="fastqsanger" name="outputPESecond"/>
76 <data format="text" name="outputMutations"/>
77 </outputs>
78
79 <help>
80 This tools simulate reads from a given fasta file.
81 For more information, please see https://sourceforge.net/apps/mediawiki/dnaa/index.php?title=Whole_Genome_Simulation
82 </help>
83
84 </tool>