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1 <tool id="art_illumina" name="ART Illumina" version="2014.11.03.0">
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2 <description>simulates sequencing data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="stdio" />
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7 <command><![CDATA[
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8 art_illumina
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9
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10 #if str($sam) == "-s":
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11 --samout
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12 #end if
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13
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14 #if not str($aln) == "-a":
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15 --noALN
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16 #end if
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17
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18 #if str($generate.choice) == "paired_end":
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19 --paired
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20 --mflen $generate.fragment_size
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21 --sdev $generate.fragment_sd
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22 #else if str($generate.choice) == "mate_pair":
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23 --matepair
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24 --mflen $generate.fragment_size
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25 --sdev $generate.fragment_sd
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26 #end if
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27
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28 --in $input_seq_file
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29 --len $read_length
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30 --fcov $fold_coverage
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31
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32 $amplicon
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33
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34 --insRate $insRate
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35 --insRate2 $insRate2
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36 --delRate $delRate
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37 --delRate2 $delRate2
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38
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39 #if $rndSeed and $rndSeed > -1:
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40 --rndSeed $rndSeed
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41 #end if
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42
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43 --out output;
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44 ]]></command>
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45 <inputs>
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46 <param label="DNA/RNA reference sequence" format="fasta" name="input_seq_file" type="data"/>
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47 <param label="the fold of read coverage over the reference sequences" name="fold_coverage" type="integer" value="20"/>
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48 <param label="length of reads to be simulated" name="read_length" type="integer" value="100"/>
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49 <param label="amplicon sequencing simulation" name="amplicon" type="boolean" truevalue="--amplicon" falsevalue="" />
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50
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51 <conditional name="generate">
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52 <param name="choice" type="select" label="Type of data to generate">
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53 <option value="single_end">Single-End</option>
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54 <option value="paired_end">Paired-End</option>
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55 <option value="mate_pair">Mate-Pair</option>
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56 </param>
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57 <when value="single_end">
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58 </when>
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59 <when value="paired_end">
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60 <expand macro="frag_len_sd" />
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61 </when>
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62 <when value="mate_pair">
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63 <expand macro="frag_len_sd" />
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64 </when>
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65 </conditional>
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66
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67 <expand macro="aln" />
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68 <expand macro="sam" />
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69
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70 <param label="the first-read insertion rate" help="(--insRate)" name="insRate" type="float" value="0.00009" />
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71 <param label="the second-read insertion rate" help="(--insRate2)" name="insRate2" type="float" value="0.00015" />
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72 <param label="the first-read deletion rate" help="(--delRate)" name="delRate" type="float" value="0.00011" />
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73 <param label="the second-read deletion rate" help="(--delRate2)" name="delRate2" type="float" value="0.00023" />
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74
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75 <expand macro="rndSeed" />
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76 <!-- todo: id, errfree, masN, qShift(2), sepProf -->
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77 </inputs>
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78 <outputs>
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79 <!-- Single End -->
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80 <data format="fastq" name="output_fq1_single" from_work_dir="output.fq" label="Simulated of Illumina sequencing of $input_seq_file.name">
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81 <filter>generate['choice'] == "single_end"</filter>
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82 </data>
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83
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84 <!-- Paired End -->
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85 <data format="fastq" name="output_fq1_paired" from_work_dir="output1.fq" label="Simulated of Illumina sequencing of $input_seq_file.name (Forward)">
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86 <filter>generate['choice'] != "single_end"</filter>
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87 </data>
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88 <data format="fastq" name="output_fq2_paired" from_work_dir="output2.fq" label="Simulated of Illumina sequencing of $input_seq_file.name (Reverse)">
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89 <filter>generate['choice'] != "single_end"</filter>
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90 </data>
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91 <data format="sam" name="output_sam" from_work_dir="output.sam" label="Mapping of Simulated Illumina data to $input_seq_file.name">
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92 <filter>sam</filter>
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93 </data>
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94
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95 <!-- Single End -->
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96 <data format="aln" name="output_aln1_single" from_work_dir="output.aln" label="Alignment of Simulated Illumina data to $input_seq_file.name">
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97 <filter>aln and generate['choice'] == "single_end"</filter>
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98 </data>
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99
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100 <!-- paired end -->
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101 <data format="aln" name="output_aln1_paired" from_work_dir="output1.aln" label="Alignment of Simulated Illumina data to $input_seq_file.name">
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102 <filter>aln and generate['choice'] != "single_end"</filter>
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103 </data>
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104 <data format="aln" name="output_aln2_paired" from_work_dir="output2.aln" label="Alignment of Simulated Illumina data to $input_seq_file.name">
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105 <filter>aln and generate['choice'] != "single_end"</filter>
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106 </data>
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107 </outputs>
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108 <tests>
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109 <test>
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110 <param name="rndSeed" value="42" />
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111 <param name="input_seq_file" value="input.fa" />
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112 <param name="fold_coverage" value="20" />
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113 <param name="read_length" value="200" />
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114 <param name="choice" value="single_end" />
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115 <param name="aln" value="True" />
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116 <param name="sam" value="True" />
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117
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118 <output name="output_fq1_single" file="art.illumina.01.fq" />
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119 <output name="output_aln1_single" file="art.illumina.01.aln" lines_diff="2"/>
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120 <output name="output_sam" file="art.illumina.01.sam" lines_diff="2"/>
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121 </test>
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122 <test>
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123 <param name="rndSeed" value="42" />
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124 <param name="input_seq_file" value="input.fa" />
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125 <param name="fold_coverage" value="20" />
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126 <param name="read_length" value="200" />
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127 <param name="choice" value="paired_end" />
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128 <param name="fragment_size" value="300" />
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129 <param name="fragment_sd" value="10" />
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130 <param name="aln" value="True" />
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131 <param name="sam" value="True" />
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132
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133 <output name="output_fq1_paired" file="art.illumina.021.fq" />
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134 <output name="output_fq2_paired" file="art.illumina.022.fq" />
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135 <output name="output_aln1_paired" file="art.illumina.021.aln" lines_diff="2"/>
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136 <output name="output_aln2_paired" file="art.illumina.022.aln" lines_diff="2"/>
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137 <output name="output_sam" file="art.illumina.02.sam" lines_diff="2"/>
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138 </test>
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139 </tests>
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140 <help><![CDATA[
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141 Art Illumina Simulator
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142 ======================
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143
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144 ART (art_Illumina Q version) is a simulation program to generate sequence read
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145 data of Illumina sequencers. ART generates reads according to the empirical
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146 read quality profile summarized from large real read data. ART has been using
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147 for testing or benchmarking a variety of methods or tools for next-generation
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148 sequencing data analysis, including read alignment, de novo assembly, detection
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149 of SNP, CNV, or other structure variation.
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150
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151 art_Illumina can generate single-end, paired-end, mate-pair reads, and
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152 amplicon sequencing simulation of Illumina sequencing platform. Its outputs
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153 include FASTQ read, ALN and/or SAM alignment files.
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154
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155 ]]></help>
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156 <expand macro="citation" />
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157 </tool>
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158
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