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1 <tool id="art_solid" name="ART SOLiD" version="2014.11.03.0">
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2 <description>simulates SOLiD 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_SOLiD
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9
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10 $sam
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11
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12 #if $rndSeed and $rndSeed > -1:
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13 -r $rndSeed
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14 #end if
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15
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16 #if $generate.amplicon.use_amplicon == "amplicon_true":
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17 -A
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18
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19 #if $generate.choice == "single_end":
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20 s
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21 #else if $generate.choice == "paired_end":
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22 p
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23 #else:
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24 m
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25 #end if
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26
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27 #end if
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28
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29 $input_seq_file
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30 output
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31
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32 #if $generate.choice == "single_end":
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33 $generate.LEN_READ
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34 $fold_coverage
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35 #else if $generate.choice == "paired_end":
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36 $generate.LEN_READ_F3
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37 $generate.LEN_READ_F5
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38 $fold_coverage
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39 $generate.fragment_size
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40 $generate.fragment_sd
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41 #else:
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42 $generate.LEN_READ
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43 $fold_coverage
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44 $generate.fragment_size
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45 $generate.fragment_sd
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46 #end if
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47
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48 #if $generate.amplicon.use_amplicon == "amplicon_true":
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49 #if $generate.choice == "single_end":
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50 $generate.amplicon.reads_per_amplicon
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51 #else:
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52 $generate.amplicon.read_pairs_per_amplicon
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53 #end if
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54 #end if
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55 ]]></command>
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56 <inputs>
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57 <param label="DNA/RNA reference sequence" format="fasta" name="input_seq_file" type="data"/>
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58 <param label="the fold of read coverage over the reference sequences" name="fold_coverage" type="integer" value="20"/>
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59
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60 <conditional name="generate">
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61 <param name="choice" type="select" label="Type of data to generate">
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62 <option value="single_end">Single-End</option>
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63 <option value="paired_end">Paired-End</option>
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64 <option value="paired_end">Mate Pair</option>
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65 </param>
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66 <when value="single_end">
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67 <param name="LEN_READ" type="integer" label="Length of F3/R3 reads" value="100" />
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68 <expand macro="amplicon" />
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69 </when>
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70 <when value="paired_end">
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71 <param name="LEN_READ_F3" type="integer" label="Length of F3 reads" value="100" />
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72 <param name="LEN_READ_F5" type="integer" label="Length of F5 reads" value="100" />
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73 <expand macro="frag_len_sd" />
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74 <expand macro="amplicon_pair" />
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75 </when>
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76 <when value="mate_pair">
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77 <param name="LEN_READ" type="integer" label="Length of F3/R3 reads" value="100" />
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78 <expand macro="frag_len_sd" />
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79 <expand macro="amplicon_pair" />
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80 </when>
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81 </conditional>
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82
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83 <expand macro="sam" />
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84 <expand macro="rndSeed" />
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85
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86 </inputs>
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87 <outputs>
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88
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89 <!-- Single End -->
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90 <data format="fastq" name="output_fq1_single" from_work_dir="output.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name">
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91 <filter>generate['choice'] == "single_end"</filter>
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92 </data>
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93
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94 <!-- Paired End -->
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95 <data format="fastq" name="output_fq1_paired" from_work_dir="output_F3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (F3)">
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96 <filter>generate['choice'] == "paired_end"</filter>
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97 </data>
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98 <data format="fastq" name="output_fq2_paired" from_work_dir="output_F5.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (F5)">
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99 <filter>generate['choice'] == "paired_end"</filter>
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100 </data>
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101
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102 <!-- Mate Pair -->
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103 <data format="fastq" name="output_fq1_mate" from_work_dir="output_F3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (Forward)">
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104 <filter>generate['choice'] == "mate_pair"</filter>
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105 </data>
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106 <data format="fastq" name="output_fq2_mate" from_work_dir="output_R3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (Reverse)">
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107 <filter>generate['choice'] == "mate_pair"</filter>
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108 </data>
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109
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110 <data format="sam" name="output_sam" from_work_dir="output.sam" label="Mapping of Simulated SOLiD data to $input_seq_file.name">
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111 <filter>sam</filter>
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112 </data>
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113 <!-- todo? map file -->
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114 </outputs>
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115 <tests>
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116 <!-- Single End tests -->
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117 <test>
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118 <param name="rndSeed" value="42" />
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119 <param name="input_seq_file" value="input.fa" />
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120 <param name="LEN_READ" value="25" />
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121 <param name="fold_coverage" value="10" />
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122 <param name="choice" value="single_end" />
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123 <param name="sam" value="False" />
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124
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125 <output name="output_fq1_single" file="art.solid.01.fq" />
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126 </test>
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127 <test>
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128 <param name="rndSeed" value="42" />
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129 <param name="input_seq_file" value="input.fa" />
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130 <param name="fold_coverage" value="20" />
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131 <param name="choice" value="paired_end" />
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132 <param name="LEN_READ_F3" value="50" />
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133 <param name="LEN_READ_F5" value="50" />
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134 <param name="fragment_size" value="75" />
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135 <param name="fragment_sd" value="10" />
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136 <param name="sam" value="True" />
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137
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138 <output name="output_fq1_paired" file="art.solid.02_F3.fq" />
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139 <output name="output_fq2_paired" file="art.solid.02_F5.fq" />
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140 <output name="output_sam" file="art.solid.02.sam" lines_diff="2"/>
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141 </test>
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142 </tests>
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143 <help><![CDATA[
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144 Art SOLiD Simulator
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145 ===================
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146
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147 ART_SOLiD is a simulation program to generate sequence read data of SOLiD
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148 sequencing reads. ART generates reads according to a SOLiD read error profile.
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149 The built-in error profile is an empiricial error profile summarized from large
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150 SOLiD sequencing data. ART has been using for testing or benchmarking a variety
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151 of method or tools for next-generation sequencing data analysis, including read
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152 alignment, de novo assembly, detection of SNP, CNV, or other structure
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153 variation.
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154
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155 art_SOLiD can generate both single-end, matepair, and paired-end of SOLiD
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156 sequencing platform. art_SOLiD also support amplicon sequencing simulation with
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157 RNA references.
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158 ]]></help>
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159 <expand macro="citation" />
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160 </tool>
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161
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