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4
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1 <tool id="svdetect_run_parallel" name="Detect clusters of anomalously mapped pairs">
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2
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3 <description>and identify structural variants</description>
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4
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5 <command interpreter="perl">SVDetect_run_parallel.pl
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6
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7 #if $getLinks.linking == "linking"
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8 linking
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9 <!-- -out1 '$links_file' -->
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10 #end if
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11 #if $getFilteredLinks.filtering == "filtering"
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12 filtering
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13 <!--- out2 '$flinks_file' -->
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14 #if str($getFilteredLinks.links2SV) == "create"
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15 links2SV
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16 -out3 '$sv_file'
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17 #end if
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18 #if $getFilteredLinks.file_conversion.file_conversion_select=="convert" and str($getFilteredLinks.file_conversion.links2circos) == "create"
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19 links2circos
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20 -out4 '$circos_file'
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21 #end if
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22 #if $getFilteredLinks.file_conversion.file_conversion_select=="convert" and str($getFilteredLinks.file_conversion.links2bed) == "create"
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23 links2bed
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24 -out5 '$bed_file'
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25 #end if
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26 #end if
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27 -conf '$config_file'
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28 -l '$log_file'
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29 -N '$sample_name'
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30
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31 </command>
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32
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33 <inputs>
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34 <param name="sample_name" type="text" value="sample" label="Sample Name"/>
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35 <param name="mates_file" format="bam" type="data" label="Input BAM file (.ab.bam)"/>
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36 <param name="cmap_file" format="len" type="data" label="Chromosomes list file (.len)" help="Tabulated file format with Chromosome ID (integer from 1), name and length"/>
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37 <param name="mates_orientation" type="select" format="txt" label="Type of sequencing technology and libraries">
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38 <option value="FR">Illumina paired-ends</option>
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39 <option value="RF">Illumina mate-pairs</option>
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40 <option value="FR">SOLiD paired-ends</option>
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41 <option value="RR">SOLiD mate-pairs</option>
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42 </param>
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43 <param name="read1_length" type="integer" size="10" value="50" label="Read 1 length (bp)" help="Length of the first read in a pair (left read)"/>
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44 <param name="read2_length" type="integer" size="10" value="50" label="Read 2 length (bp)" help="Length of the second read in a pair (right read)"/>
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45 <param name="sv_type" type="select" format="txt" label="Type of SV to detect">
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46 <option value="all">all types of SVs</option>
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47 <option value="intra">intrachromosomal SVs only</option>
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48 <option value="inter">interchromosomal SVs only</option>
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49 </param>
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50
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51 <conditional name="getLinks">
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52 <param name="linking" type="select" label="Linking procedure" help="Detection and isolation of links">
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53 <option value="linking">Yes</option>
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54 <option value="">No, already done</option>
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55 </param>
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56 <when value="">
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57 <!-- do nothing here -->
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58 </when>
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59 <when value="linking">
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60 <param name="splitmate" label="Do you want to split the original mate file per chromosome for parallel computing?" type="boolean" truevalue="split" falsevalue="do_not_split" checked="True" help="Untick it if already done"/>
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61 <param name="window_size" type="integer" size="20" value="3000" label="Window size (bp)" help="Equal to at least “2µ+2√2σ"/>
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62 <param name="step_length" type="integer" size="20" value="250" label="Step length size (bp)" help="Equal to 1/2 or 1/4 of the window size"/>
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63 </when>
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64 </conditional>
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65
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66 <conditional name="getFilteredLinks">
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67 <param name="filtering" type="select" label="Filtering procedure" help="Filtering of links according different parameters and thresholds">
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68 <option value="filtering">Yes</option>
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69 <option value="">No</option>
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70 </param>
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71 <when value="">
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72 <!-- do nothing here -->
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73 </when>
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74 <when value="filtering">
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75
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76 <param name="splitlink" label="Do you want to split the original link file per chromosome for parallel computing?" type="boolean" truevalue="split" falsevalue="do_not_split" checked="False" help="Untick it if (the linking is) already done"/>
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77 <param name="chromosomes" type="text" size="20" label="List of chromosome names to keep or exclude"/>
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78 <param name="nb_pairs_threshold" type="integer" size="20" value="5" label="Minimum number of pairs in a cluster"/>
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79
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80 <conditional name="filter1">
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81 <param name="strand_filtering" type="select" label="Strand filtering procedure">
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82 <option value="strand">Yes</option>
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83 <option value="">No</option>
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84 </param>
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85 <when value="">
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86 <!-- do nothing here -->
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87 </when>
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88 <when value="strand">
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89
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90 <conditional name="filter2">
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91 <param name="order_filtering" type="select" label="Order filtering procedure">
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92 <option value="order">Yes</option>
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93 <option value="">No</option>
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94 </param>
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95 <when value="">
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96 <!-- do nothing here -->
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97 </when>
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98 <when value="order">
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99
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100 <conditional name="filter3">
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101 <param name="insert_size_filtering" type="select" label="Insert-size filtering procedure">
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102 <option value="insert">Yes</option>
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103 <option value="">No</option>
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104 </param>
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105 <when value="">
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106 <!-- do nothing here -->
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107 </when>
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108 <when value="insert">
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109 <param name="indel_sigma_threshold" type="float" size="20" value="3" label="Minimal number of sigma fold for the insert size filtering and to call insertions and deletions"/>
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110 <param name="dup_sigma_threshold" type="float" size="20" value="3" label="minimal number of sigma fold for the insert size filtering to call tandem duplications"/>
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111 <param name="singleton_sigma_threshold" type="float" size="20" value="4" label="Minimal number of sigma fold for the insert size filtering to call singletons" help="for Illumina mate-pairs only"/>
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112 </when>
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113 </conditional>
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114
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115 <param name="mu_length" type="integer" size="20" value="3000" label="Mean insert size value (µ) of normally mapped mate-pairs, in bp"/>
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116 <param name="sigma_length" type="integer" size="20" value="250" label="Calculated sd value (σ) from the distribution of normally mapped mate-pairs, in bp"/>
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117 <param name="nb_pairs_order_threshold" type="integer" size="20" value="2" label="Minimal number of pairs in a subgroup of paired-end reads for balanced events"/>
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118 </when>
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119 </conditional>
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120
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121 <param name="final_score_threshold" type="float" size="20" value="1.0" label="Minimal final filtering score for calling SVs" help="A value of 1 means all the pairs in a cluster were consistent between each other after applying filters"/>
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122 </when>
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123 </conditional>
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124
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125 <param name="links2SV" label="Do you want to have filtered links in a tabulated file format showing significant SVs?" type="boolean" truevalue="create" falsevalue="do_not_create" checked="True"/>
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126
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127 <conditional name="file_conversion">
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128 <param name="file_conversion_select" type="select" label="Output file conversion" help="Converts filtered links to Circos/BED files format for graphical view of SVs">
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129 <option value="do_not_convert">No</option>
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130 <option value="convert">Yes</option>
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131 </param>
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132 <when value="do_not_convert">
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133 <!-- do nothing here -->
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134 </when>
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135 <when value="convert">
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136 <param name="links2circos" label="Converts the link list to the Circos link format" type="boolean" truevalue="create" falsevalue="do_not_create" checked="True"/>
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137 <param name="links2bed" label="Converts the link list to the UCSC BED format" type="boolean" truevalue="create" falsevalue="do_not_create" checked="False"/>
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138 <param name="organism_id" type="text" size="10" value="hs" label="Organism ID"/>
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139 <repeat name="color_code" title="Color-code" min="1" max="7">
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140 <param name="color" type="select" label="Color">
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141 <option value="grey">grey</option>
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142 <option value="black">black</option>
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143 <option value="blue">blue</option>
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144 <option value="green">green</option>
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145 <option value="purple">purple</option>
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146 <option value="orange">orange</option>
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147 <option value="red">red</option>
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148 </param>
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149 <param name="interval" type="text" value="1,3" label="Interval"/>
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150 </repeat>
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151 </when>
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152 </conditional>
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153 </when>
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154 </conditional>
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155 </inputs>
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156
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157
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158 <outputs>
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159 <!--<data format="txt" name="links_file" label="svdetect.links">
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160 <filter>getLinks['linking']=="linking"</filter>
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161 </data>
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162 <data format="txt" name="flinks_file" label="svdetect.links.filtered">
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163 <filter>getFilteredLinks['filtering']=="filtering"</filter>
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164 </data>-->
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165 <data format="sv" name="sv_file" label="${sample_name}.sv">
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166 <filter>(
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167 getFilteredLinks['filtering']=="filtering" and
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168 getFilteredLinks['links2SV'] is True
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169 )
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170 </filter>
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171 </data>
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172 <data format="segdup" name="circos_file" label="${sample_name}.segdup">
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173 <filter>(
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174 getFilteredLinks['filtering']=="filtering" and
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175 getFilteredLinks['file_conversion']['file_conversion_select']=="convert" and
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176 getFilteredLinks['file_conversion']['links2circos'] is True
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177 )
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178 </filter>
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179 </data>
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180 <data format="bed" name="bed_file" label="${sample_name}.bed">
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181 <filter>(
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182 getFilteredLinks['filtering']=="filtering" and
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183 getFilteredLinks['file_conversion']['file_conversion_select']=="convert" and
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184 getFilteredLinks['file_conversion']['links2bed'] is True
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185 )
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186 </filter>
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187 </data>
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188 <data format="txt" name="log_file" label="${sample_name}.svdetect_run.log"/>
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189 </outputs>
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190
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191
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192
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193 <configfiles>
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194 <configfile name="config_file">
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195 <general>
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196 input_format = bam
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197 sv_type = ${sv_type}
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198 mates_orientation=${mates_orientation}
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199 read1_length=${read1_length}
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200 read2_length=${read2_length}
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201 mates_file=${mates_file}
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202 cmap_file=${cmap_file}
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203 tmp_dir=$__new_file_path__/svdetect/tmp
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204 output_dir=$__new_file_path__/svdetect
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205 num_threads=8
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206 </general>
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207
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208 #if $getLinks.linking == "linking"
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209 <detection>
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210 #if str($getLinks.splitmate) == "split"
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211 split_mate_file=1
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212 #else
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213 split_mate_file=0
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214 #end if
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215 window_size=${getLinks.window_size}
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216 step_length=${getLinks.step_length}
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217 </detection>
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218 #end if
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219
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220 #if $getFilteredLinks.filtering == "filtering"
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221 <filtering>
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222 #if str($getFilteredLinks.splitlink) == "split"
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223 split_link_file=1
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224 #else
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225 split_link_file=0
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226 #end if
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227 #if str($getFilteredLinks.chromosomes) != ""
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228 chromosomes=${getFilteredLinks.chromosomes}
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229 #end if
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230 nb_pairs_threshold=${getFilteredLinks.nb_pairs_threshold}
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231 #if $getFilteredLinks.filter1.strand_filtering == "strand"
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232 strand_filtering=1
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233 final_score_threshold=${getFilteredLinks.filter1.final_score_threshold}
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234 #if $getFilteredLinks.filter1.filter2.order_filtering == "order"
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235 order_filtering=1
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236 mu_length=${getFilteredLinks.filter1.filter2.mu_length}
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237 sigma_length=${getFilteredLinks.filter1.filter2.sigma_length}
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238 nb_pairs_order_threshold=${getFilteredLinks.filter1.filter2.nb_pairs_order_threshold}
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239 #if $getFilteredLinks.filter1.filter2.filter3.insert_size_filtering == "insert"
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240 insert_size_filtering=1
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241 indel_sigma_threshold=${getFilteredLinks.filter1.filter2.filter3.indel_sigma_threshold}
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242 dup_sigma_threshold=${getFilteredLinks.filter1.filter2.filter3.dup_sigma_threshold}
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243 singleton_sigma_threshold=${getFilteredLinks.filter1.filter2.filter3.singleton_sigma_threshold}
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244 #else
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245 insert_size_filtering=0
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246 #end if
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247 #else
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248 order_filtering=0
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249 #end if
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250 #else
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251 strand_filtering=0
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252 #end if
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253 </filtering>
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254 #end if
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255
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256 #if $getFilteredLinks.filtering == "filtering"
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257 #if $getFilteredLinks.file_conversion.file_conversion_select == "convert"
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258 #if str($getFilteredLinks.file_conversion.links2circos) == "create"
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259 <circos>
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260 organism_id=${getFilteredLinks.file_conversion.organism_id}
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261 <colorcode>
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262 #for $color_repeat in $getFilteredLinks.file_conversion.color_code
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263 ${color_repeat.color}=${color_repeat.interval}
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264 #end for
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265 </colorcode>
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266 </circos>
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267 #end if
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268 #if str($getFilteredLinks.file_conversion.links2bed) == "create"
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269 <bed>
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270 <colorcode>
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271 #for $color_repeat in $getFilteredLinks.file_conversion.color_code
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272 #if str($color_repeat.color)== "grey"
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273 190,190,190=${color_repeat.interval}
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274 #end if
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275 #if str($color_repeat.color)== "black"
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276 0,0,0=${color_repeat.interval}
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277 #end if
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278 #if str($color_repeat.color)== "blue"
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279 0,0,255=${color_repeat.interval}
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280 #end if
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281 #if str($color_repeat.color)== "green"
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282 0,255,0=${color_repeat.interval}
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283 #end if
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284 #if str($color_repeat.color)== "purple"
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285 153,50,205=${color_repeat.interval}
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286 #end if
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287 #if str($color_repeat.color)== "orange"
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288 255,140,0=${color_repeat.interval}
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289 #end if
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290 #if str($color_repeat.color)== "red"
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291 255,0,0=${color_repeat.interval}
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292 #end if
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293 #end for
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294 </colorcode>
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295 </bed>
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296 #end if
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297 #end if
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298 #end if
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299 </configfile>
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300 </configfiles>
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301
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302 <help>
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303 **What it does**
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304
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305 SVDetect - Version : 0.8
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306
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307 Parallel version (nCPU=8)
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308
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309 SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies
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310
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311 This tool aims to identifying structural variations (SVs) with both clustering and sliding-window strategies, and helping in their visualization at the genome scale.
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312 SVDetect is compatible with SOLiD and Illumina (>=1.3) reads.
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313
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314 Manual documentation available at the http://svdetect.sourceforge.net/Site/Manual.html
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315
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316 -----
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317
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318 .. class:: infomark
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319
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320 Contact Bruno Zeitouni (bruno.zeitouni@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect.
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321
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322 </help>
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323
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324 </tool>
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