annotate macros.xml @ 9:e7e1aa83d5b1 draft

planemo upload for repository https://github.com/gbcs-embl/Je/tree/master/src/galaxy commit e9754a8ec64b4606a620fe3b62fd186e659fc4e0
author gbcs-embl-heidelberg
date Thu, 05 Jul 2018 07:31:08 -0400
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children bd3cdf128bcb
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1 <macros>
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3 <token name="@VERSION_STRING@">1.2.1</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="1.2">je-suite</requirement>
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7 </requirements>
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8 </xml>
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9 <xml name="version_command">
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10 <version_command>je version 2&gt;&amp;1 | tail -n 1</version_command>
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11 </xml>
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13 <token name="@single_or_paired_cmd@">
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14 #if str( $library.type ) == "single":
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15 F1=${library.input_1}
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16 #elif str( $library.type ) == "paired":
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17 F1=${library.input_1}
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18 F2=${library.input_2}
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19 SAME_HEADERS=${library.SAME_HEADERS}
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20 #else
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21 ## prepare paired-end collection
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22 F1=${library.input_1.forward}
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23 F2=${library.input_1.reverse}
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24 SAME_HEADERS=${library.SAME_HEADERS}
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25 #end if
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26 </token>
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27
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28 <xml name="paired_options">
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29 <when value="paired">
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30 <param name="input_1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" label="FASTQ file #1"/>
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31 <param name="input_2" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" label="FASTQ file #2"/>
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32 <yield />
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33 <param name="SAME_HEADERS" type="boolean"
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34 label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)"
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35 help="Only applies if barcodes are added to the header (option ADD)"
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36 truevalue="true"
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37 falsevalue="false" checked="false"/>
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38 </when>
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39 <when value="paired_collection">
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40 <param name="input_1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired"
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41 label="FASTQ Paired Dataset"/>
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42 <yield />
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43 <param name="SAME_HEADERS" type="boolean"
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44 label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)"
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45 help="Only applies if barcodes are added to the header (option ADD)"
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46 truevalue="true"
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47 falsevalue="false" checked="false"/>
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48 </when>
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49 </xml>
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50
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51 <token name="@single_or_paired_illu_cmd@">
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52 @single_or_paired_cmd@
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53 I1=$library.I1
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54 #if str( $library.type ) != "single":
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55 #if str( $library.I2_CONDITIONAL.I2_AVAILABLE ) == "true":
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56 I2=${library.I2_CONDITIONAL.I2}
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57 BRED=${library.I2_CONDITIONAL.BRED_CONDITIONAL.BRED}
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58 #if str( $library.I2_CONDITIONAL.BRED_CONDITIONAL.BRED ) == "true":
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59 STRICT=${library.I2_CONDITIONAL.BRED_CONDITIONAL.STRICT}
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60 #end if
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61 #end if
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62 #end if
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63 </token>
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64
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65 <xml name="single_or_paired_illu">
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66 <conditional name="library">
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67 <param name="type" type="select" label="Is this single or paired library">
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68 <option value="single">Single-end</option>
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69 <option value="paired">Paired-end</option>
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70 <option value="paired_collection">Paired-end Dataset Collection</option>
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71 </param>
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72 <when value="single">
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73 <param name="input_1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" label="FASTQ file"/>
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74 <param name="I1" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="First Index File"/>
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75 </when>
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76 <expand macro="paired_options">
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77 <param name="I1" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="First Index File"/>
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78 <conditional name="I2_CONDITIONAL">
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79 <param name="I2_AVAILABLE" type="select" label="Do you have a second index file?">
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80 <option value="true">Yes</option>
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81 <option value="false" selected="true">No</option>
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82 </param>
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83 <when value="true">
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84 <param name="I2" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="Second Index File"/>
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85 <expand macro="bred_conditional"/>
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86 </when>
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87 <when value="false"/>
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88 </conditional>
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89 </expand>
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90 </conditional>
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91 </xml>
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92
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93 <xml name="single_or_paired_general">
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94 <conditional name="library">
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95 <param name="type" type="select" label="Is this single or paired library">
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96 <option value="single">Single-end</option>
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97 <option value="paired">Paired-end</option>
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98 <option value="paired_collection">Paired-end Dataset Collection</option>
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99 </param>
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100 <when value="single">
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101 <param name="input_1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" label="FASTQ file"/>
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102 </when>
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103 <expand macro="paired_options">
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104 <yield />
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105 </expand>
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106 </conditional>
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107 </xml>
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108
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109 <token name="@demultiplex_paired_end_cmd_options@">
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110 BPOS=$library.BPOS_CONDITIONAL.BPOS
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111 #if str( $library.BPOS_CONDITIONAL.BPOS ) == "BOTH":
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112 BM=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BM}
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113 #if str( $library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BM ) == "BOTH":
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114 BRED=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.BRED}
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115 #if str( $library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.BRED ) == "true":
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116 STRICT=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.STRICT}
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117 #end if
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118 #end if
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119 #end if
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120 </token>
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121
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122 <xml name="demultiplex_paired_end_options">
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123 <conditional name="BPOS_CONDITIONAL">
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124 <param name="BPOS" type="select" label="Barcode read position (BPOS)" help="where are the barcodes">
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125 <option value="READ_1" selected="true">READ_1 (beginning of read from the first fastq file)</option>
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126 <option value="READ_2">READ_2 (beginning of read from the second fastq file)</option>
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127 <option value="BOTH">BOTH (beginning of both reads)</option>
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128 </param>
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129 <when value="READ_1"/>
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130 <when value="READ_2"/>
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131 <when value="BOTH">
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132 <conditional name="BM_CONDITIIONAL">
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133 <param name="BM" type="select" label="Barcode for sample matching (BM)"
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134 help="which barcode should be used for sample look up (BM option)." >
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135 <option value="READ_1" selected="true">
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136 READ_1 (beginning of read from the first fastq file)
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137 </option>
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138 <option value="READ_2">
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139 READ_2 (beginning of read from the second fastq file)
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140 </option>
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141 <option value="BOTH">
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142 BOTH (beginning of both reads)
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143 </option>
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144 </param>
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145 <when value="READ_1"/>
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146 <when value="READ_2"/>
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147 <when value="BOTH">
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148 <expand macro="bred_conditional"/>
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149 </when>
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150 </conditional>
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151 </when>
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152 </conditional>
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153 </xml>
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154
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155 <xml name="bred_conditional">
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156 <conditional name="BRED_CONDITIONAL">
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157 <param name="BRED" type="select" label="Redundant barcodes (BRED)"
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158 help="are the barcodes REDUNDANT i.e. do they both resolve to the same sample.">
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159 <option value="true" selected="true">Yes</option>
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160 <option value="false">No</option>
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161 </param>
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162 <when value="true">
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163 <param name="STRICT" type="boolean" label="Strict (S)"
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164 truevalue="true"
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165 falsevalue="false"
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166 checked="false"
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167 />
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168 </when>
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169 <when value="false"/>
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170 </conditional>
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171 </xml>
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172
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173 <token name="@barcode_option_cmd@">
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174 #if str( $barcodes.barcode_list_type_con ) == "text":
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175 BARCODE_FILE=${barcode_file_from_text}
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176 #else if str( $barcodes.barcode_list_type_con ) == "file":
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177 BARCODE_FILE=${barcodes.BARCODE_FILE}
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178 #end if
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179 </token>
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180
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181 <xml name="barcode_option">
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182 <conditional name="barcodes">
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183 <param name="barcode_list_type_con" type="select" label="Barcode list input type">
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184 <option value="file" selected="true">Use a tab-delimited file from the history</option>
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185 <option value="text">Paste the barcodes list in a text field within the form</option>
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186 </param>
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187
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188 <when value="file">
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189 <param name="BARCODE_FILE" type="data" format="tabular,txt" label="Barcode List"
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190 help="Barcode list format: one sample per line. First column is sample name and second is the
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191 barcode, separated by tab or space. A third and fourth column can be used to specify the resulting
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192 file names. See help below."/>
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193 </when>
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194
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195 <when value="text">
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196 <param name="barcode_text" type="text" area="True" size="10x30"
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197 value="sample_name &lt;tab&gt; barcode" label="Barcode List"
0
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198 help="Barcode list format: one sample per line. First column is sample name and second is the
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199 barcode, separated by tab or space. A third and fourth column can be used to specify the resulting
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200 file names. See help below.">
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201 <sanitizer>
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202 <valid initial="string.printable"></valid>
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203 <mapping initial="none"/>
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204 </sanitizer>
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205 </param>
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206 </when>
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207 </conditional>
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208 </xml>
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209
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210 <xml name="barcode_config_file">
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211 <configfile name="barcode_file_from_text">#set from_text_area = ''
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212 #if str( $barcodes.barcode_list_type_con ) == "text":
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213 #set from_text_area = $barcodes.barcode_text
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214 #end if
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215 ${from_text_area}</configfile>
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216 </xml>
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217
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218 <token name="@barcode_len_cmd@">
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219 #if str( $LEN ) != "":
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220 BCLEN=$LEN
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221 #end if
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222 </token>
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223
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224 <xml name="barcode_len_option">
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225 <param name="LEN" type="text" value="" label="Barcode Length (LEN)"
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226 help="If 'Barcode read position'=BOTH and 'Redundant barcodes'=False, two distinct
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227 lengths can be provided using the syntax LEN=X:Z where X and Z are 2 integers representing
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228 the barcode length for read_1 and read_2 respectively. Default: empty"/>
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229 </xml>
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230 <xml name="clip_barcode">
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231 <param name="CLIP_BARCODE" type="boolean" label="Remove barcode sequence from read (C)"
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232 truevalue="true" falsevalue="false" checked="true"/>
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233 </xml>
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234
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235 <token name="@demultiplexer_common_options_cmd@">
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236 ADD=${ADD}
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237 MM=$MM
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238 MMD=$MMD
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239 Q=$MIN_BASE_QUALITY
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240 QUALITY_FORMAT=$QUALITY_FORMAT
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241 </token>
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242 <xml name="demultiplexer_common_options">
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243 <param name="ADD" type="boolean"
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244 label="Add matched barcode at the end of the read header (ADD)"
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245 truevalue="true"
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246 falsevalue="false"
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247 checked="true"
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248 />
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249 <param name="MM" type="text" value="1" label="Maximum Mismatches (MM)"
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250 help="Maximum mismatches for a barcode to be considered a match." />
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251
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252 <param name="MMD" type="text" value="1" label="Minimum mismatch difference (MMD)"
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253 help="Minimum difference between number of mismatches in the best and second best barcodes for a barcode
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254 to be considered a match." />
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255
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256 <param name="MIN_BASE_QUALITY" type="text" value="10" label="Minimum base quality (Q)"
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257 help="Any barcode bases falling below this quality will be
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258 considered a mismatch even in the bases match." />
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259
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260 <param name="QUALITY_FORMAT" type="select" label="Fastq Quality Format (V)"
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261 help="How are the quality values encoded in the fastq. Either 'Solexa' for
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262 pre-pipeline 1.3 style scores (solexa scaling + 66), 'Illumina' for pipeline 1.3 and
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263 above (phred scaling + 64) or 'Standard' for phred scaled scores with a character shift
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264 of 33.">
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265 <option value="Standard" selected="true">
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266 Fastq - Illumina Casava v1.8 with Sanger coding quality (phred scaling + 33)
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267 </option>
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268 <option value="Illumina">
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269 Fastq - Illumina v1.3 or above coding of quality (phred scaling + 64)
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270 </option>
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271 <option value="Solexa">
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272 Fastq - Solexa-style quality (solexa scaling + 66)
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273 </option>
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274 <option value="null">
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275 Detect automatically
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276 </option>
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277 </param>
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278 </xml>
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279
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280 <token name="@demultiplexer_common_output_options_cmd@">
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281 KEEP_UNASSIGNED_READ=${KEEP_UNASSIGNED_READ}
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282 STATS_ONLY=${STATS_ONLY}
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283 #if str( $DIAG ) == "true":
0
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284 BARCODE_DIAG_FILE=$BARCODE_DIAG_FILE
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285 #end if
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286 </token>
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287 <xml name="demultiplexer_common_output_options">
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288 <!--<section name="output_options" title="Output Options" expanded="True">-->
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289 <param name="COLLECT_OUTPUTS" type="boolean"
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290 truevalue="true" falsevalue="false" checked="false"
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291 label="Output forward and reverse reads in dataset collections" />
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292 <param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)"
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293 truevalue="true" falsevalue="false" checked="true"/>
0
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294 <param name="DIAG" type="boolean" label="Output barcode match reporting file (DIAG)"
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295 truevalue="true" falsevalue="false" checked="false"
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296 help="This file will
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297 contain a line per read pair with the barcode best matching the read subsequence or 'null' when no
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298 match is found according to matching parameters. This file is useful for debugging or further
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299 processing in case both ends are barcoded."/>
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300 <param name="STATS_ONLY" type="boolean" label="Only produce metric and diagnostic reports (STATS_ONLY)"
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301 truevalue="true" falsevalue="false" checked="false"
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302 help="do not demultiplex." />
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303 <!--</section>-->
0
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304 </xml>
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305
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306 <token name="@common_options_cmd@">
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307 XT=${XT}
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308 ZT=${ZT}
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309 #if str( $RCHAR ) != "":
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310 RCHAR=${RCHAR}
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311 #else:
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312 RCHAR=null
0
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313 #end if
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314 GZ=${GZ}
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315 OUTPUT_DIR=results
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316 </token>
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317 <xml name="common_options">
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318 <param name="XT" type="text" value="0"
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319 label="Extra number of bases to be trimmed right after the barcode (XT)" />
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320 <param name="ZT" type="text" value="0"
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321 label="Extra number of bases to be trimmed from the read end (ZT)" />
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322
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323 <param name="RCHAR" type="text"
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324 label="Replace white space in the read name/header with speficied symbols (RCHAR)"
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325 help="Set to empty or null for no replacement."
0
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326 value=":"/>
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327
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328 <param name="GZ" type="hidden" label="Compress output (GZ)"
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329 help="will result in fastq.gz files."
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330 value="false"/>
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331 </xml>
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332
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333 <token name="@demultiplexer_common_outputs_cmd@">
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334 METRICS_FILE_NAME=$METRICS_FILE_NAME
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335 </token>
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336
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337 <xml name="demultiplexer_common_outputs">
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338 <data name="DEMULTIPLEX_RESULTS" format="tabular" label="Je-Demultiplex result placeholder" hidden="true">
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339 <filter>COLLECT_OUTPUTS == False and STATS_ONLY == False</filter>
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340 <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" directory="results" visible="true" ext="fastqsanger"/>
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341 </data>
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342 <data name="METRICS_FILE_NAME" format="tabular" label="Je-Demultiplex Metrics"/>
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343 <data name="BARCODE_DIAG_FILE" format="tabular" label="Barcode statistics">
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344 <filter>DIAG</filter>
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345 </data>
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346 <collection name="COLLECTION_1" type="list" label="${tool.name} on ${on_string} : Reads_1" >
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347 <filter>COLLECT_OUTPUTS and STATS_ONLY == False</filter>
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348 <discover_datasets pattern="(?P&lt;designation&gt;.+_1\..+)" ext="fastqsanger" directory="results" visible="false" />
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349 </collection>
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350 <collection name="COLLECTION_2" type="list" label="${tool.name} on ${on_string} : Reads_2" >
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351 <filter>COLLECT_OUTPUTS and STATS_ONLY == False</filter>
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352 <discover_datasets pattern="(?P&lt;designation&gt;.+_2\..+)" ext="fastqsanger" directory="results" visible="false" />
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353 </collection>
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354 </xml>
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355 <xml name="citations">
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356 <citations>
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357 <citation type="doi">10.1186/s12859-016-1284-2</citation>
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358 </citations>
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359 </xml>
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360 </macros>