annotate macros.xml @ 1:c6afeeade4f2 draft

use _JAVA_OPTIONS to set default memory limit
author gbcs-embl-heidelberg
date Thu, 26 Nov 2015 08:59:16 -0500
parents d39a96961423
children f6bc74863c1c
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1 <macros>
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2
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3 <token name="@single_or_paired_cmd@">
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4 #if str( $library.type ) == "single":
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5 F1=${library.input_1}
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6 #elif str( $library.type ) == "paired":
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7 F1=${library.input_1}
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8 F2=${library.input_2}
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9 SAME_HEADERS=${library.SAME_HEADERS}
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10 #else
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11 ## prepare paired-end collection
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12 F1=${library.input_1.forward}
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13 F2=${library.input_1.reverse}
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14 SAME_HEADERS=${library.SAME_HEADERS}
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15 #end if
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16 </token>
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17
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18 <xml name="paired_options">
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19 <when value="paired">
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20 <param name="input_1" format="fastq" type="data" label="FASTQ file #1"/>
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21 <param name="input_2" format="fastq" type="data" label="FASTQ file #2"/>
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22 <yield />
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23 <param name="SAME_HEADERS" type="boolean"
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24 label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)"
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25 help="Only applies if barcodes are added to the header (option ADD)"
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26 truevalue="true"
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27 falsevalue="false" checked="false"/>
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28 </when>
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29 <when value="paired_collection">
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30 <param name="input_1" format="fastq" type="data_collection" collection_type="paired"
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31 label="FASTQ Paired Dataset"/>
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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 </xml>
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40
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41 <token name="@single_or_paired_illu_cmd@">
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42 @single_or_paired_cmd@
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43 I1=$library.I1
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44 #if str( $library.type ) != "single":
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45 #if str( $library.I2_CONDITIONAL.I2_AVAILABLE ) == "true":
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46 I2=${library.I2_CONDITIONAL.I2}
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47 BRED=${library.I2_CONDITIONAL.BRED_CONDITIONAL.BRED}
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48 #if str( $library.I2_CONDITIONAL.BRED_CONDITIONAL.BRED ) == "true":
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49 STRICT=${library.I2_CONDITIONAL.BRED_CONDITIONAL.STRICT}
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50 #end if
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51 #end if
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52 #end if
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53 </token>
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54
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55 <xml name="single_or_paired_illu">
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56 <conditional name="library">
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57 <param name="type" type="select" label="Is this single or paired library">
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58 <option value="single">Single-end</option>
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59 <option value="paired">Paired-end</option>
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60 <option value="paired_collection">Paired-end Dataset Collection</option>
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61 </param>
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62 <when value="single">
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63 <param name="input_1" format="fastq" type="data" label="FASTQ file"/>
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64 <param name="I1" type="data" format="fastq" label="First Index File"/>
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65 </when>
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66 <expand macro="paired_options">
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67 <param name="I1" type="data" format="fastq" label="First Index File"/>
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68 <conditional name="I2_CONDITIONAL">
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69 <param name="I2_AVAILABLE" type="select" label="Do you have a second index file?">
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70 <option value="true">Yes</option>
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71 <option value="false" selected="true">No</option>
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72 </param>
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73 <when value="true">
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74 <param name="I2" type="data" format="fastq" label="Second Index File"/>
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75 <expand macro="bred_conditional"/>
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76 </when>
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77 <when value="false"/>
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78 </conditional>
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79 </expand>
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80 </conditional>
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81 </xml>
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82
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83 <xml name="single_or_paired_general">
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84 <conditional name="library">
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85 <param name="type" type="select" label="Is this single or paired library">
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86 <option value="single">Single-end</option>
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87 <option value="paired">Paired-end</option>
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88 <option value="paired_collection">Paired-end Dataset Collection</option>
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89 </param>
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90 <when value="single">
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91 <param name="input_1" format="fastq" type="data" label="FASTQ file"/>
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92 </when>
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93 <expand macro="paired_options">
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94 <yield />
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95 </expand>
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96 </conditional>
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97 </xml>
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98
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99 <token name="@demultiplex_paired_end_cmd_options@">
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100 BPOS=$library.BPOS_CONDITIONAL.BPOS
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101 #if str( $library.BPOS_CONDITIONAL.BPOS ) == "BOTH":
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102 BM=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BM}
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103 #if str( $library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BM ) == "BOTH":
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104 BRED=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.BRED}
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105 #if str( $library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.BRED ) == "true":
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106 STRICT=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.STRICT}
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107 #end if
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108 #end if
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109 #end if
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110 </token>
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111
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112 <xml name="demultiplex_paired_end_options">
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113 <conditional name="BPOS_CONDITIONAL">
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114 <param name="BPOS" type="select" label="Barcode read position (BPOS)" help="where are the barcodes">
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115 <option value="READ_1" selected="true">READ_1 (beginning of read from the first fastq file)</option>
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116 <option value="READ_2">READ_2 (beginning of read from the second fastq file)</option>
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117 <option value="BOTH">BOTH (beginning of both reads)</option>
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118 </param>
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119 <when value="READ_1"/>
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120 <when value="READ_2"/>
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121 <when value="BOTH">
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122 <conditional name="BM_CONDITIIONAL">
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123 <param name="BM" type="select" label="Barcode for sample matching (BM)"
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124 help="which barcode should be used for sample look up (BM option)." >
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125 <option value="READ_1" selected="true">
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126 READ_1 (beginning of read from the first fastq file)
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127 </option>
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128 <option value="READ_2">
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129 READ_2 (beginning of read from the second fastq file)
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130 </option>
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131 <option value="BOTH">
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132 BOTH (beginning of both reads)
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133 </option>
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134 </param>
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135 <when value="READ_1"/>
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136 <when value="READ_2"/>
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137 <when value="BOTH">
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138 <expand macro="bred_conditional"/>
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139 </when>
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140 </conditional>
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141 </when>
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142 </conditional>
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143 </xml>
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144
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145 <xml name="bred_conditional">
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146 <conditional name="BRED_CONDITIONAL">
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147 <param name="BRED" type="select" label="Redundant barcodes (BRED)"
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148 help="are the barcodes REDUNDANT i.e. do they both resolve to the same sample.">
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149 <option value="true" selected="true">Yes</option>
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150 <option value="false">No</option>
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151 </param>
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152 <when value="true">
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153 <param name="STRICT" type="boolean" label="Strict (S)"
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154 truevalue="true"
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155 falsevalue="false"
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156 checked="false"
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157 />
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158 </when>
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159 <when value="false"/>
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160 </conditional>
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161 </xml>
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162
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163 <token name="@barcode_option_cmd@">
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164 #if str( $barcodes.barcode_list_type_con ) == "text":
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165 BARCODE_FILE=${barcode_file_from_text}
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166 #else if str( $barcodes.barcode_list_type_con ) == "file":
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167 BARCODE_FILE=${barcodes.BARCODE_FILE}
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168 #end if
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169 </token>
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170
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171 <xml name="barcode_option">
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172 <conditional name="barcodes">
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173 <param name="barcode_list_type_con" type="select" label="Barcode list input type">
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174 <option value="file" selected="true">Use a tab-delimited file from the history</option>
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175 <option value="text">Paste the barcodes list in a text field within the form</option>
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176 </param>
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177
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178 <when value="file">
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179 <param name="BARCODE_FILE" type="data" format="tabular,txt" label="Barcode List"
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180 help="Barcode list format: one sample per line. First column is sample name and second is the
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181 barcode, separated by tab or space. A third and fourth column can be used to specify the resulting
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182 file names. See help below."/>
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183 </when>
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184
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185 <when value="text">
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186 <param name="barcode_text" type="text" area="True" size="10x30"
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187 value="sample_name\tbarcode\n" label="Barcode List"
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188 help="Barcode list format: one sample per line. First column is sample name and second is the
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189 barcode, separated by tab or space. A third and fourth column can be used to specify the resulting
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190 file names. See help below.">
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191 <sanitizer>
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192 <valid initial="string.printable"></valid>
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193 <mapping initial="none"/>
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194 </sanitizer>
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195 </param>
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196 </when>
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197 </conditional>
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198 </xml>
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199
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200 <xml name="barcode_config_file">
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201 <configfile name="barcode_file_from_text">#set from_text_area = ''
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202 #if str( $barcodes.barcode_list_type_con ) == "text":
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203 #set from_text_area = $barcodes.barcode_text
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204 #end if
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205 ${from_text_area}</configfile>
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206 </xml>
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207
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208 <token name="@barcode_len_cmd@">
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209 #if str( $LEN ) != "":
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210 BCLEN=$LEN
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211 #end if
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212 </token>
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213
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214 <xml name="barcode_len_option">
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215 <param name="LEN" type="text" value="" label="Barcode Length (LEN)"
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216 help="If 'Barcode read position'=BOTH and 'Redundant barcodes'=False, two distinct
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217 lengths can be provided using the syntax LEN=X:Z where X and Z are 2 integers representing
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218 the barcode length for read_1 and read_2 respectively. Default: empty"/>
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219 </xml>
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220 <xml name="clip_barcode">
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221 <param name="CLIP_BARCODE" type="boolean" label="Remove barcode sequence from read (C)"
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222 truevalue="true" falsevalue="false" checked="true"/>
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223 </xml>
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224
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225 <token name="@demultiplexer_common_options_cmd@">
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226 ADD=${ADD}
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227 MM=$MM
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228 MMD=$MMD
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229 Q=$MIN_BASE_QUALITY
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230 QUALITY_FORMAT=$QUALITY_FORMAT
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231 </token>
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232 <xml name="demultiplexer_common_options">
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233 <param name="ADD" type="boolean"
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234 label="Add matched barcode at the end of the read header (ADD)"
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235 truevalue="true"
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236 falsevalue="false"
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237 checked="true"
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238 />
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239 <param name="MM" type="text" value="1" label="Maximum Mismatches (MM)"
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240 help="Maximum mismatches for a barcode to be considered a match." />
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241
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242 <param name="MMD" type="text" value="1" label="Minimum mismatch difference (MMD)"
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243 help="Minimum difference between number of mismatches in the best and second best barcodes for a barcode
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244 to be considered a match." />
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245
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246 <param name="MIN_BASE_QUALITY" type="text" value="10" label="Minimum base quality (Q)"
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247 help="Any barcode bases falling below this quality will be
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248 considered a mismatch even in the bases match." />
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249
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250 <param name="QUALITY_FORMAT" type="select" label="Fastq Quality Format (V)"
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251 help="How are the quality values encoded in the fastq. Either 'Solexa' for
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252 pre-pipeline 1.3 style scores (solexa scaling + 66), 'Illumina' for pipeline 1.3 and
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253 above (phred scaling + 64) or 'Standard' for phred scaled scores with a character shift
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254 of 33.">
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255 <option value="Standard" selected="true">
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256 Fastq - Illumina Casava v1.8 with Sanger coding quality (phred scaling + 33)
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257 </option>
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258 <option value="Illumina">
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259 Fastq - Illumina v1.3 or above coding of quality (phred scaling + 64)
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260 </option>
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261 <option value="Solexa">
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262 Fastq - Solexa-style quality (solexa scaling + 66)
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263 </option>
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264 <option value="null">
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265 Detect automatically
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266 </option>
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267 </param>
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268 </xml>
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269
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270 <token name="@demultiplexer_common_output_options_cmd@">
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271 KEEP_UNASSIGNED_READ=$KEEP_UNASSIGNED_READ
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272 STATS_ONLY=${adv_options.STATS_ONLY}
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273 #if str( $adv_options.DIAG ) == "true":
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274 BARCODE_DIAG_FILE=$BARCODE_DIAG_FILE
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275 #end if
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276 </token>
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277 <xml name="demultiplexer_common_output_options">
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278 <param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)"
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279 truealue="true"
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280 falsevalue="false"
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281 checked="true"
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282 />
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283 <section name="adv_options" title="Advanced Options" expanded="False">
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284 <param name="DIAG" type="boolean" label="Output barcode match reporting file (DIAG)"
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285 truevalue="true" falsevalue="false" checked="false"
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286 help="This file will
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287 contain a line per read pair with the barcode best matching the read subsequence or 'null' when no
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288 match is found according to matching parameters. This file is useful for debugging or further
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289 processing in case both ends are barcoded."/>
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290 <param name="STATS_ONLY" type="boolean" label="Only produce metric and diagnostic reports (STATS_ONLY)"
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291 truevalue="true" falsevalue="false" checked="false"
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292 help="do not demultiplex." />
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293 </section>
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294 </xml>
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295
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296 <token name="@common_options_cmd@">
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297 XT=${XT}
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298 ZT=${ZT}
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299 #if str( $RCHAR ) != "":
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300 RCHAR=${RCHAR}
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301 #end if
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302 GZ=${GZ}
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303 OUTPUT_DIR=results
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304 </token>
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305 <xml name="common_options">
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306 <param name="XT" type="text" value="0"
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307 label="Extra number of bases to be trimmed right after the barcode (XT)" />
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308 <param name="ZT" type="text" value="0"
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309 label="Extra number of bases to be trimmed from the read end (ZT)" />
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310
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311 <param name="RCHAR" type="text"
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312 label="Replace white space in the read name/header with speficied symbols (RCHAR)"
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313 help="Set to empty for no replacement"
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314 value=":"/>
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315
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316 <param name="GZ" type="boolean" hidden="true" label="Compress output (GZ)"
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317 help="will result in fastq.gz files."
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318 truevalue="true"
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319 falsevalue="false"
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320 checked="false"/>
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321 </xml>
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322
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323 <token name="@demultiplexer_common_outputs_cmd@">
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324 METRICS_FILE_NAME=$METRICS_FILE_NAME
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325 </token>
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326 <xml name="demultiplexer_common_outputs">
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327 <data name="METRICS_FILE_NAME" format="tabular" label="Je-Demultiplex result">
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328 <!--<discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" ext="fastqsanger"-->
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329 <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" directory="results" visible="true" ext="fastqsanger"/>
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330 </data>
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331 <data name="BARCODE_DIAG_FILE" format="tabular" label="Barcode statistics">
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332 <filter>(adv_options['DIAG'] == 'true')</filter>
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333 </data>
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334 </xml>
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335
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336 </macros>