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1 <tool id="jedebarcoding" name="Jemultiplexer">
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2 <description>Demultiplexes multiplexed data</description>
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3 <requirements>
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4 <requirement type="package" version=">=1.6">java</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 jemultiplexer.py
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8 $MpxData1
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9 $output1
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10 $output1.id
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11 $bsinputtype.barcodes
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12 "$bsinputtype.barcode_list"
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13 $__new_file_path__
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14 $MpxData1.ext
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15 $bcodelen
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16 $qualityFormat
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17 $maxMismatches
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18 $minBaseQuality
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19 $minMismatchingDelta
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20 $clipBarcodeCon.xTrimLen
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21 $zTrimLen
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22 $clipBarcodeCon.clipBarcode
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23 $addBarcodeToHeader
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24 $gzipOutput
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25 $barcodeDiagFile
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26 $rChar
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27 #if $singlePaired.sPaired == "paired":
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28 $singlePaired.barcodeReadPosCon.barcodeReadPos
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29 #if $singlePaired.barcodeReadPosCon.barcodeReadPos == "BOTH":
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30 $singlePaired.barcodeReadPosCon.barcodeForSampleMatchingCon.barcodeForSampleMatching
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31 #if $singlePaired.barcodeReadPosCon.barcodeForSampleMatchingCon.barcodeForSampleMatching == "BOTH":
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32 $singlePaired.barcodeReadPosCon.barcodeForSampleMatchingCon.redundantBarcodeCon.redundantBarcode
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33 $singlePaired.barcodeReadPosCon.barcodeForSampleMatchingCon.redundantBarcodeCon.strict
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34 $singlePaired.MpxData2
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35 #else:
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36 $singlePaired.barcodeReadPosCon.barcodeForSampleMatchingCon.redundantBarcode
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37 $singlePaired.barcodeReadPosCon.barcodeForSampleMatchingCon.strict
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38 $singlePaired.MpxData2
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39 #end if
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40 #else:
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41 $singlePaired.barcodeReadPosCon.barcodeForSampleMatching
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42 $singlePaired.barcodeReadPosCon.redundantBarcode
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43 $singlePaired.barcodeReadPosCon.strict
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44 $singlePaired.MpxData2
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45 #end if
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46 #else:
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47 $singlePaired.barcodeReadPos
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48 $singlePaired.barcodeForSampleMatching
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49 $singlePaired.redundantBarcode
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50 $singlePaired.strict
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51 $singlePaired.MpxData2
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52 #end if
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53 </command>
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54 <inputs>
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55 <param type="data" format="gz,fastq" name="MpxData1" label="Compressed (or not) FASTQ file" />
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56 <conditional name="singlePaired">
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57 <param name="sPaired" type="select" label="Is this library mate-paired?">
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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 </param>
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61 <when value="single">
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62 <param name="MpxData2" type="hidden" value="single" />
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63 <param name="barcodeReadPos" type="hidden" value="none" />
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64 <param name="redundantBarcode" type="hidden" value="none" />
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65 <param name="barcodeForSampleMatching" type="hidden" value="none" />
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66 <param name="strict" type="hidden" value="none" />
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67 </when>
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68 <when value="paired">
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69 <param name="MpxData2" type="data" format="gz,fastq" label="Compressed (or not) FASTQ file" />
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70 <conditional name="barcodeReadPosCon">
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71 <param name="barcodeReadPos" type="select" label="Barcode read position (BPOS)" help="where are the barcodes">
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72 <option value="READ_1" selected="true">READ_1 (beginning of read from the first fastq file)</option>
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73 <option value="READ_2">READ_2 (beginning of read from the second fastq file)</option>
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74 <option value="BOTH">BOTH (beginning of both reads)</option>
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75 </param>
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76 <when value="READ_1">
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77 <param name="redundantBarcode" type="hidden" value="true" />
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78 <param name="barcodeForSampleMatching" type="hidden" value="BOTH" />
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79 <param name="strict" type="hidden" value="false" />
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80 </when>
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81 <when value="READ_2">
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82 <param name="redundantBarcode" type="hidden" value="true" />
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83 <param name="barcodeForSampleMatching" type="hidden" value="BOTH" />
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84 <param name="strict" type="hidden" value="false" />
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85 </when>
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86 <when value="BOTH">
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87 <conditional name="barcodeForSampleMatchingCon">
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88 <param name="barcodeForSampleMatching" type="select" label="Barcode for sample matching (BM)" help="which barcode should be used for sample look up (BM option)." >
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89 <option value="READ_1" selected="true">READ_1 (beginning of read from the first fastq file)</option>
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90 <option value="READ_2">READ_2 (beginning of read from the second fastq file)</option>
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91 <option value="BOTH">BOTH (beginning of both reads)</option>
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92 </param>
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93 <when value="READ_1">
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94 <param name="redundantBarcode" type="hidden" value="true" />
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95 <param name="strict" type="hidden" value="false" />
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96 </when>
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97 <when value="READ_2">
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98 <param name="redundantBarcode" type="hidden" value="true" />
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99 <param name="strict" type="hidden" value="false" />
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100 </when>
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101 <when value="BOTH">
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102 <conditional name="redundantBarcodeCon">
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103 <param name="redundantBarcode" type="select" label="Redundant barcodes (BRED)" help="are the barcode REDUNDANT i.e. do they both resolve to the same sample (BRED option).">
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104 <option value="true">True</option>
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105 <option value="false" selected="true">False</option>
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106 </param>
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107 <when value="true">
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108 <param name="strict" type="select" label="Strict (S)" help="tells whether both barcodes should resolve to the same sample." >
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109 <option value="true" selected="true">True</option>
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110 <option value="false">False</option>
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111 </param>
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112 </when>
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113 <when value="false">
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114 <param name="strict" type="hidden" value="false" />
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115 </when>
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116 </conditional>
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117 </when>
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118 </conditional>
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119 </when>
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120 </conditional>
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121 </when>
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122 </conditional>
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123
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124 <conditional name="bsinputtype">
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125 <param name="bsinputtype_selector" type="select" label="Barcode set input type" help="You can either submit a barcode file or paste the list in a text field. Note: one sample per line.">
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126 <option value="bs_file" selected="true">Use a .bs tab-delimited file in the history</option>
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127 <option value="bs_textfield">Paste the barcodes list in a text field within the form</option>
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128 </param>
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129 <when value="bs_file">
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130 <param name="barcodes" type="data" format="bs" label="Barcode Set" />
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131 <param name="barcode_list" type="hidden" value="none" />
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132 </when>
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133 <when value="bs_textfield">
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134 <param name="barcode_list" type="text" area="True" size="10x30" label="Barcode Set (<span style="color:brown;">one sample per line: &#60;sample_name&#62;&#60;tab or space&#62;&#60;barcode&#62;</span>)"/>
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135 <param name="barcodes" type="hidden" value="none" />
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136 </when>
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137 </conditional>
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138
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139 <param name="bcodelen" type="text" value="6" label="Barcode Length (LEN)" />
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140
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141 <param name="qualityFormat" type="select" label="Fastq Quality Format (V)" help="if you need other quality coding format, contact the galaxy administrators.">
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142 <option value="Standard" selected="true">Fastq - Illumina Casava V1.8 with Sanger coding quality (phred scaling + 33)</option>
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143 <option value="Illumina">Fastq - Illumina v1.3 or above coding of quality (phred scaling + 64)</option>
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144 <option value="Solexa">Fastq - Solexa-style quality (solexa scaling + 66)</option>
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145 </param>
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146 <param name="maxMismatches" type="text" value="1" label="Maxinum Mismatches (MM)" help="maximum mismatches for a barcode to be considered a match." />
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147 <param name="minBaseQuality" type="text" value="10" label="Minimum base quality (Q)" help="any barcode bases falling below this quality will be considered a mismatch even in the bases match." />
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148 <param name="minMismatchingDelta" type="text" value="1" label="Minimum mismatch difference (MMD)" help="Minimum difference between number of mismatches in the best and second best barcodes for a barcode to be considered a match." />
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149 <param name="zTrimLen" type="text" value="0" label="Extra number of bases to be trimmed from the barcode end (ZT)" />
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150 <conditional name="clipBarcodeCon">
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151 <param name="clipBarcode" type="select" label="Remove barcode sequence from read (C)" >
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152 <option value="true" selected="true">True</option>
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153 <option value="false">False</option>
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154 </param>
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155 <when value="true">
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156 <param name="xTrimLen" type="text" value="1" label="Extra number of base to be trimmed right after the barcode (XT)" />
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157 </when>
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158 <when value="false">
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159 <param name="xTrimLen" type="hidden" value="1" />
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160 </when>
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161 </conditional>
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162 <param name="addBarcodeToHeader" type="select" label="Add matched barcode at the end of the read header (ADD)" >
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163 <option value="true" selected="true">True</option>
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164 <option value="false">False</option>
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165 </param>
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166 <param name="gzipOutput" type="select" label="Compress output (GZ)" >
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167 <option value="true" selected="true">True</option>
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168 <option value="false">False</option>
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169 </param>
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170 <param name="barcodeDiagFile" type="select" label="Output barcode match reporting file (DIAG)" >
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171 <option value="false" selected="false">False</option>
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172 <option value="true">True</option>
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173 </param>
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174 <param name="rChar" type="select" label="Replace white space in the read name/header with speficied symbols (RCHAR)" >
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175 <option value="1" selected="1"> </option>
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176 <option value="2">:</option>
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177 <option value="3">_</option>
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178 <option value="4">-</option>
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179 </param>
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180 </inputs>
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181 <outputs>
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182 <data format="html" name="output1" label="Demultiplexing stats on ${on_string}"/>
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183 <!-- Keep this as a nice example of reformating;
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184 <data format="fastqsanger" name="output1" metadata_source="MpxData1" label="Demultiplexing stats on ${on_string}">
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185 <change_format>
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186 <when input="MpxData1.ext" value="fastqillumina" format="fastqillumina" />
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187 </change_format>
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188 </data> -->
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189 </outputs>
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190
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191 <tests>
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192 <test>
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193 <param name="MpxData1" value="C1WLBACXX_lane7_1_sequence.txt" />
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194 <param name="MpxData2" value="C1WLBACXX_lane7_2_sequence.txt" />
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195 <param name="sPaired" value="paired" />
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196 <param name="bsinputtype_selector" value="bs_file" />
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197 <param name="barcodes" value="correct_barcodes_PE_both-ends_with_fnames.txt" />
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198 <param name="barcodeReadPos" value="BOTH" />
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199 <param name="barcodeForSampleMatching" value="BOTH" />
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200 <param name="redundantBarcode" value="false" />
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201 <param name="bcodelen" value="6" />
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202 <param name="qualityFormat" value="Standard" />
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203 <param name="maxMismatches" value="3" />
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204 <param name="minBaseQuality" value="20" />
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205 <param name="minMismatchingDelta" value="2" />
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206 <param name="zTrimLen" value="0" />
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207 <param name="clipBarcode" value="true" />
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208 <param name="xTrimLen" value="1" />
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209 <param name="addBarcodeToHeader" value="true" />
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210 <param name="gzipOutput" value="true" />
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211 <param name="barcodeDiagFile" value="true" />
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212 <param name="rChar" value="1" />
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213 <output name="output1" file="result.html" ftype="html"/>
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214 </test>
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215 </tests>
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216
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217 <help>
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218
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219 **What it does**
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220
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221 Jemultiplexer : A fastq files demultiplexer with many neat options. Input files are fastq files, and can be in gzip compressed format (end in .gz).
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222
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223 Author: Charles Girardot (charles.girardot@embl.de).
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224
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225 Version: 1.0.3
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226
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227 ------
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228
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229 **Know what you are doing**
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230
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231 .. class:: warningmark
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232
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233 You will want to read the `documentation`__.
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234
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235 .. __: http://gbcs.embl.de/tikiwiki/JemultiplexerDocHome
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236
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237 ------
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238
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239 **Jemultiplexer parameter list**
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240
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241 This is an exhaustive list of Jemultiplexer options::
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242
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243 FASTQ_FILE1=File
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244 F1=File Input fastq file (optionally gzipped) for single end data, or first read in paired end data.
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245 Required.
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246
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247 FASTQ_FILE2=File
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248 F2=File Input fastq file (optionally gzipped) for the second read of paired end data.
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249 Default value: null.
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250
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251 BARCODE_FILE=File
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252 BF=File Barcode file describing sequence list and sample names. Tab-delimited file with 2
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253 columns, with the sample in col1 and the corresponding barcode in col2.
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254 Note, make sure one sample per line.
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255 If multiple barcode map to the same sample, barcodes can be combined using the OR operator '|'.
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256 i.e. the file above can be re-written like
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257 sample1 ATAT|GAGG
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258 sample2 CCAA|TGTG
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259 Finally, for the special situation of paired-end data in which barcodes differ at both
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260 ends (ie BPOS=BOTH BRED=false BM=BOTH , see BRED option description), barcodes for read_1
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261 and read_2 can be distinguished using a ':' separator i.e.
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262 sample1 ATAT:GAGG
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263 sample2 CCAA:TGTG
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264 Here understand that sample 1 is encoded with ATAT barcode at read_1 AND GAGG barcode at
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265 read_2. Note that you can still combine barcodes using | e.g.
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266 sample1 ATAT|GAGG:CCAA|TGTG
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267 would mean that sample 1 is mapped by the combination of barcode: ATAT OR GAGG at read_1
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268 AND CCAA OR TGTG at read_2.
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269 Required.
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270
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271 BARCODE_READ_POS=BarcodePosition
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272 BPOS=BarcodePosition For paired-end data, where to expect the barcode(s) : READ_1 (beginning of read from
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273 FASTQ_FILE_1), READ_2 (beginning of read from FASTQ_FILE_2), BOTH (beginning of both
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274 reads). Automatically set to READ_1 in single end mode.
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275 Default value: BOTH. This option can be set to 'null' to clear the default value.
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276 Possible values: {READ_1, READ_2, BOTH}
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277
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278 REDUNDANT_BARCODES=Boolean
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279 BRED=Boolean For paired-end data and when BARCODE_READ_POS == BOTH, this option indicates if both
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280 read's barcodes encode redundant information, which is the usual situation
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281 (REDUNDANT_BARCODES=true) i.e. barcodes are supposed to be the same at both ends or to
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282 resolve to the same sample (when a pool of barcodes has been used for each sample).
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283 When REDUNDANT_BARCODES=false, the 2 barcodes potentially encode different
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284 information. For example, only one of the barcodes encodes the sample the read belongs to
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285 while the second barcode might be a random barcode to tell apart PCR artefacts from real
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286 duplicates. Another example is when both barcodes should be used in a combined fashion
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287 to resolve the sample. In the first example, you should use BPOS=BOTH BRED=false
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288 BM=READ_1 while in the second example, you should have BPOS=BOTH BRED=false BM=BOTH (note
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289 that with BPOS=BOTH BRED=true BM=BOTH), the behavior would be different as Jemultiplexer
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290 would then check the STRICT option to perform sample resolution.
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291 Importantly, when BARCODE_READ_POS == BOTH AND REDUNDANT_BARCODES=false, BLEN, barcode
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292 matching options (MM, MMD, Q) and read trimming/clipping options (XT, ZT) accept
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293 different values for both barcodes in the form X:Z where X and Z are 2 integers.
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294 Default value: true. This option can be set to 'null' to clear the default value.
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295 Possible values: {true, false}
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296
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297 BARCODE_FOR_SAMPLE_MATCHING=BarcodePosition
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298 BM=BarcodePosition Automatically set to READ_1 in single end mode.
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299 For paired-end data and when BARCODE_READ_POS == BOTH, which barcode should be used to
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300 resolve sample :
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301 - use BM=READ_1 (beginning of read from FASTQ_FILE_1) if only this read should be used
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302 for sample matching,
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303 - use BM=READ_2 (beginning of read from FASTQ_FILE_2) if only this read should be used
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304 for sample matching,
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305 - use BM=BOTH (beginning of both reads) if both should be used ; when BM=BOTH, the
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306 behaviour of Jemultiplexer is different based on the value of REDUNDANT_BARCODES.
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307 If REDUNDANT_BARCODES=true, the two barcodes are considered to map to the same sample
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308 and Jemultiplexer uses the two barcodes according to the STRICT value.
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309 If REDUNDANT_BARCODES=false, the barcode file should map a couple of barcode to each
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310 sample (e.g. sample1 => AGAGTG:TTGATA) and Jemultiplexer needs both barcodes to find the
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311 relevant sample. Note that this is the only situation in which all barcode matching
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312 options (MM, MMD, Q) accept different values for both barcodes in the form X:Z where X
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313 and Z are 2 integers.
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314 Default value: BOTH. This option can be set to 'null' to clear the default value.
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315 Possible values: {READ_1, READ_2, BOTH}
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316
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317 STRICT=Boolean
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318 S=Boolean For paired-end data and when BARCODE_READ_POS == BOTH and BM=BOTH, tells whether both
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319 barcodes should resolve to the same sample. When true and if only one of the two reads
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320 has a barcode match, the read pair is ignored. When false and if only one of the two
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321 reads has a barcode match, the read pair is assigned to the corresponding sample ; in
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322 cases where reads resolve to different samples, the read pair is ignored.
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323 Default value: false. This option can be set to 'null' to clear the default value.
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324 Possible values: {true, false}
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325
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326 BCLEN=String
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327 LEN=String Length of the barcode sequences, optional. Taken from barcode file when not given.
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328 In situations where BARCODE_READ_POS == BOTH AND REDUNDANT_BARCODES=false, two distinct
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329 length can be provided using the syntax LEN=X:Z where X and Z are 2 integers representing
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330 the barcode length for read_1 and read_2 respectively.
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331 Default value: null.
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332
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333 MAX_MISMATCHES=String
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334 MM=String Maximum mismatches for a barcode to be considered a match. MM=null is like MM=0
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335 In situations where both barcodes are used for sample matching i.e. BPOS=BOTH BM=BOTH
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336 (note that most likely BRED=false as it does not make great sense otherwise), two
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337 distinct values can be given here using the syntax MM=X:Z where X and Z are 2 integers to
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338 use for read_1 and read_2 respectively.
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339 Default value: 1. This option can be set to 'null' to clear the default value.
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340
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341 MIN_MISMATCH_DELTA=String
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342 MMD=String Minimum difference between number of mismatches in the best and second best barcodes for
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343 a barcode to be considered a match. MMD=null is like MMD=0
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344 In situations where both barcodes are used for sample matching i.e. BPOS=BOTH BM=BOTH
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345 (note that most likely BRED=false as it does not make great sense otherwise), two
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346 distinct values can be given here using the syntax MMD=X:Z where X and Z are 2 integers
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347 to use for read_1 and read_2 respectively.
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348 Default value: 1. This option can be set to 'null' to clear the default value.
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349
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350 MIN_BASE_QUALITY=String
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351 Q=String Minimum base quality. Any barcode bases falling below this quality will be considered a
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352 mismatch even in the bases match. Q=null is like Q=0.
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353 In situations where both barcodes are used for sample matching i.e. BPOS=BOTH BM=BOTH
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354 (note that most likely BRED=false as it does not make great sense otherwise), two
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355 distinct values can be given here using the syntax Q=X:Z where X and Z are 2 integers to
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356 use for read_1 and read_2 respectively.
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357 Default value: 10. This option can be set to 'null' to clear the default value.
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358
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359 XTRIMLEN=String
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360 XT=String Extra number of base to be trimmed right after the barcode (only used if
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361 CLIP_BARCODE=true). Default is 1 as an extra 'T' (or 'A' depending how you see it) is
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362 added for barcode ligation but this default will be adapated according to the rules
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363 below. XT=null is like XT=0.
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364 When running paired-end, two distinct values can be given using the syntax XT=X:Z where X
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365 and Z are 2 integers to use for read_1 and read_2 respectively. Note that even when
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366 BPOS=READ_1 or BPOS=READ_2, a X:Y synthax can be given to trim the read w/o barcode as to
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367 end up with reads of the same length (note that this can also be operated using ZT). If a
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368 unique value is given, e.g. XT=1, while running paired-end the following rule applies :
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369 (1) BPOS=READ_1 or BPOS=READ_2, no trim is applied at the read w/o barcode ; (2)
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370 BPOS=BOTH, the value is used for both reads.
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371 Default value: 1. This option can be set to 'null' to clear the default value.
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372
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373 ZTRIMLEN=String
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374 ZT=String Extra number of bases to be trimmed from the barcode end i.e. 3' end. Pretty handy when a
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375 pipeline is set and you already know you'll trim read at a given size. ZT=null is like
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376 ZT=0.
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377 When running paired-end, two distinct values can be given here using the syntax ZT=X:Z
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378 where X and Z are 2 integers to use for read_1 and read_2 respectively. Note that even
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379 when BPOS=READ_1 or BPOS=READ_2, a X:Y synthax can be given to trim the read w/o barcode
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380 as to end up with reads of the same length (note that this can also be operated using
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381 XT). Note that if a single value is passed, the value always aplly to both reads in
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382 paired-end mode without further consideration.
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383 Default value: 0. This option can be set to 'null' to clear the default value.
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384
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385 CLIP_BARCODE=Boolean
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386 C=Boolean Remove barcode sequence from read, as well as XTRIMLEN (and ZTRIMLEN) bases if
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387 applicable, before writing to output file. If false, reads are written without
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388 modification to output file. Apply to both barcodes when BPOS=BOTH.
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389 Default value: true. This option can be set to 'null' to clear the default value.
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390 Possible values: {true, false}
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391
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392 ADD_BARCODE_TO_HEADER=Boolean
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393 ADD=Boolean Add matched barcode at the end of the read header. Apply to both barcodes when BPOS=BOTH.
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394 If true, the string ':barcode' is added at the end of the read header with a ':' added
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395 only if current read header does not end with ':'.
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396 If both reads of the pair have a barcode (i.e. BARCODE_READ_POS == BOTH), thenthe second
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397 read also has its own matched barcode written. Else, the read without a barcode receives
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398 the barcode from the barcoded read.
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399 For example :
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400 '@D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 2:N:0:'
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401 becomes
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402 '@D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 2:N:0:BARCODE'
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403 Default value: true. This option can be set to 'null' to clear the default value.
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404 Possible values: {true, false}
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405
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406 QUALITY_FORMAT=FastqQualityFormat
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407 V=FastqQualityFormat A value describing how the quality values are encoded in the fastq. Either 'Solexa' for
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408 pre-pipeline 1.3 style scores (solexa scaling + 66), 'Illumina' for pipeline 1.3 and
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409 above (phred scaling + 64) or 'Standard' for phred scaled scores with a character shift
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410 of 33. If this value is not specified (or 'null' is given), the quality format will be
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411 detected automatically.
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412 Default value: Standard. This option can be set to 'null' to clear the default value.
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413 Possible values: {Solexa, Illumina, Standard}
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414
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415 GZIP_OUTPUTS=Boolean
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416 GZ=Boolean Compress output s_l_t_barcode.txt files using gzip and append a .gz extension to the filenames.
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417 Default value: true. This option can be set to 'null' to clear the default value.
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418 Possible values: {true, false}
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419 BARCODE_DIAG_FILE=String
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420 DIAG=String Name for a barcode match reporting file (not generated by default).Either a name
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421 (in which case the file will be created in the output dir) or full path. This file will contain
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422 a line per read pair with the barcode best matching the read subsequence or 'null' when no match
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423 is found accordign to matching parameters and the final selected sample. This file is useful for
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424 debugging or further processing in case both ends are barcoded.
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425 Default value: null
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426
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427 READ_NAME_REPLACE_CHAR=String
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428 RCHAR=String Replace spaces in read name/header using provided character. This is particularly handy
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429 when you need to retain ADDed barcode in read name/header during mapping (everything
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430 after space in read name is usually clipped in BAM files). For example, with RCHAR=':' :
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431 '@D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 2:N:0:'
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432 becomes
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433 '@D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965:2:N:0:BARCODE'
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434 Default value: null.
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435 </help>
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436 </tool>
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