annotate flexbar.xml @ 5:0a7a3e7559b4

Changed tool dependency description.
author jtilman
date Sun, 30 Dec 2012 21:12:47 +0100
parents f6789b18cae8
children
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68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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2 <!-- Author: Johannes T. Roehr -->
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4 <tool id="flexbar2.3" name="Flexbar" version="2.3" force_history_refresh="True">
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f6789b18cae8 Changed tool description.
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6 <description>flexible barcode and adapter removal</description>
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8 <requirements>
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9 <requirement type="binary" version="2.3">flexbar</requirement>
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10 </requirements>
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11
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12 <version_command>flexbar --version</version_command>
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68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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14 <command interpreter="perl">
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68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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16 flexbar.pl flexbar
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17
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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18 --threads 1
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19
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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20 --reads $reads
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21
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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22 #if $cReads2.select == "on":
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23 #if $cReads2.reads2.ext == $reads.ext:
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24 --reads2 $cReads2.reads2
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25 #end if
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26 #end if
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68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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29 #if $reads.ext == "fasta":
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30 --format fasta
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31 #end if
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32 #if $reads.ext == "fastq":
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33 --format fastq
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34 #end if
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35 #if $reads.ext == "fastqsanger":
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36 --format fastq-sanger
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37 #end if
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38 #if $reads.ext == "fastqsolexa":
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39 --format fastq-solexa
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40 #end if
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41 #if $reads.ext == "fastqillumina":
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42 --format fastq-i1.3
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43 #end if
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44 #if $reads.ext == "csfasta":
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45 --format csfasta
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46 #end if
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47 #if $reads.ext == "fastqcssanger":
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48 --format csfastq
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49 #end if
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52 --max-uncalled $maxUncalled
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53 --min-readlength $minReadLen
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54
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55 #if $trimEnds.select == "on":
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56 --pre-trim-left $trimEnds.trimLeft
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57 --pre-trim-right $trimEnds.trimRight
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58 #end if
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59
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60 #if $cTrimPhred.select == "on":
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61 --pre-trim-phred $cTrimPhred.trimPhred
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62 #end if
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63
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64 #if $cTrimLen.select == "on":
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65 --post-trim-length $cTrimLen.trimLen
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66 #end if
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68
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69 #if $cBarcodes.select == "on":
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70 --barcodes $cBarcodes.barcodes
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71
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72 #if $cBarcodes.cbReads.select == "yes":
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73 --barcode-reads $cBarcodes.cbReads.bReads
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74 #end if
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75
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76 #if $cBarcodes.cbReads.select == "no":
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77 $cBarcodes.cbReads.bKeep
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78 #end if
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79
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80 --barcode-trim-end $cBarcodes.bTrimEnd
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81
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82 #if $cBarcodes.cbTailLen.select == "yes":
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83 --barcode-tail-length $cBarcodes.cbTailLen.bTailLen
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84 #end if
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85
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86 #if $cBarcodes.cbMinOverlap.select == "yes":
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87 --barcode-min-overlap $cBarcodes.cbMinOverlap.bMinOverlap
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88 #end if
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90 --barcode-threshold $cBarcodes.bThresh
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92 #if $cBarcodes.cbAlignScores.select == "yes":
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93 --barcode-match $bMatch
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94 --barcode-mismatch $bMismatch
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95 --barcode-gap $bGap
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96 #end if
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97
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98 #end if
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100
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101 #if $cAdapters.select == "yes":
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102
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103 #if $cAdapters.ccAdapters.select == "data":
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104 --adapters $cAdapters.ccAdapters.adaptersData
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105 #end if
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106
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107 #if $cAdapters.ccAdapters.select == "seq":
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108 --adapter-seq $cAdapters.ccAdapters.adapterSeq
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109 #end if
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110
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111 --adapter-trim-end $cAdapters.aTrimEnd
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112
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113 #if $cAdapters.caTailLen.select == "yes":
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114 --adapter-tail-length $cAdapters.caTailLen.aTailLen
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115 #end if
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116
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117 --adapter-min-overlap $cAdapters.aMinOverlap
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118 --adapter-threshold $cAdapters.aThresh
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119
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120 #if $cAdapters.caAlignScores.select == "on":
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121 --adapter-match $aMatch
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122 --adapter-mismatch $aMismatch
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123 --adapter-gap $aGap
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124 #end if
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125
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126 #end if
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128
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129 #if $cLogging.select == "show"
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130 $cLogging.logLevel
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131 $cLogging.noLenDist
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132 $cLogging.remTag
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133 #end if
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134
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135 #if $cLogging.select == "off"
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136 --no-length-dist
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137 #end if
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138
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139
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140 $output $output.id $__new_file_path__ $reads.ext
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141
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142 </command>
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143
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144 <inputs>
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145
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146 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/>
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147
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148
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149 <conditional name="cReads2">
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150 <param name="select" type="select" label="2nd read set (paired)">
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151 <option value="off" selected="true">Off</option>
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152 <option value="on">On</option>
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153 </param>
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154 <when value="on">
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155 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads2" type="data" label="Reads 2" optional="false" help="same format as first read set"/>
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156 </when>
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157 </conditional>
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158
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159
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160 <param name="maxUncalled" size="4" type="integer" value="0" label="1) Max uncalled" optional="false" help="allowed uncalled bases per read"/>
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161
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162 <conditional name="trimEnds">
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163 <param name="select" type="select" label="2) Trimming of ends">
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164 <option value="off" selected="true">Off</option>
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165 <option value="on">On</option>
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166 </param>
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167 <when value="on">
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168 <param name="trimLeft" size="4" type="integer" value="0" label="Left" optional="false"/>
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169 <param name="trimRight" size="4" type="integer" value="0" label="Right" optional="false" help="trims specified number of bases from read ends"/>
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170 </when>
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171 </conditional>
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172
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173 <conditional name="cTrimPhred">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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174 <param name="select" type="select" label="3) Phred-trimming">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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175 <option value="off" selected="true">Off</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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176 <option value="on">On</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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177 </param>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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178 <when value="on">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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179 <param name="trimPhred" size="4" type="integer" value="10" label="Threshold" optional="false" help="trim right end until specified or higher quality reached"/>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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180 </when>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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181 </conditional>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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182
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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183
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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184 <conditional name="cBarcodes">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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185 <param name="select" type="select" label="4) Barcode detection">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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186 <option value="off" selected="true">Off</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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187 <option value="on">On</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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188 </param>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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189 <when value="on">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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190 <param format="fasta" name="barcodes" type="data" label="Barcodes" optional="false"/>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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191 <conditional name="cbReads">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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192 <param name="select" type="select" label="Separate barcode reads">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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193 <option value="no" selected="true">No</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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194 <option value="yes">Yes</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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195 </param>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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196 <when value="yes">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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197 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="bReads" type="data" label="Separate barcode reads" optional="false"/>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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198 </when>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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199 <when value="no">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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200 <param name="bKeep" type="select" label="Remove barcodes within reads">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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201 <option value="" selected="true">Yes</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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202 <option value="--barcode-keep">No</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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203 </param>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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204 </when>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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205 </conditional>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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206 <param name="bTrimEnd" type="select" label="Trim-end mode" optional="false">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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207 <option value="ANY" selected="true">Any</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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208 <option value="RIGHT">Right</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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209 <option value="RIGHT_TAIL">Right tail</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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210 <option value="LEFT">Left</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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211 <option value="LEFT_TAIL">Left tail</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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212 </param>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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213 <conditional name="cbTailLen">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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214 <param name="select" type="select" label="Change tail length">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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215 <option value="no" selected="true">No</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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216 <option value="yes">Yes</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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217 </param>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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218 <when value="yes">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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219 <param name="bTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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220 </when>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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221 </conditional>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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222
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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223 <conditional name="cbMinOverlap">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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224 <param name="select" type="select" label="Change min-overlap" help="default: barcode length">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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225 <option value="no" selected="true">No</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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226 <option value="yes">Yes</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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227 </param>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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228 <when value="yes">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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229 <param name="bMinOverlap" size="4" type="integer" value="8" label="Min-overlap" optional="false"/>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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230 </when>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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231 </conditional>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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232
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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233 <param name="bThresh" size="4" type="integer" value="1" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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234
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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235 <conditional name="cbAlignScores">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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236 <param name="select" type="select" label="Modify alignment scores">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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237 <option value="no" selected="true">No</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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238 <option value="yes">Yes</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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239 </param>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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240 <when value="yes">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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241 <param name="bMatch" size="3" type="integer" value="1" label="Match" optional="false"/>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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242 <param name="bMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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243 <param name="bGap" size="3" type="integer" value="-7" label="Gap" optional="false"/>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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244 </when>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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245 </conditional>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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246 </when>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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247 </conditional>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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248
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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249
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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250 <conditional name="cAdapters">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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251 <param name="select" type="select" label="5) Adapter removal">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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252 <option value="off" selected="true">Off</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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253 <option value="on">On</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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254 </param>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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255
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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256 <when value="on">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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257 <conditional name="ccAdapters">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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258 <param name="select" type="select" label="Adapter source">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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259 <option value="data" selected="true">Fasta</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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260 <option value="seq">Sequence</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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261 <!-- <option value="file">File</option> -->
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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262 </param>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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263 <when value="data">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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264 <param format="fasta" name="adaptersData" type="data" label="Adapters" optional="false"/>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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265 </when>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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266 <when value="seq">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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267 <param name="adapterSeq" size="40" label="Adapter" type="text" value="AAAAAAAAAAAAAA" optional="false"/>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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268 </when>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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269 <!-- <when value="file">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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270 <param name="adaptersFile" type="file" label="Adapters file" optional="false"/>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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271 </when> -->
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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272 </conditional>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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273
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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274 <param name="aTrimEnd" type="select" label="Trim-end mode" optional="false">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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275 <option value="ANY">Any</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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276 <option value="RIGHT" selected="true">Right</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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277 <option value="RIGHT_TAIL">Right tail</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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278 <option value="LEFT">Left</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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279 <option value="LEFT_TAIL">Left tail</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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280 </param>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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281
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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282 <conditional name="caTailLen">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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283 <param name="select" type="select" label="Change tail length">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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284 <option value="no" selected="true">No</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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285 <option value="yes">Yes</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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286 </param>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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287 <when value="yes">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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288 <param name="aTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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289 </when>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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290 </conditional>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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291
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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292 <param name="aMinOverlap" size="4" type="integer" value="1" label="Min-overlap" optional="false"/>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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293 <param name="aThresh" size="4" type="integer" value="3" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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294
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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295 <conditional name="caAlignScores">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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296 <param name="select" type="select" label="Modify alignment scores">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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297 <option value="no" selected="true">No</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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298 <option value="yes">Yes</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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299 </param>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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300 <when value="yes">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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301 <param name="aMatch" size="3" type="integer" value="1" label="Match" optional="false"/>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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302 <param name="aMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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303 <param name="aGap" size="3" type="integer" value="-7" label="Gap" optional="false"/>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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304 </when>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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305 </conditional>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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306 </when>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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307 </conditional>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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308
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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309
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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310 <conditional name="cTrimLen">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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311 <param name="select" type="select" label="6) Trimming to length">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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312 <option value="off" selected="true">Off</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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313 <option value="on">On</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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314 </param>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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315 <when value="on">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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316 <param name="trimLen" size="4" type="integer" value="30" label="Length" optional="false" help="trim reads to certain length from right"/>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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317 </when>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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318 </conditional>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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319
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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320 <param name="minReadLen" size="4" type="integer" value="18" label="7) Minimum read length" optional="false" help="shorter reads are discarded"/>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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321
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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322
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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323 <conditional name="cLogging">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
parents:
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324 <param name="select" type="select" label="Logging and tagging options">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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325 <option value="off" selected="true">Off</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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326 <option value="show">Show</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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327 </param>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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328 <when value="show">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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329 <param name="logLevel" type="select" label="Alignment logging">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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330 <option value="" selected="true">Off</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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331 <option value="--log-level ALL">All</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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332 <option value="--log-level MOD">Modified</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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333 <option value="--log-level TAB">Tabular</option>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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334 </param>
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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335
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
jtilman
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336 <param name="noLenDist" type="select" label="Read length distribution">
68a4edf205f3 Uploaded Flexbar tool definition file flexbar.xml
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337 <option value="--no-length-dist" selected="true">Off</option>
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338 <option value="">On</option>
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339 </param>
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340
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341 <param name="remTag" type="select" label="Read tagging">
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342 <option value="" selected="true">Off</option>
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343 <option value="--removal-tag">Removal tags</option>
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344 </param>
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345 </when>
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346 </conditional>
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347
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348 </inputs>
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349
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350 <stdio>
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351 <exit_code range="1:" level="fatal" description="Error!" />
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352 </stdio>
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353
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354 <outputs>
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355 <data format="txt" name="output" metadata_source="reads"/>
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356 </outputs>
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357
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358
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359 <help>
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360 **Flexbar help**
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361
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362 Flexbar_ is a program to preprocess sequencing data. It demultiplexes barcoded runs and removes adapter sequences. Further, basic read trimming and filtering options are provided. Flexbar increases mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform.
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363
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364 .. _Flexbar: https://sourceforge.net/projects/flexbar
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365
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366 ------
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367
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368 **Reference**
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369
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370 Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905.
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371
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372 ------
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373
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374 **Trim-end modes**
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375
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376 **Any:** longer part of read remains
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377
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378 **Left:** align before or at read end, right part remains
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379
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380 **Right:** align after or at read start, left part remains
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381
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382 **Left tail:** consider first n bases, see tail-length options
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383
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384 **Right tail:** use only last n bases of reads in alignment
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385
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386 ------
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387
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388 **Documentation**
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389
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390 .. class:: warningmark
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391
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392 Further documentation is available on the `manual`__ wiki and via the command line help screen.
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393
3
7ba3aded92c7 Corrected webpage url.
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394 .. __: http://sourceforge.net/p/flexbar/wiki
0
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395 </help>
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396
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397 </tool>
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398