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annotate flexbar.xml @ 12:4cbf6c6d2f2b

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Fixed issue where adapter removal can not be performed and further minor issues.
author jtilman
date Thu, 17 Jan 2013 18:09:44 +0100
parents 589b4866f537
children 346a2b0979ea
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
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2 <!-- Author: Johannes T. Roehr -->
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3
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
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4 <tool id="flexbar" name="Flexbar" version="2.3" force_history_refresh="True">
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5
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6 <description>flexible barcode and adapter removal</description>
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7
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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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13
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14 <command interpreter="perl">
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16 flexbar.pl flexbar
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17
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18 --threads 1
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19
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20 --reads $reads
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21
589b4866f537 Uploaded Flexbar galaxy 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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589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
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589b4866f537 Uploaded Flexbar galaxy 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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51
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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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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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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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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 #end if
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99
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100 #if $cAdapters.select == "on":
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101
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102 #if $cAdapters.ccAdapters.select == "data":
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103 --adapters $cAdapters.ccAdapters.adaptersData
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104 #end if
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105
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106 #if $cAdapters.ccAdapters.select == "seq":
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107 --adapter-seq $cAdapters.ccAdapters.adapterSeq
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108 #end if
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109
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110 --adapter-trim-end $cAdapters.aTrimEnd
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111
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112 #if $cAdapters.caTailLen.select == "yes":
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113 --adapter-tail-length $cAdapters.caTailLen.aTailLen
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114 #end if
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115
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116 --adapter-min-overlap $cAdapters.aMinOverlap
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117 --adapter-threshold $cAdapters.aThresh
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118
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119 #if $cAdapters.caAlignScores.select == "yes":
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120 --adapter-match $aMatch
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121 --adapter-mismatch $aMismatch
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122 --adapter-gap $aGap
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123 #end if
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124 #end if
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126
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127 #if $cLogging.select == "show":
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128 $cLogging.logLevel
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129 $cLogging.noLenDist
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130 $cLogging.remTag
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131 #end if
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132
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133 #if $cLogging.select == "off":
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134 --no-length-dist
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135 #end if
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138 $output $output.id $__new_file_path__ $reads.ext
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139
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140 </command>
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142 <inputs>
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143
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144 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/>
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147 <conditional name="cReads2">
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148 <param name="select" type="select" label="2nd read set (paired)">
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149 <option value="off" selected="true">Off</option>
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150 <option value="on">On</option>
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151 </param>
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152 <when value="on">
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153 <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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154 </when>
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155 </conditional>
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158 <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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159
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160 <conditional name="trimEnds">
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161 <param name="select" type="select" label="2) Trimming of ends">
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162 <option value="off" selected="true">Off</option>
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163 <option value="on">On</option>
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164 </param>
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165 <when value="on">
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166 <param name="trimLeft" size="4" type="integer" value="0" label="Left" optional="false"/>
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167 <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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168 </when>
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169 </conditional>
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170
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171 <conditional name="cTrimPhred">
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172 <param name="select" type="select" label="3) Phred-trimming">
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173 <option value="off" selected="true">Off</option>
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174 <option value="on">On</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
175 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
176 <when value="on">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
177 <param name="trimPhred" size="4" type="integer" value="10" label="Threshold" optional="false" help="trim right end until specified or higher quality reached"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
178 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
179 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
180
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
181
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
182 <conditional name="cBarcodes">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
183 <param name="select" type="select" label="4) Barcode detection">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
184 <option value="off" selected="true">Off</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
185 <option value="on">On</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
186 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
187 <when value="on">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
188 <param format="fasta" name="barcodes" type="data" label="Barcodes" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
189 <conditional name="cbReads">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
190 <param name="select" type="select" label="Separate barcode reads">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
191 <option value="no" selected="true">No</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
192 <option value="yes">Yes</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
193 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
194 <when value="yes">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
195 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="bReads" type="data" label="Separate barcode reads" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
196 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
197 <when value="no">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
198 <param name="bKeep" type="select" label="Remove barcodes within reads">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
199 <option value="" selected="true">Yes</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
200 <option value="--barcode-keep">No</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
201 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
202 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
203 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
204 <param name="bTrimEnd" type="select" label="Trim-end mode" optional="false">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
205 <option value="ANY" selected="true">Any</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
206 <option value="RIGHT">Right</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
207 <option value="RIGHT_TAIL">Right tail</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
208 <option value="LEFT">Left</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
209 <option value="LEFT_TAIL">Left tail</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
210 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
211 <conditional name="cbTailLen">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
212 <param name="select" type="select" label="Change tail length">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
213 <option value="no" selected="true">No</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
214 <option value="yes">Yes</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
215 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
216 <when value="yes">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
217 <param name="bTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
218 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
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diff changeset
219 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
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220
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
221 <conditional name="cbMinOverlap">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
222 <param name="select" type="select" label="Change min-overlap" help="default: barcode length">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
223 <option value="no" selected="true">No</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
224 <option value="yes">Yes</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
225 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
226 <when value="yes">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
227 <param name="bMinOverlap" size="4" type="integer" value="8" label="Min-overlap" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
228 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
229 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
230
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
231 <param name="bThresh" size="4" type="integer" value="1" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
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232
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
233 <conditional name="cbAlignScores">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
234 <param name="select" type="select" label="Modify alignment scores">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
235 <option value="no" selected="true">No</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
236 <option value="yes">Yes</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
237 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
238 <when value="yes">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
239 <param name="bMatch" size="3" type="integer" value="1" label="Match" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
240 <param name="bMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
241 <param name="bGap" size="3" type="integer" value="-7" label="Gap" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
242 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
243 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
244 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
245 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
246
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
247
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
248 <conditional name="cAdapters">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
249 <param name="select" type="select" label="5) Adapter removal">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
250 <option value="off" selected="true">Off</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
251 <option value="on">On</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
252 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
253
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
254 <when value="on">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
255 <conditional name="ccAdapters">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
256 <param name="select" type="select" label="Adapter source">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
257 <option value="data" selected="true">Fasta</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
258 <option value="seq">Sequence</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
259 <!-- <option value="file">File</option> -->
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
260 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
261 <when value="data">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
262 <param format="fasta" name="adaptersData" type="data" label="Adapters" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
263 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
264 <when value="seq">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
265 <param name="adapterSeq" size="40" label="Adapter" type="text" value="AAAAAAAAAAAAAA" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
266 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
267 <!-- <when value="file">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
268 <param name="adaptersFile" type="file" label="Adapters file" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
269 </when> -->
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
270 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
271
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
272 <param name="aTrimEnd" type="select" label="Trim-end mode" optional="false">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
273 <option value="ANY">Any</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
274 <option value="RIGHT" selected="true">Right</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
275 <option value="RIGHT_TAIL">Right tail</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
276 <option value="LEFT">Left</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
277 <option value="LEFT_TAIL">Left tail</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
278 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
279
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
280 <conditional name="caTailLen">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
281 <param name="select" type="select" label="Change tail length">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
282 <option value="no" selected="true">No</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
283 <option value="yes">Yes</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
284 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
285 <when value="yes">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
286 <param name="aTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
287 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
288 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
289
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
290 <param name="aMinOverlap" size="4" type="integer" value="1" label="Min-overlap" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
291 <param name="aThresh" size="4" type="integer" value="3" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
292
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
293 <conditional name="caAlignScores">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
294 <param name="select" type="select" label="Modify alignment scores">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
295 <option value="no" selected="true">No</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
296 <option value="yes">Yes</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
297 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
298 <when value="yes">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
299 <param name="aMatch" size="3" type="integer" value="1" label="Match" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
300 <param name="aMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
301 <param name="aGap" size="3" type="integer" value="-7" label="Gap" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
302 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
303 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
304 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
305 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
306
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
307
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
308 <conditional name="cTrimLen">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
309 <param name="select" type="select" label="6) Trimming to length">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
310 <option value="off" selected="true">Off</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
311 <option value="on">On</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
312 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
313 <when value="on">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
314 <param name="trimLen" size="4" type="integer" value="30" label="Length" optional="false" help="trim reads to certain length from right"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
315 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
316 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
317
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
318 <param name="minReadLen" size="4" type="integer" value="18" label="7) Minimum read length" optional="false" help="shorter reads are discarded"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
319
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
320
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
321 <conditional name="cLogging">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
322 <param name="select" type="select" label="Logging and tagging options">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
323 <option value="off" selected="true">Off</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
324 <option value="show">Show</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
325 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
326 <when value="show">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
327 <param name="logLevel" type="select" label="Alignment logging">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
328 <option value="" selected="true">Off</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
329 <option value="--log-level ALL">All</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
330 <option value="--log-level MOD">Modified</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
331 <option value="--log-level TAB">Tabular</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
332 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
333
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
334 <param name="noLenDist" type="select" label="Read length distribution">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
335 <option value="--no-length-dist" selected="true">Off</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
336 <option value="">On</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
337 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
338
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
339 <param name="remTag" type="select" label="Read tagging">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
340 <option value="" selected="true">Off</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
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341 <option value="--removal-tag">Removal tags</option>
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342 </param>
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343 </when>
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344 </conditional>
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345
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346 </inputs>
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347
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348 <stdio>
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349 <exit_code range="1:" level="fatal" description="Error!" />
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350 </stdio>
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351
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352 <outputs>
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353 <data format="txt" name="output" metadata_source="reads"/>
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354 </outputs>
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355
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356
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357 <help>
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358 **Flexbar help**
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359
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360 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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361
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362 .. _Flexbar: https://sourceforge.net/projects/flexbar
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363
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364 ------
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365
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366 **Reference**
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367
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368 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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369
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370 ------
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371
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372 **Trim-end modes**
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373
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374 **Any:** longer part of read remains
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375
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376 **Left:** align before or at read end, right part remains
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377
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378 **Right:** align after or at read start, left part remains
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379
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380 **Left tail:** consider first n bases, see tail-length options
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381
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382 **Right tail:** use only last n bases of reads in alignment
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383
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384 ------
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385
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386 **Documentation**
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387
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388 .. class:: warningmark
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389
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390 Further documentation is available on the `manual`__ wiki and via the command line help screen.
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391
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392 .. __: http://sourceforge.net/p/flexbar/wiki
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393 </help>
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394
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395 </tool>
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396