annotate flexbar.xml @ 39:ae7d2b47ad07 draft

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author jtilman
date Sun, 01 Jul 2018 07:59:40 -0400
parents 497da23fee84
children b0847c1e320b
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2 <!-- Flexbar tool definition for Galaxy, version 3.4.2 -->
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3 <!-- Author: Johannes Roehr -->
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6 <tool id="flexbar" name="Flexbar" version="3.4.2">
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8 <description>- flexible barcode and adapter removal</description>
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10 <requirements>
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11 <requirement type="package" version="3.4.0">flexbar</requirement>
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12 </requirements>
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14 <version_command>flexbar --versions</version_command>
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16 <command detect_errors="aggressive">
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18 <![CDATA[
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20 #if $reads.mode == "se":
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21 ln -s '$reads.rs' '$rsout'_input.'$reads.rs.extension' &&
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22 #elif $reads.mode == "pe":
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23 ln -s '$reads.r1' '$r1out'_input.'$reads.r1.extension' &&
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24 ln -s '$reads.r2' '$r2out'_input.'$reads.r2.extension' &&
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25 #else:
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26 ln -s '$reads.rc.forward' '$rcout.forward'_input.'$reads.rc.forward.extension' &&
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27 ln -s '$reads.rc.reverse' '$rcout.reverse'_input.'$reads.rc.reverse.extension' &&
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28 #end if
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29
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30 '$__tool_directory__/flexbar.pl' flexbar
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0ef7736004bb Use of galaxy variable to control number of threads.
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32 --threads \${GALAXY_SLOTS:-1}
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34 #if $reads.mode == "se":
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35 --reads '$rsout'_input.'$reads.rs.extension'
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36 #elif $reads.mode == "pe":
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37 --reads '$r1out'_input.'$reads.r1.extension'
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38 --reads2 '$r2out'_input.'$reads.r2.extension'
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39 #else:
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40 --reads '$rcout.forward'_input.'$reads.rc.forward.extension'
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41 --reads2 '$rcout.reverse'_input.'$reads.rc.reverse.extension'
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42 #end if
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44 --max-uncalled $maxUncalled
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45 --min-read-length $minReadLen
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46
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47 #if $trimEnds.select == "on":
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48 --pre-trim-left $trimEnds.trimLeft
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49 --pre-trim-right $trimEnds.trimRight
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50 #end if
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51
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52
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53 #if $cTrimQual.select != "off":
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54 #if $reads.mode == "se":
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55 #if $reads.rs.ext == "fastqsanger":
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56 --qtrim-format sanger
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57 #end if
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58 #if $reads.rs.ext == "fastqsolexa":
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59 --qtrim-format solexa
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60 #end if
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61 #if $reads.rs.ext == "fastqillumina":
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62 --qtrim-format i1.3
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63 #end if
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64 #elif $reads.mode == "pe":
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65 #if $reads.r1.ext == "fastqsanger":
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66 --qtrim-format sanger
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67 #end if
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68 #if $reads.r1.ext == "fastqsolexa":
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69 --qtrim-format solexa
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70 #end if
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71 #if $reads.r1.ext == "fastqillumina":
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72 --qtrim-format i1.3
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73 #end if
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74 #else:
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75 #if $reads.rc.forward.ext == "fastqsanger":
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76 --qtrim-format sanger
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77 #end if
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78 #if $reads.rc.forward.ext == "fastqsolexa":
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79 --qtrim-format solexa
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80 #end if
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81 #if $reads.rc.forward.ext == "fastqillumina":
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82 --qtrim-format i1.3
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83 #end if
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84 #end if
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85 #end if
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87 #if $cTrimQual.select == "tail":
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88 --qtrim TAIL
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89 --qtrim-threshold $cTrimQual.trimQualTail
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90 $cTrimQual.trimQualPostTail
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91 #end if
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92 #if $cTrimQual.select == "win":
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93 --qtrim WIN
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94 --qtrim-threshold $cTrimQual.trimQualWin
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95 --qtrim-win-size $cTrimQual.trimQualWinSize
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96 $cTrimQual.trimQualPostWin
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97 #end if
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98 #if $cTrimQual.select == "bwa":
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99 --qtrim BWA
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100 --qtrim-threshold $cTrimQual.trimQualBWA
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101 $cTrimQual.trimQualPostBWA
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102 #end if
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103
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104
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105 #if $cAdapters.select == "on":
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107 #if $cAdapters.ccAdapters.select == "file":
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108 --adapters '$cAdapters.ccAdapters.adapterFile'
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109 #end if
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110 #if $cAdapters.ccAdapters.select == "files":
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111 --adapters '$cAdapters.ccAdapters.adapterFile1'
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112 --adapters2 '$cAdapters.ccAdapters.adapterFile2'
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113 #end if
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114 #if $cAdapters.ccAdapters.select == "preset":
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115 --adapter-preset '$cAdapters.ccAdapters.adapterPreset'
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116 #end if
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117 #if $cAdapters.ccAdapters.select == "seq":
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118 --adapter-seq $cAdapters.ccAdapters.adapterSeq
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119 #end if
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120
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121 --adapter-trim-end $cAdapters.aTrimEnd
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122 --adapter-min-overlap $cAdapters.aMinOverlap
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123 --adapter-error-rate $cAdapters.aThresh
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124
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125 #if $cAdapters.cPairOverlap.select == "on":
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126 --adapter-pair-overlap $cAdapters.cPairOverlap.aPairOverlap
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127 --adapter-min-poverlap $cAdapters.cPairOverlap.aMinPoverlap
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128 #end if
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129
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130 #if $cAdapters.aAdvanced.caTailLen.select == "yes":
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131 --adapter-tail-length $cAdapters.aAdvanced.caTailLen.aTailLen
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132 #end if
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133
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134 #if $cAdapters.aAdvanced.cRevComp.select == "on":
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135 --adapter-revcomp ON
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136 #if $cAdapters.aAdvanced.cRevComp.aRevCompEnd != "off":
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137 --adapter-revcomp-end $cAdapters.aAdvanced.cRevComp.aRevCompEnd
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138 #end if
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139 #end if
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140 #if $cAdapters.aAdvanced.cRevComp.select == "only":
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141 --adapter-revcomp ONLY
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142 #end if
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144 $cAdapters.aAdvanced.aReadSet
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145
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146 --adapter-cycles $cAdapters.aAdvanced.aCycles
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147
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148 #if $cAdapters.aAdvanced.caAlignScores.select == "yes":
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149 --adapter-match $cAdapters.aAdvanced.caAlignScores.aMatch
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150 --adapter-mismatch $cAdapters.aAdvanced.caAlignScores.aMismatch
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151 --adapter-gap $cAdapters.aAdvanced.caAlignScores.aGap
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152 #end if
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153 #end if
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156 #if $hTrim.select == "on":
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157 #if $hTrim.hTrimLeft != "":
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158 --htrim-left $hTrim.hTrimLeft
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159 #end if
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160 #if $hTrim.hTrimRight != "":
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161 --htrim-right $hTrim.hTrimRight
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162 #end if
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163
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164 --htrim-min-length $hTrim.hMinLength
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165 --htrim-error-rate $hTrim.hErrorRate
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166
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167 #if $hTrim.hAdvanced.hMinLength2 != "":
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168 --htrim-min-length2 $hTrim.hAdvanced.hMinLength2
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169 #end if
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170 #if $hTrim.hAdvanced.hMaxLength != "":
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171 --htrim-max-length $hTrim.hAdvanced.hMaxLength
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172 #end if
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173
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174 $hTrim.hAdvanced.hMaxFirst
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175 $hTrim.hAdvanced.hTrimAdapter
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176 #end if
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177
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178
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179 #if $cTrimLen.select == "on":
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180 --post-trim-length $cTrimLen.trimLen
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181 #end if
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182
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183 #if $cAddOptions.select == "show":
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184 $cAddOptions.logLevel
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185 $cAddOptions.numTags
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186 $cAddOptions.remTags
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187 $cAddOptions.rndTags
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188 $cAddOptions.singleReadsP
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189
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190 #if $cAddOptions.cReadBundle.select == "show":
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191 --bundle $cAddOptions.cReadBundle.bundle
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192
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193 #if $cAddOptions.cReadBundle.bundles != "":
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194 --bundles $cAddOptions.cReadBundle.bundles
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195 #end if
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196 #end if
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197 #end if
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198
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199
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200 #if $reads.mode == "se":
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201 --output-reads '$rsout'.'$reads.rs.extension'
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202 #elif $reads.mode == "pe":
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203 --output-reads '$r1out'.'$reads.r1.extension'
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204 --output-reads2 '$r2out'.'$reads.r2.extension'
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205 #else:
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206 --output-reads '$rcout.forward'.'$reads.rc.forward.extension'
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207 --output-reads2 '$rcout.reverse'.'$reads.rc.reverse.extension'
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208 #end if
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209
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210 --output-log '$outlog'
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211
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212 ]]>
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213 </command>
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214
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215
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216 <inputs>
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217
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218 <conditional name="reads">
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219 <param name="mode" type="select" label="Sequencing reads">
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220 <option value="se">Single read file</option>
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221 <option value="pe" selected="true">Paired read files</option>
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222 <option value="pc">Paired read collection</option>
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223 </param>
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224 <when value="se">
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225 <param name="rs" type="data" format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz,fastqsanger.bz2,fastqsolexa.bz2,fastqillumina.bz2" label="Fastq read file"/>
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226 </when>
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227 <when value="pe">
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228 <param name="r1" type="data" format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz,fastqsanger.bz2,fastqsolexa.bz2,fastqillumina.bz2" label="Fastq read file 1"/>
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229 <param name="r2" type="data" format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz,fastqsanger.bz2,fastqsolexa.bz2,fastqillumina.bz2" label="Fastq read file 2"/>
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230 </when>
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231 <when value="pc">
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232 <param name="rc" format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz,fastqsanger.bz2,fastqsolexa.bz2,fastqillumina.bz2" type="data_collection" collection_type="paired" label="Fastq pair collection"/>
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233 </when>
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234 </conditional>
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235
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236 <param name="maxUncalled" size="4" type="integer" value="0" label="1) Maximum uncalled bases"/>
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237
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238 <conditional name="trimEnds">
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239 <param name="select" type="select" label="2) Trimming of read ends">
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240 <option value="off" selected="true">Off</option>
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241 <option value="on">On</option>
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242 </param>
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243 <when value="off">
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244 </when>
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245 <when value="on">
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246 <param name="trimLeft" size="4" type="integer" value="0" label="Left"/>
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247 <param name="trimRight" size="4" type="integer" value="0" label="Right" help="trims specified number of bases at ends"/>
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248 </when>
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249 </conditional>
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250
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251 <conditional name="cTrimQual">
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252 <param name="select" type="select" label="3) Quality-based trimming">
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253 <option value="off" selected="true">Off</option>
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254 <option value="tail">Tail</option>
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255 <option value="win">Window</option>
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256 <option value="bwa">BWA</option>
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257 </param>
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258 <when value="off">
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259 </when>
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260 <when value="tail">
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261 <param name="trimQualTail" size="4" type="integer" value="20" label="Quality threshold" help="trim right end until specified quality or higher"/>
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262
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263 <param name="trimQualPostTail" type="select" label="After adapter removal">
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264 <option value="" selected="true">No</option>
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265 <option value="--qtrim-post-removal">Yes</option>
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266 </param>
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267 </when>
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268 <when value="win">
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269 <param name="trimQualWin" size="4" type="integer" value="20" label="Quality threshold"/>
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270 <param name="trimQualWinSize" size="4" type="integer" value="5" label="Window length" help="sliding window average quality approach from left end"/>
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271
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272 <param name="trimQualPostWin" type="select" label="After adapter removal">
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273 <option value="" selected="true">No</option>
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274 <option value="--qtrim-post-removal">Yes</option>
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275 </param>
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276 </when>
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277 <when value="bwa">
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278 <param name="trimQualBWA" size="4" type="integer" value="20" label="Quality threshold" help="trimming approach used by BWA"/>
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279
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280 <param name="trimQualPostBWA" type="select" label="After adapter removal">
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281 <option value="" selected="true">No</option>
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282 <option value="--qtrim-post-removal">Yes</option>
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283 </param>
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284 </when>
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285 </conditional>
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286
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287
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288 <conditional name="cAdapters">
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289 <param name="select" type="select" label="4) Adapter removal">
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290 <option value="off" selected="true">Off</option>
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291 <option value="on">On</option>
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292 </param>
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293 <when value="off">
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294 </when>
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295 <when value="on">
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296 <conditional name="ccAdapters">
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297 <param name="select" type="select" label="Adapter source">
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298 <option value="file" selected="true">Adapter file</option>
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299 <option value="files">Two adapter files</option>
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300 <option value="preset">Illumina preset</option>
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301 <option value="seq">Single sequence</option>
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302 </param>
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303 <when value="file">
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304 <param format="fasta" name="adapterFile" type="data" label="Fasta adapter file"/>
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305 </when>
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306 <when value="files">
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307 <param format="fasta" name="adapterFile1" type="data" label="Fasta adapter file for reads 1"/>
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308 <param format="fasta" name="adapterFile2" type="data" label="Fasta adapter file for reads 2"/>
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309 </when>
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310 <when value="preset">
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311 <param name="adapterPreset" type="select" label="Adapter preset">
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312 <option value="TruSeq" selected="true">TruSeq LT and HT-based kits</option>
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313 <option value="SmallRNA">TruSeq Small RNA</option>
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314 <option value="Methyl">TruSeq DNA Methylation and ScriptSeq</option>
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315 <option value="Ribo">TruSeq Ribo Profile</option>
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316 <option value="Nextera">Nextera, AmpliSeq, and TruSight</option>
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317 <option value="NexteraMP">Nextera Mate Pair</option>
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318 </param>
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319 </when>
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320 <when value="seq">
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321 <param name="adapterSeq" size="40" label="Adapter sequence" type="text" value=""/>
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322 </when>
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323 </conditional>
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324
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325 <param name="aMinOverlap" size="4" type="integer" value="3" label="Minimum overlap"/>
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326 <param name="aThresh" size="4" type="float" value="0.1" label="Error rate" help="allowed fraction of mismatches and indels"/>
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327
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328 <param name="aTrimEnd" type="select" label="Trim-end mode">
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329 <option value="RIGHT" selected="true">Right</option>
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330 <option value="LEFT">Left</option>
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331 <option value="RTAIL">Right tail</option>
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332 <option value="LTAIL">Left tail</option>
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333 <option value="ANY">Any</option>
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334 </param>
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335
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336 <conditional name="cPairOverlap">
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337 <param name="select" type="select" label="Pair overlap detection">
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338 <option value="off" selected="true">Off</option>
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339 <option value="on">On</option>
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340 </param>
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341 <when value="off">
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342 </when>
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343 <when value="on">
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344 <param name="aPairOverlap" type="select" label="Detection mode">
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345 <option value="ON" selected="true">Standard</option>
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346 <option value="SHORT">Trim short</option>
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347 </param>
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348 <param name="aMinPoverlap" size="4" type="integer" value="40" label="Minimum pair overlap"/>
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349 </when>
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350 </conditional>
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351
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352 <section name="aAdvanced" title="Advanced options" expanded="false">
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353
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354 <conditional name="caTailLen">
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355 <param name="select" type="select" label="Change tail length">
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356 <option value="no" selected="true">No</option>
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357 <option value="yes">Yes</option>
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358 </param>
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359 <when value="no">
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360 </when>
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361 <when value="yes">
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362 <param name="aTailLen" size="4" type="integer" value="" label="Tail length"/>
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363 </when>
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364 </conditional>
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365
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366 <conditional name="cRevComp">
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367 <param name="select" type="select" label="Reverse complements of adapters">
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368 <option value="off" selected="true">Off</option>
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369 <option value="on">On</option>
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diff changeset
370 <option value="only">Only</option>
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371 </param>
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diff changeset
372 <when value="off">
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373 </when>
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374 <when value="on">
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diff changeset
375 <param name="aRevCompEnd" type="select" label="Different trim-end for reverse complements">
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376 <option value="off" selected="true">Off</option>
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377 <option value="RIGHT">Right</option>
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378 <option value="LEFT">Left</option>
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379 <option value="RTAIL">Right tail</option>
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380 <option value="LTAIL">Left tail</option>
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381 <option value="ANY">Any</option>
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382 </param>
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383 </when>
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384 </conditional>
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385
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386
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387 <param name="aReadSet" type="select" label="Removal for single read set">
36
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diff changeset
388 <option value="" selected="true">Off</option>
34
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diff changeset
389 <option value="--adapter-read-set 1">1st</option>
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390 <option value="--adapter-read-set 2">2nd</option>
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391 </param>
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392
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393 <param name="aCycles" size="4" type="integer" value="1" label="Number of removal cycles"/>
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394
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diff changeset
395 <conditional name="caAlignScores">
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diff changeset
396 <param name="select" type="select" label="Modify alignment scores">
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397 <option value="no" selected="true">No</option>
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398 <option value="yes">Yes</option>
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399 </param>
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400 <when value="no">
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401 </when>
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diff changeset
402 <when value="yes">
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diff changeset
403 <param name="aMatch" size="3" type="integer" value="1" label="Match"/>
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diff changeset
404 <param name="aMismatch" size="3" type="integer" value="-1" label="Mismatch"/>
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405 <param name="aGap" size="3" type="integer" value="-6" label="Gap"/>
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406 </when>
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407 </conditional>
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408 </section>
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409 </when>
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410 </conditional>
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411
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412
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diff changeset
413 <conditional name="hTrim">
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414 <param name="select" type="select" label="5) Trimming of homopolymers">
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415 <option value="off" selected="true">Off</option>
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416 <option value="on">On</option>
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417 </param>
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418 <when value="off">
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419 </when>
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420 <when value="on">
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421 <param name="hTrimLeft" size="4" label="Trim homopolymers on left end" type="text" value="" optional="true"/>
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422 <param name="hTrimRight" size="4" label="Trim homopolymers on right end" type="text" value="" optional="true" help="for example AT"/>
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423
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424 <param name="hMinLength" size="4" type="integer" value="3" label="Minimum length"/>
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425 <param name="hErrorRate" size="4" type="float" value="0.1" label="Error rate"/>
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426
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diff changeset
427 <section name="hAdvanced" title="Advanced options" expanded="false">
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428
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429 <param name="hMaxLength" size="4" type="integer" value="" label="Maximum length" optional="true"/>
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430
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431 <param name="hMaxFirst" type="select" label="Maximum length only for first one">
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432 <option value="" selected="true">Off</option>
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433 <option value="--htrim-max-first">On</option>
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434 </param>
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435
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436 <param name="hMinLength2" size="4" type="integer" value="" label="Minimum length after first one" optional="true"/>
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437
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438 <param name="hTrimAdapter" type="select" label="Only in case of adapter on same side">
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439 <option value="" selected="true">Off</option>
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440 <option value="--htrim-adapter">On</option>
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441 </param>
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442 </section>
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443 </when>
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444 </conditional>
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445
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446
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447 <conditional name="cTrimLen">
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448 <param name="select" type="select" label="6) Trimming to length">
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449 <option value="off" selected="true">Off</option>
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450 <option value="on">On</option>
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451 </param>
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452 <when value="off">
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parents: 21
diff changeset
453 </when>
34
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454 <when value="on">
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diff changeset
455 <param name="trimLen" size="4" type="integer" value="" label="Length" help="trim reads to certain length from right"/>
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456 </when>
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457 </conditional>
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458
36
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459 <param name="minReadLen" size="4" type="integer" value="20" label="7) Minimum read length"/>
34
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460
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diff changeset
461 <conditional name="cAddOptions">
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diff changeset
462 <param name="select" type="select" label="Additional options">
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diff changeset
463 <option value="hide" selected="true">Hide</option>
19
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464 <option value="show">Show</option>
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465 </param>
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466 <when value="hide">
20
83e3813084f2 Adjustment of when tags.
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467 </when>
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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468 <when value="show">
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469 <param name="logLevel" type="select" label="Alignment logging">
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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470 <option value="" selected="true">Off</option>
31
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471 <option value="--align-log ALL">All</option>
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472 <option value="--align-log MOD">Modified</option>
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473 <option value="--align-log TAB">Tabular</option>
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474 </param>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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475
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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476 <param name="numTags" type="select" label="Number tags">
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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477 <option value="" selected="true">Off</option>
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478 <option value="--number-tags">On</option>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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479 </param>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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480
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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481 <param name="remTags" type="select" label="Removal tags">
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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482 <option value="" selected="true">Off</option>
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483 <option value="--removal-tags">On</option>
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484 </param>
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485
31
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486 <param name="rndTags" type="select" label="UMI tags">
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487 <option value="" selected="true">Off</option>
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diff changeset
488 <option value="--umi-tags">On</option>
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489 </param>
34
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490
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491 <param name="singleReadsP" type="select" label="Single reads as paired">
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492 <option value="" selected="true">Off</option>
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493 <option value="--single-reads-paired">On</option>
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494 </param>
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495
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496 <conditional name="cReadBundle">
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497 <param name="select" type="select" label="Read bundle options">
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498 <option value="hide" selected="true">Hide</option>
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499 <option value="show">Show</option>
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500 </param>
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501 <when value="hide">
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502 </when>
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503 <when value="show">
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504 <param name="bundle" size="4" type="integer" value="256" label="Number of paired reads per bundle"/>
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505 <param name="bundles" size="4" type="integer" value="" optional="true" label="Only certain number of bundles for testing"/>
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506 </when>
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507 </conditional>
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508 </when>
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509 </conditional>
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510
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511 </inputs>
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0ef7736004bb Use of galaxy variable to control number of threads.
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diff changeset
512
19
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513 <outputs>
34
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514 <data name="outlog" format="txt" label="Flexbar log for ${on_string}"/>
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515
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516 <data name="rsout" label="Flexbar on ${reads.rs.name}" format_source="rs">
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517 <filter>reads['mode'] == 'se'</filter>
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518 </data>
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519
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520 <data name="r1out" label="Flexbar on ${reads.r1.name}" format_source="r1">
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521 <filter>reads['mode'] == "pe"</filter>
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522 </data>
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523 <data name="r2out" label="Flexbar on ${reads.r2.name}" format_source="r2">
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524 <filter>reads['mode'] == "pe"</filter>
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525 </data>
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526
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527 <collection name="rcout" type="paired" label="Flexbar on ${on_string}">
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528 <filter>reads['mode'] == "pc"</filter>
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diff changeset
529 <data name="forward" label="Flexbar on ${reads.rc.forward.name}" format_source="rc['forward']"/>
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530 <data name="reverse" label="Flexbar on ${reads.rc.reverse.name}" format_source="rc['reverse']"/>
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531 </collection>
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532 </outputs>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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533
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jtilman
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534 <help>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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535
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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536 **Description**
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537
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538 The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome as well as transcriptome assemblies. Unique molecular identifiers can be extracted in a flexible way. The program supports sequencing data in fastq format, e.g. from the Illumina platform. Flexbar is available on the project_ page.
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539
24
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diff changeset
540 .. _project: https://github.com/seqan/flexbar
19
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parents:
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541
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parents:
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542 ------
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
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543
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
544 **Trim-end modes**
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
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545
22
12e4b3bb38c6 Adjusted tool definition to Flexbar release 2.4
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diff changeset
546 **Any:** longer side of read remains after overlap removal
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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parents:
diff changeset
547
22
12e4b3bb38c6 Adjusted tool definition to Flexbar release 2.4
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diff changeset
548 **Left:** right side remains after removal, align before or at read end
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
549
22
12e4b3bb38c6 Adjusted tool definition to Flexbar release 2.4
jtilman
parents: 21
diff changeset
550 **Right:** left part remains after removal, align after or at read start
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
551
22
12e4b3bb38c6 Adjusted tool definition to Flexbar release 2.4
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diff changeset
552 **Left tail:** consider first n bases of reads in alignment
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
553
22
12e4b3bb38c6 Adjusted tool definition to Flexbar release 2.4
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diff changeset
554 **Right tail:** use only last n bases, see tail-length options
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
555
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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556 ------
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
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557
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
558 **Documentation**
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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parents:
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559
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560 Further documentation is available on the `manual`__ page and via the command line help screen.
19
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parents:
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561
24
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diff changeset
562 .. __: https://github.com/seqan/flexbar/wiki
19
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563
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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564 ------
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
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565
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diff changeset
566 **References**
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
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567
31
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568 Johannes T. Roehr, Christoph Dieterich, Knut Reinert:
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diff changeset
569 Flexbar 3.0 – SIMD and multicore parallelization. Bioinformatics 2017.
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570
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diff changeset
571 Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich:
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diff changeset
572 Flexbar – flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012.
19
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573
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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574 </help>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
575
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
576 </tool>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
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577