annotate flexbar.xml @ 43:afaa5daf84ac draft

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author jtilman
date Tue, 07 May 2019 10:24:05 -0400
parents b0847c1e320b
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2 <!-- Flexbar tool definition for Galaxy, version 3.5.0 -->
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3 <!-- Author: Johannes Roehr -->
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6 <tool id="flexbar" name="Flexbar" version="3.5.0">
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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="3.5.0">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' '$outlog'_input1.'$reads.rs.extension' &&
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22 #elif $reads.mode == "pe":
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23 ln -s '$reads.r1' '$outlog'_input1.'$reads.r1.extension' &&
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24 ln -s '$reads.r2' '$outlog'_input2.'$reads.r2.extension' &&
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25 #else:
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26 ln -s '$reads.rc.forward' '$outlog'_input1.'$reads.rc.forward.extension' &&
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27 ln -s '$reads.rc.reverse' '$outlog'_input2.'$reads.rc.reverse.extension' &&
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28 #end if
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29
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30 #if $cBarcodes.select == "on":
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31
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32 mkdir flexbar_barcoded &&
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33
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34 #if $cBarcodes.bAdvanced.cbReads.select == "yes":
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35 ln -s '$cBarcodes.bAdvanced.cbReads.bReads' '$outlog'_input3.'$cBarcodes.bAdvanced.cbReads.bReads.extension' &&
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36 #end if
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37 #end if
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38
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39
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40 '$__tool_directory__/flexbar.pl' flexbar
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42 --threads \${GALAXY_SLOTS:-1}
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44 #if $reads.mode == "se":
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45 --reads '$outlog'_input1.'$reads.rs.extension'
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46 #elif $reads.mode == "pe":
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47 --reads '$outlog'_input1.'$reads.r1.extension'
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48 --reads2 '$outlog'_input2.'$reads.r2.extension'
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49 #else:
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50 --reads '$outlog'_input1.'$reads.rc.forward.extension'
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51 --reads2 '$outlog'_input2.'$reads.rc.reverse.extension'
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52 #end if
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54 --max-uncalled $maxUncalled
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55 --min-read-length $minReadLen
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57 #if $trimEnds.select == "on":
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58 --pre-trim-left $trimEnds.trimLeft
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59 --pre-trim-right $trimEnds.trimRight
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60 #end if
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62
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63 #if $cTrimQual.select != "off":
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64 #if $reads.mode == "se":
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65 #if $reads.rs.ext == "fastqsanger":
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66 --qtrim-format sanger
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67 #end if
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68 #if $reads.rs.ext == "fastqsolexa":
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69 --qtrim-format solexa
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70 #end if
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71 #if $reads.rs.ext == "fastqillumina":
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72 --qtrim-format i1.3
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73 #end if
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74 #elif $reads.mode == "pe":
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75 #if $reads.r1.ext == "fastqsanger":
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76 --qtrim-format sanger
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77 #end if
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78 #if $reads.r1.ext == "fastqsolexa":
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79 --qtrim-format solexa
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80 #end if
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81 #if $reads.r1.ext == "fastqillumina":
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82 --qtrim-format i1.3
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83 #end if
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84 #else:
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85 #if $reads.rc.forward.ext == "fastqsanger":
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86 --qtrim-format sanger
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87 #end if
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88 #if $reads.rc.forward.ext == "fastqsolexa":
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89 --qtrim-format solexa
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90 #end if
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91 #if $reads.rc.forward.ext == "fastqillumina":
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92 --qtrim-format i1.3
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93 #end if
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94 #end if
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95 #end if
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96
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97 #if $cTrimQual.select == "tail":
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98 --qtrim TAIL
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99 --qtrim-threshold $cTrimQual.trimQualTail
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100 $cTrimQual.trimQualPostTail
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101 #end if
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102 #if $cTrimQual.select == "win":
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103 --qtrim WIN
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104 --qtrim-threshold $cTrimQual.trimQualWin
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105 --qtrim-win-size $cTrimQual.trimQualWinSize
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106 $cTrimQual.trimQualPostWin
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107 #end if
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108 #if $cTrimQual.select == "bwa":
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109 --qtrim BWA
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110 --qtrim-threshold $cTrimQual.trimQualBWA
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111 $cTrimQual.trimQualPostBWA
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112 #end if
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113
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114
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115 #if $cBarcodes.select == "on":
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116
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117 --target flexbar_barcoded/flexbarOut
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118
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119 #if $cBarcodes.ccBarcodes.select == "file":
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120 --barcodes $cBarcodes.ccBarcodes.barcodeFile
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121 #end if
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122 #if $cBarcodes.ccBarcodes.select == "files":
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123 --barcodes $cBarcodes.ccBarcodes.barcodeFile1
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124 --barcodes2 $cBarcodes.ccBarcodes.barcodeFile2
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125 #end if
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126
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127 --barcode-error-rate $cBarcodes.bThresh
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128
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129 --barcode-trim-end $cBarcodes.bTrimEnd
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130
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131 #if $cBarcodes.bAdvanced.cbReads.select == "yes":
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132 --barcode-reads '$outlog'_input3.'$cBarcodes.bAdvanced.cbReads.bReads.extension'
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133 #end if
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134
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135 #if $cBarcodes.bAdvanced.cbMinOverlap.select == "yes":
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136 --barcode-min-overlap $cBarcodes.bAdvanced.cbMinOverlap.bMinOverlap
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137 #end if
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138
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139 $cBarcodes.bAdvanced.bKeep
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140 $cBarcodes.bAdvanced.bUnassigned
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141
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142 #if $cBarcodes.bAdvanced.cbTailLen.select == "yes":
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143 --barcode-tail-length $cBarcodes.bAdvanced.cbTailLen.bTailLen
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144 #end if
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145
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146 #if $cBarcodes.bAdvanced.cbAlignScores.select == "yes":
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147 --barcode-match $cBarcodes.bAdvanced.cbAlignScores.bMatch
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148 --barcode-mismatch $cBarcodes.bAdvanced.cbAlignScores.bMismatch
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149 --barcode-gap $cBarcodes.bAdvanced.cbAlignScores.bGap
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150 #end if
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151 #end if
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152
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153
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154 #if $cAdapters.select == "on":
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155
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156 #if $cAdapters.ccAdapters.select == "file":
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157 --adapters '$cAdapters.ccAdapters.adapterFile'
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158 #end if
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159 #if $cAdapters.ccAdapters.select == "files":
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160 --adapters '$cAdapters.ccAdapters.adapterFile1'
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161 --adapters2 '$cAdapters.ccAdapters.adapterFile2'
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162 #end if
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163 #if $cAdapters.ccAdapters.select == "preset":
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164 --adapter-preset '$cAdapters.ccAdapters.adapterPreset'
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165 #end if
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166 #if $cAdapters.ccAdapters.select == "seq":
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167 --adapter-seq $cAdapters.ccAdapters.adapterSeq
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168 #end if
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169
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170 --adapter-trim-end $cAdapters.aTrimEnd
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171 --adapter-min-overlap $cAdapters.aMinOverlap
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172 --adapter-error-rate $cAdapters.aThresh
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173
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174 #if $cAdapters.cPairOverlap.select == "on":
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175 --adapter-pair-overlap $cAdapters.cPairOverlap.aPairOverlap
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176 --adapter-min-poverlap $cAdapters.cPairOverlap.aMinPoverlap
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177 #end if
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178
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179 #if $cAdapters.aAdvanced.caTailLen.select == "yes":
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180 --adapter-tail-length $cAdapters.aAdvanced.caTailLen.aTailLen
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181 #end if
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182
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183 #if $cAdapters.aAdvanced.cRevComp.select == "on":
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184 --adapter-revcomp ON
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185 #if $cAdapters.aAdvanced.cRevComp.aRevCompEnd != "off":
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186 --adapter-revcomp-end $cAdapters.aAdvanced.cRevComp.aRevCompEnd
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187 #end if
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188 #end if
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189 #if $cAdapters.aAdvanced.cRevComp.select == "only":
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190 --adapter-revcomp ONLY
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191 #end if
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192
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193 $cAdapters.aAdvanced.aReadSet
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194
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195 --adapter-cycles $cAdapters.aAdvanced.aCycles
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196
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197 #if $cAdapters.aAdvanced.caAlignScores.select == "yes":
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198 --adapter-match $cAdapters.aAdvanced.caAlignScores.aMatch
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199 --adapter-mismatch $cAdapters.aAdvanced.caAlignScores.aMismatch
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200 --adapter-gap $cAdapters.aAdvanced.caAlignScores.aGap
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201 #end if
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202 #end if
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203
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204
36
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205 #if $hTrim.select == "on":
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206 #if $hTrim.hTrimLeft != "":
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207 --htrim-left $hTrim.hTrimLeft
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208 #end if
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209 #if $hTrim.hTrimRight != "":
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210 --htrim-right $hTrim.hTrimRight
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211 #end if
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212
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213 --htrim-min-length $hTrim.hMinLength
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214 --htrim-error-rate $hTrim.hErrorRate
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215
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216 #if $hTrim.hAdvanced.hMinLength2 != "":
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217 --htrim-min-length2 $hTrim.hAdvanced.hMinLength2
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218 #end if
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219 #if $hTrim.hAdvanced.hMaxLength != "":
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220 --htrim-max-length $hTrim.hAdvanced.hMaxLength
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221 #end if
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222
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223 $hTrim.hAdvanced.hMaxFirst
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224 $hTrim.hAdvanced.hTrimAdapter
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225 #end if
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226
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227
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228 #if $cTrimLen.select == "on":
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229 --post-trim-length $cTrimLen.trimLen
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230 #end if
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231
34
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232 #if $cAddOptions.select == "show":
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233 $cAddOptions.logLevel
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234 $cAddOptions.numTags
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235 $cAddOptions.remTags
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diff changeset
236 $cAddOptions.rndTags
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237 $cAddOptions.singleReadsP
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238
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239 #if $cAddOptions.cReadBundle.select == "show":
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240 --bundle $cAddOptions.cReadBundle.bundle
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241
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242 #if $cAddOptions.cReadBundle.bundles != "":
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243 --bundles $cAddOptions.cReadBundle.bundles
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244 #end if
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245 #end if
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246 #end if
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247
41
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248 #if $cBarcodes.select == "off":
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249 #if $reads.mode == "se":
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250 --output-reads '$rsout'.'$reads.rs.extension'
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251 #elif $reads.mode == "pe":
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252 --output-reads '$r1out'.'$reads.r1.extension'
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253 --output-reads2 '$r2out'.'$reads.r2.extension'
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254 #else:
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255 --output-reads '$rcout.forward'.'$reads.rc.forward.extension'
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256 --output-reads2 '$rcout.reverse'.'$reads.rc.reverse.extension'
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257 #end if
34
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258 #end if
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259
34
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260 --output-log '$outlog'
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261
41
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262 #if $cBarcodes.select == "on":
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263 flexbar_barcoded
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264 #end if
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265
34
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266 ]]>
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267 </command>
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268
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269
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270 <inputs>
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271
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272 <conditional name="reads">
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273 <param name="mode" type="select" label="Sequencing reads">
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274 <option value="se">Single read file</option>
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275 <option value="pe" selected="true">Paired read files</option>
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276 <option value="pc">Paired read collection</option>
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277 </param>
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278 <when value="se">
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279 <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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280 </when>
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281 <when value="pe">
39
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282 <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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283 <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"/>
34
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284 </when>
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285 <when value="pc">
39
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286 <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"/>
19
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287 </when>
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288 </conditional>
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289
34
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290 <param name="maxUncalled" size="4" type="integer" value="0" label="1) Maximum uncalled bases"/>
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291
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292 <conditional name="trimEnds">
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293 <param name="select" type="select" label="2) Trimming of read ends">
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294 <option value="off" selected="true">Off</option>
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295 <option value="on">On</option>
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296 </param>
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297 <when value="off">
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298 </when>
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299 <when value="on">
34
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300 <param name="trimLeft" size="4" type="integer" value="0" label="Left"/>
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301 <param name="trimRight" size="4" type="integer" value="0" label="Right" help="trims specified number of bases at ends"/>
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302 </when>
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303 </conditional>
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304
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305 <conditional name="cTrimQual">
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306 <param name="select" type="select" label="3) Quality-based trimming">
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307 <option value="off" selected="true">Off</option>
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308 <option value="tail">Tail</option>
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309 <option value="win">Window</option>
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310 <option value="bwa">BWA</option>
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311 </param>
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312 <when value="off">
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313 </when>
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314 <when value="tail">
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315 <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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diff changeset
316
34
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317 <param name="trimQualPostTail" type="select" label="After adapter removal">
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318 <option value="" selected="true">No</option>
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319 <option value="--qtrim-post-removal">Yes</option>
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320 </param>
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321 </when>
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322 <when value="win">
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323 <param name="trimQualWin" size="4" type="integer" value="20" label="Quality threshold"/>
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324 <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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325
34
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326 <param name="trimQualPostWin" type="select" label="After adapter removal">
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327 <option value="" selected="true">No</option>
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328 <option value="--qtrim-post-removal">Yes</option>
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329 </param>
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330 </when>
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331 <when value="bwa">
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332 <param name="trimQualBWA" size="4" type="integer" value="20" label="Quality threshold" help="trimming approach used by BWA"/>
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333
34
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334 <param name="trimQualPostBWA" type="select" label="After adapter removal">
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335 <option value="" selected="true">No</option>
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336 <option value="--qtrim-post-removal">Yes</option>
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337 </param>
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338 </when>
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339 </conditional>
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340
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341
41
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342 <conditional name="cBarcodes">
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343 <param name="select" type="select" label="4) Barcode detection">
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344 <option value="off" selected="true">Off</option>
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345 <option value="on">On</option>
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346 </param>
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347 <when value="off">
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348 </when>
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349 <when value="on">
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350 <conditional name="ccBarcodes">
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351 <param name="select" type="select" label="Barcodes">
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352 <option value="file" selected="true">Barcode file</option>
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diff changeset
353 <option value="files">Two barcode files</option>
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354 </param>
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355 <when value="file">
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356 <param format="fasta" name="barcodeFile" type="data" label="Fasta file with barcodes for reads 1"/>
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357 </when>
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358 <when value="files">
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359 <param format="fasta" name="barcodeFile1" type="data" label="Fasta file with barcodes for reads 1"/>
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360 <param format="fasta" name="barcodeFile2" type="data" label="Fasta file with barcodes for reads 2"/>
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361 </when>
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362 </conditional>
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363
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diff changeset
364 <param name="bThresh" size="4" type="float" value="0.0" label="Error rate" help="allowed fraction of mismatches and indels"/>
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365
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366 <param name="bTrimEnd" type="select" label="Trim-end mode">
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diff changeset
367 <option value="LTAIL" selected="true">Left tail</option>
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368 <option value="LEFT">Left</option>
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369 <option value="RTAIL">Right tail</option>
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370 <option value="RIGHT">Right</option>
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371 <option value="ANY">Any</option>
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372 </param>
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373
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diff changeset
374 <section name="bAdvanced" title="Advanced options" expanded="false">
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375
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diff changeset
376 <conditional name="cbReads">
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diff changeset
377 <param name="select" type="select" label="Separate barcode reads">
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378 <option value="no" selected="true">No</option>
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379 <option value="yes">Yes</option>
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380 </param>
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diff changeset
381 <when value="no">
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382 </when>
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383 <when value="yes">
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diff changeset
384 <param name="bReads" type="data" label="Fastq file with separate barcode reads" format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz,fastqsanger.bz2,fastqsolexa.bz2,fastqillumina.bz2"/>
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385 </when>
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386 </conditional>
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387
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diff changeset
388 <conditional name="cbMinOverlap">
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diff changeset
389 <param name="select" type="select" label="Change minimum overlap" help="default: barcode length">
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390 <option value="no" selected="true">No</option>
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diff changeset
391 <option value="yes">Yes</option>
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392 </param>
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diff changeset
393 <when value="no">
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parents: 39
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394 </when>
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diff changeset
395 <when value="yes">
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396 <param name="bMinOverlap" size="4" type="integer" value="" label="Minimum overlap"/>
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parents: 39
diff changeset
397 </when>
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398 </conditional>
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399
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parents: 39
diff changeset
400 <param name="bKeep" type="select" label="Remove barcodes within reads">
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parents: 39
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401 <option value="" selected="true">Yes</option>
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diff changeset
402 <option value="--barcode-keep">No</option>
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403 </param>
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parents: 39
diff changeset
404
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parents: 39
diff changeset
405 <param name="bUnassigned" type="select" label="Include unassigned reads">
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diff changeset
406 <option value="" selected="true">No</option>
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parents: 39
diff changeset
407 <option value="--barcode-unassigned">Yes</option>
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408 </param>
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409
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parents: 39
diff changeset
410 <conditional name="cbTailLen">
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parents: 39
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411 <param name="select" type="select" label="Change tail length">
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412 <option value="no" selected="true">No</option>
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parents: 39
diff changeset
413 <option value="yes">Yes</option>
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414 </param>
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diff changeset
415 <when value="no">
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416 </when>
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parents: 39
diff changeset
417 <when value="yes">
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parents: 39
diff changeset
418 <param name="bTailLen" size="4" type="integer" value="" label="Tail length"/>
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parents: 39
diff changeset
419 </when>
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diff changeset
420 </conditional>
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parents: 39
diff changeset
421
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parents: 39
diff changeset
422 <conditional name="cbAlignScores">
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parents: 39
diff changeset
423 <param name="select" type="select" label="Modify alignment scores">
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parents: 39
diff changeset
424 <option value="no" selected="true">No</option>
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parents: 39
diff changeset
425 <option value="yes">Yes</option>
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jtilman
parents: 39
diff changeset
426 </param>
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parents: 39
diff changeset
427 <when value="no">
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parents: 39
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428 </when>
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parents: 39
diff changeset
429 <when value="yes">
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parents: 39
diff changeset
430 <param name="bMatch" size="3" type="integer" value="1" label="Match"/>
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jtilman
parents: 39
diff changeset
431 <param name="bMismatch" size="3" type="integer" value="-1" label="Mismatch"/>
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parents: 39
diff changeset
432 <param name="bGap" size="3" type="integer" value="-9" label="Gap"/>
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parents: 39
diff changeset
433 </when>
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diff changeset
434 </conditional>
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parents: 39
diff changeset
435 </section>
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diff changeset
436 </when>
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jtilman
parents: 39
diff changeset
437 </conditional>
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parents: 39
diff changeset
438
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parents: 39
diff changeset
439
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
440 <conditional name="cAdapters">
41
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parents: 39
diff changeset
441 <param name="select" type="select" label="5) Adapter removal">
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
442 <option value="off" selected="true">Off</option>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
443 <option value="on">On</option>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
444 </param>
20
83e3813084f2 Adjustment of when tags.
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diff changeset
445 <when value="off">
83e3813084f2 Adjustment of when tags.
jtilman
parents: 19
diff changeset
446 </when>
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
447 <when value="on">
34
4a095317caca Uploaded
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parents: 31
diff changeset
448 <conditional name="ccAdapters">
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parents: 31
diff changeset
449 <param name="select" type="select" label="Adapter source">
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parents: 31
diff changeset
450 <option value="file" selected="true">Adapter file</option>
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parents: 31
diff changeset
451 <option value="files">Two adapter files</option>
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parents: 31
diff changeset
452 <option value="preset">Illumina preset</option>
4a095317caca Uploaded
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parents: 31
diff changeset
453 <option value="seq">Single sequence</option>
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parents: 31
diff changeset
454 </param>
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jtilman
parents: 31
diff changeset
455 <when value="file">
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parents: 31
diff changeset
456 <param format="fasta" name="adapterFile" type="data" label="Fasta adapter file"/>
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parents: 31
diff changeset
457 </when>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
458 <when value="files">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
459 <param format="fasta" name="adapterFile1" type="data" label="Fasta adapter file for reads 1"/>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
460 <param format="fasta" name="adapterFile2" type="data" label="Fasta adapter file for reads 2"/>
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jtilman
parents: 31
diff changeset
461 </when>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
462 <when value="preset">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
463 <param name="adapterPreset" type="select" label="Adapter preset">
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jtilman
parents: 31
diff changeset
464 <option value="TruSeq" selected="true">TruSeq LT and HT-based kits</option>
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parents: 31
diff changeset
465 <option value="SmallRNA">TruSeq Small RNA</option>
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jtilman
parents: 31
diff changeset
466 <option value="Methyl">TruSeq DNA Methylation and ScriptSeq</option>
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jtilman
parents: 31
diff changeset
467 <option value="Ribo">TruSeq Ribo Profile</option>
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jtilman
parents: 31
diff changeset
468 <option value="Nextera">Nextera, AmpliSeq, and TruSight</option>
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parents: 31
diff changeset
469 <option value="NexteraMP">Nextera Mate Pair</option>
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parents: 31
diff changeset
470 </param>
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jtilman
parents: 31
diff changeset
471 </when>
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jtilman
parents: 31
diff changeset
472 <when value="seq">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
473 <param name="adapterSeq" size="40" label="Adapter sequence" type="text" value=""/>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
474 </when>
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jtilman
parents: 31
diff changeset
475 </conditional>
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jtilman
parents: 31
diff changeset
476
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jtilman
parents: 31
diff changeset
477 <param name="aMinOverlap" size="4" type="integer" value="3" label="Minimum overlap"/>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
478 <param name="aThresh" size="4" type="float" value="0.1" label="Error rate" help="allowed fraction of mismatches and indels"/>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
479
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
480 <param name="aTrimEnd" type="select" label="Trim-end mode">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
481 <option value="RIGHT" selected="true">Right</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
482 <option value="LEFT">Left</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
483 <option value="RTAIL">Right tail</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
484 <option value="LTAIL">Left tail</option>
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jtilman
parents: 31
diff changeset
485 <option value="ANY">Any</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
486 </param>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
487
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jtilman
parents: 31
diff changeset
488 <conditional name="cPairOverlap">
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jtilman
parents: 31
diff changeset
489 <param name="select" type="select" label="Pair overlap detection">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
490 <option value="off" selected="true">Off</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
491 <option value="on">On</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
492 </param>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
493 <when value="off">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
494 </when>
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jtilman
parents: 31
diff changeset
495 <when value="on">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
496 <param name="aPairOverlap" type="select" label="Detection mode">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
497 <option value="ON" selected="true">Standard</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
498 <option value="SHORT">Trim short</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
499 </param>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
500 <param name="aMinPoverlap" size="4" type="integer" value="40" label="Minimum pair overlap"/>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
501 </when>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
502 </conditional>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
503
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
504 <section name="aAdvanced" title="Advanced options" expanded="false">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
505
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
506 <conditional name="caTailLen">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
507 <param name="select" type="select" label="Change tail length">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
508 <option value="no" selected="true">No</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
509 <option value="yes">Yes</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
510 </param>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
511 <when value="no">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
512 </when>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
513 <when value="yes">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
514 <param name="aTailLen" size="4" type="integer" value="" label="Tail length"/>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
515 </when>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
516 </conditional>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
517
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
518 <conditional name="cRevComp">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
519 <param name="select" type="select" label="Reverse complements of adapters">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
520 <option value="off" selected="true">Off</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
521 <option value="on">On</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
522 <option value="only">Only</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
523 </param>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
524 <when value="off">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
525 </when>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
526 <when value="on">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
527 <param name="aRevCompEnd" type="select" label="Different trim-end for reverse complements">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
528 <option value="off" selected="true">Off</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
529 <option value="RIGHT">Right</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
530 <option value="LEFT">Left</option>
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jtilman
parents: 31
diff changeset
531 <option value="RTAIL">Right tail</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
532 <option value="LTAIL">Left tail</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
533 <option value="ANY">Any</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
534 </param>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
535 </when>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
536 </conditional>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
537
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jtilman
parents: 31
diff changeset
538
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
539 <param name="aReadSet" type="select" label="Removal for single read set">
36
4e47e1caf21a Uploaded
jtilman
parents: 34
diff changeset
540 <option value="" selected="true">Off</option>
34
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
541 <option value="--adapter-read-set 1">1st</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
542 <option value="--adapter-read-set 2">2nd</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
543 </param>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
544
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
545 <param name="aCycles" size="4" type="integer" value="1" label="Number of removal cycles"/>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
546
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
547 <conditional name="caAlignScores">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
548 <param name="select" type="select" label="Modify alignment scores">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
549 <option value="no" selected="true">No</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
550 <option value="yes">Yes</option>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
551 </param>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
552 <when value="no">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
553 </when>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
554 <when value="yes">
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
555 <param name="aMatch" size="3" type="integer" value="1" label="Match"/>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
556 <param name="aMismatch" size="3" type="integer" value="-1" label="Mismatch"/>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
557 <param name="aGap" size="3" type="integer" value="-6" label="Gap"/>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
558 </when>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
559 </conditional>
4a095317caca Uploaded
jtilman
parents: 31
diff changeset
560 </section>
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
561 </when>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
562 </conditional>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
563
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
564
36
4e47e1caf21a Uploaded
jtilman
parents: 34
diff changeset
565 <conditional name="hTrim">
41
b0847c1e320b Uploaded
jtilman
parents: 39
diff changeset
566 <param name="select" type="select" label="6) Trimming of homopolymers">
36
4e47e1caf21a Uploaded
jtilman
parents: 34
diff changeset
567 <option value="off" selected="true">Off</option>
4e47e1caf21a Uploaded
jtilman
parents: 34
diff changeset
568 <option value="on">On</option>
4e47e1caf21a Uploaded
jtilman
parents: 34
diff changeset
569 </param>
4e47e1caf21a Uploaded
jtilman
parents: 34
diff changeset
570 <when value="off">
4e47e1caf21a Uploaded
jtilman
parents: 34
diff changeset
571 </when>
4e47e1caf21a Uploaded
jtilman
parents: 34
diff changeset
572 <when value="on">
4e47e1caf21a Uploaded
jtilman
parents: 34
diff changeset
573 <param name="hTrimLeft" size="4" label="Trim homopolymers on left end" type="text" value="" optional="true"/>
4e47e1caf21a Uploaded
jtilman
parents: 34
diff changeset
574 <param name="hTrimRight" size="4" label="Trim homopolymers on right end" type="text" value="" optional="true" help="for example AT"/>
4e47e1caf21a Uploaded
jtilman
parents: 34
diff changeset
575
4e47e1caf21a Uploaded
jtilman
parents: 34
diff changeset
576 <param name="hMinLength" size="4" type="integer" value="3" label="Minimum length"/>
4e47e1caf21a Uploaded
jtilman
parents: 34
diff changeset
577 <param name="hErrorRate" size="4" type="float" value="0.1" label="Error rate"/>
4e47e1caf21a Uploaded
jtilman
parents: 34
diff changeset
578
4e47e1caf21a Uploaded
jtilman
parents: 34
diff changeset
579 <section name="hAdvanced" title="Advanced options" expanded="false">
4e47e1caf21a Uploaded
jtilman
parents: 34
diff changeset
580
4e47e1caf21a Uploaded
jtilman
parents: 34
diff changeset
581 <param name="hMaxLength" size="4" type="integer" value="" label="Maximum length" optional="true"/>
4e47e1caf21a Uploaded
jtilman
parents: 34
diff changeset
582
4e47e1caf21a Uploaded
jtilman
parents: 34
diff changeset
583 <param name="hMaxFirst" type="select" label="Maximum length only for first one">
4e47e1caf21a Uploaded
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parents: 34
diff changeset
584 <option value="" selected="true">Off</option>
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diff changeset
585 <option value="--htrim-max-first">On</option>
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586 </param>
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587
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diff changeset
588 <param name="hMinLength2" size="4" type="integer" value="" label="Minimum length after first one" optional="true"/>
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parents: 34
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589
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590 <param name="hTrimAdapter" type="select" label="Only in case of adapter on same side">
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591 <option value="" selected="true">Off</option>
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diff changeset
592 <option value="--htrim-adapter">On</option>
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593 </param>
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594 </section>
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595 </when>
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596 </conditional>
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597
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598
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599 <conditional name="cTrimLen">
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600 <param name="select" type="select" label="7) Trimming to length">
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601 <option value="off" selected="true">Off</option>
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602 <option value="on">On</option>
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12e4b3bb38c6 Adjusted tool definition to Flexbar release 2.4
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603 </param>
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604 <when value="off">
12e4b3bb38c6 Adjusted tool definition to Flexbar release 2.4
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parents: 21
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605 </when>
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606 <when value="on">
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607 <param name="trimLen" size="4" type="integer" value="" label="Length" help="trim reads to certain length from right"/>
22
12e4b3bb38c6 Adjusted tool definition to Flexbar release 2.4
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608 </when>
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609 </conditional>
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621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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610
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611 <param name="minReadLen" size="4" type="integer" value="20" label="8) Minimum read length"/>
34
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612
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613 <conditional name="cAddOptions">
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614 <param name="select" type="select" label="Additional options">
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615 <option value="hide" selected="true">Hide</option>
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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616 <option value="show">Show</option>
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617 </param>
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618 <when value="hide">
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83e3813084f2 Adjustment of when tags.
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619 </when>
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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620 <when value="show">
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621 <param name="logLevel" type="select" label="Alignment logging">
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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622 <option value="" selected="true">Off</option>
31
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623 <option value="--align-log ALL">All</option>
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624 <option value="--align-log MOD">Modified</option>
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625 <option value="--align-log TAB">Tabular</option>
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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626 </param>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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627
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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628 <param name="numTags" type="select" label="Number tags">
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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629 <option value="" selected="true">Off</option>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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630 <option value="--number-tags">On</option>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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631 </param>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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632
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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633 <param name="remTags" type="select" label="Removal tags">
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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634 <option value="" selected="true">Off</option>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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parents:
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635 <option value="--removal-tags">On</option>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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636 </param>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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637
31
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638 <param name="rndTags" type="select" label="UMI tags">
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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639 <option value="" selected="true">Off</option>
31
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diff changeset
640 <option value="--umi-tags">On</option>
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641 </param>
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642
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643 <param name="singleReadsP" type="select" label="Single reads as paired">
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parents: 31
diff changeset
644 <option value="" selected="true">Off</option>
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parents: 31
diff changeset
645 <option value="--single-reads-paired">On</option>
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diff changeset
646 </param>
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647
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648 <conditional name="cReadBundle">
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649 <param name="select" type="select" label="Read bundle options">
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parents: 31
diff changeset
650 <option value="hide" selected="true">Hide</option>
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parents: 31
diff changeset
651 <option value="show">Show</option>
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parents: 31
diff changeset
652 </param>
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diff changeset
653 <when value="hide">
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654 </when>
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diff changeset
655 <when value="show">
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diff changeset
656 <param name="bundle" size="4" type="integer" value="256" label="Number of paired reads per bundle"/>
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657 <param name="bundles" size="4" type="integer" value="" optional="true" label="Only certain number of bundles for testing"/>
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658 </when>
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659 </conditional>
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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660 </when>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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661 </conditional>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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662
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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663 </inputs>
23
0ef7736004bb Use of galaxy variable to control number of threads.
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diff changeset
664
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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665 <outputs>
34
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666 <data name="outlog" format="txt" label="Flexbar log for ${on_string}"/>
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667
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668 <data name="rsout" label="Flexbar on ${reads.rs.name}" format_source="rs">
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diff changeset
669 <filter>reads['mode'] == 'se'</filter>
41
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diff changeset
670 <filter>cBarcodes['select'] == "off"</filter>
34
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671 </data>
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diff changeset
672
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673 <data name="r1out" label="Flexbar on ${reads.r1.name}" format_source="r1">
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diff changeset
674 <filter>reads['mode'] == "pe"</filter>
41
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diff changeset
675 <filter>cBarcodes['select'] == "off"</filter>
34
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676 </data>
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diff changeset
677 <data name="r2out" label="Flexbar on ${reads.r2.name}" format_source="r2">
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diff changeset
678 <filter>reads['mode'] == "pe"</filter>
41
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diff changeset
679 <filter>cBarcodes['select'] == "off"</filter>
34
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680 </data>
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diff changeset
681
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diff changeset
682 <collection name="rcout" type="paired" label="Flexbar on ${on_string}">
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diff changeset
683 <filter>reads['mode'] == "pc"</filter>
41
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diff changeset
684 <filter>cBarcodes['select'] == "off"</filter>
34
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diff changeset
685 <data name="forward" label="Flexbar on ${reads.rc.forward.name}" format_source="rc['forward']"/>
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parents: 31
diff changeset
686 <data name="reverse" label="Flexbar on ${reads.rc.reverse.name}" format_source="rc['reverse']"/>
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diff changeset
687 </collection>
41
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parents: 39
diff changeset
688
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parents: 39
diff changeset
689 <collection type="list" label="Flexbar on ${on_string}" name="barcoded">
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parents: 39
diff changeset
690 <filter>cBarcodes['select'] == "on"</filter>
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parents: 39
diff changeset
691 <discover_datasets pattern="__designation_and_ext__" directory="flexbar_barcoded" visible="true"/>
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parents: 39
diff changeset
692 </collection>
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parents: 39
diff changeset
693
19
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jtilman
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694 </outputs>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
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695
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
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696 <help>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
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697
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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698 **Description**
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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699
31
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700 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.
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
701
24
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diff changeset
702 .. _project: https://github.com/seqan/flexbar
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
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parents:
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703
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
704 ------
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
705
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
706 **Trim-end modes**
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
707
22
12e4b3bb38c6 Adjusted tool definition to Flexbar release 2.4
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parents: 21
diff changeset
708 **Any:** longer side of read remains after overlap removal
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
709
22
12e4b3bb38c6 Adjusted tool definition to Flexbar release 2.4
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parents: 21
diff changeset
710 **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
711
22
12e4b3bb38c6 Adjusted tool definition to Flexbar release 2.4
jtilman
parents: 21
diff changeset
712 **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
713
22
12e4b3bb38c6 Adjusted tool definition to Flexbar release 2.4
jtilman
parents: 21
diff changeset
714 **Left tail:** consider first n bases of reads in alignment
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
715
22
12e4b3bb38c6 Adjusted tool definition to Flexbar release 2.4
jtilman
parents: 21
diff changeset
716 **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
717
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
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diff changeset
718 ------
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
719
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
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720 **Documentation**
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
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721
31
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722 Further documentation is available on the `manual`__ page and via the command line help screen.
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
723
24
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diff changeset
724 .. __: https://github.com/seqan/flexbar/wiki
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
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725
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
726 ------
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
727
31
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diff changeset
728 **References**
19
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
729
31
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diff changeset
730 Johannes T. Roehr, Christoph Dieterich, Knut Reinert:
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diff changeset
731 Flexbar 3.0 – SIMD and multicore parallelization. Bioinformatics 2017.
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732
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diff changeset
733 Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich:
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diff changeset
734 Flexbar – flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012.
19
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735
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
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diff changeset
736 </help>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
737
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
738 </tool>
621fa3daa2a1 Updated tool definition for Flexbar 2.33 release
jtilman
parents:
diff changeset
739