Mercurial > repos > jtilman > flexbar

annotate flexbar.xml @ 10:f0bdf862ba39

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Simplified perl wrapper.
author jtilman
date Mon, 31 Dec 2012 18:40:01 +0100
parents 589b4866f537
children 4cbf6c6d2f2b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
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1
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
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2 <!-- Author: Johannes T. Roehr -->
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3
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
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4 <tool id="flexbar" name="Flexbar" version="2.3" force_history_refresh="True">
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5
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6 <description>flexible barcode and adapter removal</description>
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7
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8 <requirements>
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9 <requirement type="binary" version="2.3">flexbar</requirement>
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10 </requirements>
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11
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12 <version_command>flexbar --version</version_command>
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13
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14 <command interpreter="perl">
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15
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16 flexbar.pl flexbar
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17
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18 --threads 1
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19
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
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20 --reads $reads
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21
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
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22 #if $cReads2.select == "on":
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23 #if $cReads2.reads2.ext == $reads.ext:
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24 --reads2 $cReads2.reads2
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25 #end if
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26 #end if
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589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
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28
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
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29 #if $reads.ext == "fasta":
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30 --format fasta
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31 #end if
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32 #if $reads.ext == "fastq":
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33 --format fastq
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34 #end if
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35 #if $reads.ext == "fastqsanger":
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36 --format fastq-sanger
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37 #end if
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38 #if $reads.ext == "fastqsolexa":
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39 --format fastq-solexa
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40 #end if
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41 #if $reads.ext == "fastqillumina":
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42 --format fastq-i1.3
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43 #end if
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44 #if $reads.ext == "csfasta":
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45 --format csfasta
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46 #end if
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47 #if $reads.ext == "fastqcssanger":
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48 --format csfastq
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49 #end if
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51
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
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52 --max-uncalled $maxUncalled
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53 --min-readlength $minReadLen
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54
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55 #if $trimEnds.select == "on":
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56 --pre-trim-left $trimEnds.trimLeft
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57 --pre-trim-right $trimEnds.trimRight
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58 #end if
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59
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60 #if $cTrimPhred.select == "on":
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61 --pre-trim-phred $cTrimPhred.trimPhred
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62 #end if
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63
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
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64 #if $cTrimLen.select == "on":
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65 --post-trim-length $cTrimLen.trimLen
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66 #end if
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68
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69 #if $cBarcodes.select == "on":
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70 --barcodes $cBarcodes.barcodes
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71
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72 #if $cBarcodes.cbReads.select == "yes":
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73 --barcode-reads $cBarcodes.cbReads.bReads
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74 #end if
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75
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76 #if $cBarcodes.cbReads.select == "no":
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77 $cBarcodes.cbReads.bKeep
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78 #end if
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79
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80 --barcode-trim-end $cBarcodes.bTrimEnd
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81
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82 #if $cBarcodes.cbTailLen.select == "yes":
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83 --barcode-tail-length $cBarcodes.cbTailLen.bTailLen
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84 #end if
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85
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86 #if $cBarcodes.cbMinOverlap.select == "yes":
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87 --barcode-min-overlap $cBarcodes.cbMinOverlap.bMinOverlap
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88 #end if
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89
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90 --barcode-threshold $cBarcodes.bThresh
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91
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92 #if $cBarcodes.cbAlignScores.select == "yes":
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93 --barcode-match $bMatch
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94 --barcode-mismatch $bMismatch
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95 --barcode-gap $bGap
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96 #end if
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97
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98 #end if
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100
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
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101 #if $cAdapters.select == "yes":
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102
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103 #if $cAdapters.ccAdapters.select == "data":
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104 --adapters $cAdapters.ccAdapters.adaptersData
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105 #end if
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106
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107 #if $cAdapters.ccAdapters.select == "seq":
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108 --adapter-seq $cAdapters.ccAdapters.adapterSeq
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109 #end if
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110
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111 --adapter-trim-end $cAdapters.aTrimEnd
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112
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113 #if $cAdapters.caTailLen.select == "yes":
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114 --adapter-tail-length $cAdapters.caTailLen.aTailLen
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115 #end if
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116
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117 --adapter-min-overlap $cAdapters.aMinOverlap
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118 --adapter-threshold $cAdapters.aThresh
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119
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120 #if $cAdapters.caAlignScores.select == "on":
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121 --adapter-match $aMatch
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122 --adapter-mismatch $aMismatch
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123 --adapter-gap $aGap
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124 #end if
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125
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126 #end if
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128
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129 #if $cLogging.select == "show"
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130 $cLogging.logLevel
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131 $cLogging.noLenDist
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132 $cLogging.remTag
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133 #end if
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134
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135 #if $cLogging.select == "off"
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136 --no-length-dist
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137 #end if
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139
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140 $output $output.id $__new_file_path__ $reads.ext
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141
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142 </command>
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143
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144 <inputs>
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145
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146 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/>
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147
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148
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149 <conditional name="cReads2">
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150 <param name="select" type="select" label="2nd read set (paired)">
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151 <option value="off" selected="true">Off</option>
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152 <option value="on">On</option>
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153 </param>
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154 <when value="on">
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155 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads2" type="data" label="Reads 2" optional="false" help="same format as first read set"/>
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156 </when>
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157 </conditional>
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159
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160 <param name="maxUncalled" size="4" type="integer" value="0" label="1) Max uncalled" optional="false" help="allowed uncalled bases per read"/>
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161
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162 <conditional name="trimEnds">
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163 <param name="select" type="select" label="2) Trimming of ends">
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164 <option value="off" selected="true">Off</option>
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165 <option value="on">On</option>
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166 </param>
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167 <when value="on">
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168 <param name="trimLeft" size="4" type="integer" value="0" label="Left" optional="false"/>
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169 <param name="trimRight" size="4" type="integer" value="0" label="Right" optional="false" help="trims specified number of bases from read ends"/>
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170 </when>
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171 </conditional>
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172
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173 <conditional name="cTrimPhred">
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174 <param name="select" type="select" label="3) Phred-trimming">
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175 <option value="off" selected="true">Off</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
176 <option value="on">On</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
177 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
178 <when value="on">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
179 <param name="trimPhred" size="4" type="integer" value="10" label="Threshold" optional="false" help="trim right end until specified or higher quality reached"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
180 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
181 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
182
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
183
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
184 <conditional name="cBarcodes">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
185 <param name="select" type="select" label="4) Barcode detection">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
186 <option value="off" selected="true">Off</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
187 <option value="on">On</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
188 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
189 <when value="on">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
190 <param format="fasta" name="barcodes" type="data" label="Barcodes" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
191 <conditional name="cbReads">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
192 <param name="select" type="select" label="Separate barcode reads">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
193 <option value="no" selected="true">No</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
194 <option value="yes">Yes</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
195 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
196 <when value="yes">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
197 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="bReads" type="data" label="Separate barcode reads" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
198 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
199 <when value="no">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
200 <param name="bKeep" type="select" label="Remove barcodes within reads">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
201 <option value="" selected="true">Yes</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
202 <option value="--barcode-keep">No</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
203 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
204 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
205 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
206 <param name="bTrimEnd" type="select" label="Trim-end mode" optional="false">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
207 <option value="ANY" selected="true">Any</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
208 <option value="RIGHT">Right</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
209 <option value="RIGHT_TAIL">Right tail</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
210 <option value="LEFT">Left</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
211 <option value="LEFT_TAIL">Left tail</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
212 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
213 <conditional name="cbTailLen">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
214 <param name="select" type="select" label="Change tail length">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
215 <option value="no" selected="true">No</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
216 <option value="yes">Yes</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
217 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
218 <when value="yes">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
219 <param name="bTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
220 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
221 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
222
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
223 <conditional name="cbMinOverlap">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
224 <param name="select" type="select" label="Change min-overlap" help="default: barcode length">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
225 <option value="no" selected="true">No</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
226 <option value="yes">Yes</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
227 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
228 <when value="yes">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
229 <param name="bMinOverlap" size="4" type="integer" value="8" label="Min-overlap" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
230 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
231 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
232
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
233 <param name="bThresh" size="4" type="integer" value="1" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
234
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
235 <conditional name="cbAlignScores">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
236 <param name="select" type="select" label="Modify alignment scores">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
237 <option value="no" selected="true">No</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
238 <option value="yes">Yes</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
239 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
240 <when value="yes">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
241 <param name="bMatch" size="3" type="integer" value="1" label="Match" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
242 <param name="bMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
243 <param name="bGap" size="3" type="integer" value="-7" label="Gap" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
244 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
245 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
246 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
247 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
248
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
249
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
250 <conditional name="cAdapters">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
251 <param name="select" type="select" label="5) Adapter removal">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
252 <option value="off" selected="true">Off</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
253 <option value="on">On</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
254 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
255
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
256 <when value="on">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
257 <conditional name="ccAdapters">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
258 <param name="select" type="select" label="Adapter source">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
259 <option value="data" selected="true">Fasta</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
260 <option value="seq">Sequence</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
261 <!-- <option value="file">File</option> -->
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
262 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
263 <when value="data">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
264 <param format="fasta" name="adaptersData" type="data" label="Adapters" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
265 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
266 <when value="seq">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
267 <param name="adapterSeq" size="40" label="Adapter" type="text" value="AAAAAAAAAAAAAA" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
268 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
269 <!-- <when value="file">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
270 <param name="adaptersFile" type="file" label="Adapters file" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
271 </when> -->
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
272 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
273
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
274 <param name="aTrimEnd" type="select" label="Trim-end mode" optional="false">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
275 <option value="ANY">Any</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
276 <option value="RIGHT" selected="true">Right</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
277 <option value="RIGHT_TAIL">Right tail</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
278 <option value="LEFT">Left</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
279 <option value="LEFT_TAIL">Left tail</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
280 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
281
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
282 <conditional name="caTailLen">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
283 <param name="select" type="select" label="Change tail length">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
284 <option value="no" selected="true">No</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
285 <option value="yes">Yes</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
286 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
287 <when value="yes">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
288 <param name="aTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
289 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
290 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
291
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
292 <param name="aMinOverlap" size="4" type="integer" value="1" label="Min-overlap" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
293 <param name="aThresh" size="4" type="integer" value="3" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
294
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
295 <conditional name="caAlignScores">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
296 <param name="select" type="select" label="Modify alignment scores">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
297 <option value="no" selected="true">No</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
298 <option value="yes">Yes</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
299 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
300 <when value="yes">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
301 <param name="aMatch" size="3" type="integer" value="1" label="Match" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
302 <param name="aMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
303 <param name="aGap" size="3" type="integer" value="-7" label="Gap" optional="false"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
304 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
305 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
306 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
307 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
308
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
309
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
310 <conditional name="cTrimLen">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
311 <param name="select" type="select" label="6) Trimming to length">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
312 <option value="off" selected="true">Off</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
313 <option value="on">On</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
314 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
315 <when value="on">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
316 <param name="trimLen" size="4" type="integer" value="30" label="Length" optional="false" help="trim reads to certain length from right"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
317 </when>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
318 </conditional>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
319
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
320 <param name="minReadLen" size="4" type="integer" value="18" label="7) Minimum read length" optional="false" help="shorter reads are discarded"/>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
321
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
322
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
323 <conditional name="cLogging">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
324 <param name="select" type="select" label="Logging and tagging options">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
325 <option value="off" selected="true">Off</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
326 <option value="show">Show</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
327 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
328 <when value="show">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
329 <param name="logLevel" type="select" label="Alignment logging">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
330 <option value="" selected="true">Off</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
331 <option value="--log-level ALL">All</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
332 <option value="--log-level MOD">Modified</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
333 <option value="--log-level TAB">Tabular</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
334 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
335
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
336 <param name="noLenDist" type="select" label="Read length distribution">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
337 <option value="--no-length-dist" selected="true">Off</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
338 <option value="">On</option>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
339 </param>
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
340
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
diff changeset
341 <param name="remTag" type="select" label="Read tagging">
589b4866f537 Uploaded Flexbar galaxy tool definition file flexbar.xml
jtilman
parents:
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342 <option value="" selected="true">Off</option>
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343 <option value="--removal-tag">Removal tags</option>
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344 </param>
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345 </when>
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346 </conditional>
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347
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348 </inputs>
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349
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350 <stdio>
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351 <exit_code range="1:" level="fatal" description="Error!" />
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352 </stdio>
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353
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354 <outputs>
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355 <data format="txt" name="output" metadata_source="reads"/>
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356 </outputs>
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357
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358
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359 <help>
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360 **Flexbar help**
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361
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362 Flexbar_ is a program to preprocess sequencing data. It demultiplexes barcoded runs and removes adapter sequences. Further, basic read trimming and filtering options are provided. Flexbar increases mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform.
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363
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364 .. _Flexbar: https://sourceforge.net/projects/flexbar
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365
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366 ------
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367
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368 **Reference**
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369
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370 Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905.
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371
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372 ------
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373
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374 **Trim-end modes**
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375
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376 **Any:** longer part of read remains
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377
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378 **Left:** align before or at read end, right part remains
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379
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380 **Right:** align after or at read start, left part remains
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381
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382 **Left tail:** consider first n bases, see tail-length options
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383
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384 **Right tail:** use only last n bases of reads in alignment
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385
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386 ------
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387
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388 **Documentation**
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389
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390 .. class:: warningmark
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391
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392 Further documentation is available on the `manual`__ wiki and via the command line help screen.
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393
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394 .. __: http://sourceforge.net/p/flexbar/wiki
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395 </help>
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396
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397 </tool>
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398