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1 <?xml version="1.0" ?>
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2 <tool id="qiime_cutadapt_trim-paired" name="qiime cutadapt trim-paired" version="2018.4">
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3 <description> - Find and remove adapters in demultiplexed paired-end sequences.</description>
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4 <requirements>
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5 <requirement type="package" version="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8
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9 qiime cutadapt trim-paired --i-demultiplexed-sequences=$idemultiplexedsequences
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10
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11 #if str($padapterf):
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12 --p-adapter-f="$padapterf"
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13 #end if
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14
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15 --o-trimmed-sequences=otrimmedsequences
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16
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17 #if str($cmdconfig) != 'None':
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18 --cmd-config=$cmdconfig
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19 #end if
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20
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21 #if '__sq__' in str($panywheref):
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22 #set $panywheref_temp = $panywheref.replace('__sq__', "'")
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23 #set $panywheref = $panywheref_temp
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24 #end if
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25
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26 #if str($panywheref):
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27 --p-anywhere-f="$panywheref"
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28 #end if
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29
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30 #if $poverlap:
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31 --p-overlap=$poverlap
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32 #end if
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33
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34 #if '__sq__' in str($panywherer):
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35 #set $panywherer_temp = $panywherer.replace('__sq__', "'")
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36 #set $panywherer = $panywherer_temp
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37 #end if
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38
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39 #if str($panywherer):
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40 --p-anywhere-r="$panywherer"
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41 #end if
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42
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43 #if $ptimes:
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44 --p-times=$ptimes
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45 #end if
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46
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47 #if $pindels:
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48 --p-indels
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49 #end if
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50
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51 #if str($padapterr):
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52 --p-adapter-r="$padapterr"
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53 #end if
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54
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55 #if $perrorrate:
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56 --p-error-rate=$perrorrate
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57 #end if
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58
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59 #if $pmatchadapterwildcards:
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60 --p-match-adapter-wildcards
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61 #end if
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62
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63 #set $slots = '${GALAXY_SLOTS:-4}'
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64 --p-cores=$slots
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65
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66 #if str($pfrontr):
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67 --p-front-r="$pfrontr"
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68 #end if
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69
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70 #if str($pfrontf):
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71 --p-front-f="$pfrontf"
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72 #end if
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73
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74 #if $pmatchreadwildcards:
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75 --p-match-read-wildcards
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76 #end if
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77 ;
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78
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79 cp otrimmedsequences.qza $otrimmedsequences
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80
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81 ]]></command>
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82 <inputs>
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83 <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: SampleData[PairedEndSequencesWithQuality] The paired-end sequences to be trimmed. [required]" name="idemultiplexedsequences" optional="False" type="data"/>
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84
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85 <param label="--p-adapter-f: Sequence of an adapter ligated to the 3' end. The adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. Search in forward read. If your sequence of interest is 'framed' by a 5' and a 3' adapter, use this parameter to define a 'linked' primer - see https://cutadapt.readthedocs.io for complete details. [optional]" name="padapterf" optional="True" type="text"/>
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86 <param label="--p-front-f: Sequence of an adapter ligated to the 5' end. The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a `^` character is prepended, the adapter is only found if it is at the beginning of the read. Search in forward read. [optional]" name="pfrontf" optional="True" type="text"/>
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87 <param label="--p-anywhere-f: Sequence of an adapter that may be ligated to the 5' or 3' end. Both types of matches as described under `adapter` and `front` are allowed. If the first base of the read is part of the match, the behavior is as with `front`, otherwise as with `adapter`. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to. Search in forward read. [optional]" name="panywheref" optional="True" type="text"/>
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88
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89 <param label="--p-adapter-r: Sequence of an adapter ligated to the 3' end. The adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. Search in reverse read. If your sequence of interest is 'framed' by a 5' and a 3' adapter, use this parameter to define a 'linked' primer - see https://cutadapt.readthedocs.io for complete details. [optional]" name="padapterr" optional="True" type="text"/>
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90 <param label="--p-front-r: Sequence of an adapter ligated to the 5' end. The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a `^` character is prepended, the adapter is only found if it is at the beginning of the read. Search in reverse read. [optional]" name="pfrontr" optional="True" type="text"/>
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91 <param label="--p-anywhere-r: Sequence of an adapter that may be ligated to the 5' or 3' end. Both types of matches as described under `adapter` and `front` are allowed. If the first base of the read is part of the match, the behavior is as with `front`, otherwise as with `adapter`. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to. Search in reverse read. [optional]" name="panywherer" optional="True" type="text"/>
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92
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93 <param label="--p-error-rate: Maximum allowed error rate. [default: 0.1]" name="perrorrate" optional="True" type="float" value="0.1"/>
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94
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95 <param label="--p-indels: --p-no-indels Allow insertions or deletions of bases when matching adapters. [default: True]" name="pindels" checked="False" type="boolean"/>
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96
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97 <param label="--p-times: Remove multiple occurrences of an adapter if it is repeated, up to `times` times. [default: 1]" name="ptimes" optional="True" type="integer" value="1"/>
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98
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99 <param label="--p-overlap: Require at least `overlap` bases of overlap between read and adapter for an adapter to be found. [default: 3]" name="poverlap" optional="True" type="integer" value="3"/>
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100
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101 <param label="--p-match-read-wildcards: --p-no-match-read-wildcards Interpret IUPAC wildcards (e.g., N) in reads. [default: False]" name="pmatchreadwildcards" checked="False" type="boolean"/>
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102
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103 <param label="--p-match-adapter-wildcards: --p-no-match-adapter-wildcards Interpret IUPAC wildcards (e.g., N) in adapters. [default: True]" name="pmatchadapterwildcards" checked="False" type="boolean"/>
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104
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105 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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106 </inputs>
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107 <outputs>
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108 <data format="qza" label="${tool.name} on ${on_string}: trimmed-sequences.qza" name="otrimmedsequences"/>
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109 </outputs>
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110 <help><![CDATA[
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111 Find and remove adapters in demultiplexed paired-end sequences.
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112 ----------------------------------------------------------------
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113
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114 Search demultiplexed paired-end sequences for adapters and remove them. The
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115 parameter descriptions in this method are adapted from the official
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116 cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
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117 for complete details.
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118
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119 Parameters
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120 ----------
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121 demultiplexed_sequences : SampleData[PairedEndSequencesWithQuality]
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122 The paired-end sequences to be trimmed.
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123 adapter_f : List[Str], optional
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124 Sequence of an adapter ligated to the 3' end. The adapter and any
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125 subsequent bases are trimmed. If a `$` is appended, the adapter is only
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126 found if it is at the end of the read. Search in forward read. If your
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127 sequence of interest is "framed" by a 5' and a 3' adapter, use this
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128 parameter to define a "linked" primer - see
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129 https://cutadapt.readthedocs.io for complete details.
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130 front_f : List[Str], optional
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131 Sequence of an adapter ligated to the 5' end. The adapter and any
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132 preceding bases are trimmed. Partial matches at the 5' end are allowed.
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133 If a `^` character is prepended, the adapter is only found if it is at
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134 the beginning of the read. Search in forward read.
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135 anywhere_f : List[Str], optional
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136 Sequence of an adapter that may be ligated to the 5' or 3' end. Both
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137 types of matches as described under `adapter` and `front` are allowed.
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138 If the first base of the read is part of the match, the behavior is as
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139 with `front`, otherwise as with `adapter`. This option is mostly for
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140 rescuing failed library preparations - do not use if you know which end
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141 your adapter was ligated to. Search in forward read.
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142 adapter_r : List[Str], optional
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143 Sequence of an adapter ligated to the 3' end. The adapter and any
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144 subsequent bases are trimmed. If a `$` is appended, the adapter is only
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145 found if it is at the end of the read. Search in reverse read. If your
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146 sequence of interest is "framed" by a 5' and a 3' adapter, use this
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147 parameter to define a "linked" primer - see
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148 https://cutadapt.readthedocs.io for complete details.
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149 front_r : List[Str], optional
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150 Sequence of an adapter ligated to the 5' end. The adapter and any
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151 preceding bases are trimmed. Partial matches at the 5' end are allowed.
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152 If a `^` character is prepended, the adapter is only found if it is at
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153 the beginning of the read. Search in reverse read.
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154 anywhere_r : List[Str], optional
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155 Sequence of an adapter that may be ligated to the 5' or 3' end. Both
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156 types of matches as described under `adapter` and `front` are allowed.
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157 If the first base of the read is part of the match, the behavior is as
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158 with `front`, otherwise as with `adapter`. This option is mostly for
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159 rescuing failed library preparations - do not use if you know which end
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160 your adapter was ligated to. Search in reverse read.
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161 error_rate : Float % Range(0, 1, inclusive_end=True), optional
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162 Maximum allowed error rate.
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163 indels : Bool, optional
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164 Allow insertions or deletions of bases when matching adapters.
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165 times : Int % Range(1, None), optional
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166 Remove multiple occurrences of an adapter if it is repeated, up to
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167 `times` times.
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168 overlap : Int % Range(1, None), optional
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169 Require at least `overlap` bases of overlap between read and adapter
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170 for an adapter to be found.
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171 match_read_wildcards : Bool, optional
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172 Interpret IUPAC wildcards (e.g., N) in reads.
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173 match_adapter_wildcards : Bool, optional
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174 Interpret IUPAC wildcards (e.g., N) in adapters.
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175
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176 Returns
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177 -------
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178 trimmed_sequences : SampleData[PairedEndSequencesWithQuality]
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179 The resulting trimmed sequences.
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180 ]]>
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181 </help>
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182 <macros>
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183 <import>qiime_citation.xml</import>
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184 </macros>
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185 <expand macro="qiime_citation" />
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186 </tool>
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