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1 <?xml version="1.0" ?>
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2 <tool id="qiime_cutadapt_trim-single" name="qiime cutadapt trim-single"
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3 version="2020.8">
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4 <description>Find and remove adapters in demultiplexed single-end sequences.</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime cutadapt trim-single
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10
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11 --i-demultiplexed-sequences=$idemultiplexedsequences
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12
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13 --p-cores=$pcores
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14
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15 #if $padapter:
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16 --p-adapter
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17 #end if
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18
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19 #if str($pfront):
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20 --p-front=$pfront
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21 #end if
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22 #if '__ob__' in str($panywhere):
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23 #set $panywhere_temp = $panywhere.replace('__ob__', '[')
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24 #set $panywhere = $panywhere_temp
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25 #end if
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26 #if '__cb__' in str($panywhere):
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27 #set $panywhere_temp = $panywhere.replace('__cb__', ']')
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28 #set $panywhere = $panywhere_temp
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29 #end if
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30 #if 'X' in str($panywhere):
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31 #set $panywhere_temp = $panywhere.replace('X', '\\')
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32 #set $panywhere = $panywhere_temp
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33 #end if
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34 #if '__sq__' in str($panywhere):
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35 #set $panywhere_temp = $panywhere.replace('__sq__', "'")
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36 #set $panywhere = $panywhere_temp
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37 #end if
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38 #if '__db__' in str($panywhere):
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39 #set $panywhere_temp = $panywhere.replace('__db__', '"')
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40 #set $panywhere = $panywhere_temp
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41 #end if
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42
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43 #if str($panywhere):
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44 --p-anywhere=$panywhere
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45 #end if
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46
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47 --p-error-rate=$perrorrate
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48
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49 #if $pnoindels:
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50 --p-no-indels
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51 #end if
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52
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53 --p-times=$ptimes
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54
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55 --p-overlap=$poverlap
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56
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57 #if $pmatchreadwildcards:
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58 --p-match-read-wildcards
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59 #end if
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60
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61 #if $pnomatchadapterwildcards:
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62 --p-no-match-adapter-wildcards
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63 #end if
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64
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65 --p-minimum-length=$pminimumlength
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66
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67 #if $pdiscarduntrimmed:
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68 --p-discard-untrimmed
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69 #end if
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70
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71 --o-trimmed-sequences=otrimmedsequences
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72
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73 #if str($examples) != 'None':
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74 --examples=$examples
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75 #end if
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76
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77 ;
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78 cp otrimmedsequences.qza $otrimmedsequences
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79
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80 ]]></command>
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81 <inputs>
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82 <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[SequencesWithQuality] The single-end sequences to be trimmed. [required]" name="idemultiplexedsequences" optional="False" type="data" />
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83 <param label="--p-adapter: --p-adapter: TEXT... Sequence of an adapter ligated to the 3\' end. The List[Str] adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. 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="padapter" selected="False" type="boolean" />
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84 <param label="--p-front: TEXT... Sequence of an adapter ligated to the 5\' end. The List[Str] 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. [optional]" name="pfront" optional="False" type="text" />
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85 <param label="--p-anywhere: TEXT... Sequence of an adapter that may be ligated to the 5\' List[Str] 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. [optional]" name="panywhere" optional="False" type="text" />
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86 <param exclude_max="False" label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) Maximum allowed error rate. [default: 0.1]" max="1" min="0" name="perrorrate" optional="True" type="float" value="0.1" />
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87 <param label="--p-no-indels: Do not allow insertions or deletions of bases when matching adapters. [default: True]" name="pnoindels" selected="False" type="boolean" />
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88 <param label="--p-times: INTEGER Remove multiple occurrences of an adapter if it is Range(1, None) repeated, up to `times` times. [default: 1]" min="1" name="ptimes" optional="True" type="integer" value="1" />
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89 <param label="--p-overlap: INTEGER Require at least `overlap` bases of overlap between Range(1, None) read and adapter for an adapter to be found. [default: 3]" min="1" name="poverlap" optional="True" type="integer" value="3" />
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90 <param label="--p-match-read-wildcards: --p-match-read-wildcards: / --p-no-match-read-wildcards Interpret IUPAC wildcards (e.g., N) in reads. [default: False]" name="pmatchreadwildcards" selected="False" type="boolean" />
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91 <param label="--p-no-match-adapter-wildcards: Do not interpret IUPAC wildcards (e.g., N) in adapters. [default: True]" name="pnomatchadapterwildcards" selected="False" type="boolean" />
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92 <param label="--p-minimum-length: INTEGER Range(1, None) Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records. [default: 1]" min="1" name="pminimumlength" optional="True" type="integer" value="1" />
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93 <param label="--p-discard-untrimmed: --p-discard-untrimmed: / --p-no-discard-untrimmed Discard reads in which no adapter was found. [default: False]" name="pdiscarduntrimmed" selected="False" type="boolean" />
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94 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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95
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96 </inputs>
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97
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98 <outputs>
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99 <data format="qza" label="${tool.name} on ${on_string}: trimmedsequences.qza" name="otrimmedsequences" />
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100
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101 </outputs>
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102
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103 <help><![CDATA[
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104 Find and remove adapters in demultiplexed single-end sequences.
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105 ###############################################################
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106
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107 Search demultiplexed single-end sequences for adapters and remove them. The
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108 parameter descriptions in this method are adapted from the official
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109 cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
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110 for complete details.
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111
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112 Parameters
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113 ----------
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114 demultiplexed_sequences : SampleData[SequencesWithQuality]
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115 The single-end sequences to be trimmed.
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116 cores : Int % Range(1, None), optional
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117 Number of CPU cores to use.
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118 adapter : List[Str], optional
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119 Sequence of an adapter ligated to the 3' end. The adapter and any
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120 subsequent bases are trimmed. If a `$` is appended, the adapter is only
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121 found if it is at the end of the read. If your sequence of interest is
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122 "framed" by a 5' and a 3' adapter, use this parameter to define a
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123 "linked" primer - see https://cutadapt.readthedocs.io for complete
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124 details.
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125 front : List[Str], optional
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126 Sequence of an adapter ligated to the 5' end. The adapter and any
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127 preceding bases are trimmed. Partial matches at the 5' end are allowed.
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128 If a `^` character is prepended, the adapter is only found if it is at
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129 the beginning of the read.
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130 anywhere : List[Str], optional
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131 Sequence of an adapter that may be ligated to the 5' or 3' end. Both
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132 types of matches as described under `adapter` and `front` are allowed.
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133 If the first base of the read is part of the match, the behavior is as
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134 with `front`, otherwise as with `adapter`. This option is mostly for
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135 rescuing failed library preparations - do not use if you know which end
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136 your adapter was ligated to.
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137 error_rate : Float % Range(0, 1, inclusive_end=True), optional
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138 Maximum allowed error rate.
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139 indels : Bool, optional
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140 Allow insertions or deletions of bases when matching adapters.
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141 times : Int % Range(1, None), optional
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142 Remove multiple occurrences of an adapter if it is repeated, up to
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143 `times` times.
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144 overlap : Int % Range(1, None), optional
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145 Require at least `overlap` bases of overlap between read and adapter
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146 for an adapter to be found.
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147 match_read_wildcards : Bool, optional
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148 Interpret IUPAC wildcards (e.g., N) in reads.
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149 match_adapter_wildcards : Bool, optional
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150 Interpret IUPAC wildcards (e.g., N) in adapters.
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151 minimum_length : Int % Range(1, None), optional
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152 Discard reads shorter than specified value. Note, the cutadapt default
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153 of 0 has been overridden, because that value produces empty sequence
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154 records.
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155 discard_untrimmed : Bool, optional
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156 Discard reads in which no adapter was found.
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157
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158 Returns
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159 -------
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160 trimmed_sequences : SampleData[SequencesWithQuality]
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161 The resulting trimmed sequences.
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162 ]]></help>
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163 <macros>
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164 <import>qiime_citation.xml</import>
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165 </macros>
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166 <expand macro="qiime_citation"/>
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167 </tool> |
