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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" version="2018.4">
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3 <description> - Find and remove adapters in demultiplexed single-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-single --i-demultiplexed-sequences=$idemultiplexedsequences
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10
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11 #if '__sq__' in str($panywhere):
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12 #set $panywhere_temp = $panywhere.replace('__sq__', "'")
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13 #set $panywhere = $panywhere_temp
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14 #end if
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15
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16 #if str($panywhere):
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17 --p-anywhere="$panywhere"
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18 #end if
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19
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20
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21 #if str($cmdconfig) != 'None':
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22 --cmd-config=$cmdconfig
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23 #end if
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24
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25 #if $poverlap:
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26 --p-overlap=$poverlap
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27 #end if
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28
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29 #if str($pfront):
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30 --p-front="$pfront"
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31 #end if
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32
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33 #if $ptimes:
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34 --p-times=$ptimes
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35 #end if
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36
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37 --o-trimmed-sequences=otrimmedsequences
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38
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39 #if $pindels:
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40 --p-indels
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41 #end if
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42
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43 #if $perrorrate:
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44 --p-error-rate=$perrorrate
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45 #end if
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46
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47 #if $pmatchadapterwildcards:
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48 --p-match-adapter-wildcards
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49 #end if
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50
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51 #set $slots = '${GALAXY_SLOTS:-4}'
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52 --p-cores=$slots
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53
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54 #if str($padapter):
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55 --p-adapter="$padapter"
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56 #end if
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57
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58 #if $pmatchreadwildcards:
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59 --p-match-read-wildcards
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60 #end if
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61 ;
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62 cp otrimmedsequences.qza $otrimmedsequences
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63
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64 ]]></command>
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65 <inputs>
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66 <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: SampleData[SequencesWithQuality] The single-end sequences to be trimmed. [required]" name="idemultiplexedsequences" optional="False" type="data"/>
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67
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68 <param label="--p-adapter: Sequence of an adapter ligated to the 3' end. The adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. 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" optional="True" type="text"/>
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69
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70 <param label="--p-front: 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. [optional]" name="pfront" optional="True" type="text"/>
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71 <param label="--p-anywhere: 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. [optional]" name="panywhere" optional="True" type="text"/>
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72
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73 <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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74
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75 <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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76 <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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77
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78 <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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79
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80 <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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81 <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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82
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83 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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84 </inputs>
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85 <outputs>
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86 <data format="qza" label="${tool.name} on ${on_string}: trimmed-sequences.qza" name="otrimmedsequences"/>
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87 </outputs>
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88 <help><![CDATA[
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89 Find and remove adapters in demultiplexed single-end sequences.
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90 ----------------------------------------------------------------
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91
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92 Search demultiplexed single-end sequences for adapters and remove them. The
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93 parameter descriptions in this method are adapted from the official
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94 cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
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95 for complete details.
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96
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97 Parameters
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98 ----------
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99 demultiplexed_sequences : SampleData[SequencesWithQuality]
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100 The single-end sequences to be trimmed.
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101 adapter : List[Str], optional
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102 Sequence of an adapter ligated to the 3' end. The adapter and any
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103 subsequent bases are trimmed. If a `$` is appended, the adapter is only
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104 found if it is at the end of the read. If your sequence of interest is
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105 "framed" by a 5' and a 3' adapter, use this parameter to define a
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106 "linked" primer - see https://cutadapt.readthedocs.io for complete
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107 details.
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108 front : List[Str], optional
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109 Sequence of an adapter ligated to the 5' end. The adapter and any
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110 preceding bases are trimmed. Partial matches at the 5' end are allowed.
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111 If a `^` character is prepended, the adapter is only found if it is at
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112 the beginning of the read.
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113 anywhere : List[Str], optional
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114 Sequence of an adapter that may be ligated to the 5' or 3' end. Both
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115 types of matches as described under `adapter` and `front` are allowed.
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116 If the first base of the read is part of the match, the behavior is as
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117 with `front`, otherwise as with `adapter`. This option is mostly for
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118 rescuing failed library preparations - do not use if you know which end
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119 your adapter was ligated to.
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120 error_rate : Float % Range(0, 1, inclusive_end=True), optional
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121 Maximum allowed error rate.
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122 indels : Bool, optional
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123 Allow insertions or deletions of bases when matching adapters.
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124 times : Int % Range(1, None), optional
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125 Remove multiple occurrences of an adapter if it is repeated, up to
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126 `times` times.
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127 overlap : Int % Range(1, None), optional
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128 Require at least `overlap` bases of overlap between read and adapter
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129 for an adapter to be found.
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130 match_read_wildcards : Bool, optional
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131 Interpret IUPAC wildcards (e.g., N) in reads.
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132 match_adapter_wildcards : Bool, optional
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133 Interpret IUPAC wildcards (e.g., N) in adapters.
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134
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135 Returns
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136 -------
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137 trimmed_sequences : SampleData[SequencesWithQuality]
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138 The resulting trimmed sequences.
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139 ]]>
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140 </help>
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141 </tool>
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