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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="2019.7">
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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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9
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5 <requirement type="package" version="2019.7">qiime2</requirement>
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0
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6 </requirements>
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7 <command><![CDATA[
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8 qiime cutadapt trim-single
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9 --i-demultiplexed-sequences=$idemultiplexedsequences
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10
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11 #set $pcores = '${GALAXY_SLOTS:-4}'
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12 #if str($pcores):
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13 --p-cores=$pcores
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14 #end if
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15
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4
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16
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17 #if '__sq__' in str($padapter):
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18 #set $padapter_temp = $padapter.replace('__sq__', "'")
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19 #set $padapter = $padapter_temp
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20 #end if
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21
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22 #if 'X' in str($padapter):
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23 #set $padapter_temp = $padapter.replace('X', "$")
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24 #set $padapter = $padapter_temp
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25 #end if
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26
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0
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27 #if str($padapter):
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28 --p-adapter="$padapter"
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29 #end if
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30
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4
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31
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32
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33
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34
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35 #if '__sq__' in str($pfront):
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36 #set $pfront_temp = $pfront.replace('__sq__', "'")
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37 #set $pfront = $pfront_temp
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38 #end if
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39
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0
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40 #if str($pfront):
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41 --p-front="$pfront"
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42 #end if
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43
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4
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44
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45
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46
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47
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0
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48 #if '__sq__' in str($panywhere):
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49 #set $panywhere_temp = $panywhere.replace('__sq__', "'")
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50 #set $panywhere = $panywhere_temp
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51 #end if
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52
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53 #if str($panywhere):
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54 --p-anywhere="$panywhere"
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55 #end if
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56
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57
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4
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58
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59
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5
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60 #if str($perrorrate):
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0
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61 --p-error-rate=$perrorrate
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62 #end if
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63
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64 #if $pnoindels:
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65 --p-no-indels
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66 #end if
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67
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5
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68 #if str($ptimes):
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0
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69 --p-times=$ptimes
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70 #end if
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71
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5
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72 #if str($poverlap):
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0
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73 --p-overlap=$poverlap
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74 #end if
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75
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76 #if $pmatchreadwildcards:
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77 --p-match-read-wildcards
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78 #end if
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79
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80 #if $pnomatchadapterwildcards:
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81 --p-no-match-adapter-wildcards
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82 #end if
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83
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5
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84 #if str($pminimumlength):
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0
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85 --p-minimum-length=$pminimumlength
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86 #end if
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87
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88 #if $pdiscarduntrimmed:
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89 --p-discard-untrimmed
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90 #end if
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91
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92 --o-trimmed-sequences=otrimmedsequences
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93
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94 ;
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95 cp otrimmedsequences.qza $otrimmedsequences
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96 ]]></command>
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97 <inputs>
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98 <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[SequencesWithQuality] The single-end sequences to be trimmed. [required]" name="idemultiplexedsequences" optional="False" type="data"/>
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99 <param label="--p-adapter: TEXT... Sequence of an adapter ligated to the 3' end. The List[Str] adapter and any subsequent bases are trimmed. If a `$` 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" optional="True" type="text"/>
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100 <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="True" type="text"/>
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101 <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="True" type="text"/>
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102
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103 <param label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) Maximum allowed error rate. [default: 0.1]" name="perrorrate" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.1"/>
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104 <param label="--p-no-indels: Do not allow insertions or deletions of bases when matching adapters. [default: False]" name="pnoindels" selected="False" type="boolean"/>
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105 <param label="--p-times: INTEGER Remove multiple occurrences of an adapter if it is Range(1, None) repeated, up to `times` times. [default: 1]" name="ptimes" optional="True" type="integer" min="1" value="1"/>
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106 <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]" name="poverlap" optional="True" type="integer" min="1" value="3"/>
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107 <param label="--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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108 <param label="--p-no-match-adapter-wildcards: Do not interpret IUPAC wildcards (e.g., N) in adapters. [default: False]" name="pnomatchadapterwildcards" selected="False" type="boolean"/>
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109 <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]" name="pminimumlength" optional="True" type="integer" min="1" value="1"/>
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110 <param label="--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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111 </inputs>
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112 <outputs>
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113 <data format="qza" label="${tool.name} on ${on_string}: trimmedsequences.qza" name="otrimmedsequences"/>
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114 </outputs>
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115 <help><![CDATA[
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116 Find and remove adapters in demultiplexed single-end sequences.
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117 ###############################################################
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118
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119 Search demultiplexed single-end sequences for adapters and remove them. The
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120 parameter descriptions in this method are adapted from the official
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121 cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
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122 for complete details.
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123
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124 Parameters
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125 ----------
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126 demultiplexed_sequences : SampleData[SequencesWithQuality]
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127 The single-end sequences to be trimmed.
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128 adapter : List[Str], optional
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129 Sequence of an adapter ligated to the 3' end. The adapter and any
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130 subsequent bases are trimmed. If a `$` is appended, the adapter is only
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131 found if it is at the end of the read. If your sequence of interest is
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132 "framed" by a 5' and a 3' adapter, use this parameter to define a
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133 "linked" primer - see https://cutadapt.readthedocs.io for complete
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134 details.
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135 front : List[Str], optional
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136 Sequence of an adapter ligated to the 5' end. The adapter and any
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137 preceding bases are trimmed. Partial matches at the 5' end are allowed.
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138 If a `^` character is prepended, the adapter is only found if it is at
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139 the beginning of the read.
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140 anywhere : List[Str], optional
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141 Sequence of an adapter that may be ligated to the 5' or 3' end. Both
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142 types of matches as described under `adapter` and `front` are allowed.
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143 If the first base of the read is part of the match, the behavior is as
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144 with `front`, otherwise as with `adapter`. This option is mostly for
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145 rescuing failed library preparations - do not use if you know which end
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146 your adapter was ligated to.
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147 error_rate : Float % Range(0, 1, inclusive_end=True), optional
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148 Maximum allowed error rate.
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149 indels : Bool, optional
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150 Allow insertions or deletions of bases when matching adapters.
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151 times : Int % Range(1, None), optional
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152 Remove multiple occurrences of an adapter if it is repeated, up to
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153 `times` times.
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154 overlap : Int % Range(1, None), optional
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155 Require at least `overlap` bases of overlap between read and adapter
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156 for an adapter to be found.
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157 match_read_wildcards : Bool, optional
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158 Interpret IUPAC wildcards (e.g., N) in reads.
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159 match_adapter_wildcards : Bool, optional
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160 Interpret IUPAC wildcards (e.g., N) in adapters.
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161 minimum_length : Int % Range(1, None), optional
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162 Discard reads shorter than specified value. Note, the cutadapt default
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163 of 0 has been overridden, because that value produces empty sequence
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164 records.
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165 discard_untrimmed : Bool, optional
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166 Discard reads in which no adapter was found.
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167
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168 Returns
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169 -------
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170 trimmed_sequences : SampleData[SequencesWithQuality]
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171 The resulting trimmed sequences.
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172 ]]></help>
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173 <macros>
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174 <import>qiime_citation.xml</import>
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175 </macros>
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176 <expand macro="qiime_citation"/>
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177 </tool>
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