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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"
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3 version="2020.8">
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4 <description>Find and remove adapters in demultiplexed paired-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-paired
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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 str($padapterf):
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16 --p-adapter-f=$padapterf
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17 #end if
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18 #if str($pfrontf):
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19 --p-front-f=$pfrontf
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20 #end if
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21 #if '__ob__' in str($panywheref):
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22 #set $panywheref_temp = $panywheref.replace('__ob__', '[')
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23 #set $panywheref = $panywheref_temp
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24 #end if
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25 #if '__cb__' in str($panywheref):
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26 #set $panywheref_temp = $panywheref.replace('__cb__', ']')
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27 #set $panywheref = $panywheref_temp
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28 #end if
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29 #if 'X' in str($panywheref):
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30 #set $panywheref_temp = $panywheref.replace('X', '\\')
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31 #set $panywheref = $panywheref_temp
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32 #end if
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33 #if '__sq__' in str($panywheref):
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34 #set $panywheref_temp = $panywheref.replace('__sq__', "'")
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35 #set $panywheref = $panywheref_temp
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36 #end if
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37 #if '__db__' in str($panywheref):
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38 #set $panywheref_temp = $panywheref.replace('__db__', '"')
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39 #set $panywheref = $panywheref_temp
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40 #end if
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41
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42 #if str($panywheref):
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43 --p-anywhere-f=$panywheref
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44 #end if
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45
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46 #if str($padapterr):
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47 --p-adapter-r=$padapterr
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48 #end if
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49 #if str($pfrontr):
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50 --p-front-r=$pfrontr
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51 #end if
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52 #if '__ob__' in str($panywherer):
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53 #set $panywherer_temp = $panywherer.replace('__ob__', '[')
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54 #set $panywherer = $panywherer_temp
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55 #end if
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56 #if '__cb__' in str($panywherer):
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57 #set $panywherer_temp = $panywherer.replace('__cb__', ']')
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58 #set $panywherer = $panywherer_temp
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59 #end if
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60 #if 'X' in str($panywherer):
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61 #set $panywherer_temp = $panywherer.replace('X', '\\')
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62 #set $panywherer = $panywherer_temp
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63 #end if
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64 #if '__sq__' in str($panywherer):
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65 #set $panywherer_temp = $panywherer.replace('__sq__', "'")
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66 #set $panywherer = $panywherer_temp
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67 #end if
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68 #if '__db__' in str($panywherer):
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69 #set $panywherer_temp = $panywherer.replace('__db__', '"')
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70 #set $panywherer = $panywherer_temp
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71 #end if
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72
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73 #if str($panywherer):
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74 --p-anywhere-r=$panywherer
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75 #end if
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76
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77 --p-error-rate=$perrorrate
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78
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79 #if $pnoindels:
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80 --p-no-indels
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81 #end if
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82
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83 --p-times=$ptimes
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84
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85 --p-overlap=$poverlap
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86
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87 #if $pmatchreadwildcards:
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88 --p-match-read-wildcards
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89 #end if
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90
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91 #if $pnomatchadapterwildcards:
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92 --p-no-match-adapter-wildcards
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93 #end if
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94
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95 --p-minimum-length=$pminimumlength
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96
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97 #if $pdiscarduntrimmed:
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98 --p-discard-untrimmed
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99 #end if
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100
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101 --o-trimmed-sequences=otrimmedsequences
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102
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103 #if str($examples) != 'None':
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104 --examples=$examples
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105 #end if
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106
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107 ;
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108 cp otrimmedsequences.qza $otrimmedsequences
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109
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110 ]]></command>
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111 <inputs>
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112 <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[PairedEndSequencesWithQuality] The paired-end sequences to be trimmed. [required]" name="idemultiplexedsequences" optional="False" type="data" />
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113 <param label="--p-adapter-f: TEXT... Sequence of an adapter ligated to the 3\' end. The List[Str] adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. 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="False" type="text" value="False" />
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114 <param label="--p-front-f: 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. Search in forward read. [optional]" name="pfrontf" optional="False" type="text" />
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115 <param label="--p-anywhere-f: TEXT... Sequence of an adapter that may be ligated to the List[Str] 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="False" type="text" />
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116 <param label="--p-adapter-r: 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. 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="False" type="text" value="False" />
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117 <param label="--p-front-r: 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. Search in reverse read. [optional]" name="pfrontr" optional="False" type="text" />
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118 <param label="--p-anywhere-r: TEXT... Sequence of an adapter that may be ligated to the List[Str] 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="False" type="text" />
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119 <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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120 <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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121 <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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122 <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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123 <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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124 <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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125 <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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126 <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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127 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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128
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129 </inputs>
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130
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131 <outputs>
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132 <data format="qza" label="${tool.name} on ${on_string}: trimmedsequences.qza" name="otrimmedsequences" />
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133
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134 </outputs>
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135
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136 <help><![CDATA[
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137 Find and remove adapters in demultiplexed paired-end sequences.
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138 ###############################################################
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139
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140 Search demultiplexed paired-end sequences for adapters and remove them. The
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141 parameter descriptions in this method are adapted from the official
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142 cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
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143 for complete details.
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144
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145 Parameters
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146 ----------
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147 demultiplexed_sequences : SampleData[PairedEndSequencesWithQuality]
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148 The paired-end sequences to be trimmed.
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149 cores : Int % Range(1, None), optional
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150 Number of CPU cores to use.
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151 adapter_f : List[Str], optional
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152 Sequence of an adapter ligated to the 3' end. The adapter and any
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153 subsequent bases are trimmed. If a `$` is appended, the adapter is only
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154 found if it is at the end of the read. Search in forward read. If your
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155 sequence of interest is "framed" by a 5' and a 3' adapter, use this
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156 parameter to define a "linked" primer - see
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157 https://cutadapt.readthedocs.io for complete details.
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158 front_f : List[Str], optional
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159 Sequence of an adapter ligated to the 5' end. The adapter and any
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160 preceding bases are trimmed. Partial matches at the 5' end are allowed.
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161 If a `^` character is prepended, the adapter is only found if it is at
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162 the beginning of the read. Search in forward read.
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163 anywhere_f : List[Str], optional
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164 Sequence of an adapter that may be ligated to the 5' or 3' end. Both
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165 types of matches as described under `adapter` and `front` are allowed.
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166 If the first base of the read is part of the match, the behavior is as
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167 with `front`, otherwise as with `adapter`. This option is mostly for
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168 rescuing failed library preparations - do not use if you know which end
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169 your adapter was ligated to. Search in forward read.
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170 adapter_r : List[Str], optional
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171 Sequence of an adapter ligated to the 3' end. The adapter and any
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172 subsequent bases are trimmed. If a `$` is appended, the adapter is only
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173 found if it is at the end of the read. Search in reverse read. If your
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174 sequence of interest is "framed" by a 5' and a 3' adapter, use this
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175 parameter to define a "linked" primer - see
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176 https://cutadapt.readthedocs.io for complete details.
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177 front_r : List[Str], optional
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178 Sequence of an adapter ligated to the 5' end. The adapter and any
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179 preceding bases are trimmed. Partial matches at the 5' end are allowed.
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180 If a `^` character is prepended, the adapter is only found if it is at
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181 the beginning of the read. Search in reverse read.
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182 anywhere_r : List[Str], optional
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183 Sequence of an adapter that may be ligated to the 5' or 3' end. Both
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184 types of matches as described under `adapter` and `front` are allowed.
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185 If the first base of the read is part of the match, the behavior is as
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186 with `front`, otherwise as with `adapter`. This option is mostly for
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187 rescuing failed library preparations - do not use if you know which end
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188 your adapter was ligated to. Search in reverse read.
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189 error_rate : Float % Range(0, 1, inclusive_end=True), optional
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190 Maximum allowed error rate.
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191 indels : Bool, optional
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192 Allow insertions or deletions of bases when matching adapters.
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193 times : Int % Range(1, None), optional
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194 Remove multiple occurrences of an adapter if it is repeated, up to
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195 `times` times.
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196 overlap : Int % Range(1, None), optional
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197 Require at least `overlap` bases of overlap between read and adapter
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198 for an adapter to be found.
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199 match_read_wildcards : Bool, optional
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200 Interpret IUPAC wildcards (e.g., N) in reads.
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201 match_adapter_wildcards : Bool, optional
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202 Interpret IUPAC wildcards (e.g., N) in adapters.
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203 minimum_length : Int % Range(1, None), optional
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204 Discard reads shorter than specified value. Note, the cutadapt default
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205 of 0 has been overridden, because that value produces empty sequence
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206 records.
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207 discard_untrimmed : Bool, optional
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208 Discard reads in which no adapter was found.
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209
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210 Returns
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211 -------
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212 trimmed_sequences : SampleData[PairedEndSequencesWithQuality]
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213 The resulting trimmed sequences.
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214 ]]></help>
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215 <macros>
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216 <import>qiime_citation.xml</import>
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217 </macros>
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218 <expand macro="qiime_citation"/>
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219 </tool> |
