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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="2019.4">
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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="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime cutadapt trim-paired
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9
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10 --i-demultiplexed-sequences=$idemultiplexedsequences
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11
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12 #set $pcores = '${GALAXY_SLOTS:-4}'
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13 #if str($pcores):
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14 --p-cores=$pcores
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15 #end if
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16
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17 #if str($padapterf):
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18 --p-adapter-f="$padapterf"
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19 #end if
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20
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21 #if str($pfrontf):
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22 --p-front-f="$pfrontf"
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23 #end if
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24
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25 #if '__sq__' in str($panywheref):
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26 #set $panywheref_temp = $panywheref.replace('__sq__', "'")
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27 #set $panywheref = $panywheref_temp
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28 #end if
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29
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30 #if str($panywheref):
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31 --p-anywhere-f="$panywheref"
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32 #end if
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33
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34
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35 #if str($padapterr):
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36 --p-adapter-r="$padapterr"
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37 #end if
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38
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39 #if str($pfrontr):
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40 --p-front-r="$pfrontr"
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41 #end if
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42
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43 #if '__sq__' in str($panywherer):
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44 #set $panywherer_temp = $panywherer.replace('__sq__', "'")
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45 #set $panywherer = $panywherer_temp
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46 #end if
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47
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48 #if str($panywherer):
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49 --p-anywhere-r="$panywherer"
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50 #end if
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51
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52 #if $perrorrate:
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53 --p-error-rate=$perrorrate
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54 #end if
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55
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56 #if $pnoindels:
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57 --p-no-indels
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58 #end if
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59
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60 #if $ptimes:
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61 --p-times=$ptimes
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62 #end if
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63
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64 #if $poverlap:
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65 --p-overlap=$poverlap
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66 #end if
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67
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68 #if $pmatchreadwildcards:
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69 --p-match-read-wildcards
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70 #end if
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71
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72 #if $pnomatchadapterwildcards:
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73 --p-no-match-adapter-wildcards
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74 #end if
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75
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76 #if $pminimumlength:
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77 --p-minimum-length=$pminimumlength
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78 #end if
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79
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80 #if $pdiscarduntrimmed:
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81 --p-discard-untrimmed
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82 #end if
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83
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84 --o-trimmed-sequences=otrimmedsequences
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85 ;
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86
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87 cp otrimmedsequences.qza $otrimmedsequences
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88 ]]></command>
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89 <inputs>
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90 <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[PairedEndSequencesWithQuality] The paired-end sequences to be trimmed. [required]" name="idemultiplexedsequences" optional="False" type="data"/>
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91 <param label="--p-adapter-f: TEXT... Sequence of an adapter ligated to the 3' end. The List[Str] adapter and any subsequent bases are trimmed. If a `$` 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="True" type="text"/>
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92 <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="True" type="text"/>
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93 <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="True" type="text"/>
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94 <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="True" type="text"/>
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95 <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="True" type="text"/>
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96 <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="True" type="text"/>
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97 <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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98 <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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99 <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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100 <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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101 <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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102 <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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103 <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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104 <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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105 </inputs>
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106 <outputs>
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107 <data format="qza" label="${tool.name} on ${on_string}: trimmedsequences.qza" name="otrimmedsequences"/>
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108 </outputs>
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109 <help><![CDATA[
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110 Find and remove adapters in demultiplexed paired-end sequences.
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111 ###############################################################
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112
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113 Search demultiplexed paired-end sequences for adapters and remove them. The
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114 parameter descriptions in this method are adapted from the official
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115 cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
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116 for complete details.
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117
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118 Parameters
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119 ----------
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120 demultiplexed_sequences : SampleData[PairedEndSequencesWithQuality]
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121 The paired-end sequences to be trimmed.
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122 adapter_f : List[Str], optional
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123 Sequence of an adapter ligated to the 3' end. The adapter and any
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124 subsequent bases are trimmed. If a `$` is appended, the adapter is only
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125 found if it is at the end of the read. Search in forward read. If your
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126 sequence of interest is "framed" by a 5' and a 3' adapter, use this
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127 parameter to define a "linked" primer - see
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128 https://cutadapt.readthedocs.io for complete details.
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129 front_f : List[Str], optional
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130 Sequence of an adapter ligated to the 5' end. The adapter and any
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131 preceding bases are trimmed. Partial matches at the 5' end are allowed.
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132 If a `^` character is prepended, the adapter is only found if it is at
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133 the beginning of the read. Search in forward read.
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134 anywhere_f : List[Str], optional
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135 Sequence of an adapter that may be ligated to the 5' or 3' end. Both
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136 types of matches as described under `adapter` and `front` are allowed.
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137 If the first base of the read is part of the match, the behavior is as
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138 with `front`, otherwise as with `adapter`. This option is mostly for
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139 rescuing failed library preparations - do not use if you know which end
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140 your adapter was ligated to. Search in forward read.
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141 adapter_r : List[Str], optional
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142 Sequence of an adapter ligated to the 3' end. The adapter and any
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143 subsequent bases are trimmed. If a `$` is appended, the adapter is only
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144 found if it is at the end of the read. Search in reverse read. If your
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145 sequence of interest is "framed" by a 5' and a 3' adapter, use this
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146 parameter to define a "linked" primer - see
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147 https://cutadapt.readthedocs.io for complete details.
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148 front_r : List[Str], optional
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149 Sequence of an adapter ligated to the 5' end. The adapter and any
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150 preceding bases are trimmed. Partial matches at the 5' end are allowed.
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151 If a `^` character is prepended, the adapter is only found if it is at
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152 the beginning of the read. Search in reverse read.
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153 anywhere_r : List[Str], optional
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154 Sequence of an adapter that may be ligated to the 5' or 3' end. Both
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155 types of matches as described under `adapter` and `front` are allowed.
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156 If the first base of the read is part of the match, the behavior is as
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157 with `front`, otherwise as with `adapter`. This option is mostly for
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158 rescuing failed library preparations - do not use if you know which end
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159 your adapter was ligated to. Search in reverse read.
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160 error_rate : Float % Range(0, 1, inclusive_end=True), optional
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161 Maximum allowed error rate.
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162 indels : Bool, optional
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163 Allow insertions or deletions of bases when matching adapters.
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164 times : Int % Range(1, None), optional
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165 Remove multiple occurrences of an adapter if it is repeated, up to
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166 `times` times.
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167 overlap : Int % Range(1, None), optional
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168 Require at least `overlap` bases of overlap between read and adapter
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169 for an adapter to be found.
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170 match_read_wildcards : Bool, optional
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171 Interpret IUPAC wildcards (e.g., N) in reads.
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172 match_adapter_wildcards : Bool, optional
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173 Interpret IUPAC wildcards (e.g., N) in adapters.
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174 minimum_length : Int % Range(1, None), optional
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175 Discard reads shorter than specified value. Note, the cutadapt default
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176 of 0 has been overridden, because that value produces empty sequence
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177 records.
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178 discard_untrimmed : Bool, optional
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179 Discard reads in which no adapter was found.
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180
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181 Returns
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182 -------
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183 trimmed_sequences : SampleData[PairedEndSequencesWithQuality]
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184 The resulting trimmed sequences.
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185 ]]></help>
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186 <macros>
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187 <import>qiime_citation.xml</import>
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188 </macros>
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189 <expand macro="qiime_citation"/>
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190 </tool>
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