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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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4
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17
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18
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19 #if '__sq__' in str($padapterf):
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20 #set $padapterf_temp = $padapterf.replace('__sq__', "'")
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21 #set $padapterf = $padapterf_temp
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22 #end if
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23
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24 #if 'X' in str($padapterf):
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25 #set $padapterf_temp = $padapterf.replace('X', "$")
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26 #set $padapterf = $padapterf_temp
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27 #end if
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28
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0
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29 #if str($padapterf):
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30 --p-adapter-f="$padapterf"
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31 #end if
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32
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4
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33
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34
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35
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36 #if '__sq__' in str($pfrontf):
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37 #set $pfrontf_temp = $pfrontf.replace('__sq__', "'")
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38 #set $pfrontf = $pfrontf_temp
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39 #end if
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40
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0
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41 #if str($pfrontf):
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42 --p-front-f="$pfrontf"
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43 #end if
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44
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4
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45
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46
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47
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0
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48 #if '__sq__' in str($panywheref):
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49 #set $panywheref_temp = $panywheref.replace('__sq__', "'")
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50 #set $panywheref = $panywheref_temp
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51 #end if
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52
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53 #if str($panywheref):
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54 --p-anywhere-f="$panywheref"
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55 #end if
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56
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57
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4
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58
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59
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60
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61 #if '__sq__' in str($padapterr):
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62 #set $padapterr_temp = $padapterr.replace('__sq__', "'")
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63 #set $padapterr = $padapterr_temp
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64 #end if
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65
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66 #if 'X' in str($padapterr):
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67 #set $padapterr_temp = $padapterr.replace('X', "$")
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68 #set $padapterr = $padapterr_temp
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69 #end if
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70
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0
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71 #if str($padapterr):
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72 --p-adapter-r="$padapterr"
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73 #end if
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74
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4
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75
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76
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77 #if '__sq__' in str($pfrontr):
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78 #set $pfrontr_temp = $pfrontr.replace('__sq__', "'")
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79 #set $pfrontr = $pfrontr_temp
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80 #end if
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81
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0
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82 #if str($pfrontr):
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83 --p-front-r="$pfrontr"
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84 #end if
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85
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4
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86
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87
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0
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88 #if '__sq__' in str($panywherer):
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89 #set $panywherer_temp = $panywherer.replace('__sq__', "'")
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90 #set $panywherer = $panywherer_temp
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91 #end if
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92
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93 #if str($panywherer):
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94 --p-anywhere-r="$panywherer"
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95 #end if
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96
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4
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97
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98
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5
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99 #if str($perrorrate):
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0
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100 --p-error-rate=$perrorrate
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101 #end if
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102
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103 #if $pnoindels:
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104 --p-no-indels
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105 #end if
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106
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107 #if $ptimes:
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108 --p-times=$ptimes
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109 #end if
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110
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5
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111 #if str($poverlap):
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0
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112 --p-overlap=$poverlap
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113 #end if
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114
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115 #if $pmatchreadwildcards:
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116 --p-match-read-wildcards
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117 #end if
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118
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119 #if $pnomatchadapterwildcards:
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120 --p-no-match-adapter-wildcards
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121 #end if
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122
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123 #if $pminimumlength:
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124 --p-minimum-length=$pminimumlength
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125 #end if
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126
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127 #if $pdiscarduntrimmed:
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128 --p-discard-untrimmed
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129 #end if
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130
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131 --o-trimmed-sequences=otrimmedsequences
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132 ;
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133
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134 cp otrimmedsequences.qza $otrimmedsequences
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135 ]]></command>
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136 <inputs>
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137 <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[PairedEndSequencesWithQuality] The paired-end sequences to be trimmed. [required]" name="idemultiplexedsequences" optional="False" type="data"/>
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138 <param label="--p-adapter-f: TEXT... Sequence of an adapter ligated to the 3' end. The List[Str] adapter and any subsequent bases are trimmed. If a `$` 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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139 <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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140 <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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141 <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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142 <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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143 <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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144 <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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145 <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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146 <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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147 <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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148 <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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149 <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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150 <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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151 <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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152 </inputs>
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153 <outputs>
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154 <data format="qza" label="${tool.name} on ${on_string}: trimmedsequences.qza" name="otrimmedsequences"/>
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155 </outputs>
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156 <help><![CDATA[
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157 Find and remove adapters in demultiplexed paired-end sequences.
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158 ###############################################################
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159
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160 Search demultiplexed paired-end sequences for adapters and remove them. The
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161 parameter descriptions in this method are adapted from the official
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162 cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
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163 for complete details.
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164
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165 Parameters
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166 ----------
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167 demultiplexed_sequences : SampleData[PairedEndSequencesWithQuality]
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168 The paired-end sequences to be trimmed.
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169 adapter_f : List[Str], optional
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170 Sequence of an adapter ligated to the 3' end. The adapter and any
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171 subsequent bases are trimmed. If a `$` is appended, the adapter is only
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172 found if it is at the end of the read. Search in forward read. If your
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173 sequence of interest is "framed" by a 5' and a 3' adapter, use this
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174 parameter to define a "linked" primer - see
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175 https://cutadapt.readthedocs.io for complete details.
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176 front_f : List[Str], optional
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177 Sequence of an adapter ligated to the 5' end. The adapter and any
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178 preceding bases are trimmed. Partial matches at the 5' end are allowed.
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179 If a `^` character is prepended, the adapter is only found if it is at
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180 the beginning of the read. Search in forward read.
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181 anywhere_f : List[Str], optional
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182 Sequence of an adapter that may be ligated to the 5' or 3' end. Both
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183 types of matches as described under `adapter` and `front` are allowed.
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184 If the first base of the read is part of the match, the behavior is as
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185 with `front`, otherwise as with `adapter`. This option is mostly for
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186 rescuing failed library preparations - do not use if you know which end
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187 your adapter was ligated to. Search in forward read.
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188 adapter_r : List[Str], optional
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189 Sequence of an adapter ligated to the 3' end. The adapter and any
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190 subsequent bases are trimmed. If a `$` is appended, the adapter is only
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191 found if it is at the end of the read. Search in reverse read. If your
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192 sequence of interest is "framed" by a 5' and a 3' adapter, use this
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193 parameter to define a "linked" primer - see
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194 https://cutadapt.readthedocs.io for complete details.
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195 front_r : List[Str], optional
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196 Sequence of an adapter ligated to the 5' end. The adapter and any
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197 preceding bases are trimmed. Partial matches at the 5' end are allowed.
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198 If a `^` character is prepended, the adapter is only found if it is at
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199 the beginning of the read. Search in reverse read.
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200 anywhere_r : List[Str], optional
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201 Sequence of an adapter that may be ligated to the 5' or 3' end. Both
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202 types of matches as described under `adapter` and `front` are allowed.
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203 If the first base of the read is part of the match, the behavior is as
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204 with `front`, otherwise as with `adapter`. This option is mostly for
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205 rescuing failed library preparations - do not use if you know which end
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206 your adapter was ligated to. Search in reverse read.
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207 error_rate : Float % Range(0, 1, inclusive_end=True), optional
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208 Maximum allowed error rate.
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209 indels : Bool, optional
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210 Allow insertions or deletions of bases when matching adapters.
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211 times : Int % Range(1, None), optional
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212 Remove multiple occurrences of an adapter if it is repeated, up to
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213 `times` times.
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214 overlap : Int % Range(1, None), optional
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215 Require at least `overlap` bases of overlap between read and adapter
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216 for an adapter to be found.
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217 match_read_wildcards : Bool, optional
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218 Interpret IUPAC wildcards (e.g., N) in reads.
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219 match_adapter_wildcards : Bool, optional
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220 Interpret IUPAC wildcards (e.g., N) in adapters.
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221 minimum_length : Int % Range(1, None), optional
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222 Discard reads shorter than specified value. Note, the cutadapt default
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223 of 0 has been overridden, because that value produces empty sequence
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224 records.
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225 discard_untrimmed : Bool, optional
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226 Discard reads in which no adapter was found.
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227
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228 Returns
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229 -------
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230 trimmed_sequences : SampleData[PairedEndSequencesWithQuality]
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231 The resulting trimmed sequences.
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232 ]]></help>
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233 <macros>
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234 <import>qiime_citation.xml</import>
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235 </macros>
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236 <expand macro="qiime_citation"/>
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237 </tool>
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