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