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1 <?xml version="1.0" ?>
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2 <tool id="qiime_feature-classifier_classify-consensus-vsearch" name="qiime feature-classifier classify-consensus-vsearch" version="2019.4">
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3 <description> - VSEARCH consensus taxonomy classifier</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 feature-classifier classify-consensus-vsearch
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9
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10 --i-query=$iquery
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11 --i-reference-reads=$ireferencereads
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12
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13
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14 #if str( $id_to_taxonomy_fp.selector ) == 'history'
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15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
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16 --i-reference-taxonomy '$tax'
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17 #else:
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18 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
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19 --i-reference-taxonomy '$tax'
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20 #end if
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21
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22
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4
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23
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0
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24 #if $pmaxaccepts:
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25 --p-maxaccepts=$pmaxaccepts
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26 #end if
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27
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28 #if $ppercidentity:
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29 --p-perc-identity=$ppercidentity
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30 #end if
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31
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32 #if $pquerycov:
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33 --p-query-cov=$pquerycov
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34 #end if
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35
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36 #if str($pstrand) != 'None':
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37 --p-strand=$pstrand
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38 #end if
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39
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40 #if $pminconsensus:
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41 --p-min-consensus=$pminconsensus
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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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48 #if '__sq__' in str($punassignablelabel):
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49 #set $punassignablelabel_temp = $punassignablelabel.replace('__sq__', "'")
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50 #set $punassignablelabel = $punassignablelabel_temp
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51 #end if
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52
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0
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53 #if str($punassignablelabel):
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54 --p-unassignable-label="$punassignablelabel"
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55 #end if
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56
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4
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57
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58
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59
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0
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60 #set $pthreads = '${GALAXY_SLOTS:-4}'
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61 #if str($pthreads):
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62 --p-threads="$pthreads"
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63 #end if
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64
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65 --o-classification=oclassification
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66 ;
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67 cp oclassification.qza $oclassification
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68 ]]></command>
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69 <inputs>
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70 <param format="qza,no_unzip.zip" label="--i-query: ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically. [required]" name="iquery" optional="False" type="data"/>
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71 <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] reference sequences. [required]" name="ireferencereads" optional="False" type="data"/>
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72
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73 <conditional name="id_to_taxonomy_fp" optional="True">
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74 <param name="selector" type="select" label="Reference taxonomy to query">
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75 <option value="cached">Public databases</option>
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76 <option value="history">Databases from your history</option>
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77 </param>
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78 <when value="cached">
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79 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
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80 <options from_data_table="qiime_taxonomy" />
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81 </param>
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82 </when>
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83 <when value="history">
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84 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
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85 </when>
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86 </conditional>
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87
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88 <param label="--p-maxaccepts: INTEGER Maximum number of hits to keep for each query. Set Range(0, None) to 0 to keep all hits > perc-identity similarity. Must be in range [0, infinity]. [default: 10]" name="pmaxaccepts" optional="True" type="integer" min="0" value="10"/>
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89 <param label="--p-perc-identity: PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to query is lower. Must be in range [0.0, 1.0]. [default: 0.8]" name="ppercidentity" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.8"/>
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90 <param label="--p-query-cov: PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if query alignment coverage per high-scoring pair is lower. Must be in range [0.0, 1.0]. [default: 0.8]" name="pquerycov" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.8"/>
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91 <param label="--p-strand: Align against reference sequences in forward ('plus') or both directions ('both'). [default: 'both']" name="pstrand" optional="True" type="select">
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92 <option value="None">Selection is Optional</option>
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93 <option selected="True" value="both">both</option>
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94 <option value="plus">plus</option>
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95 </param>
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96 <param label="--p-min-consensus: NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True) Minimum fraction of assignments must match top hit to be accepted as consensus assignment. Must be in range (0.5, 1.0]. [default: 0.51]" name="pminconsensus" optional="True" type="float" min="0.5" max="1" exclude_min="True" exclude_max="False" value="0.51"/>
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4
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97 <param label="--p-unassignable-label: TEXT [default: 'Unassigned']" name="punassignablelabel" optional="True" type="text" value="Unassigned"/>
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0
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98 </inputs>
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99 <outputs>
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100 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
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101 </outputs>
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102 <help><![CDATA[
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103 VSEARCH consensus taxonomy classifier
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104 #####################################
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105
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106 Assign taxonomy to query sequences using VSEARCH. Performs VSEARCH global
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107 alignment between query and reference_reads, then assigns consensus
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108 taxonomy to each query sequence from among maxaccepts top hits,
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109 min_consensus of which share that taxonomic assignment. Unlike classify-
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110 consensus-blast, this method searches the entire reference database before
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111 choosing the top N hits, not the first N hits.
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112
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113 Parameters
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114 ----------
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115 query : FeatureData[Sequence]
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116 Sequences to classify taxonomically.
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117 reference_reads : FeatureData[Sequence]
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118 reference sequences.
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119 reference_taxonomy : FeatureData[Taxonomy]
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120 reference taxonomy labels.
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121 maxaccepts : Int % Range(0, None), optional
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122 Maximum number of hits to keep for each query. Set to 0 to keep all
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123 hits > perc_identity similarity. Must be in range [0, infinity].
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124 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
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125 Reject match if percent identity to query is lower. Must be in range
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126 [0.0, 1.0].
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127 query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional
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128 Reject match if query alignment coverage per high-scoring pair is
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129 lower. Must be in range [0.0, 1.0].
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130 strand : Str % Choices('both', 'plus'), optional
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131 Align against reference sequences in forward ("plus") or both
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132 directions ("both").
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133 min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional
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134 Minimum fraction of assignments must match top hit to be accepted as
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135 consensus assignment. Must be in range (0.5, 1.0].
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136 unassignable_label : Str, optional
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137 \
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138
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139 Returns
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140 -------
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141 classification : FeatureData[Taxonomy]
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142 The resulting taxonomy classifications.
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143 ]]></help>
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144 <macros>
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145 <import>qiime_citation.xml</import>
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146 </macros>
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147 <expand macro="qiime_citation"/>
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148 </tool>
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