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1 <?xml version="1.0" ?>
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2 <tool id="qiime_feature-classifier_classify-consensus-blast" name="qiime feature-classifier classify-consensus-blast" version="2019.7">
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3 <description> - BLAST+ consensus taxonomy classifier</description>
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4 <requirements>
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5 <requirement type="package" version="2019.7">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-blast
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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 #if str( $id_to_taxonomy_fp.selector ) == 'history'
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14 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
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15 --i-reference-taxonomy '$tax'
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16 #else:
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17 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
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18 --i-reference-taxonomy '$tax'
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19 #end if
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20
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21
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22 #if str($pmaxaccepts):
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0
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23 --p-maxaccepts=$pmaxaccepts
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24 #end if
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25
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6
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26 #if str($ppercidentity):
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27 --p-perc-identity=$ppercidentity
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28 #end if
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29
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30 #if str($pquerycov):
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31 --p-query-cov=$pquerycov
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32 #end if
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33
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34 #if str($pstrand) != 'None':
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35 --p-strand=$pstrand
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36 #end if
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37
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38 #if str($pevalue):
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39 --p-evalue=$pevalue
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40 #end if
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41
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6
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42 #if str($pminconsensus):
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43 --p-min-consensus=$pminconsensus
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44 #end if
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45
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4
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46
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47
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48
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49
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50 #if '__sq__' in str($punassignablelabel):
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51 #set $punassignablelabel_temp = $punassignablelabel.replace('__sq__', "'")
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52 #set $punassignablelabel = $punassignablelabel_temp
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53 #end if
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54
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55 #if str($punassignablelabel):
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56 --p-unassignable-label="$punassignablelabel"
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57 #end if
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58
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4
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59
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60
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61 --o-classification=oclassification
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62 ;
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63 cp oclassification.qza $oclassification
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64 ]]></command>
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65 <inputs>
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66 <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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67 <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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68
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69 <conditional name="id_to_taxonomy_fp" optional="True">
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70 <param name="selector" type="select" label="Reference taxonomy to query">
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71 <option value="cached">Public databases</option>
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72 <option value="history">Databases from your history</option>
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73 </param>
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74 <when value="cached">
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75 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
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76 <options from_data_table="qiime_taxonomy" />
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77 </param>
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78 </when>
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79 <when value="history">
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80 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
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81 </when>
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82 </conditional>
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83
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84 <param label="--p-maxaccepts: INTEGER Maximum number of hits to keep for each query. Must Range(1, None) be in range [1, infinity]. BLAST will choose the first N hits in the reference database that exceed perc-identity similarity to query. [default: 10]" name="pmaxaccepts" optional="True" type="integer" min="1" value="10"/>
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85 <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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86 <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. Note: this uses blastn's qcov_hsp_perc parameter, and may not behave identically to the query-cov parameter used by classify-consensus-vsearch. Must be in range [0.0, 1.0]. [default: 0.8]" name="pquerycov" optional="True" min="0" max="1" exclude_max="False" type="float" value="0.8"/>
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87 <param label="--p-strand: " name="pstrand" optional="True" type="select">
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88 <option selected="True" value="None">Selection is Optional</option>
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89 <option value="both">both</option>
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90 <option value="plus">plus</option>
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91 <option value="minus">minus</option>
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92 </param>
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93 <param label="--p-evalue: NUMBER BLAST expectation value (E) threshold for saving hits. [default: 0.001]" name="pevalue" optional="True" type="float" value="0.001"/>
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94 <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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95 <param label="--p-unassignable-label: TEXT [default: 'Unassigned']" name="punassignablelabel" optional="True" type="text" value="Unassigned"/>
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96 </inputs>
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97 <outputs>
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98 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
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99 </outputs>
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100 <help><![CDATA[
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101 BLAST+ consensus taxonomy classifier
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102 ####################################
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103
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104 Assign taxonomy to query sequences using BLAST+. Performs BLAST+ local
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105 alignment between query and reference_reads, then assigns consensus
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106 taxonomy to each query sequence from among maxaccepts hits, min_consensus
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107 of which share that taxonomic assignment. Note that maxaccepts selects the
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108 first N hits with > perc_identity similarity to query, not the top N
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109 matches. For top N hits, use classify-consensus-vsearch.
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110
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111 Parameters
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112 ----------
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113 query : FeatureData[Sequence]
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114 Sequences to classify taxonomically.
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115 reference_reads : FeatureData[Sequence]
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116 reference sequences.
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117 reference_taxonomy : FeatureData[Taxonomy]
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118 reference taxonomy labels.
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119 maxaccepts : Int % Range(1, None), optional
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120 Maximum number of hits to keep for each query. Must be in range [1,
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121 infinity]. BLAST will choose the first N hits in the reference database
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122 that exceed perc_identity similarity to query.
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123 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
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124 Reject match if percent identity to query is lower. Must be in range
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125 [0.0, 1.0].
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126 query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional
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127 Reject match if query alignment coverage per high-scoring pair is
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128 lower. Note: this uses blastn's qcov_hsp_perc parameter, and may not
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129 behave identically to the query_cov parameter used by classify-
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130 consensus-vsearch. Must be in range [0.0, 1.0].
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131 strand : Str % Choices('both', 'plus', 'minus'), optional
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132 Align against reference sequences in forward ("plus"), reverse
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133 ("minus"), or both directions ("both").
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134 evalue : Float, optional
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135 BLAST expectation value (E) threshold for saving hits.
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136 min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional
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137 Minimum fraction of assignments must match top hit to be accepted as
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138 consensus assignment. Must be in range (0.5, 1.0].
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139 unassignable_label : Str, optional
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140 \
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141
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142 Returns
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143 -------
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144 classification : FeatureData[Taxonomy]
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145 Taxonomy classifications of query 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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