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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"
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3 version="2020.8">
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4 <description>BLAST+ consensus taxonomy classifier</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime feature-classifier classify-consensus-blast
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10
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11 --i-query=$iquery
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12
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13 --i-reference-reads=$ireferencereads
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14
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15 --i-reference-taxonomy=$ireferencetaxonomy
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16
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17 --p-maxaccepts=$pmaxaccepts
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18
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19 --p-perc-identity=$ppercidentity
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20
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21 --p-query-cov=$pquerycov
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22
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23 #if str($pstrand) != 'None':
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24 --p-strand=$pstrand
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25 #end if
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26
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27 --p-evalue=$pevalue
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28
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29 --p-min-consensus=$pminconsensus
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30
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31 #if str($punassignablelabel):
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32 --p-unassignable-label=$punassignablelabel
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33 #end if
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34 --o-classification=oclassification
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35
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36 #if str($examples) != 'None':
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37 --examples=$examples
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38 #end if
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39
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40 ;
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41 cp oclassification.qza $oclassification
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42
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43 ]]></command>
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44 <inputs>
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45 <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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46 <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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47 <param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] reference taxonomy labels. [required]" name="ireferencetaxonomy" optional="False" type="data" />
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48 <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]" min="1" name="pmaxaccepts" optional="True" type="integer" value="10" />
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49 <param exclude_max="False" 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]" max="1.0" min="0.0" name="ppercidentity" optional="True" type="float" value="0.8" />
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50 <param exclude_max="False" 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]" max="1.0" min="0.0" name="pquerycov" optional="True" type="float" value="0.8" />
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51 <param label="--p-strand: " name="pstrand" optional="True" type="select">
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52 <option selected="True" value="None">Selection is Optional</option>
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53 <option value="both">both</option>
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54 <option value="plus">plus</option>
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55 <option value="minus">minus</option>
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56 </param>
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57 <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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58 <param exclude_max="False" exclude_min="True" 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]" max="1.0" min="0.5" name="pminconsensus" optional="True" type="float" value="0.51" />
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59 <param label="--p-unassignable-label: TEXT [default: \'Unassigned\']" name="punassignablelabel" optional="False" type="text" value="\'Unassigned\'" />
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60 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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61
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62 </inputs>
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63
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64 <outputs>
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65 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification" />
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66
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67 </outputs>
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68
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69 <help><![CDATA[
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70 BLAST+ consensus taxonomy classifier
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71 ###############################################################
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72
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73 Assign taxonomy to query sequences using BLAST+. Performs BLAST+ local
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74 alignment between query and reference_reads, then assigns consensus
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75 taxonomy to each query sequence from among maxaccepts hits, min_consensus
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76 of which share that taxonomic assignment. Note that maxaccepts selects the
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77 first N hits with > perc_identity similarity to query, not the top N
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78 matches. For top N hits, use classify-consensus-vsearch.
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79
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80 Parameters
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81 ----------
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82 query : FeatureData[Sequence]
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83 Sequences to classify taxonomically.
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84 reference_reads : FeatureData[Sequence]
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85 reference sequences.
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86 reference_taxonomy : FeatureData[Taxonomy]
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87 reference taxonomy labels.
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88 maxaccepts : Int % Range(1, None), optional
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89 Maximum number of hits to keep for each query. Must be in range [1,
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90 infinity]. BLAST will choose the first N hits in the reference database
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91 that exceed perc_identity similarity to query.
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92 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
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93 Reject match if percent identity to query is lower. Must be in range
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94 [0.0, 1.0].
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95 query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional
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96 Reject match if query alignment coverage per high-scoring pair is
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97 lower. Note: this uses blastn's qcov_hsp_perc parameter, and may not
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98 behave identically to the query_cov parameter used by classify-
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99 consensus-vsearch. Must be in range [0.0, 1.0].
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100 strand : Str % Choices('both', 'plus', 'minus'), optional
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101 Align against reference sequences in forward ("plus"), reverse
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102 ("minus"), or both directions ("both").
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103 evalue : Float, optional
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104 BLAST expectation value (E) threshold for saving hits.
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105 min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional
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106 Minimum fraction of assignments must match top hit to be accepted as
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107 consensus assignment. Must be in range (0.5, 1.0].
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108 unassignable_label : Str, optional
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109
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110 Returns
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111 -------
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112 classification : FeatureData[Taxonomy]
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113 Taxonomy classifications of query sequences.
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114 ]]></help>
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115 <macros>
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116 <import>qiime_citation.xml</import>
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117 </macros>
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118 <expand macro="qiime_citation"/>
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119 </tool> |
