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comparison qiime2/qiime_feature-classifier_classify-consensus-vsearch.xml @ 9:f190567fe3f6 draft

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author florianbegusch
date Wed, 14 Aug 2019 15:12:48 -0400
parents de4c22a52df4
children a0a8d77a991c
comparison
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8:d66c7509e8f9 9:f190567fe3f6
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-classifier_classify-consensus-vsearch" name="qiime feature-classifier classify-consensus-vsearch" version="2019.4"> 2 <tool id="qiime_feature-classifier_classify-consensus-vsearch" name="qiime feature-classifier classify-consensus-vsearch" version="2019.7">
3 <description> - VSEARCH consensus taxonomy classifier</description> 3 <description> - VSEARCH consensus taxonomy classifier</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement> 5 <requirement type="package" version="2019.7">qiime2</requirement>
6 </requirements> 6 </requirements>
7 <command><![CDATA[ 7 <command><![CDATA[
8 qiime feature-classifier classify-consensus-vsearch 8 qiime feature-classifier classify-consensus-vsearch
9 9
10 --i-query=$iquery 10 --i-query=$iquery
15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp 15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
16 --i-reference-taxonomy '$tax' 16 --i-reference-taxonomy '$tax'
17 #else: 17 #else:
18 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path 18 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
19 --i-reference-taxonomy '$tax' 19 --i-reference-taxonomy '$tax'
20 #end if
21
22
23 #if $psearchexact:
24 --p-search-exact
25 #end if
26
27
28 #if $ptophitsonly:
29 --p-top-hits-only
20 #end if 30 #end if
21 31
22 32
23 33
24 #if str($pmaxaccepts): 34 #if str($pmaxaccepts):
61 #if str($pthreads): 71 #if str($pthreads):
62 --p-threads="$pthreads" 72 --p-threads="$pthreads"
63 #end if 73 #end if
64 74
65 --o-classification=oclassification 75 --o-classification=oclassification
76
66 ; 77 ;
67 cp oclassification.qza $oclassification 78 cp oclassification.qza $oclassification
68 ]]></command> 79 ]]></command>
69 <inputs> 80 <inputs>
70 <param format="qza,no_unzip.zip" label="--i-query: ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically. [required]" name="iquery" optional="False" type="data"/> 81 <param format="qza,no_unzip.zip" label="--i-query: ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically. [required]" name="iquery" optional="False" type="data"/>
93 <option selected="True" value="both">both</option> 104 <option selected="True" value="both">both</option>
94 <option value="plus">plus</option> 105 <option value="plus">plus</option>
95 </param> 106 </param>
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"/> 107 <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"/>
97 <param label="--p-unassignable-label: TEXT [default: 'Unassigned']" name="punassignablelabel" optional="True" type="text" value="Unassigned"/> 108 <param label="--p-unassignable-label: TEXT [default: 'Unassigned']" name="punassignablelabel" optional="True" type="text" value="Unassigned"/>
109
110
111 <param label="--p-search-exact: Search for exact full-length matches to the query sequences. Only 100% exact matches are reported and this command is much faster than the default. If True, the perc-identity and query-cov settings are ignored. Note: query and reference reads must be trimmed to the exact same DNA locus (e.g., primer site) because only exact matches will be reported. [default: False]" name="psearchexact" selected="False" type="boolean"/>
112 <param label="--p-top-hits-only: Only the top hits between the query and reference sequence sets are reported. For each query, the top hit is the one presenting the highest percentage of identity. Multiple equally scored top hits will be used for consensus taxonomic assignment if maxaccepts is greater than 1. [default: False]" name="ptophitsonly" selected="False" type="boolean"/>
113
98 </inputs> 114 </inputs>
99 <outputs> 115 <outputs>
100 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/> 116 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
101 </outputs> 117 </outputs>
102 <help><![CDATA[ 118 <help><![CDATA[
103 VSEARCH consensus taxonomy classifier 119 VSEARCH-based consensus taxonomy classifier
104 #####################################
105 120
106 Assign taxonomy to query sequences using VSEARCH. Performs VSEARCH global 121 Assign taxonomy to query sequences using VSEARCH. Performs VSEARCH global
107 alignment between query and reference_reads, then assigns consensus 122 alignment between query and reference_reads, then assigns consensus
108 taxonomy to each query sequence from among maxaccepts top hits, 123 taxonomy to each query sequence from among maxaccepts top hits,
109 min_consensus of which share that taxonomic assignment. Unlike classify- 124 min_consensus of which share that taxonomic assignment. Unlike classify-
116 Sequences to classify taxonomically. 131 Sequences to classify taxonomically.
117 reference_reads : FeatureData[Sequence] 132 reference_reads : FeatureData[Sequence]
118 reference sequences. 133 reference sequences.
119 reference_taxonomy : FeatureData[Taxonomy] 134 reference_taxonomy : FeatureData[Taxonomy]
120 reference taxonomy labels. 135 reference taxonomy labels.
121 maxaccepts : Int % Range(0, None), optional 136 maxaccepts : Int % Range(1, None) | Str % Choices('all'), optional
122 Maximum number of hits to keep for each query. Set to 0 to keep all 137 Maximum number of hits to keep for each query. Set to "all" to keep all
123 hits > perc_identity similarity. Must be in range [0, infinity]. 138 hits > perc_identity similarity.
124 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional 139 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
125 Reject match if percent identity to query is lower. Must be in range 140 Reject match if percent identity to query is lower.
126 [0.0, 1.0].
127 query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional 141 query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional
128 Reject match if query alignment coverage per high-scoring pair is 142 Reject match if query alignment coverage per high-scoring pair is
129 lower. Must be in range [0.0, 1.0]. 143 lower.
130 strand : Str % Choices('both', 'plus'), optional 144 strand : Str % Choices('both', 'plus'), optional
131 Align against reference sequences in forward ("plus") or both 145 Align against reference sequences in forward ("plus") or both
132 directions ("both"). 146 directions ("both").
133 min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional 147 min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional
134 Minimum fraction of assignments must match top hit to be accepted as 148 Minimum fraction of assignments must match top hit to be accepted as
135 consensus assignment. Must be in range (0.5, 1.0]. 149 consensus assignment.
136 unassignable_label : Str, optional 150 unassignable_label : Str, optional
137 \ 151 search_exact : Bool, optional
152 Search for exact full-length matches to the query sequences. Only 100%
153 exact matches are reported and this command is much faster than the
154 default. If True, the perc_identity and query_cov settings are ignored.
155 Note: query and reference reads must be trimmed to the exact same DNA
156 locus (e.g., primer site) because only exact matches will be reported.
157 top_hits_only : Bool, optional
158 Only the top hits between the query and reference sequence sets are
159 reported. For each query, the top hit is the one presenting the highest
160 percentage of identity. Multiple equally scored top hits will be used
161 for consensus taxonomic assignment if maxaccepts is greater than 1.
162 threads : Int % Range(1, None), optional
163 Number of threads to use for job parallelization.
138 164
139 Returns 165 Returns
140 ------- 166 -------
141 classification : FeatureData[Taxonomy] 167 classification : FeatureData[Taxonomy]
142 The resulting taxonomy classifications. 168 The resulting taxonomy classifications.