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comparison qiime2/qiime_feature-classifier_classify-consensus-vsearch.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-classifier_classify-consensus-vsearch" name="qiime feature-classifier classify-consensus-vsearch"
3 version="2020.8">
4 <description>VSEARCH-based consensus taxonomy classifier</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime feature-classifier classify-consensus-vsearch
10
11 --i-query=$iquery
12
13 --i-reference-reads=$ireferencereads
14
15 --i-reference-taxonomy=$ireferencetaxonomy
16
17 #if str($pmaxaccepts) != 'None':
18 --p-maxaccepts=$pmaxaccepts
19 #end if
20
21 --p-perc-identity=$ppercidentity
22
23 --p-query-cov=$pquerycov
24
25 #if str($pstrand) != 'None':
26 --p-strand=$pstrand
27 #end if
28
29 --p-min-consensus=$pminconsensus
30
31 #if str($punassignablelabel):
32 --p-unassignable-label=$punassignablelabel
33 #end if
34 #if $psearchexact:
35 --p-search-exact
36 #end if
37
38 #if $ptophitsonly:
39 --p-top-hits-only
40 #end if
41
42 #if str($pmaxhits) != 'None':
43 --p-maxhits=$pmaxhits
44 #end if
45
46 #if str($pmaxrejects) != 'None':
47 --p-maxrejects=$pmaxrejects
48 #end if
49
50 #if $pnooutputnohits:
51 --p-no-output-no-hits
52 #end if
53
54 --p-weak-id=$pweakid
55
56 --p-threads=$pthreads
57
58 --o-classification=oclassification
59
60 #if str($examples) != 'None':
61 --examples=$examples
62 #end if
63
64 ;
65 cp oclassification.qza $oclassification
66
67 ]]></command>
68 <inputs>
69 <param format="qza,no_unzip.zip" label="--i-query: ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically. [required]" name="iquery" optional="False" type="data" />
70 <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] reference sequences. [required]" name="ireferencereads" optional="False" type="data" />
71 <param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] reference taxonomy labels. [required]" name="ireferencetaxonomy" optional="False" type="data" />
72 <param label="--p-maxaccepts: " name="pmaxaccepts" optional="True" type="select">
73 <option selected="True" value="None">Selection is Optional</option>
74 <option value="Int % Range(1">Int % Range(1</option>
75 <option value="None">None</option>
76 </param>
77 <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. [default: 0.8]" max="1.0" min="0.0" name="ppercidentity" optional="True" type="float" value="0.8" />
78 <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. [default: 0.8]" max="1.0" min="0.0" name="pquerycov" optional="True" type="float" value="0.8" />
79 <param label="--p-strand: " name="pstrand" optional="True" type="select">
80 <option selected="True" value="None">Selection is Optional</option>
81 <option value="both">both</option>
82 <option value="plus">plus</option>
83 </param>
84 <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. [default: 0.51]" max="1.0" min="0.5" name="pminconsensus" optional="True" type="float" value="0.51" />
85 <param label="--p-unassignable-label: TEXT [default: \'Unassigned\']" name="punassignablelabel" optional="False" type="text" value="\'Unassigned\'" />
86 <param label="--p-search-exact: --p-search-exact: / --p-no-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" />
87 <param label="--p-top-hits-only: --p-top-hits-only: / --p-no-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" />
88 <param label="--p-maxhits: " name="pmaxhits" optional="True" type="select">
89 <option selected="True" value="None">Selection is Optional</option>
90 <option value="Int % Range(1">Int % Range(1</option>
91 <option value="None">None</option>
92 </param>
93 <param label="--p-maxrejects: " name="pmaxrejects" optional="True" type="select">
94 <option selected="True" value="None">Selection is Optional</option>
95 <option value="Int % Range(1">Int % Range(1</option>
96 <option value="None">None</option>
97 </param>
98 <param label="--p-no-output-no-hits: Do not report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs. [default: True]" name="pnooutputnohits" selected="False" type="boolean" />
99 <param exclude_max="False" label="--p-weak-id: PROPORTION Range(0.0, 1.0, inclusive_end=True) Show hits with percentage of identity of at least N, without terminating the search. A normal search stops as soon as enough hits are found (as defined by maxaccepts, maxrejects, and perc-identity). As weak-id reports weak hits that are not deduced from maxaccepts, high perc-identity values can be used, hence preserving both speed and sensitivity. Logically, weak-id must be smaller than the value indicated by perc-identity, otherwise this option will be ignored. [default: 0.0]" max="1.0" min="0.0" name="pweakid" optional="True" type="float" value="0.0" />
100 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
101
102 </inputs>
103
104 <outputs>
105 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification" />
106
107 </outputs>
108
109 <help><![CDATA[
110 VSEARCH-based consensus taxonomy classifier
111 ###############################################################
112
113 Assign taxonomy to query sequences using VSEARCH. Performs VSEARCH global
114 alignment between query and reference_reads, then assigns consensus
115 taxonomy to each query sequence from among maxaccepts top hits,
116 min_consensus of which share that taxonomic assignment. Unlike classify-
117 consensus-blast, this method searches the entire reference database before
118 choosing the top N hits, not the first N hits.
119
120 Parameters
121 ----------
122 query : FeatureData[Sequence]
123 Sequences to classify taxonomically.
124 reference_reads : FeatureData[Sequence]
125 reference sequences.
126 reference_taxonomy : FeatureData[Taxonomy]
127 reference taxonomy labels.
128 maxaccepts : Int % Range(1, None) | Str % Choices('all'), optional
129 Maximum number of hits to keep for each query. Set to "all" to keep all
130 hits > perc_identity similarity. Note that if strand=both, maxaccepts
131 will keep N hits for each direction (if searches in the opposite
132 direction yield results that exceed the minimum perc_identity). In
133 those cases use maxhits to control the total number of hits returned.
134 This option works in pair with maxrejects. The search process sorts
135 target sequences by decreasing number of k-mers they have in common
136 with the query sequence, using that information as a proxy for sequence
137 similarity. After pairwise alignments, if the first target sequence
138 passes the acceptation criteria, it is accepted as best hit and the
139 search process stops for that query. If maxaccepts is set to a higher
140 value, more hits are accepted. If maxaccepts and maxrejects are both
141 set to "all", the complete database is searched.
142 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
143 Reject match if percent identity to query is lower.
144 query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional
145 Reject match if query alignment coverage per high-scoring pair is
146 lower.
147 strand : Str % Choices('both', 'plus'), optional
148 Align against reference sequences in forward ("plus") or both
149 directions ("both").
150 min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional
151 Minimum fraction of assignments must match top hit to be accepted as
152 consensus assignment.
153 unassignable_label : Str, optional
154 search_exact : Bool, optional
155 Search for exact full-length matches to the query sequences. Only 100%
156 exact matches are reported and this command is much faster than the
157 default. If True, the perc_identity and query_cov settings are ignored.
158 Note: query and reference reads must be trimmed to the exact same DNA
159 locus (e.g., primer site) because only exact matches will be reported.
160 top_hits_only : Bool, optional
161 Only the top hits between the query and reference sequence sets are
162 reported. For each query, the top hit is the one presenting the highest
163 percentage of identity. Multiple equally scored top hits will be used
164 for consensus taxonomic assignment if maxaccepts is greater than 1.
165 maxhits : Int % Range(1, None) | Str % Choices('all'), optional
166 Maximum number of hits to show once the search is terminated.
167 maxrejects : Int % Range(1, None) | Str % Choices('all'), optional
168 Maximum number of non-matching target sequences to consider before
169 stopping the search. This option works in pair with maxaccepts (see
170 maxaccepts description for details).
171 output_no_hits : Bool, optional
172 Report both matching and non-matching queries. WARNING: always use the
173 default setting for this option unless if you know what you are doing!
174 If you set this option to False, your sequences and feature table will
175 need to be filtered to exclude unclassified sequences, otherwise you
176 may run into errors downstream from missing feature IDs.
177 weak_id : Float % Range(0.0, 1.0, inclusive_end=True), optional
178 Show hits with percentage of identity of at least N, without
179 terminating the search. A normal search stops as soon as enough hits
180 are found (as defined by maxaccepts, maxrejects, and perc_identity). As
181 weak_id reports weak hits that are not deduced from maxaccepts, high
182 perc_identity values can be used, hence preserving both speed and
183 sensitivity. Logically, weak_id must be smaller than the value
184 indicated by perc_identity, otherwise this option will be ignored.
185 threads : Int % Range(1, None), optional
186 Number of threads to use for job parallelization.
187
188 Returns
189 -------
190 classification : FeatureData[Taxonomy]
191 The resulting taxonomy classifications.
192 ]]></help>
193 <macros>
194 <import>qiime_citation.xml</import>
195 </macros>
196 <expand macro="qiime_citation"/>
197 </tool>