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comparison qiime2/qiime_feature-classifier_classify-consensus-vsearch.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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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" version="2019.4">
3 <description> - VSEARCH consensus taxonomy classifier</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime feature-classifier classify-consensus-vsearch
9
10 --i-query=$iquery
11 --i-reference-reads=$ireferencereads
12
13
14 #if str( $id_to_taxonomy_fp.selector ) == 'history'
15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
16 --i-reference-taxonomy '$tax'
17 #else:
18 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
19 --i-reference-taxonomy '$tax'
20 #end if
21
22
23 #if $pmaxaccepts:
24 --p-maxaccepts=$pmaxaccepts
25 #end if
26
27 #if $ppercidentity:
28 --p-perc-identity=$ppercidentity
29 #end if
30
31 #if $pquerycov:
32 --p-query-cov=$pquerycov
33 #end if
34
35 #if str($pstrand) != 'None':
36 --p-strand=$pstrand
37 #end if
38
39 #if $pminconsensus:
40 --p-min-consensus=$pminconsensus
41 #end if
42
43 #if str($punassignablelabel):
44 --p-unassignable-label="$punassignablelabel"
45 #end if
46
47 #set $pthreads = '${GALAXY_SLOTS:-4}'
48 #if str($pthreads):
49 --p-threads="$pthreads"
50 #end if
51
52 --o-classification=oclassification
53 ;
54 cp oclassification.qza $oclassification
55 ]]></command>
56 <inputs>
57 <param format="qza,no_unzip.zip" label="--i-query: ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically. [required]" name="iquery" optional="False" type="data"/>
58 <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] reference sequences. [required]" name="ireferencereads" optional="False" type="data"/>
59
60 <conditional name="id_to_taxonomy_fp" optional="True">
61 <param name="selector" type="select" label="Reference taxonomy to query">
62 <option value="cached">Public databases</option>
63 <option value="history">Databases from your history</option>
64 </param>
65 <when value="cached">
66 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
67 <options from_data_table="qiime_taxonomy" />
68 </param>
69 </when>
70 <when value="history">
71 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
72 </when>
73 </conditional>
74
75 <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"/>
76 <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"/>
77 <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"/>
78 <param label="--p-strand: Align against reference sequences in forward ('plus') or both directions ('both'). [default: 'both']" name="pstrand" optional="True" type="select">
79 <option value="None">Selection is Optional</option>
80 <option selected="True" value="both">both</option>
81 <option value="plus">plus</option>
82 </param>
83 <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"/>
84 <param label="--p-unassignable-label: TEXT [default: 'Unassigned']" name="punassignablelabel" optional="True" type="text" value="'Unassigned'"/>
85 </inputs>
86 <outputs>
87 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
88 </outputs>
89 <help><![CDATA[
90 VSEARCH consensus taxonomy classifier
91 #####################################
92
93 Assign taxonomy to query sequences using VSEARCH. Performs VSEARCH global
94 alignment between query and reference_reads, then assigns consensus
95 taxonomy to each query sequence from among maxaccepts top hits,
96 min_consensus of which share that taxonomic assignment. Unlike classify-
97 consensus-blast, this method searches the entire reference database before
98 choosing the top N hits, not the first N hits.
99
100 Parameters
101 ----------
102 query : FeatureData[Sequence]
103 Sequences to classify taxonomically.
104 reference_reads : FeatureData[Sequence]
105 reference sequences.
106 reference_taxonomy : FeatureData[Taxonomy]
107 reference taxonomy labels.
108 maxaccepts : Int % Range(0, None), optional
109 Maximum number of hits to keep for each query. Set to 0 to keep all
110 hits > perc_identity similarity. Must be in range [0, infinity].
111 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
112 Reject match if percent identity to query is lower. Must be in range
113 [0.0, 1.0].
114 query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional
115 Reject match if query alignment coverage per high-scoring pair is
116 lower. Must be in range [0.0, 1.0].
117 strand : Str % Choices('both', 'plus'), optional
118 Align against reference sequences in forward ("plus") or both
119 directions ("both").
120 min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional
121 Minimum fraction of assignments must match top hit to be accepted as
122 consensus assignment. Must be in range (0.5, 1.0].
123 unassignable_label : Str, optional
124 \
125
126 Returns
127 -------
128 classification : FeatureData[Taxonomy]
129 The resulting taxonomy classifications.
130 ]]></help>
131 <macros>
132 <import>qiime_citation.xml</import>
133 </macros>
134 <expand macro="qiime_citation"/>
135 </tool>