|
0
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_feature-classifier_classify-consensus-blast" name="qiime feature-classifier classify-consensus-blast" version="2019.4">
|
|
|
3 <description> - BLAST+ 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-blast
|
|
|
9
|
|
|
10 --i-query=$iquery
|
|
|
11 --i-reference-reads=$ireferencereads
|
|
|
12
|
|
|
13 #if str( $id_to_taxonomy_fp.selector ) == 'history'
|
|
|
14 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
|
|
|
15 --i-reference-taxonomy '$tax'
|
|
|
16 #else:
|
|
|
17 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
|
|
|
18 --i-reference-taxonomy '$tax'
|
|
|
19 #end if
|
|
|
20
|
|
|
21
|
|
6
|
22 #if str($pmaxaccepts):
|
|
0
|
23 --p-maxaccepts=$pmaxaccepts
|
|
|
24 #end if
|
|
|
25
|
|
6
|
26 #if str($ppercidentity):
|
|
0
|
27 --p-perc-identity=$ppercidentity
|
|
|
28 #end if
|
|
|
29
|
|
6
|
30 #if str($pquerycov):
|
|
0
|
31 --p-query-cov=$pquerycov
|
|
|
32 #end if
|
|
|
33
|
|
|
34 #if str($pstrand) != 'None':
|
|
|
35 --p-strand=$pstrand
|
|
|
36 #end if
|
|
|
37
|
|
6
|
38 #if str($pevalue):
|
|
0
|
39 --p-evalue=$pevalue
|
|
|
40 #end if
|
|
|
41
|
|
6
|
42 #if str($pminconsensus):
|
|
0
|
43 --p-min-consensus=$pminconsensus
|
|
|
44 #end if
|
|
|
45
|
|
4
|
46
|
|
|
47
|
|
|
48
|
|
|
49
|
|
|
50 #if '__sq__' in str($punassignablelabel):
|
|
|
51 #set $punassignablelabel_temp = $punassignablelabel.replace('__sq__', "'")
|
|
|
52 #set $punassignablelabel = $punassignablelabel_temp
|
|
|
53 #end if
|
|
|
54
|
|
0
|
55 #if str($punassignablelabel):
|
|
|
56 --p-unassignable-label="$punassignablelabel"
|
|
|
57 #end if
|
|
|
58
|
|
4
|
59
|
|
|
60
|
|
0
|
61 --o-classification=oclassification
|
|
|
62 ;
|
|
|
63 cp oclassification.qza $oclassification
|
|
|
64 ]]></command>
|
|
|
65 <inputs>
|
|
|
66 <param format="qza,no_unzip.zip" label="--i-query: ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically. [required]" name="iquery" optional="False" type="data"/>
|
|
|
67 <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] reference sequences. [required]" name="ireferencereads" optional="False" type="data"/>
|
|
|
68
|
|
|
69 <conditional name="id_to_taxonomy_fp" optional="True">
|
|
|
70 <param name="selector" type="select" label="Reference taxonomy to query">
|
|
|
71 <option value="cached">Public databases</option>
|
|
|
72 <option value="history">Databases from your history</option>
|
|
|
73 </param>
|
|
|
74 <when value="cached">
|
|
|
75 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
|
|
|
76 <options from_data_table="qiime_taxonomy" />
|
|
|
77 </param>
|
|
|
78 </when>
|
|
|
79 <when value="history">
|
|
|
80 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
|
|
|
81 </when>
|
|
|
82 </conditional>
|
|
|
83
|
|
|
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"/>
|
|
|
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"/>
|
|
|
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"/>
|
|
|
87 <param label="--p-strand: " name="pstrand" optional="True" type="select">
|
|
|
88 <option selected="True" value="None">Selection is Optional</option>
|
|
|
89 <option value="both">both</option>
|
|
|
90 <option value="plus">plus</option>
|
|
|
91 <option value="minus">minus</option>
|
|
|
92 </param>
|
|
|
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"/>
|
|
|
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"/>
|
|
4
|
95 <param label="--p-unassignable-label: TEXT [default: 'Unassigned']" name="punassignablelabel" optional="True" type="text" value="Unassigned"/>
|
|
0
|
96 </inputs>
|
|
|
97 <outputs>
|
|
|
98 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
|
|
|
99 </outputs>
|
|
|
100 <help><![CDATA[
|
|
|
101 BLAST+ consensus taxonomy classifier
|
|
|
102 ####################################
|
|
|
103
|
|
|
104 Assign taxonomy to query sequences using BLAST+. Performs BLAST+ local
|
|
|
105 alignment between query and reference_reads, then assigns consensus
|
|
|
106 taxonomy to each query sequence from among maxaccepts hits, min_consensus
|
|
|
107 of which share that taxonomic assignment. Note that maxaccepts selects the
|
|
|
108 first N hits with > perc_identity similarity to query, not the top N
|
|
|
109 matches. For top N hits, use classify-consensus-vsearch.
|
|
|
110
|
|
|
111 Parameters
|
|
|
112 ----------
|
|
|
113 query : FeatureData[Sequence]
|
|
|
114 Sequences to classify taxonomically.
|
|
|
115 reference_reads : FeatureData[Sequence]
|
|
|
116 reference sequences.
|
|
|
117 reference_taxonomy : FeatureData[Taxonomy]
|
|
|
118 reference taxonomy labels.
|
|
|
119 maxaccepts : Int % Range(1, None), optional
|
|
|
120 Maximum number of hits to keep for each query. Must be in range [1,
|
|
|
121 infinity]. BLAST will choose the first N hits in the reference database
|
|
|
122 that exceed perc_identity similarity to query.
|
|
|
123 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
|
|
|
124 Reject match if percent identity to query is lower. Must be in range
|
|
|
125 [0.0, 1.0].
|
|
|
126 query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional
|
|
|
127 Reject match if query alignment coverage per high-scoring pair is
|
|
|
128 lower. Note: this uses blastn's qcov_hsp_perc parameter, and may not
|
|
|
129 behave identically to the query_cov parameter used by classify-
|
|
|
130 consensus-vsearch. Must be in range [0.0, 1.0].
|
|
|
131 strand : Str % Choices('both', 'plus', 'minus'), optional
|
|
|
132 Align against reference sequences in forward ("plus"), reverse
|
|
|
133 ("minus"), or both directions ("both").
|
|
|
134 evalue : Float, optional
|
|
|
135 BLAST expectation value (E) threshold for saving hits.
|
|
|
136 min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional
|
|
|
137 Minimum fraction of assignments must match top hit to be accepted as
|
|
|
138 consensus assignment. Must be in range (0.5, 1.0].
|
|
|
139 unassignable_label : Str, optional
|
|
|
140 \
|
|
|
141
|
|
|
142 Returns
|
|
|
143 -------
|
|
|
144 classification : FeatureData[Taxonomy]
|
|
|
145 Taxonomy classifications of query sequences.
|
|
|
146 ]]></help>
|
|
|
147 <macros>
|
|
|
148 <import>qiime_citation.xml</import>
|
|
|
149 </macros>
|
|
|
150 <expand macro="qiime_citation"/>
|
|
|
151 </tool>
|
