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comparison qiime2-2020.8/qiime_feature-classifier_classify-consensus-blast.xml @ 20:d93d8888f0b0 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
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19:6c48f8d82424 20:d93d8888f0b0
1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-classifier_classify-consensus-blast" name="qiime feature-classifier classify-consensus-blast"
3 version="2020.8">
4 <description>BLAST+ 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-blast
10
11 --i-query=$iquery
12
13 --i-reference-reads=$ireferencereads
14
15 --i-reference-taxonomy=$ireferencetaxonomy
16
17 --p-maxaccepts=$pmaxaccepts
18
19 --p-perc-identity=$ppercidentity
20
21 --p-query-cov=$pquerycov
22
23 #if str($pstrand) != 'None':
24 --p-strand=$pstrand
25 #end if
26
27 --p-evalue=$pevalue
28
29 --p-min-consensus=$pminconsensus
30
31 #if str($punassignablelabel):
32 --p-unassignable-label=$punassignablelabel
33 #end if
34 --o-classification=oclassification
35
36 #if str($examples) != 'None':
37 --examples=$examples
38 #end if
39
40 ;
41 cp oclassification.qza $oclassification
42
43 ]]></command>
44 <inputs>
45 <param format="qza,no_unzip.zip" label="--i-query: ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically. [required]" name="iquery" optional="False" type="data" />
46 <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] reference sequences. [required]" name="ireferencereads" optional="False" type="data" />
47 <param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] reference taxonomy labels. [required]" name="ireferencetaxonomy" optional="False" type="data" />
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" />
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" />
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" />
51 <param label="--p-strand: " name="pstrand" optional="True" type="select">
52 <option selected="True" value="None">Selection is Optional</option>
53 <option value="both">both</option>
54 <option value="plus">plus</option>
55 <option value="minus">minus</option>
56 </param>
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" />
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" />
59 <param label="--p-unassignable-label: TEXT [default: \'Unassigned\']" name="punassignablelabel" optional="False" type="text" value="\'Unassigned\'" />
60 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
61
62 </inputs>
63
64 <outputs>
65 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification" />
66
67 </outputs>
68
69 <help><![CDATA[
70 BLAST+ consensus taxonomy classifier
71 ###############################################################
72
73 Assign taxonomy to query sequences using BLAST+. Performs BLAST+ local
74 alignment between query and reference_reads, then assigns consensus
75 taxonomy to each query sequence from among maxaccepts hits, min_consensus
76 of which share that taxonomic assignment. Note that maxaccepts selects the
77 first N hits with > perc_identity similarity to query, not the top N
78 matches. For top N hits, use classify-consensus-vsearch.
79
80 Parameters
81 ----------
82 query : FeatureData[Sequence]
83 Sequences to classify taxonomically.
84 reference_reads : FeatureData[Sequence]
85 reference sequences.
86 reference_taxonomy : FeatureData[Taxonomy]
87 reference taxonomy labels.
88 maxaccepts : Int % Range(1, None), optional
89 Maximum number of hits to keep for each query. Must be in range [1,
90 infinity]. BLAST will choose the first N hits in the reference database
91 that exceed perc_identity similarity to query.
92 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
93 Reject match if percent identity to query is lower. Must be in range
94 [0.0, 1.0].
95 query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional
96 Reject match if query alignment coverage per high-scoring pair is
97 lower. Note: this uses blastn's qcov_hsp_perc parameter, and may not
98 behave identically to the query_cov parameter used by classify-
99 consensus-vsearch. Must be in range [0.0, 1.0].
100 strand : Str % Choices('both', 'plus', 'minus'), optional
101 Align against reference sequences in forward ("plus"), reverse
102 ("minus"), or both directions ("both").
103 evalue : Float, optional
104 BLAST expectation value (E) threshold for saving hits.
105 min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional
106 Minimum fraction of assignments must match top hit to be accepted as
107 consensus assignment. Must be in range (0.5, 1.0].
108 unassignable_label : Str, optional
109
110 Returns
111 -------
112 classification : FeatureData[Taxonomy]
113 Taxonomy classifications of query sequences.
114 ]]></help>
115 <macros>
116 <import>qiime_citation.xml</import>
117 </macros>
118 <expand macro="qiime_citation"/>
119 </tool>