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comparison qiime2/qiime_feature-classifier_classify-consensus-blast.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-classifier_classify-consensus-blast" name="qiime feature-classifier classify-consensus-blast" version="2019.7"> 2 <tool id="qiime_feature-classifier_classify-consensus-blast" name="qiime feature-classifier classify-consensus-blast"
3 <description> - BLAST+ consensus taxonomy classifier</description> 3 version="2020.8">
4 <requirements> 4 <description>BLAST+ consensus taxonomy classifier</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime feature-classifier classify-consensus-blast 9 qiime feature-classifier classify-consensus-blast
9 10
10 --i-query=$iquery 11 --i-query=$iquery
12
11 --i-reference-reads=$ireferencereads 13 --i-reference-reads=$ireferencereads
12 14
13 #if str( $id_to_taxonomy_fp.selector ) == 'history' 15 --i-reference-taxonomy=$ireferencetaxonomy
14 #set $tax = $id_to_taxonomy_fp.taxonomy_fp 16
15 --i-reference-taxonomy '$tax' 17 --p-maxaccepts=$pmaxaccepts
16 #else: 18
17 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path 19 --p-perc-identity=$ppercidentity
18 --i-reference-taxonomy '$tax' 20
21 --p-query-cov=$pquerycov
22
23 #if str($pstrand) != 'None':
24 --p-strand=$pstrand
19 #end if 25 #end if
20 26
27 --p-evalue=$pevalue
21 28
22 #if str($pmaxaccepts): 29 --p-min-consensus=$pminconsensus
23 --p-maxaccepts=$pmaxaccepts 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
24 #end if 38 #end if
25 39
26 #if str($ppercidentity):
27 --p-perc-identity=$ppercidentity
28 #end if
29
30 #if str($pquerycov):
31 --p-query-cov=$pquerycov
32 #end if
33
34 #if str($pstrand) != 'None':
35 --p-strand=$pstrand
36 #end if
37
38 #if str($pevalue):
39 --p-evalue=$pevalue
40 #end if
41
42 #if str($pminconsensus):
43 --p-min-consensus=$pminconsensus
44 #end if
45
46
47
48
49
50 #if '__sq__' in str($punassignablelabel):
51 #set $punassignablelabel_temp = $punassignablelabel.replace('__sq__', "'")
52 #set $punassignablelabel = $punassignablelabel_temp
53 #end if
54
55 #if str($punassignablelabel):
56 --p-unassignable-label="$punassignablelabel"
57 #end if
58
59
60
61 --o-classification=oclassification
62 ; 40 ;
63 cp oclassification.qza $oclassification 41 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 42
69 <conditional name="id_to_taxonomy_fp" optional="True"> 43 ]]></command>
70 <param name="selector" type="select" label="Reference taxonomy to query"> 44 <inputs>
71 <option value="cached">Public databases</option> 45 <param format="qza,no_unzip.zip" label="--i-query: ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically. [required]" name="iquery" optional="False" type="data" />
72 <option value="history">Databases from your history</option> 46 <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] reference sequences. [required]" name="ireferencereads" optional="False" type="data" />
73 </param> 47 <param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] reference taxonomy labels. [required]" name="ireferencetaxonomy" optional="False" type="data" />
74 <when value="cached"> 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" />
75 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True"> 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" />
76 <options from_data_table="qiime_taxonomy" /> 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" />
77 </param> 51 <param label="--p-strand: " name="pstrand" optional="True" type="select">
78 </when> 52 <option selected="True" value="None">Selection is Optional</option>
79 <when value="history"> 53 <option value="both">both</option>
80 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" /> 54 <option value="plus">plus</option>
81 </when> 55 <option value="minus">minus</option>
82 </conditional> 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>
83 63
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"/> 64 <outputs>
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"/> 65 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification" />
86 <param label="--p-query-cov: PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if query alignment coverage per high-scoring pair is lower. Note: this uses blastn's qcov_hsp_perc parameter, and may not behave identically to the query-cov parameter used by classify-consensus-vsearch. Must be in range [0.0, 1.0]. [default: 0.8]" name="pquerycov" optional="True" min="0" max="1" exclude_max="False" type="float" value="0.8"/> 66
87 <param label="--p-strand: " name="pstrand" optional="True" type="select"> 67 </outputs>
88 <option selected="True" value="None">Selection is Optional</option> 68
89 <option value="both">both</option> 69 <help><![CDATA[
90 <option value="plus">plus</option>
91 <option value="minus">minus</option>
92 </param>
93 <param label="--p-evalue: NUMBER BLAST expectation value (E) threshold for saving hits. [default: 0.001]" name="pevalue" optional="True" type="float" value="0.001"/>
94 <param label="--p-min-consensus: NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True) Minimum fraction of assignments must match top hit to be accepted as consensus assignment. Must be in range (0.5, 1.0]. [default: 0.51]" name="pminconsensus" optional="True" type="float" min="0.5" max="1" exclude_min="True" exclude_max="False" value="0.51"/>
95 <param label="--p-unassignable-label: TEXT [default: 'Unassigned']" name="punassignablelabel" optional="True" type="text" value="Unassigned"/>
96 </inputs>
97 <outputs>
98 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
99 </outputs>
100 <help><![CDATA[
101 BLAST+ consensus taxonomy classifier 70 BLAST+ consensus taxonomy classifier
102 #################################### 71 ###############################################################
103 72
104 Assign taxonomy to query sequences using BLAST+. Performs BLAST+ local 73 Assign taxonomy to query sequences using BLAST+. Performs BLAST+ local
105 alignment between query and reference_reads, then assigns consensus 74 alignment between query and reference_reads, then assigns consensus
106 taxonomy to each query sequence from among maxaccepts hits, min_consensus 75 taxonomy to each query sequence from among maxaccepts hits, min_consensus
107 of which share that taxonomic assignment. Note that maxaccepts selects the 76 of which share that taxonomic assignment. Note that maxaccepts selects the
135 BLAST expectation value (E) threshold for saving hits. 104 BLAST expectation value (E) threshold for saving hits.
136 min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional 105 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 106 Minimum fraction of assignments must match top hit to be accepted as
138 consensus assignment. Must be in range (0.5, 1.0]. 107 consensus assignment. Must be in range (0.5, 1.0].
139 unassignable_label : Str, optional 108 unassignable_label : Str, optional
140 \
141 109
142 Returns 110 Returns
143 ------- 111 -------
144 classification : FeatureData[Taxonomy] 112 classification : FeatureData[Taxonomy]
145 Taxonomy classifications of query sequences. 113 Taxonomy classifications of query sequences.
146 ]]></help> 114 ]]></help>
147 <macros> 115 <macros>
148 <import>qiime_citation.xml</import> 116 <import>qiime_citation.xml</import>
149 </macros> 117 </macros>
150 <expand macro="qiime_citation"/> 118 <expand macro="qiime_citation"/>
151 </tool> 119 </tool>