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comparison qiime_feature-classifier_classify-consensus-blast.xml @ 0:09b7bcb72fa7 draft

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author florianbegusch
date Thu, 24 May 2018 02:11:44 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-classifier_classify-consensus-blast" name="qiime feature-classifier classify-consensus-blast" version="2018.4">
3 <description>- BLAST+ consensus taxonomy classifier</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime feature-classifier classify-consensus-blast --i-query=$iquery
9
10 #if str( $id_to_taxonomy_fp.selector ) == 'history'
11 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
12 --i-reference-taxonomy '$tax'
13 #else:
14 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
15 --i-reference-taxonomy '$tax'
16 #end if
17
18 --i-reference-reads=$ireferencereads
19 #if $ppercidentity:
20 --p-perc-identity=$ppercidentity
21 #end if
22
23 #if str($cmdconfig) != 'None':
24 --cmd-config=$cmdconfig
25 #end if
26
27 #if $pminconsensus:
28 --p-min-consensus=$pminconsensus
29 #end if
30
31 #if str($pstrand) != 'None':
32 --p-strand=$pstrand
33 #end if
34
35 #if str($punassignablelabel):
36 --p-unassignable-label="$punassignablelabel"
37 #end if
38
39 #if $pevalue:
40 --p-evalue=$pevalue
41 #end if
42 --o-classification=oclassification
43 #if $pmaxaccepts:
44 --p-maxaccepts=$pmaxaccepts
45 #end if
46 ;
47 cp oclassification.qza $oclassification;
48 ]]></command>
49 <inputs>
50 <param format="qza,no_unzip.zip" label="--i-query: FeatureData[Sequence] Sequences to classify taxonomically. [required]" name="iquery" optional="False" type="data"/>
51 <param format="qza,no_unzip.zip" label="--i-reference-reads: FeatureData[Sequence] reference sequences. [required]" name="ireferencereads" optional="False" type="data"/>
52
53 <conditional name="id_to_taxonomy_fp" optional="True">
54 <param name="selector" type="select" label="Reference taxonomy to query">
55 <option value="cached">Public databases</option>
56 <option value="history">Databases from your history</option>
57 </param>
58 <when value="cached">
59 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
60 <options from_data_table="qiime_taxonomy" />
61 </param>
62 </when>
63 <when value="history">
64 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
65 </when>
66 </conditional>
67
68 <param label="--p-maxaccepts: Maximum number of hits to keep for each query. Must be in range [0, infinity]. [default: 10]" name="pmaxaccepts" optional="True" type="integer" value="10"/>
69 <param label="--p-perc-identity: 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" value="0.8"/>
70 <param label="--p-strand: [both|plus|minus] Align against reference sequences in forward ('plus'), reverse ('minus'), or both directions ('both'). [default: both]" name="pstrand" optional="True" type="select">
71 <option selected="True" value="both">both</option>
72 <option value="plus">plus</option>
73 <option value="minus">minus</option>
74 </param>
75 <param label="--p-evalue: BLAST expectation value (E) threshold for saving hits. [default: 0.001]" name="pevalue" optional="True" type="float" value="0.001"/>
76 <param label="--p-min-consensus: 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" value="0.51"/>
77 <param label="--p-unassignable-label: [default: Unassigned]" name="punassignablelabel" optional="True" type="text" value="Unassigned"/>
78 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
79 </inputs>
80 <outputs>
81 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
82 </outputs>
83 <help><![CDATA[
84 BLAST+ consensus taxonomy classifier
85 ------------------------------------
86
87 Assign taxonomy to query sequences using BLAST+. Performs BLAST+ local
88 alignment between query and reference_reads, then assigns consensus
89 taxonomy to each query sequence from among maxaccepts top hits,
90 min_consensus of which share that taxonomic assignment.
91
92 Parameters
93 ----------
94 query : FeatureData[Sequence]
95 Sequences to classify taxonomically.
96 reference_reads : FeatureData[Sequence]
97 reference sequences.
98 reference_taxonomy : FeatureData[Taxonomy]
99 reference taxonomy labels.
100 maxaccepts : Int % Range(1, None), optional
101 Maximum number of hits to keep for each query. Must be in range [0,
102 infinity].
103 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
104 Reject match if percent identity to query is lower. Must be in range
105 [0.0, 1.0].
106 strand : Str % Choices({'both', 'minus', 'plus'}), optional
107 Align against reference sequences in forward ("plus"), reverse
108 ("minus"), or both directions ("both").
109 evalue : Float, optional
110 BLAST expectation value (E) threshold for saving hits.
111 min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional
112 Minimum fraction of assignments must match top hit to be accepted as
113 consensus assignment. Must be in range (0.5, 1.0].
114 unassignable_label : Str, optional
115 \
116
117 Returns
118 -------
119 classification : FeatureData[Taxonomy]
120 Taxonomy classifications of query sequences.
121 ]]>
122 </help>
123 </tool>