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comparison qiime_feature-classifier_classify-consensus-vsearch.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-vsearch" name="qiime feature-classifier classify-consensus-vsearch" version="2018.4">
3 <description> - VSEARCH 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-vsearch --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 --o-classification=oclassification
36
37 #if str($punassignablelabel):
38 --p-unassignable-label="$punassignablelabel"
39 #end if
40
41 #set $pthreads = '${GALAXY_SLOTS:-4}'
42 --p-threads="$pthreads"
43
44 #if $pmaxaccepts:
45 --p-maxaccepts=$pmaxaccepts
46 #end if
47 ;
48 cp oclassification.qza $oclassification;
49 ]]></command>
50 <inputs>
51 <param format="qza,no_unzip.zip" label="--i-query: FeatureData[Sequence] Sequences to classify taxonomically. [required]" name="iquery" optional="False" type="data"/>
52 <param format="qza,no_unzip.zip" label="--i-reference-reads: FeatureData[Sequence] reference sequences. [required]" name="ireferencereads" optional="False" type="data"/>
53
54 <conditional name="id_to_taxonomy_fp" optional="True">
55 <param name="selector" type="select" label="Reference taxonomy to query">
56 <option value="cached">Public databases</option>
57 <option value="history">Databases from your history</option>
58 </param>
59 <when value="cached">
60 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
61 <options from_data_table="qiime_taxonomy" />
62 </param>
63 </when>
64 <when value="history">
65 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
66 </when>
67 </conditional>
68
69 <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"/>
70 <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"/>
71 <param label="--p-strand: [both|plus] Align against reference sequences in forward ('plus') or both directions ('both'). [default: both]" name="pstrand" optional="True" type="select">
72 <option selected="True" value="both">both</option>
73 <option value="plus">plus</option>
74 </param>
75 <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"/>
76 <param label="--p-unassignable-label: [default: Unassigned]" name="punassignablelabel" optional="True" type="text" value="Unassigned"/>
77 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
78 </inputs>
79 <outputs>
80 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
81 </outputs>
82 <help><![CDATA[
83 VSEARCH consensus taxonomy classifier
84 -------------------------------------
85
86 Assign taxonomy to query sequences using VSEARCH. Performs VSEARCH global
87 alignment between query and reference_reads, then assigns consensus
88 taxonomy to each query sequence from among maxaccepts top hits,
89 min_consensus of which share that taxonomic assignment.
90
91 Parameters
92 ----------
93 query : FeatureData[Sequence]
94 Sequences to classify taxonomically.
95 reference_reads : FeatureData[Sequence]
96 reference sequences.
97 reference_taxonomy : FeatureData[Taxonomy]
98 reference taxonomy labels.
99 maxaccepts : Int % Range(1, None), optional
100 Maximum number of hits to keep for each query. Must be in range [0,
101 infinity].
102 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
103 Reject match if percent identity to query is lower. Must be in range
104 [0.0, 1.0].
105 strand : Str % Choices({'both', 'plus'}), optional
106 Align against reference sequences in forward ("plus") or both
107 directions ("both").
108 min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional
109 Minimum fraction of assignments must match top hit to be accepted as
110 consensus assignment. Must be in range (0.5, 1.0].
111 unassignable_label : Str, optional
112 \
113
114 Returns
115 -------
116 classification : FeatureData[Taxonomy]
117 The resulting taxonomy classifications.
118 ]]>
119 </help>
120 </tool>