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comparison qiime2-2020.8/qiime_vsearch_cluster-features-closed-reference.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_vsearch_cluster-features-closed-reference" name="qiime vsearch cluster-features-closed-reference"
3 version="2020.8">
4 <description> Closed-reference clustering of features.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime vsearch cluster-features-closed-reference
10
11 --i-sequences=$isequences
12
13 --i-table=$itable
14
15 --i-reference-sequences=$ireferencesequences
16
17 --p-perc-identity=$ppercidentity
18
19 #if str($pstrand) != 'None':
20 --p-strand=$pstrand
21 #end if
22
23 --p-threads=$pthreads
24
25 --o-clustered-table=oclusteredtable
26
27 --o-clustered-sequences=oclusteredsequences
28
29 --o-unmatched-sequences=ounmatchedsequences
30
31 #if str($examples) != 'None':
32 --examples=$examples
33 #end if
34
35 ;
36 cp ounmatchedsequences.qza $ounmatchedsequences
37
38 ]]></command>
39 <inputs>
40 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table. [required]" name="isequences" optional="False" type="data" />
41 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to be clustered. [required]" name="itable" optional="False" type="data" />
42 <param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] The sequences to use as cluster centroids. [required]" name="ireferencesequences" optional="False" type="data" />
43 <param label="--p-perc-identity: PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True) The percent identity at which clustering should be performed. This parameter maps to vsearch\'s --id parameter. [required]" name="ppercidentity" optional="False" type="text" />
44 <param label="--p-strand: " name="pstrand" optional="True" type="select">
45 <option selected="True" value="None">Selection is Optional</option>
46 <option value="plus">plus</option>
47 <option value="both">both</option>
48 </param>
49 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
50
51 </inputs>
52
53 <outputs>
54 <data format="qza" label="${tool.name} on ${on_string}: clusteredtable.qza" name="oclusteredtable" />
55 <data format="qza" label="${tool.name} on ${on_string}: clusteredsequences.qza" name="oclusteredsequences" />
56 <data format="qza" label="${tool.name} on ${on_string}: unmatchedsequences.qza" name="ounmatchedsequences" />
57
58 </outputs>
59
60 <help><![CDATA[
61 Closed-reference clustering of features.
62 ###############################################################
63
64 Given a feature table and the associated feature sequences, cluster the
65 features against a reference database based on user-specified percent
66 identity threshold of their sequences. This is not a general-purpose
67 closed-reference clustering method, but rather is intended to be used for
68 clustering the results of quality-filtering/dereplication methods, such as
69 DADA2, or for re-clustering a FeatureTable at a lower percent identity than
70 it was originally clustered at. When a group of features in the input table
71 are clustered into a single feature, the frequency of that single feature
72 in a given sample is the sum of the frequencies of the features that were
73 clustered in that sample. Feature identifiers will be inherited from the
74 centroid feature of each cluster. See the vsearch documentation for details
75 on how sequence clustering is performed.
76
77 Parameters
78 ----------
79 sequences : FeatureData[Sequence]
80 The sequences corresponding to the features in table.
81 table : FeatureTable[Frequency]
82 The feature table to be clustered.
83 reference_sequences : FeatureData[Sequence]
84 The sequences to use as cluster centroids.
85 perc_identity : Float % Range(0, 1, inclusive_start=False, inclusive_end=True)
86 The percent identity at which clustering should be performed. This
87 parameter maps to vsearch's --id parameter.
88 strand : Str % Choices('plus', 'both'), optional
89 Search plus (i.e., forward) or both (i.e., forward and reverse
90 complement) strands.
91 threads : Int % Range(0, 256, inclusive_end=True), optional
92 The number of threads to use for computation. Passing 0 will launch one
93 thread per CPU core.
94
95 Returns
96 -------
97 clustered_table : FeatureTable[Frequency]
98 The table following clustering of features.
99 clustered_sequences : FeatureData[Sequence]
100 The sequences representing clustered features, relabeled by the
101 reference IDs.
102 unmatched_sequences : FeatureData[Sequence]
103 The sequences which failed to match any reference sequences. This
104 output maps to vsearch's --notmatched parameter.
105 ]]></help>
106 <macros>
107 <import>qiime_citation.xml</import>
108 </macros>
109 <expand macro="qiime_citation"/>
110 </tool>