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comparison qiime2/qiime_vsearch_cluster-features-closed-reference.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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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" version="2018.4">
3 <description> - Closed-reference clustering of features.</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime vsearch cluster-features-closed-reference --p-perc-identity="$ppercidentity" --i-table=$itable --i-sequences=$isequences --i-reference-sequences=$ireferencesequences --o-unmatched-sequences=ounmatchedsequences
10
11 #if str($cmdconfig) != 'None':
12 --cmd-config=$cmdconfig
13 #end if
14 --o-clustered-table=oclusteredtable
15 #if str($pstrand) != 'None':
16 --p-strand=$pstrand
17 #end if
18 --o-clustered-sequences=oclusteredsequences
19 #set $pthreads = '${GALAXY_SLOTS:-4}'
20
21 #if str($pthreads):
22 --p-threads="$pthreads"
23 #end if
24 ;
25 cp ounmatchedsequences.qza $ounmatchedsequences;
26 cp oclusteredtable.qza $oclusteredtable;
27 cp oclusteredsequences.qza $oclusteredsequences
28 ]]>
29 </command>
30 <inputs>
31 <param format="qza,no_unzip.zip" label="--i-sequences: FeatureData[Sequence] The sequences corresponding to the features in table. [required]" name="isequences" optional="False" type="data"/>
32 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table to be clustered. [required]" name="itable" optional="False" type="data"/>
33 <param format="qza,no_unzip.zip" label="--i-reference-sequences: FeatureData[Sequence] The sequences to use as cluster centroids. [required]" name="ireferencesequences" optional="False" type="data"/>
34
35 <param label="--p-perc-identity: The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter. [required]" name="ppercidentity" optional="False" type="text"/>
36
37 <param label="--p-strand: Search plus (i.e., forward) or both (i.e.,
38 forward and reverse complement) strands.
39 [default: plus]" name="pstrand" optional="True" type="select">
40 <option selected="True" value="None">Selection is Optional</option>
41 <option value="both">both</option>
42 <option value="plus">plus</option>
43 </param>
44
45 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
46 </inputs>
47 <outputs>
48 <data format="qza" label="${tool.name} on ${on_string}: unmatched-sequences.qza" name="ounmatchedsequences"/>
49 <data format="qza" label="${tool.name} on ${on_string}: clustered-table.qza" name="oclusteredtable"/>
50 <data format="qza" label="${tool.name} on ${on_string}: clustered-sequences.qza" name="oclusteredsequences"/>
51 </outputs>
52 <help>
53 <![CDATA[
54 Closed-reference clustering of features.
55 -----------------------------------------
56
57 Given a feature table and the associated feature sequences, cluster the
58 features against a reference database based on user-specified percent
59 identity threshold of their sequences. This is not a general-purpose
60 closed-reference clustering method, but rather is intended to be used for
61 clustering the results of quality-filtering/dereplication methods, such as
62 DADA2, or for re-clustering a FeatureTable at a lower percent identity than
63 it was originally clustered at. When a group of features in the input table
64 are clustered into a single feature, the frequency of that single feature
65 in a given sample is the sum of the frequencies of the features that were
66 clustered in that sample. Feature identifiers will be inherited from the
67 centroid feature of each cluster. See the vsearch documentation for details
68 on how sequence clustering is performed.
69
70 Parameters
71 ----------
72 sequences : FeatureData[Sequence]
73 The sequences corresponding to the features in table.
74 table : FeatureTable[Frequency]
75 The feature table to be clustered.
76 reference_sequences : FeatureData[Sequence]
77 The sequences to use as cluster centroids.
78 perc_identity : Float % Range(0, 1, inclusive_start=False, inclusive_end=True)
79 The percent identity at which clustering should be performed. This
80 parameter maps to vsearch's --id parameter.
81 strand : Str % Choices({'both', 'plus'}), optional
82 Search plus (i.e., forward) or both (i.e., forward and reverse
83 complement) strands.
84
85 Returns
86 -------
87 clustered_table : FeatureTable[Frequency]
88 The table following clustering of features.
89 clustered_sequences : FeatureData[Sequence]
90 The sequences representing clustered features, relabeled by the
91 reference IDs.
92 unmatched_sequences : FeatureData[Sequence]
93 The sequences which failed to match any reference sequences. This
94 output maps to vsearch's --notmatched parameter.
95 ]]>
96 </help>
97 <macros>
98 <import>qiime_citation.xml</import>
99 </macros>
100 <expand macro="qiime_citation" />
101 </tool>