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comparison qiime_vsearch_cluster-features-de-novo.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_vsearch_cluster-features-de-novo" name="qiime vsearch cluster-features-de-novo" version="2018.4">
3 <description> - De novo 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-de-novo --p-perc-identity="$ppercidentity" --i-table=$itable --i-sequences=$isequences
10
11 #if str($cmdconfig) != 'None':
12 --cmd-config=$cmdconfig
13 #end if
14 --o-clustered-table=oclusteredtable --o-clustered-sequences=oclusteredsequences
15 #set $pthreads = '${GALAXY_SLOTS:-4}'
16
17 #if str($pthreads):
18 --p-threads="$pthreads"
19 #end if
20
21 ;
22 cp oclusteredtable.qza $oclusteredtable;
23 cp oclusteredsequences.qza $oclusteredsequences
24 ]]>
25 </command>
26 <inputs>
27 <param format="qza,no_unzip.zip" label="--i-sequences: FeatureData[Sequence] The sequences corresponding to the features in table. [required]" name="isequences" optional="False" type="data"/>
28 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table to be clustered. [required]" name="itable" optional="False" type="data"/>
29
30 <param label="--p-perc-identity: The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter. [required]" name="ppercidentity" optional="False" type="text"/>
31
32 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
33 </inputs>
34 <outputs>
35 <data format="qza" label="${tool.name} on ${on_string}: clustered-table.qza" name="oclusteredtable"/>
36 <data format="qza" label="${tool.name} on ${on_string}: clustered-sequences.qza" name="oclusteredsequences"/>
37 </outputs>
38 <help>
39 <![CDATA[
40 De novo clustering of features.
41 --------------------------------
42
43 Given a feature table and the associated feature sequences, cluster the
44 features based on user-specified percent identity threshold of their
45 sequences. This is not a general-purpose de novo clustering method, but
46 rather is intended to be used for clustering the results of quality-
47 filtering/dereplication methods, such as DADA2, or for re-clustering a
48 FeatureTable at a lower percent identity than it was originally clustered
49 at. When a group of features in the input table are clustered into a single
50 feature, the frequency of that single feature in a given sample is the sum
51 of the frequencies of the features that were clustered in that sample.
52 Feature identifiers and sequences will be inherited from the centroid
53 feature of each cluster. See the vsearch documentation for details on how
54 sequence clustering is performed.
55
56 Parameters
57 ----------
58 sequences : FeatureData[Sequence]
59 The sequences corresponding to the features in table.
60 table : FeatureTable[Frequency]
61 The feature table to be clustered.
62 perc_identity : Float % Range(0, 1, inclusive_start=False, inclusive_end=True)
63 The percent identity at which clustering should be performed. This
64 parameter maps to vsearch's --id parameter.
65
66 Returns
67 -------
68 clustered_table : FeatureTable[Frequency]
69 The table following clustering of features.
70 clustered_sequences : FeatureData[Sequence]
71 Sequences representing clustered features.
72 ]]>
73 </help>
74 </tool>