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+++ b/qiime2/qiime_vsearch_cluster-features-de-novo.xml	Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,86 @@
+<?xml version="1.0" ?>
+<tool id="qiime_vsearch_cluster-features-de-novo" name="qiime vsearch cluster-features-de-novo"
+      version="2020.8">
+  <description>De novo clustering of features.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime vsearch cluster-features-de-novo
+
+--i-sequences=$isequences
+
+--i-table=$itable
+
+--p-perc-identity=$ppercidentity
+
+--p-threads=$pthreads
+
+--o-clustered-table=oclusteredtable
+
+--o-clustered-sequences=oclusteredsequences
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp oclusteredsequences.qza $oclusteredsequences
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table.                                    [required]" name="isequences" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to be clustered.        [required]" name="itable" optional="False" type="data" />
+    <param label="--p-perc-identity: PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True)   The percent identity at which clustering should be performed. This parameter maps to vsearch\'s --id parameter.                                [required]" name="ppercidentity" optional="False" type="text" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: clusteredtable.qza" name="oclusteredtable" />
+    <data format="qza" label="${tool.name} on ${on_string}: clusteredsequences.qza" name="oclusteredsequences" />
+    
+  </outputs>
+
+  <help><![CDATA[
+De novo clustering of features.
+###############################################################
+
+Given a feature table and the associated feature sequences, cluster the
+features based on user-specified percent identity threshold of their
+sequences. This is not a general-purpose de novo clustering method, but
+rather is intended to be used for clustering the results of quality-
+filtering/dereplication methods, such as DADA2, or for re-clustering a
+FeatureTable at a lower percent identity than it was originally clustered
+at. When a group of features in the input table are clustered into a single
+feature, the frequency of that single feature in a given sample is the sum
+of the frequencies of the features that were clustered in that sample.
+Feature identifiers and sequences will be inherited from the centroid
+feature of each cluster. See the vsearch documentation for details on how
+sequence clustering is performed.
+
+Parameters
+----------
+sequences : FeatureData[Sequence]
+    The sequences corresponding to the features in table.
+table : FeatureTable[Frequency]
+    The feature table to be clustered.
+perc_identity : Float % 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.
+threads : Int % Range(0, 256, inclusive_end=True), optional
+    The number of threads to use for computation. Passing 0 will launch one
+    thread per CPU core.
+
+Returns
+-------
+clustered_table : FeatureTable[Frequency]
+    The table following clustering of features.
+clustered_sequences : FeatureData[Sequence]
+    Sequences representing clustered features.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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