--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_vsearch_cluster-features-de-novo.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,72 @@
+<?xml version="1.0" ?>
+<tool id="qiime_vsearch_cluster-features-de-novo" name="qiime vsearch cluster-features-de-novo" version="2019.4">
+	<description> - De novo clustering of features.</description>
+	<requirements>
+		<requirement type="package" version="2019.4">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+qiime vsearch cluster-features-de-novo
+
+--i-sequences=$isequences
+--i-table=$itable
+--p-perc-identity="$ppercidentity"
+
+#set $pthreads = '${GALAXY_SLOTS:-4}'
+#if str($pthreads):
+ --p-threads="$pthreads"
+#end if
+
+--o-clustered-table=oclusteredtable
+--o-clustered-sequences=oclusteredsequences
+;
+cp oclusteredtable.qza $oclusteredtable;
+cp oclusteredsequences.qza $oclusteredsequences
+	]]></command>
+	<inputs>
+		<param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table.                                    [required]" name="isequences" optional="False" type="data"/>
+		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to be clustered.        [required]" name="itable" optional="False" type="data"/>
+		
+		<param label="--p-perc-identity: PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True)   The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter.                                [required]" name="ppercidentity" optional="False" min="0" max="1" value="" exclude_min="True" exclude_max="False" type="float"/>
+	</inputs>
+	<outputs>
+		<data format="qza" label="${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.
+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>