<?xml version="1.0" ?>
<tool id="qiime_vsearch_dereplicate-sequences" name="qiime vsearch dereplicate-sequences" version="2018.4">
	<description> - Dereplicate sequences.</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command>
	<![CDATA[
	qiime vsearch dereplicate-sequences --i-sequences=$isequences --o-dereplicated-sequences=odereplicatedsequences

	#if str($cmdconfig) != 'None':
	 --cmd-config=$cmdconfig
	#end if
	 --o-dereplicated-table=odereplicatedtable;

	cp odereplicatedsequences.qza $odereplicatedsequences;
	cp odereplicatedtable.qza $odereplicatedtable;
	]]>
	</command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-sequences: SampleData[JoinedSequencesWithQuality] | SampleData[SequencesWithQuality] | SampleData[Sequences] The sequences to be dereplicated. [required]" name="isequences" optional="False" type="data"/>

		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: dereplicated-sequences.qza" name="odereplicatedsequences"/>
		<data format="qza" label="${tool.name} on ${on_string}: dereplicated-table.qza" name="odereplicatedtable"/>
	</outputs>
	<help>
		<![CDATA[
Dereplicate sequences.
-----------------------

Dereplicate sequence data and create a feature table and feature
representative sequences. Feature identfiers in the resulting artifacts
will be the sha1 hash of the sequence defining each feature. If clustering
of features into OTUs is desired, the resulting artifacts can be passed to
the cluster_features_* methods in this plugin.

Parameters
----------
sequences : SampleData[JoinedSequencesWithQuality] | SampleData[SequencesWithQuality] | SampleData[Sequences]
    The sequences to be dereplicated.

Returns
-------
dereplicated_table : FeatureTable[Frequency]
    The table of dereplicated sequences.
dereplicated_sequences : FeatureData[Sequence]
    The dereplicated sequences.
		]]>
	</help>
</tool>