<?xml version="1.0" ?>
<tool id="qiime_vsearch_cluster-features-closed-reference" name="qiime vsearch cluster-features-closed-reference" version="2018.4">
	<description> -  Closed-reference clustering of features.</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command>
	<![CDATA[
	qiime vsearch cluster-features-closed-reference --p-perc-identity="$ppercidentity" --i-table=$itable --i-sequences=$isequences --i-reference-sequences=$ireferencesequences --o-unmatched-sequences=ounmatchedsequences

	#if str($cmdconfig) != 'None':
	 --cmd-config=$cmdconfig
	#end if
	 --o-clustered-table=oclusteredtable
	#if str($pstrand) != 'None':
	 --p-strand=$pstrand
	#end if
	 --o-clustered-sequences=oclusteredsequences
	#set $pthreads = '${GALAXY_SLOTS:-4}'

	#if str($pthreads):
	 --p-threads="$pthreads"
	#end if
	;
	cp ounmatchedsequences.qza $ounmatchedsequences;
	cp oclusteredtable.qza $oclusteredtable;
	cp oclusteredsequences.qza $oclusteredsequences
	]]>
	</command>
	<inputs>
		<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"/>
		<param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table to be clustered. [required]" name="itable" optional="False" type="data"/>
		<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"/>

		<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"/>

		<param label="--p-strand: Search plus (i.e., forward) or both (i.e.,
                                  forward and reverse complement) strands.
                                  [default: plus]" name="pstrand" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="both">both</option>
			<option value="plus">plus</option>
		</param>

		<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 ${on_string}: unmatched-sequences.qza" name="ounmatchedsequences"/>
		<data format="qza" label="${tool.name} on ${on_string}: clustered-table.qza" name="oclusteredtable"/>
		<data format="qza" label="${tool.name} on ${on_string}: clustered-sequences.qza" name="oclusteredsequences"/>
	</outputs>
	<help>
		<![CDATA[
Closed-reference clustering of features.
-----------------------------------------

Given a feature table and the associated feature sequences, cluster the
features against a reference database based on user-specified percent
identity threshold of their sequences. This is not a general-purpose
closed-reference 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 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.
reference_sequences : FeatureData[Sequence]
    The sequences to use as cluster centroids.
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.
strand : Str % Choices({'both', 'plus'}), optional
    Search plus (i.e., forward) or both (i.e., forward and reverse
    complement) strands.

Returns
-------
clustered_table : FeatureTable[Frequency]
    The table following clustering of features.
clustered_sequences : FeatureData[Sequence]
    The sequences representing clustered features, relabeled by the
    reference IDs.
unmatched_sequences : FeatureData[Sequence]
    The sequences which failed to match any reference sequences. This
    output maps to vsearch's --notmatched parameter.
    ]]>
	</help>
</tool>