<?xml version="1.0" ?>
<tool id="qiime_feature-classifier_classify-consensus-vsearch" name="qiime feature-classifier classify-consensus-vsearch" version="2019.4">
	<description> - VSEARCH consensus taxonomy classifier</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime feature-classifier classify-consensus-vsearch

--i-query=$iquery
--i-reference-reads=$ireferencereads


#if str( $id_to_taxonomy_fp.selector ) == 'history'
#set $tax = $id_to_taxonomy_fp.taxonomy_fp
--i-reference-taxonomy '$tax'
#else:
#set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
--i-reference-taxonomy '$tax'
#end if


#if $pmaxaccepts:
 --p-maxaccepts=$pmaxaccepts
#end if

#if $ppercidentity:
 --p-perc-identity=$ppercidentity
#end if

#if $pquerycov:
 --p-query-cov=$pquerycov
#end if

#if str($pstrand) != 'None':
 --p-strand=$pstrand
#end if

#if $pminconsensus:
 --p-min-consensus=$pminconsensus
#end if

#if str($punassignablelabel):
 --p-unassignable-label="$punassignablelabel"
#end if

#set $pthreads = '${GALAXY_SLOTS:-4}'
#if str($pthreads):
 --p-threads="$pthreads"
#end if

--o-classification=oclassification
;
cp oclassification.qza $oclassification
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-query: ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically.      [required]" name="iquery" optional="False" type="data"/>
		<param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] reference sequences.                      [required]" name="ireferencereads" optional="False" type="data"/>

		<conditional name="id_to_taxonomy_fp" optional="True">
		   <param name="selector" type="select" label="Reference taxonomy to query">
			  <option value="cached">Public databases</option>
			  <option value="history">Databases from your history</option>
		   </param>
		   <when value="cached">
			  <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
				 <options from_data_table="qiime_taxonomy" />
			  </param>
		   </when>
		   <when value="history">
			  <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
		   </when>
		</conditional>

		<param label="--p-maxaccepts: INTEGER  Maximum number of hits to keep for each query. Set Range(0, None)        to 0 to keep all hits > perc-identity similarity. Must be in range [0, infinity].        [default: 10]" name="pmaxaccepts" optional="True" type="integer" min="0" value="10"/>
		<param label="--p-perc-identity: PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to query is lower. Must be in range [0.0, 1.0].          [default: 0.8]" name="ppercidentity" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.8"/>
		<param label="--p-query-cov: PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if query alignment coverage per high-scoring pair is lower. Must be in range [0.0, 1.0].                                 [default: 0.8]" name="pquerycov" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.8"/>
		<param label="--p-strand: Align against reference sequences in forward   ('plus') or both directions ('both').  [default: 'both']" name="pstrand" optional="True" type="select">
			<option value="None">Selection is Optional</option>
			<option selected="True" value="both">both</option>
			<option value="plus">plus</option>
		</param>
		<param label="--p-min-consensus: NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True)   Minimum fraction of assignments must match top hit to be accepted as consensus assignment. Must be in range (0.5, 1.0].                    [default: 0.51]" name="pminconsensus" optional="True" type="float" min="0.5" max="1" exclude_min="True" exclude_max="False" value="0.51"/>
		<param label="--p-unassignable-label: TEXT [default: 'Unassigned']" name="punassignablelabel" optional="True" type="text" value="'Unassigned'"/>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
	</outputs>
	<help><![CDATA[
VSEARCH consensus taxonomy classifier
#####################################

Assign taxonomy to query sequences using VSEARCH. Performs VSEARCH global
alignment between query and reference_reads, then assigns consensus
taxonomy to each query sequence from among maxaccepts top hits,
min_consensus of which share that taxonomic assignment. Unlike classify-
consensus-blast, this method searches the entire reference database before
choosing the top N hits, not the first N hits.

Parameters
----------
query : FeatureData[Sequence]
    Sequences to classify taxonomically.
reference_reads : FeatureData[Sequence]
    reference sequences.
reference_taxonomy : FeatureData[Taxonomy]
    reference taxonomy labels.
maxaccepts : Int % Range(0, None), optional
    Maximum number of hits to keep for each query. Set to 0 to keep all
    hits > perc_identity similarity. Must be in range [0, infinity].
perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
    Reject match if percent identity to query is lower. Must be in range
    [0.0, 1.0].
query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional
    Reject match if query alignment coverage per high-scoring pair is
    lower. Must be in range [0.0, 1.0].
strand : Str % Choices('both', 'plus'), optional
    Align against reference sequences in forward ("plus") or both
    directions ("both").
min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional
    Minimum fraction of assignments must match top hit to be accepted as
    consensus assignment. Must be in range (0.5, 1.0].
unassignable_label : Str, optional
	\

Returns
-------
classification : FeatureData[Taxonomy]
    The resulting taxonomy classifications.
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>