--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-classifier_classify-hybrid-vsearch-sklearn.xml	Tue Aug 13 07:46:48 2019 -0400
@@ -0,0 +1,116 @@
+<?xml version="1.0" ?>
+<tool id="qiime_feature-classifier_classify-hybrid-vsearch-sklearn" name="qiime feature-classifier classify-hybrid-vsearch-sklearn" version="2019.7">
+	<description> -  ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier</description>
+	<requirements>
+		<requirement type="package" version="2019.7">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+qiime feature-classifier classify-hybrid-vsearch-sklearn
+    
+--i-query=$iquery
+--i-reference-reads=$ireferencereads
+--i-reference-taxonomy=$ireferencetaxonomy
+--i-classifier=$iclassifier
+
+#if str($pmaxaccepts) != 'None':
+ --p-maxaccepts=$pmaxaccepts
+#end if
+
+#if str($ppercidentity):
+ --p-perc-identity=$ppercidentity
+#end if
+
+#if str($pquerycov):
+ --p-query-cov=$pquerycov
+#end if
+
+#if str($pstrand) != 'None':
+ --p-strand=$pstrand
+#end if
+
+#if str($pminconsensus):
+ --p-min-consensus=$pminconsensus
+#end if
+
+#if str($pconfidence) != 'None':
+ --p-confidence=$pconfidence
+#end if
+
+#if str($preadorientation) != 'None':
+ --p-read-orientation=$preadorientation
+#end if
+
+#set $pthreads = '${GALAXY_SLOTS:-4}'
+
+#if str($pthreads):
+
+#if str($pthreads):
+ --p-threads="$pthreads"
+#end if
+
+#end if
+
+
+#if $pprefilter:
+ --p-prefilter
+#end if
+
+#if str($psamplesize):
+ --p-sample-size=$psamplesize
+#end if
+
+#if str($prandseed):
+ --p-randseed=$prandseed
+#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"/>
+		<param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] reference taxonomy labels.                  [required]" name="ireferencetaxonomy" optional="False" type="data"/>
+		<param format="qza,no_unzip.zip" label="--i-classifier: ARTIFACT TaxonomicClassifier Pre-trained sklearn taxonomic classifier for classifying the reads.                      [required]" name="iclassifier" optional="False" type="data"/>
+		<param label="--p-maxaccepts: " name="pmaxaccepts" optional="True" type="select">
+			<option selected="True" value="None">Selection is Optional</option>
+			<option value="Int % Range(1">Int % Range(1</option>
+			<option value="None">None</option>
+		</param>
+		<param label="--p-perc-identity: PROPORTION Range(0.0, 1.0, inclusive_end=True) Percent sequence similarity to use for PREFILTER. Reject match if percent identity to query is lower. Set to a lower value to perform a rough pre-filter. This parameter is ignored if `prefilter` is disabled. [default: 0.5]" name="ppercidentity" optional="True" type="float" value="0.5"/>
+		<param label="--p-query-cov: PROPORTION Range(0.0, 1.0, inclusive_end=True) Query coverage threshold to use for PREFILTER. Reject match if query alignment coverage per high-scoring pair is lower. Set to a lower value to perform a rough pre-filter. This parameter is ignored if `prefilter` is disabled.                            [default: 0.8]" name="pquerycov" optional="True" type="float" value="0.8"/>
+		<param label="--p-strand: " 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="--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.   [default: 0.51]" name="pminconsensus" optional="True" type="float" value="0.51"/>
+		<param label="--p-confidence: " name="pconfidence" optional="True" type="select">
+			<option selected="True" value="None">Selection is Optional</option>
+			<option value="Float % Range(0">Float % Range(0</option>
+			<option value="1">1</option>
+			<option value="inclusive_end=True">inclusive_end=True</option>
+		</param>
+		<param label="--p-read-orientation: " name="preadorientation" optional="True" type="select">
+			<option selected="True" value="None">Selection is Optional</option>
+			<option value="same">same</option>
+			<option value="reverse-complement">reverse-complement</option>
+			<option value="auto">auto</option>
+		</param>
+		<param label="--p-prefilter: --p-no-prefilter Toggle positive filter of query sequences on or off. [default: True]" name="pprefilter" selected="False" type="boolean"/>
+		<param label="--p-sample-size: INTEGER Range(1, None)      Randomly extract the given number of sequences from the reference database to use for prefiltering. This parameter is ignored if `prefilter` is disabled. [default: 1000]" name="psamplesize" optional="True" type="integer" value="1000"/>
+		<param label="--p-randseed: INTEGER  Use integer as a seed for the pseudo-random generator Range(0, None)      used during prefiltering. A given seed always produces the same output, which is useful for replicability. Set to 0 to use a pseudo-random seed. This parameter is ignored if `prefilter` is disabled.    [default: 0]" name="prandseed" optional="True" type="integer" value="0"/>
+	</inputs>
+	<outputs>
+		<data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
+	</outputs>
+	<help><![CDATA[
+
+	]]></help>
+<macros>
+    <import>qiime_citation.xml</import>
+</macros>
+<expand macro="qiime_citation"/>
+</tool>