--- a/qiime2/qiime_feature-classifier_classify-sklearn.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_feature-classifier_classify-sklearn.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,75 +1,64 @@
 <?xml version="1.0" ?>
-<tool id="qiime_feature-classifier_classify-sklearn" name="qiime feature-classifier classify-sklearn" version="2019.7">
-	<description> - Pre-fitted sklearn-based taxonomy classifier</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_feature-classifier_classify-sklearn" name="qiime feature-classifier classify-sklearn"
+      version="2020.8">
+  <description>Pre-fitted sklearn-based taxonomy classifier</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime feature-classifier classify-sklearn
 
-
-#if str( $id_to_classifier_fp.selector ) == 'history'
-#set $classifier = $id_to_classifier_fp.classifier_fp
---i-classifier '$classifier'
-#else:
-#set $classifier = $id_to_classifier_fp.classifier_fp.fields.path
---i-classifier '$classifier'
-#end if
-
-
 --i-reads=$ireads
 
-#set $pnjobs = '${GALAXY_SLOTS:-4}'
-
-#if str($pnjobs):
- --p-n-jobs="$pnjobs"
-#end if
+--i-classifier=$iclassifier
 
+--p-n-jobs=$pnjobs
 
-#if str($pconfidence) != '':
-  #if float($pconfidence) >= 0.0:
-	--p-confidence=$pconfidence
-  #end if
+#if str($pconfidence) != 'None':
+--p-confidence=$pconfidence
 #end if
 
 #if str($preadorientation) != 'None':
- --p-read-orientation=$preadorientation
+--p-read-orientation=$preadorientation
 #end if
 
 --o-classification=oclassification
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
 cp oclassification.qza $oclassification
-	]]></command>
-	<inputs>
-		<conditional name="id_to_classifier_fp" optional="True">
-		   <param name="selector" type="select" label="Reference classifier to query">
-			  <option value="cached">Public classifiers</option>
-			  <option value="history">Classifiers from your history</option>
-		   </param>
-		   <when value="cached">
-			  <param name="classifier_fp" label="Reference classifier" type="select" optional="True">
-				 <options from_data_table="qiime_rep_set" />
-			  </param>
-		   </when>
-		   <when value="history">
-			  <param name="classifier_fp" type="data" format="qza,no_unzip.zip" label="Reference classifier" optional="True" />
-		   </when>
-		</conditional>
 
-		<param format="qza,no_unzip.zip" label="--i-reads: ARTIFACT FeatureData[Sequence] The feature data to be classified.         [required]" name="ireads" optional="False" type="data"/>
-		<param label="--p-confidence: NUMBER  Confidence threshold for limiting taxonomic depth. Provide -1 to disable confidence calculation, or 0 to calculate confidence but not apply it to limit the taxonomic depth of the assignments.    [default: 0.7]" name="pconfidence" optional="True" type="float" value="0.7"/>
-		<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>
-		</param>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
-	</outputs>
-	<help><![CDATA[
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-reads: ARTIFACT FeatureData[Sequence] The feature data to be classified.         [required]" name="ireads" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-classifier: ARTIFACT TaxonomicClassifier  The taxonomic classifier for classifying the reads. [required]" name="iclassifier" optional="False" type="data" />
+    <param label="--p-confidence: " name="pconfidence" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="Float % Range(0">Float % Range(0</option>
+      <option value="1">1</option>
+      <option value="inclusive_end=True">inclusive_end=True</option>
+    </param>
+    <param label="--p-read-orientation: " name="preadorientation" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="same">same</option>
+      <option value="reverse-complement">reverse-complement</option>
+      <option value="auto">auto</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Pre-fitted sklearn-based taxonomy classifier
-############################################
+###############################################################
 
 Classify reads by taxon using a fitted classifier.
 
@@ -80,27 +69,33 @@
 classifier : TaxonomicClassifier
     The taxonomic classifier for classifying the reads.
 reads_per_batch : Int % Range(0, None), optional
-    Number of reads to process in each batch. If 0, this parameter is
+    Number of reads to process in each batch. If "auto", this parameter is
     autoscaled to min( number of query sequences / n_jobs, 20000).
+n_jobs : Int, optional
+    The maximum number of concurrently worker processes. If -1 all CPUs are
+    used. If 1 is given, no parallel computing code is used at all, which
+    is useful for debugging. For n_jobs below -1, (n_cpus + 1 + n_jobs) are
+    used. Thus for n_jobs = -2, all CPUs but one are used.
 pre_dispatch : Str, optional
     "all" or expression, as in "3*n_jobs". The number of batches (of tasks)
     to be pre-dispatched.
-confidence : Float, optional
-    Confidence threshold for limiting taxonomic depth. Provide -1 to
+confidence : Float % Range(0, 1, inclusive_end=True) | Str % Choices('disable'), optional
+    Confidence threshold for limiting taxonomic depth. Set to "disable" to
     disable confidence calculation, or 0 to calculate confidence but not
     apply it to limit the taxonomic depth of the assignments.
-read_orientation : Str % Choices('same', 'reverse-complement'), optional
+read_orientation : Str % Choices('same', 'reverse-complement', 'auto'), optional
     Direction of reads with respect to reference sequences. same will cause
     reads to be classified unchanged; reverse-complement will cause reads
-    to be reversed and complemented prior to classification. Default is to
-    autodetect based on the confidence estimates for the first 100 reads.
+    to be reversed and complemented prior to classification. "auto" will
+    autodetect orientation based on the confidence estimates for the first
+    100 reads.
 
 Returns
 -------
 classification : FeatureData[Taxonomy]
-	]]></help>
-<macros>
+  ]]></help>
+  <macros>
     <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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