--- a/qiime2/qiime_sample-classifier_predict-classification.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_sample-classifier_predict-classification.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,35 +1,47 @@
 <?xml version="1.0" ?>
-<tool id="qiime_sample-classifier_predict-classification" name="qiime sample-classifier predict-classification" version="2019.7">
-	<description> - Use trained classifier to predict target values for new samples.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_sample-classifier_predict-classification" name="qiime sample-classifier predict-classification"
+      version="2020.8">
+  <description>Use trained classifier to predict target values for new samples.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime sample-classifier predict-classification
 
 --i-table=$itable
+
 --i-sample-estimator=$isampleestimator
 
-#set $pnjobs = '${GALAXY_SLOTS:-4}'
-
-#if str($pnjobs):
- --p-n-jobs="$pnjobs"
-#end if
+--p-n-jobs=$pnjobs
 
 --o-predictions=opredictions
+
+--o-probabilities=oprobabilities
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
-cp opredictions.qza $opredictions
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table containing all features that should be used for target prediction.                  [required]" name="itable" optional="False" type="data"/>
-		<param format="qza,no_unzip.zip" label="--i-sample-estimator: ARTIFACT SampleEstimator[Classifier] Sample classifier trained with fit_classifier. [required]" name="isampleestimator" optional="False" type="data"/>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: predictions.qza" name="opredictions"/>
-	</outputs>
-	<help><![CDATA[
+cp oprobabilities.qza $oprobabilities
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table containing all features that should be used for target prediction.                  [required]" name="itable" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-sample-estimator: ARTIFACT SampleEstimator[Classifier] Sample classifier trained with fit_classifier. [required]" name="isampleestimator" optional="False" type="data" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: predictions.qza" name="opredictions" />
+    <data format="qza" label="${tool.name} on ${on_string}: probabilities.qza" name="oprobabilities" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Use trained classifier to predict target values for new samples.
-################################################################
+###############################################################
 
 Use trained estimator to predict target values for new samples. These will
 typically be unseen samples, e.g., test data (derived manually or from
@@ -44,14 +56,18 @@
     prediction.
 sample_estimator : SampleEstimator[Classifier]
     Sample classifier trained with fit_classifier.
+n_jobs : Int, optional
+    Number of jobs to run in parallel.
 
 Returns
 -------
 predictions : SampleData[ClassifierPredictions]
     Predicted target values for each input sample.
-	]]></help>
-<macros>
+probabilities : SampleData[Probabilities]
+    Predicted class probabilities for each input sample.
+  ]]></help>
+  <macros>
     <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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