--- a/qiime2/qiime_sample-classifier_confusion-matrix.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_sample-classifier_confusion-matrix.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,83 +1,148 @@
 <?xml version="1.0" ?>
-<tool id="qiime_sample-classifier_confusion-matrix" name="qiime sample-classifier confusion-matrix" version="2019.7">
-	<description> - Make a confusion matrix from sample classifier predictions.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_sample-classifier_confusion-matrix" name="qiime sample-classifier confusion-matrix"
+      version="2020.8">
+  <description>Make a confusion matrix from sample classifier predictions.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime sample-classifier confusion-matrix
 
 --i-predictions=$ipredictions
---m-truth-column="$mtruthcolumn"
---m-truth-file=mtruthfile
+
+#if str($iprobabilities) != 'None':
+--i-probabilities=$iprobabilities
+#end if
+
+#if str($mtruthfile) != 'None':
+--m-truth-file=$mtruthfile
+#end if
+
+#if '__ob__' in str($mtruthcolumn):
+  #set $mtruthcolumn_temp = $mtruthcolumn.replace('__ob__', '[')
+  #set $mtruthcolumn = $mtruthcolumn_temp
+#end if
+#if '__cb__' in str($mtruthcolumn):
+  #set $mtruthcolumn_temp = $mtruthcolumn.replace('__cb__', ']')
+  #set $mtruthcolumn = $mtruthcolumn_temp
+#end if
+#if 'X' in str($mtruthcolumn):
+  #set $mtruthcolumn_temp = $mtruthcolumn.replace('X', '\\')
+  #set $mtruthcolumn = $mtruthcolumn_temp
+#end if
+#if '__sq__' in str($mtruthcolumn):
+  #set $mtruthcolumn_temp = $mtruthcolumn.replace('__sq__', "'")
+  #set $mtruthcolumn = $mtruthcolumn_temp
+#end if
+#if '__db__' in str($mtruthcolumn):
+  #set $mtruthcolumn_temp = $mtruthcolumn.replace('__db__', '"')
+  #set $mtruthcolumn = $mtruthcolumn_temp
+#end if
+
+--m-truth-column=$mtruthcolumn
+
 
 #if str($pmissingsamples) != 'None':
- --p-missing-samples=$pmissingsamples
+--p-missing-samples=$pmissingsamples
+#end if
+
+#if str($pvmin) != 'None':
+--p-vmin=$pvmin
+#end if
+
+#if str($pvmax) != 'None':
+--p-vmax=$pvmax
 #end if
 
 #if str($ppalette) != 'None':
- --p-palette=$ppalette
+--p-palette=$ppalette
 #end if
 
 --o-visualization=ovisualization
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
-qiime tools export --input-path ovisualization.qzv --output-path out   && mkdir -p '$ovisualization.files_path'
+cp oprobabilities.qza $oprobabilities
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$ovisualization.files_path'
 && cp -r out/* '$ovisualization.files_path'
-&& mv '$ovisualization.files_path/index.html' '$ovisualization';
-cp mtruthfile.qza $mtruthfile
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-predictions: ARTIFACT SampleData[ClassifierPredictions] Predicted values to plot on x axis. Should be predictions of categorical data produced by a sample classifier.                                  [required]" name="ipredictions" optional="False" type="data"/>
-		<param label="--m-truth-column: COLUMN  MetadataColumn[Categorical] Metadata column (true values) to plot on y axis. [required]" name="mtruthcolumn" optional="False" type="text"/>
-		<param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="error">error</option>
-			<option value="ignore">ignore</option>
-		</param>
-		<param label="--p-palette: " name="ppalette" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="YellowOrangeBrown">YellowOrangeBrown</option>
-			<option value="YellowOrangeRed">YellowOrangeRed</option>
-			<option value="OrangeRed">OrangeRed</option>
-			<option value="PurpleRed">PurpleRed</option>
-			<option value="RedPurple">RedPurple</option>
-			<option value="BluePurple">BluePurple</option>
-			<option value="GreenBlue">GreenBlue</option>
-			<option value="PurpleBlue">PurpleBlue</option>
-			<option value="YellowGreen">YellowGreen</option>
-			<option value="summer">summer</option>
-			<option value="copper">copper</option>
-			<option value="viridis">viridis</option>
-			<option value="plasma">plasma</option>
-			<option value="inferno">inferno</option>
-			<option value="magma">magma</option>
-			<option value="sirocco">sirocco</option>
-			<option value="drifting">drifting</option>
-			<option value="melancholy">melancholy</option>
-			<option value="enigma">enigma</option>
-			<option value="eros">eros</option>
-			<option value="spectre">spectre</option>
-			<option value="ambition">ambition</option>
-			<option value="mysteriousstains">mysteriousstains</option>
-			<option value="daydream">daydream</option>
-			<option value="solano">solano</option>
-			<option value="navarro">navarro</option>
-			<option value="dandelions">dandelions</option>
-			<option value="deepblue">deepblue</option>
-			<option value="verve">verve</option>
-			<option value="greyscale">greyscale</option>
-		</param>
-	</inputs>
-	<outputs>
-		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
-		<data format="qza" label="${tool.name} on ${on_string}: truthfile.qza" name="mtruthfile"/>
-	</outputs>
-	<help><![CDATA[
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-predictions: ARTIFACT SampleData[ClassifierPredictions] Predicted values to plot on x axis. Should be predictions of categorical data produced by a sample classifier.                                  [required]" name="ipredictions" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-probabilities: ARTIFACT SampleData[Probabilities] Predicted class probabilities for each input sample. [optional]" name="iprobabilities" optional="False" type="data" />
+    <param label="--m-truth-file: METADATA" name="mtruthfile" optional="False" type="data" />
+    <param label="--m-truth-column: COLUMN  MetadataColumn[Categorical] Metadata column (true values) to plot on y axis. [required]" name="mtruthcolumn" optional="False" type="text" />
+    <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="error">error</option>
+      <option value="ignore">ignore</option>
+    </param>
+    <param label="--p-vmin: " name="pvmin" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="auto">auto</option>
+    </param>
+    <param label="--p-vmax: " name="pvmax" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="auto">auto</option>
+    </param>
+    <param label="--p-palette: " name="ppalette" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="YellowOrangeBrown">YellowOrangeBrown</option>
+      <option value="YellowOrangeRed">YellowOrangeRed</option>
+      <option value="OrangeRed">OrangeRed</option>
+      <option value="PurpleRed">PurpleRed</option>
+      <option value="RedPurple">RedPurple</option>
+      <option value="BluePurple">BluePurple</option>
+      <option value="GreenBlue">GreenBlue</option>
+      <option value="PurpleBlue">PurpleBlue</option>
+      <option value="YellowGreen">YellowGreen</option>
+      <option value="summer">summer</option>
+      <option value="copper">copper</option>
+      <option value="viridis">viridis</option>
+      <option value="cividis">cividis</option>
+      <option value="plasma">plasma</option>
+      <option value="inferno">inferno</option>
+      <option value="magma">magma</option>
+      <option value="sirocco">sirocco</option>
+      <option value="drifting">drifting</option>
+      <option value="melancholy">melancholy</option>
+      <option value="enigma">enigma</option>
+      <option value="eros">eros</option>
+      <option value="spectre">spectre</option>
+      <option value="ambition">ambition</option>
+      <option value="mysteriousstains">mysteriousstains</option>
+      <option value="daydream">daydream</option>
+      <option value="solano">solano</option>
+      <option value="navarro">navarro</option>
+      <option value="dandelions">dandelions</option>
+      <option value="deepblue">deepblue</option>
+      <option value="verve">verve</option>
+      <option value="greyscale">greyscale</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Make a confusion matrix from sample classifier predictions.
-###########################################################
+###############################################################
 
 Make a confusion matrix and calculate accuracy of predicted vs. true values
-for a set of samples classified using a sample classifier.
+for a set of samples classified using a sample classifier. If per-sample
+class probabilities are provided, will also generate Receiver Operating
+Characteristic curves and calculate area under the curve for each class.
 
 Parameters
 ----------
@@ -86,20 +151,28 @@
     categorical data produced by a sample classifier.
 truth : MetadataColumn[Categorical]
     Metadata column (true values) to plot on y axis.
+probabilities : SampleData[Probabilities], optional
+    Predicted class probabilities for each input sample.
 missing_samples : Str % Choices('error', 'ignore'), optional
     How to handle missing samples in metadata. "error" will fail if missing
     samples are detected. "ignore" will cause the feature table and
     metadata to be filtered, so that only samples found in both files are
     retained.
-palette : Str % Choices('YellowOrangeBrown', 'YellowOrangeRed', 'OrangeRed', 'PurpleRed', 'RedPurple', 'BluePurple', 'GreenBlue', 'PurpleBlue', 'YellowGreen', 'summer', 'copper', 'viridis', 'plasma', 'inferno', 'magma', 'sirocco', 'drifting', 'melancholy', 'enigma', 'eros', 'spectre', 'ambition', 'mysteriousstains', 'daydream', 'solano', 'navarro', 'dandelions', 'deepblue', 'verve', 'greyscale'), optional
+vmin : Float | Str % Choices('auto'), optional
+    The minimum value to use for anchoring the colormap. If "auto", vmin is
+    set to the minimum value in the data.
+vmax : Float | Str % Choices('auto'), optional
+    The maximum value to use for anchoring the colormap. If "auto", vmax is
+    set to the maximum value in the data.
+palette : Str % Choices('YellowOrangeBrown', 'YellowOrangeRed', 'OrangeRed', 'PurpleRed', 'RedPurple', 'BluePurple', 'GreenBlue', 'PurpleBlue', 'YellowGreen', 'summer', 'copper', 'viridis', 'cividis', 'plasma', 'inferno', 'magma', 'sirocco', 'drifting', 'melancholy', 'enigma', 'eros', 'spectre', 'ambition', 'mysteriousstains', 'daydream', 'solano', 'navarro', 'dandelions', 'deepblue', 'verve', 'greyscale'), optional
     The color palette to use for plotting.
 
 Returns
 -------
 visualization : Visualization
-	]]></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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