--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2-2020.8/qiime_sample-classifier_confusion-matrix.xml	Fri Sep 04 12:44:24 2020 +0000
@@ -0,0 +1,178 @@
+<?xml version="1.0" ?>
+<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=$ipredictions
+
+#if str($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
+#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
+#end if
+
+--o-visualization=ovisualization
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+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'
+
+  ]]></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. If per-sample
+class probabilities are provided, will also generate Receiver Operating
+Characteristic curves and calculate area under the curve for each class.
+
+Parameters
+----------
+predictions : SampleData[ClassifierPredictions]
+    Predicted values to plot on x axis. Should be predictions of
+    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.
+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>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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