--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_sample-classifier_scatterplot.xml	Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,107 @@
+<?xml version="1.0" ?>
+<tool id="qiime_sample-classifier_scatterplot" name="qiime sample-classifier scatterplot"
+      version="2020.8">
+  <description>Make 2D scatterplot and linear regression of regressor predictions.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime sample-classifier scatterplot
+
+--i-predictions=$ipredictions
+
+#if str($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
+
+--o-visualization=ovisualization
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp ofeatureimportance.qza $ofeatureimportance
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$ovisualization.files_path'
+&& cp -r out/* '$ovisualization.files_path'
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-predictions: ARTIFACT SampleData[RegressorPredictions] Predicted values to plot on y axis. Must be predictions of numeric data produced by a sample regressor.                                   [required]" name="ipredictions" optional="False" type="data" />
+    <param label="--m-truth-file: METADATA" name="mtruthfile" optional="False" type="data" />
+    <param label="--m-truth-column: COLUMN  MetadataColumn[Numeric] Metadata column (true values) to plot on x axis. [required]" name="mtruthcolumn" optional="False" type="text" />
+    <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="error">error</option>
+      <option value="ignore">ignore</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Make 2D scatterplot and linear regression of regressor predictions.
+###############################################################
+
+Make a 2D scatterplot and linear regression of predicted vs. true values
+for a set of samples predicted using a sample regressor.
+
+Parameters
+----------
+predictions : SampleData[RegressorPredictions]
+    Predicted values to plot on y axis. Must be predictions of numeric data
+    produced by a sample regressor.
+truth : MetadataColumn[Numeric]
+    Metadata column (true values) to plot on x axis.
+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.
+
+Returns
+-------
+visualization : Visualization
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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