--- a/qiime2/qiime_sample-classifier_scatterplot.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_sample-classifier_scatterplot.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,45 +1,84 @@
 <?xml version="1.0" ?>
-<tool id="qiime_sample-classifier_scatterplot" name="qiime sample-classifier scatterplot" version="2019.7">
-	<description> - Make 2D scatterplot and linear regression of regressor predictions.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<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=$ipredictions
---m-truth-column="$mtruthcolumn"
+
+#if str($mtruthfile) != 'None':
+--m-truth-file=$mtruthfile
+#end if
 
---m-truth-file="$mtruthfile"
+#if '__ob__' in str($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
 
 --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 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' '$ovisualization';
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-predictions: ARTIFACT SampleData[RegressorPredictions] Predicted values to plot on y axis. Must be predictions of numeric data produced by a sample regressor.                                   [required]" name="ipredictions" optional="False" type="data"/>
-		<param label="--m-truth-column: COLUMN  MetadataColumn[Numeric] Metadata column (true values) to plot on x axis. [required]" name="mtruthcolumn" optional="False" type="text"/>
-		<param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="error">error</option>
-			<option value="ignore">ignore</option>
-		</param>
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
 
-		<param label="--m-truth-file: Metadata file or artifact viewable as metadata." name="mtruthfile" type="data" format="tabular,qza,no_unzip.zip" />
+  ]]></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>
 
-	</inputs>
-	<outputs>
-		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
-	</outputs>
-	<help><![CDATA[
+  <outputs>
+    <data format="html" label="${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.
@@ -60,9 +99,9 @@
 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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