--- a/plotwithscale.xml	Wed May 31 16:26:29 2017 -0400
+++ b/plotwithscale.xml	Thu Jun 08 16:44:13 2017 -0400
@@ -132,12 +132,43 @@
   </inputs>
 
   <outputs>
-    <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.testandplot.stackerr.txt" />-->
-    <data format="txt" name="adjustedpvalue" label="${tool.name} on ${on_string}: Adjusted p-value" from_work_dir="iwtomics.testandplot.adjustedpvalue.txt" />
-    <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.testandplot.iwtomicstestresults.pdf" />
-    <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.testandplot.summaryplot.pdf" />
+    <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.plotwithscale.stackerr.txt" />-->
+    <data format="txt" name="adjustedpvalue" label="${tool.name} on ${on_string}: Adjusted p-value" from_work_dir="iwtomics.plotwithscale.adjustedpvalue.txt" />
+    <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.plotwithscale.iwtomicstestresults.pdf" />
+    <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.plotwithscale.summaryplot.pdf" />
   </outputs>
 
+  <tests>
+    <test>
+      <param name="rdata" value="output_testandplot/iwtomics.testandplot.RData" ftype="rdata" />
+      <param name="testids" value="output_testandplot/iwtomics.testandplot.tests.txt" ftype="tabular" />
+      <param name="featureids" value="output_testandplot/iwtomics.testandplot.selectedfeatures.txt" ftype="tabular" />
+      <repeat name="thresholdontestscale">
+        <param name="test" value="1" />
+        <param name="feature" value="1" />
+        <param name="scale" value="10" />
+      </repeat>
+      <repeat name="thresholdontestscale">
+        <param name="test" value="1,2,3" />
+        <param name="feature" value="2" />
+        <param name="scale" value="20" />
+      </repeat>
+      <param name="alpha" value="0.05" />
+      <param name="average" value="TRUE" />
+      <param name="size" value="TRUE" />
+      <param name="plottype" value="boxplot" />
+      <param name="prob0" value="0.25" />
+      <param name="prob1" value="0.5" />
+      <param name="prob2" value="0.75" />
+      <param name="groupby" value="feature" />
+      <param name="featurealphaplot" value="0.05" />
+      <param name="featureonlysig" value="TRUE" />
+      <output name="adjustedpvalue" file="output_plotwithscale/iwtomics.plotwithscale.adjustedpvalue.txt" compare="sim_size" />
+      <output name="iwtomicsrespdf" file="output_plotwithscale/iwtomics.plotwithscale.iwtomicstestresults.pdf" compare="sim_size" />
+      <output name="iwtomicssumpdf" file="output_plotwithscale/iwtomics.plotwithscale.summaryplot.pdf" compare="sim_size" />
+    </test>
+  </tests>
+
   <help>
 This tool allows to select the scale for the Interval-Wise Testing results. In particular, it returns the p-value curves
 for the different tests performed at the selected scale, and it creates a graphical representation of the