--- a/plotwithscale.xml	Mon Jun 19 12:09:26 2017 -0400
+++ b/plotwithscale.xml	Tue Jun 20 12:57:03 2017 -0400
@@ -3,7 +3,7 @@
   <macros>
     <import>macros.xml</import>
   </macros>
-  <expand macro="requirements" />
+  <!--<expand macro="requirements" />-->
   
   <command detect_errors="exit_code">
 <![CDATA[
@@ -40,13 +40,7 @@
         summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}'
         only_significant='${plotsum.conditionalgroupby.featureonlysig}'
       #end if
-
-      >& /dev/null
 ]]>
-    <!--
-    to print the stack add the following line at the end of the command and enable the corresponding entry in output
-    2> "${stackerr}"
-    -->
   </command>
 
   <inputs>
@@ -70,55 +64,14 @@
     <section name="plotres" title="Plot IWTomics test results" expanded="True">
       <!-- alpha -->
       <param name="alpha" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
-      <!-- average -->
-      <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" />
-      <!-- average -->
-      <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" />
-      <!-- conditional plot type -->
-      <conditional name="conditionalplottype">
-        <!-- plot type -->
-        <param name="plottype" type="select" label="Plot type">
-          <option value="boxplot">Pointwise quantile curves (boxplot)</option>
-          <option value="curves">Curves (aligned)</option>
-        </param>
-        <!-- conditional choice: plottype=boxplot -->
-        <when value="boxplot">
-          <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
-            <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
-            <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
-            <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
-            <repeat name="probabilities" title="Probabilities">
-              <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
-            </repeat>
-          </section>
-        </when>
-      </conditional>
+      <expand macro="plot-params" />
     </section>
 
     <!-- summary plot -->
-    <section name="plotsum" title="Summary plot" expanded="True">
-      <!-- conditional group by -->
-      <conditional name="conditionalgroupby">
-        <!-- group by -->
-        <param name="groupby" type="select" label="Group by" help="How tests should be grouped.">
-          <option value="none">No plot</option>
-          <option value="test">Group by test</option>
-          <option value="feature">Group by feature</option>
-        </param>
-        <when value="test">
-          <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
-          <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
-        </when>
-        <when value="feature">
-          <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
-          <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
-        </when>
-      </conditional>
-    </section>
+    <expand macro="plot-sum" />
   </inputs>
 
   <outputs>
-    <!--<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" />