# HG changeset patch
# User fabio
# Date 1497977823 14400
# Node ID 7dcc25a1a0624649b72d7244b3203634ef21da53
# Parent  0a17de046de0acecec0ddbcf3a7833172a769fc6
Uploaded 20170620

diff -r 0a17de046de0 -r 7dcc25a1a062 ._loadandplot.R
Binary file ._loadandplot.R has changed
diff -r 0a17de046de0 -r 7dcc25a1a062 ._plotwithscale.R
Binary file ._plotwithscale.R has changed
diff -r 0a17de046de0 -r 7dcc25a1a062 ._testandplot.R
Binary file ._testandplot.R has changed
diff -r 0a17de046de0 -r 7dcc25a1a062 loadandplot.xml
--- a/loadandplot.xml	Mon Jun 19 12:09:26 2017 -0400
+++ b/loadandplot.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[
@@ -36,28 +36,25 @@
       #if $conditionaltype.smoothing == 'no':
         alignment="'${conditionaltype.alignment}'"
       #elif $conditionaltype.smoothing == 'locpoly':
-        alignment="'${conditionaltype.locpolyconditionalscale.alignment}'"
-        #if $conditionaltype.locpolyconditionalscale.alignment == 'scale':
-          scale='${conditionaltype.locpolyconditionalscale.scalegrid}'
-        #end if
         bandwidth='${conditionaltype.locpolybandwidth}'
         degree='${conditionaltype.locpolydegree}'
-        fill_gaps='${conditionaltype.fillgaps}'
+        alignment="'${conditionaltype.conditionalscale.alignment}'"
       #elif $conditionaltype.smoothing == 'kernel':
-        alignment="'${conditionaltype.kernelconditionalscale.alignment}'"
-        #if $conditionaltype.kernelconditionalscale.alignment == 'scale':
-          scale='${conditionaltype.kernelconditionalscale.scalegrid}'
-        #end if
         bandwidth='${conditionaltype.kernelbandwidth}'
-        fill_gaps='${conditionaltype.fillgaps}'
+        alignment="'${conditionaltype.conditionalscale.alignment}'"
       #elif $conditionaltype.smoothing == 'splines':
-        alignment="'${conditionaltype.splinesconditionalscale.alignment}'"
-        #if $conditionaltype.splinesconditionalscale.alignment == 'scale':
-          scale='${conditionaltype.splinesconditionalscale.scalegrid}'
-        #end if
         degree='${conditionaltype.splinesdegree}'
         dist_knots='${conditionaltype.splinesdistknots}'
-        fill_gaps='${conditionaltype.fillgaps}'
+        alignment="'${conditionaltype.conditionalscale.alignment}'"
+      #end if
+
+      #if $conditionaltype.smoothing != 'no':
+        #if $conditionaltype.conditionalscale.alignment == 'scale':
+          scale='${conditionaltype.conditionalscale.scalegrid}'
+          fill_gaps='TRUE'
+        #else
+          fill_gaps='${conditionaltype.conditionalscale.fillgaps}'
+        #end if
       #end if
 
       average='${plotres.average}'
@@ -104,101 +101,33 @@
       </param>
       <!-- conditional choice: smoothing=no -->
       <when value="no">
-        <param name="alignment" type="select" label="Region alignment" help="">
-          <option value="center">Center - Alignment on the central position</option>
-          <option value="left">Left - Alignment on the starting position</option>
-          <option value="right">Right - Alignment on the ending position</option>
-        </param>
+        <expand macro="alignment" />
       </when>
       <!-- conditional choice: smoothing=locpoly -->
       <when value="locpoly">
-        <!-- conditional region alignment -->
-        <conditional name="locpolyconditionalscale">
-          <param name="alignment" type="select" label="Region alignment" help="">
-            <option value="center">Center - Alignment on the central position</option>
-            <option value="left">Left - Alignment on the starting position</option>
-            <option value="right">Right - Alignment on the ending position</option>
-            <option value="scale">Scale - Scaling all regions to the same length</option>
-          </param>
-          <when value="scale">
-            <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
-          </when>
-        </conditional>
-
         <param name="locpolybandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
         <param name="locpolydegree" type="integer" value="3" min="0" label="Degree of local polynomial" help="" />
-
-        <!-- fill gaps -->
-        <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
+        <!-- conditional region alignment -->
+        <expand macro="alignment-s" />
       </when>
       <!-- conditional choice: smoothing=kernel -->
       <when value="kernel">
+        <param name="kernelbandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
         <!-- conditional region alignment -->
-        <conditional name="kernelconditionalscale">
-          <param name="alignment" type="select" label="Region alignment" help="">
-            <option value="center">Center - Alignment on the central position</option>
-            <option value="left">Left - Alignment on the starting position</option>
-            <option value="right">Right - Alignment on the ending position</option>
-            <option value="scale">Scale - Scaling all regions to the same length</option>
-          </param>
-          <when value="scale">
-            <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
-          </when>
-        </conditional>
-
-        <param name="kernelbandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
-
-        <!-- fill gaps -->
-        <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
+        <expand macro="alignment-s" />
       </when>
       <!-- conditional choice: smoothing=splines -->
       <when value="splines">
-        <!-- conditional region alignment -->
-        <conditional name="splinesconditionalscale">
-          <param name="alignment" type="select" label="Region alignment" help="">
-            <option value="center">Center - Alignment on the central position</option>
-            <option value="left">Left - Alignment on the starting position</option>
-            <option value="right">Right - Alignment on the ending position</option>
-            <option value="scale">Scale - Scaling all regions to the same length</option>
-          </param>
-          <when value="scale">
-            <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
-          </when>
-        </conditional>
-
         <param name="splinesdegree" type="integer" value="3" min="0" label="Degree of B-splines" help="" />
         <param name="splinesdistknots" type="integer" value="10" min="2" label="Distance between nodes (approximate)" help="" />
-
-        <!-- fill gaps -->
-        <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
+        <!-- conditional region alignment -->
+        <expand macro="alignment-s" />
       </when>
     </conditional>
 
     <!-- plot IWTomics results -->
     <section name="plotres" title="Plot data" expanded="True">
-      <!-- average -->
-      <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" help="" />
-      <!-- sample size in each position -->
-      <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" help="" />
-      <!-- conditional plot type -->
-      <conditional name="conditionalplottype">
-        <!-- plot type -->
-        <param name="plottype" type="select" label="Plot type" help="">
-          <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>
   </inputs>
 
diff -r 0a17de046de0 -r 7dcc25a1a062 macros.xml
--- a/macros.xml	Mon Jun 19 12:09:26 2017 -0400
+++ b/macros.xml	Tue Jun 20 12:57:03 2017 -0400
@@ -6,24 +6,48 @@
             <requirement type="package" version="@VERSION@">bioconductor-iwtomics</requirement>
         </requirements>
     </xml>
+    
+    <xml name="alignment-s">
+        <conditional name="conditionalscale">
+            <param name="alignment" type="select" label="Region alignment" help="">
+                <option value="center">Center - Alignment on the central position</option>
+                <option value="left">Left - Alignment on the starting position</option>
+                <option value="right">Right - Alignment on the ending position</option>
+                <option value="scale">Scale - Scaling all regions to the same length</option>
+            </param>
+            <when value="center">
+                <!-- fill gaps -->
+                <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
+            </when>
+            <when value="left">
+                <!-- fill gaps -->
+                <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
+            </when>
+            <when value="right">
+                <!-- fill gaps -->
+                <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
+            </when>
+            <when value="scale">
+                <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
+            </when>
+        </conditional>
+    </xml>
+
+    <xml name="alignment">
+        <param name="alignment" type="select" label="Region alignment" help="">
+            <option value="center">Center - Alignment on the central position</option>
+            <option value="left">Left - Alignment on the starting position</option>
+            <option value="right">Right - Alignment on the ending position</option>
+        </param>
+    </xml>
+
     <xml name="citations">
         <citations>
-            <citation type="bibtex">
-                @ARTICLE{
-                        iwt-functional-data,
-                        author = {Pini, Alessia and Vantini, Simone},
-                        title = {Interval-Wise Testing for functional data},
-                        journal = {Journal of Nonparametric Statistics},
-                        year = {2017},
-                        volume = {29},
-                        number = {2},
-                        pages = {407-424}
-                }
-            </citation>
+            <citation type="doi">10.1080/10485252.2017.1306627</citation>
             <citation type="bibtex">
                 @MANUAL{
                         iwtomics,
-                        author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
+                        author = {Cremona, M.A. and Pini, A. and Chiaromonte, F. and Vantini, S.},
                         title = {IWTomics: Interval-Wise Testing for Omics Data},
                         note = {R package version 1.0.0},
                         year = {2017}
@@ -31,4 +55,52 @@
             </citation>
         </citations>
     </xml>
+
+    <xml name="plot-params">
+        <!-- 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>
+    </xml>
+
+    <xml name="plot-sum">
+        <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>
+    </xml>
 </macros>
\ No newline at end of file
diff -r 0a17de046de0 -r 7dcc25a1a062 plotwithscale.xml
--- 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" />
diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/._.DS_Store
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/input/._Controls_regions.bed
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/input/._Elements1_regions.bed
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/input/._Elements2_regions.bed
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/input/._Elements3_regions.bed
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/input/._Feature1.bed
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/input/._Feature2.bed
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/input/._features.header.bed.txt
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/input/._regions.header.txt
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/output_loadandplot/._iwtomics.loadandplot.RData
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/output_loadandplot/._iwtomics.loadandplot.features.txt
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/output_loadandplot/._iwtomics.loadandplot.pdf
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/output_loadandplot/._iwtomics.loadandplot.regions.txt
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/output_plotwithscale/._iwtomics.plotwithscale.adjustedpvalue.txt
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/output_plotwithscale/._iwtomics.plotwithscale.iwtomicstestresults.pdf
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/output_plotwithscale/._iwtomics.plotwithscale.summaryplot.pdf
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/output_testandplot/._iwtomics.testandplot.RData
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/output_testandplot/._iwtomics.testandplot.adjustedpvalue.matrix.txt
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/output_testandplot/._iwtomics.testandplot.iwtomicstestresults.pdf
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/output_testandplot/._iwtomics.testandplot.selectedfeatures.txt
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/output_testandplot/._iwtomics.testandplot.summaryplot.pdf
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diff -r 0a17de046de0 -r 7dcc25a1a062 test-data/output_testandplot/._iwtomics.testandplot.tests.txt
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diff -r 0a17de046de0 -r 7dcc25a1a062 testandplot.xml
--- a/testandplot.xml	Mon Jun 19 12:09:26 2017 -0400
+++ b/testandplot.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[
@@ -48,13 +48,7 @@
         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>
@@ -102,55 +96,14 @@
     <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.testandplot.stackerr.txt" />-->
     <data format="txt" name="adjustedpvaluematrix" label="${tool.name} on ${on_string}: Adjusted p-value Matrix" from_work_dir="iwtomics.testandplot.adjustedpvalue.matrix.txt" />
     <data format="pdf" name="iwtomicsrespdf" label="${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" />