--- 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>
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