--- a/limma_voom.xml	Wed May 09 13:27:14 2018 -0400
+++ b/limma_voom.xml	Tue May 15 02:36:36 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="limma_voom" name="limma" version="3.34.9.3">
+<tool id="limma_voom" name="limma" version="3.34.9.4">
     <description>
         Perform differential expression with limma-voom or limma-trend
     </description>
@@ -72,6 +72,10 @@
     #end if
 #end if
 
+#if $out.plots:
+    -P $out.plots
+#end if
+
 #if $out.normCounts:
     -x
 #end if
@@ -202,9 +206,9 @@
 
         <!-- Contrasts -->
         <repeat name="rep_contrast" title="Contrast" min="1" default="1">
-            <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">
+            <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For differences between contrasts use e.g. (Mut1-WT)-(Mut2-WT). For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">
                 <validator type="empty_field" />
-                <validator type="regex" message="Please only use letters, numbers or underscores">^[\w-]+$</validator>
+                <validator type="regex" message="Please only use letters, numbers or underscores">^[\(\w\)-]+$</validator>
             </param>
         </repeat>
 
@@ -250,6 +254,15 @@
 
         <!-- Output Options -->
         <section name="out" expanded="false" title="Output Options">
+            <param name="plots" type="select" display="checkboxes" multiple="True" optional="True" label="Additional Plots" help="Select additional plots to output in the report and as PDFs">
+                <option value="d">Density Plots (if filtering)</option>
+                <option value="c">CpmsVsCounts Plots (if filtering on cpms)</option>
+                <option value="b">Box Plots (if normalising)</option>
+                <option value="x">MDS Extra (Dims 2vs3 and 3vs4)</option>
+                <option value="m">MD Plots for individual samples</option>
+                <option value="h">Heatmaps (top DE genes) </option>
+                <option value="s">Stripcharts (top DE genes)</option>
+            </param>
             <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
                 label="Output Normalised Counts Table?"
                 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
@@ -278,9 +291,9 @@
             <param name="treat" type="boolean" truevalue="1" falsevalue="0" checked="False"
                 label="Test significance relative to a fold-change threshold (TREAT)"
                 help="If you want to apply a cut-off on a fold change the TREAT function can be used, see Help section below. Default: No"/>
-            <param name="topgenes" type="integer" value="10" min="0"
-                label="Number of genes to highlight in Volcano plot and Heatmap"
-                help="The top DE genes will be highlighted in the Volcano plot for each contrast and output in a heatmap PDF. Default: 10."/>
+            <param name="topgenes" type="integer" value="10" min="0" max="100"
+                label="Number of genes to highlight in Volcano plot, Heatmap and Stripcharts"
+                help="The top DE genes will be highlighted in the Volcano plot for each contrast and can be output in heatmap and stripchart PDFs (max 100). Default: 10."/>
             <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM">
                 <option value="TMM" selected="true">TMM</option>
                 <option value="RLE">RLE</option>