--- a/heatmap2.xml	Fri Oct 11 13:12:37 2024 +0000
+++ b/heatmap2.xml	Tue Nov 12 16:44:40 2024 +0000
@@ -1,7 +1,7 @@
 <tool id="ggplot2_heatmap2" name="heatmap2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
     <macros>
         <token name="@TOOL_VERSION@">3.2.0</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">r-gplots</requirement>
@@ -79,6 +79,9 @@
     #if $cluster_cond.cluster_cols_rows == "both"
         reorder_cols <- TRUE
         reorder_rows <- TRUE
+        # Layout is:
+        # 4 = color key           | 3 = dendrogram for columns
+        # 2 = dendrogram for rows | 1 = heatmap
         layout_matrix <- rbind(c(4,3), c(2,1))
         key_margins <- list(mar=c(4,0.5,2,1))
         lheight <- c(1, 5)
@@ -86,6 +89,9 @@
     #elif $cluster_cond.cluster_cols_rows == "row"
         reorder_cols <- FALSE
         reorder_rows <- TRUE
+        # Layout is:
+        # 3 = dendrogram for columns (not plotted) + title | 4 = color key
+        # 2 = dendrogram for rows                          | 1 = heatmap
         layout_matrix <- rbind(c(3,4), c(2,1))
         key_margins <- list(mar=c(3,5,1,10))
         lheight <- c(1,7)
@@ -93,10 +99,14 @@
     #elif $cluster_cond.cluster_cols_rows == "column"
         reorder_cols <- TRUE
         reorder_rows <- FALSE
-        layout_matrix <- rbind(c(4), c(3), c(1), c(2))
-        key_margins <- list(mar=c(4,0.5,2,1))
-        lheight <- c(0.3, 2, 6, 1)
-        lwidth <- c(1)
+        # Layout is:
+        # nothing                               | 4 = color key
+        # nothing                               | 3 = dendrogram for columns
+        # 2 = dendrogram for rows (not plotted) | 1 = heatmap
+        layout_matrix <- rbind(c(0, 4), c(0, 3), c(2, 1))
+        key_margins <- list(mar=c(1, 5, 1, 10))
+        lheight <- c(0.5, 1, 5)
+        lwidth <- c(0.01, 1)
     #end if
     hclust_fun <- function(x) hclust(x, method='$cluster_cond.clustering')
     #if $cluster_cond.distance == 'pearson_correlation':
@@ -283,7 +293,7 @@
             <param name="input1" value="mtcars.txt"/>
             <param name="cluster" value="no"/>
             <param name="image_file_format" value="png"/>
-            <output name="output1" file="result2.png" compare="sim_size" delta="12000" />
+            <output name="output1" file="result2.png" compare="image_diff" />
         </test>
         <test>
             <param name="input1" value="mtcars.txt"/>
@@ -293,7 +303,7 @@
             <param name="labels" value="rows"/>
             <param name="type" value="three"/>
             <param name="image_file_format" value="png"/>
-            <output name="output1" file="result3.png" compare="sim_size"/>
+            <output name="output1" file="result3.png" compare="image_diff"/>
         </test>
         <test>
             <param name="input1" value="mtcars.txt"/>
@@ -307,7 +317,7 @@
             <param name="zscore" value="rows"/>
             <param name="type" value="three"/>
             <param name="image_file_format" value="png"/>
-            <output name="output1" file="result4.png" compare="sim_size" delta="12000" />
+            <output name="output1" file="result4.png" compare="image_diff" />
         </test>
         <test>
             <param name="input1" value="mtcars.txt"/>
@@ -316,7 +326,7 @@
             <param name="scale" value="row"/>
             <param name="type" value="three"/>
             <param name="image_file_format" value="png"/>
-            <output name="output1" file="result5.png" compare="sim_size" delta="12000" />
+            <output name="output1" file="result5.png" compare="image_diff" />
         </test>
         <test>
             <param name="input1" value="mtcars.txt"/>
@@ -325,7 +335,18 @@
             <param name="scale" value="column"/>
             <param name="type" value="three"/>
             <param name="image_file_format" value="png"/>
-            <output name="output1" file="result6.png" compare="sim_size" delta="12000" />
+            <output name="output1" file="result6.png" compare="image_diff" />
+        </test>
+        <test>
+            <param name="input1" value="mtcars.txt"/>
+            <param name="cluster" value="yes"/>
+            <param name="cluster_cols_rows" value="column"/>
+            <param name="distance" value="pearson_correlation"/>
+            <param name="scale" value="row"/>
+            <param name="type" value="palettes"/>
+            <param name="name" value="YlOrBr"/>
+            <param name="image_file_format" value="png"/>
+            <output name="output1" file="result7.png" compare="image_diff" />
         </test>
     </tests>
     <help><![CDATA[