Merge pull request #6130 from MaraBesemer/main

add color palette to ampvis2 heatmap
galaxyproject · Nov 16, 2024 · 94142a1 · 94142a1
2 parents 64c7062 + 0807ba5
commit 94142a1
Showing 1 changed file with 18 additions and 3 deletions.
diff --git a/tools/ampvis2/heatmap.xml b/tools/ampvis2/heatmap.xml
@@ -1,4 +1,4 @@
-<tool id="ampvis2_heatmap" name="ampvis2 heatmap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
+<tool id="ampvis2_heatmap" name="ampvis2 heatmap" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" license="MIT">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -63,7 +63,7 @@
                 #if $scale_by
                     scale_by = "$scale_by",
                 #end if
-                ## color_vector = NULL
+                 color_vector = c("$color_palette_start", "$color_palette_end"),
                 ## round = 1,
                 #if $output_options.out_format == "tabular"
                     textmap = TRUE,
@@ -150,6 +150,8 @@
                 </param>
             </when>
         </conditional>
+        <param argument="color_palette_start" type="color" label="Start color for the heatmap" help="Choose the start color for the heatmap."/>
+        <param argument="color_palette_end" type="color" label="End color for the heatmap" help="Choose the end color for the heatmap."/>
         <!-- https://github.com/KasperSkytte/ampvis2/issues/168 
             if this is possible again reuse: metadata_sample_or_variable_select ? -->
         <expand macro="metadata_sample_select" argument="normalise_by" label="Normalize counts by a variable or a specific sample"/>
@@ -294,6 +296,19 @@
             </conditional>
             <output name="plot" value="AalborgWWTPs-heatmap-plot_foo_file.pdf" ftype="pdf" compare="sim_size"/>
         </test>
+        <!-- test with different color palettes -->
+        <test expect_num_outputs="1">
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
+            <param name="color_palette_start" value="red"/>
+            <param name="color_palette_end" value="yellow"/>
+            <output name="plot" value="AalborgWWTPs-heatmap-red-yellow.pdf" ftype="pdf" compare="sim_size"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
+            <param name="color_palette_start" value="blue"/>
+            <param name="color_palette_end" value="green"/>
+            <output name="plot" value="AalborgWWTPs-heatmap-blue-green.pdf" ftype="pdf" compare="sim_size"/>
+        </test>
 
     </tests>
     <help><![CDATA[
@@ -330,4 +345,4 @@ Heatmap in the chosen output format.
 If table output is chosen the data presented in the heatmap is written into a tabular dataset.
     ]]></help>
     <expand macro="citations"/>
-</tool>
+</tool>