From b4ca101a2d1f8a6b9cf930092e3390a25ee9fbb2 Mon Sep 17 00:00:00 2001
From: MaraBesemer <118823479+MaraBesemer@users.noreply.github.com>
Date: Sun, 7 Jul 2024 11:31:13 +0200
Subject: [PATCH 1/6] add color palette to ampvis2 heatmap

---
 tools/ampvis2/heatmap.xml | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/tools/ampvis2/heatmap.xml b/tools/ampvis2/heatmap.xml
index 7f419595c88..c39ae73f985 100644
--- a/tools/ampvis2/heatmap.xml
+++ b/tools/ampvis2/heatmap.xml
@@ -63,6 +63,7 @@
                 #if $scale_by
                     scale_by = "$scale_by",
                 #end if
+                color_palette = "$color_palette",
                 ## color_vector = NULL
                 ## round = 1,
                 #if $output_options.out_format == "tabular"
@@ -150,6 +151,18 @@
                 </param>
             </when>
         </conditional>
+         <param argument="color_palette" type="select" label="Color Palette" help="Choose the color palette for the heatmap.">
+            <option value="red">Red</option>
+            <option value="green">Green</option>
+            <option value="blue">Blue</option>
+            <option value="yellow">Yellow</option>
+            <option value="orange">Orange</option>
+            <option value="purple">Purple</option>
+            <option value="brown">Brown</option>
+            <option value="pink">Pink</option>
+            <option value="gray">Gray</option>
+            <option value="cyan">Cyan</option>
+        </param>
         <!-- 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"/>
@@ -330,4 +343,4 @@ 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>
\ No newline at end of file
+</tool>

From 450b8e00d630c9e0885b12e868e46e1361042c8e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Sun, 7 Jul 2024 13:18:48 +0200
Subject: [PATCH 2/6] we need to bump the version number

---
 tools/ampvis2/heatmap.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/ampvis2/heatmap.xml b/tools/ampvis2/heatmap.xml
index c39ae73f985..33b49db814f 100644
--- 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@+galaxy2" profile="@PROFILE@" license="MIT">
     <description></description>
     <macros>
         <import>macros.xml</import>

From d0f97a402dc498cbd4395c94197b6993b92dd6d2 Mon Sep 17 00:00:00 2001
From: MaraBesemer <118823479+MaraBesemer@users.noreply.github.com>
Date: Mon, 8 Jul 2024 15:26:51 +0200
Subject: [PATCH 3/6] Update heatmap.xml

add tests for color_palette
---
 tools/ampvis2/heatmap.xml | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/tools/ampvis2/heatmap.xml b/tools/ampvis2/heatmap.xml
index 33b49db814f..ced04b53422 100644
--- a/tools/ampvis2/heatmap.xml
+++ b/tools/ampvis2/heatmap.xml
@@ -307,6 +307,17 @@
             </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" value="red"/>
+            <output name="plot" value="AalborgWWTPs-heatmap-red.pdf" ftype="pdf" compare="sim_size"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
+            <param name="color_palette" value="blue"/>
+            <output name="plot" value="AalborgWWTPs-heatmap-blue.pdf" ftype="pdf" compare="sim_size"/>
+        </test>
     
     </tests>
     <help><![CDATA[

From 5db4811a266d08fc775b051e39b00023616f2296 Mon Sep 17 00:00:00 2001
From: MaraBesemer <118823479+MaraBesemer@users.noreply.github.com>
Date: Thu, 11 Jul 2024 13:55:25 +0200
Subject: [PATCH 4/6] change color_palette into a two dimensional vector

---
 tools/ampvis2/heatmap.xml | 26 +++++++++-----------------
 1 file changed, 9 insertions(+), 17 deletions(-)

diff --git a/tools/ampvis2/heatmap.xml b/tools/ampvis2/heatmap.xml
index ced04b53422..a7f7747582e 100644
--- a/tools/ampvis2/heatmap.xml
+++ b/tools/ampvis2/heatmap.xml
@@ -63,7 +63,7 @@
                 #if $scale_by
                     scale_by = "$scale_by",
                 #end if
-                color_palette = "$color_palette",
+                 color_palette = c("$color_palette_start", "$color_palette_end"),
                 ## color_vector = NULL
                 ## round = 1,
                 #if $output_options.out_format == "tabular"
@@ -151,18 +151,8 @@
                 </param>
             </when>
         </conditional>
-         <param argument="color_palette" type="select" label="Color Palette" help="Choose the color palette for the heatmap.">
-            <option value="red">Red</option>
-            <option value="green">Green</option>
-            <option value="blue">Blue</option>
-            <option value="yellow">Yellow</option>
-            <option value="orange">Orange</option>
-            <option value="purple">Purple</option>
-            <option value="brown">Brown</option>
-            <option value="pink">Pink</option>
-            <option value="gray">Gray</option>
-            <option value="cyan">Cyan</option>
-        </param>
+        <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"/>
@@ -310,13 +300,15 @@
         <!-- test with different color palettes -->
         <test expect_num_outputs="1">
             <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
-            <param name="color_palette" value="red"/>
-            <output name="plot" value="AalborgWWTPs-heatmap-red.pdf" ftype="pdf" compare="sim_size"/>
+            <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" value="blue"/>
-            <output name="plot" value="AalborgWWTPs-heatmap-blue.pdf" ftype="pdf" compare="sim_size"/>
+            <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>

From cea68fd58a06ad3de76da5ad36e283aa64fe9837 Mon Sep 17 00:00:00 2001
From: MaraBesemer <118823479+MaraBesemer@users.noreply.github.com>
Date: Wed, 17 Jul 2024 13:48:35 +0200
Subject: [PATCH 5/6] Update heatmap.xml

chance color_palette to color_vector
---
 tools/ampvis2/heatmap.xml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tools/ampvis2/heatmap.xml b/tools/ampvis2/heatmap.xml
index a7f7747582e..92a330acf92 100644
--- a/tools/ampvis2/heatmap.xml
+++ b/tools/ampvis2/heatmap.xml
@@ -63,8 +63,7 @@
                 #if $scale_by
                     scale_by = "$scale_by",
                 #end if
-                 color_palette = c("$color_palette_start", "$color_palette_end"),
-                ## color_vector = NULL
+                 color_vector = c("$color_palette_start", "$color_palette_end"),
                 ## round = 1,
                 #if $output_options.out_format == "tabular"
                     textmap = TRUE,

From 0807ba5edd5d98ae2210f93b20003ad8c4183bda Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Sat, 16 Nov 2024 16:13:43 +0100
Subject: [PATCH 6/6] Update tools/ampvis2/heatmap.xml

---
 tools/ampvis2/heatmap.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/ampvis2/heatmap.xml b/tools/ampvis2/heatmap.xml
index 92a330acf92..7fdf009ba73 100644
--- a/tools/ampvis2/heatmap.xml
+++ b/tools/ampvis2/heatmap.xml
@@ -1,4 +1,4 @@
-<tool id="ampvis2_heatmap" name="ampvis2 heatmap" version="@TOOL_VERSION@+galaxy2" 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>