From e9750324f7d9bb128d2fd485a8573f632c979ffa Mon Sep 17 00:00:00 2001
From: Leonid Kostrykin <void@evoid.de>
Date: Thu, 14 Mar 2024 10:27:03 +0100
Subject: [PATCH 1/6] Fix requirements

---
 tools/points2binaryimage/points2binaryimage.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/points2binaryimage/points2binaryimage.xml b/tools/points2binaryimage/points2binaryimage.xml
index 360dc016..6e6f4b92 100644
--- a/tools/points2binaryimage/points2binaryimage.xml
+++ b/tools/points2binaryimage/points2binaryimage.xml
@@ -11,7 +11,7 @@
         <requirement type="package" version="1.15.4">numpy</requirement>
         <requirement type="package" version="0.23.4">pandas</requirement>
         <requirement type="package" version="2018.7">pytz</requirement><!--pandas seems to have additional requirements that are not automatically installed-->
-        <requirement type="package" version="2.4.1">dateutil</requirement>
+        <requirement type="package" version="2.5.2">python-dateutil</requirement>
         <requirement type="package" version="0.15.1">tifffile</requirement>
     </requirements>
     <command detect_errors="aggressive">

From f9ecd89cf7abb2c9070cff3a7d3d181cb39376be Mon Sep 17 00:00:00 2001
From: Leonid Kostrykin <void@evoid.de>
Date: Thu, 14 Mar 2024 10:31:29 +0100
Subject: [PATCH 2/6] Update help

---
 tools/points2binaryimage/points2binaryimage.xml | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/tools/points2binaryimage/points2binaryimage.xml b/tools/points2binaryimage/points2binaryimage.xml
index 6e6f4b92..68cdfdd7 100644
--- a/tools/points2binaryimage/points2binaryimage.xml
+++ b/tools/points2binaryimage/points2binaryimage.xml
@@ -1,5 +1,9 @@
-<tool id="ip_points_to_binaryimage" name="Convert point coordinates to binary image" version="0.2-1">
+<tool id="ip_points_to_binaryimage" name="Convert point coordinates to binary image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
     <description></description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.2</token>
+        <token name="@VERSION_SUFFIX@">2</token>
+    </macros>
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>
     </edam_operations>
@@ -40,9 +44,13 @@
         </test>
     </tests>
     <help>
-    **What it does**
 
-    Converts CSV point file to binary image.
+        This tool converts a CSV list of points to a binary image by rasterizing the point coordinates.
+
+        The created image is a single-channel image with 16 bits per pixel (unsigned integer).
+        The points are rasterized with value 32767 (white).
+        Pixels not corresponding to any points in the CSV are assigned the value 0 (black).
+
     </help>
     <citations>
         <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 

From 8453a6f133c3d32b0845f69198f777c880dc9186 Mon Sep 17 00:00:00 2001
From: Leonid Kostrykin <void@evoid.de>
Date: Thu, 14 Mar 2024 11:25:20 +0100
Subject: [PATCH 3/6] Add creators

Squashed commit of the following:

commit 4e2755b003e87ad598bd6d223161b3423d147850
Author: Leonid Kostrykin <void@evoid.de>
Date:   Thu Mar 14 10:21:48 2024 +0000

    Add creators
---
 macros/creators/bmcv.xml                        | 5 +++++
 tools/points2binaryimage/bmcv.xml               | 1 +
 tools/points2binaryimage/points2binaryimage.xml | 1 +
 3 files changed, 7 insertions(+)
 create mode 100644 macros/creators/bmcv.xml
 create mode 120000 tools/points2binaryimage/bmcv.xml

diff --git a/macros/creators/bmcv.xml b/macros/creators/bmcv.xml
new file mode 100644
index 00000000..2f9b13f5
--- /dev/null
+++ b/macros/creators/bmcv.xml
@@ -0,0 +1,5 @@
+<macros>
+    <xml name="creator">
+        <organization name="Biomedical Computer Vision Group" alternateName="BMCV" url="http://www.bioquant.uni-heidelberg.de/research/groups/biomedical_computer_vision.html" />
+    </xml>
+</macros>
\ No newline at end of file
diff --git a/tools/points2binaryimage/bmcv.xml b/tools/points2binaryimage/bmcv.xml
new file mode 120000
index 00000000..8c33e2c4
--- /dev/null
+++ b/tools/points2binaryimage/bmcv.xml
@@ -0,0 +1 @@
+../../macros/creators/bmcv.xml
\ No newline at end of file
diff --git a/tools/points2binaryimage/points2binaryimage.xml b/tools/points2binaryimage/points2binaryimage.xml
index 68cdfdd7..c869df81 100644
--- a/tools/points2binaryimage/points2binaryimage.xml
+++ b/tools/points2binaryimage/points2binaryimage.xml
@@ -1,6 +1,7 @@
 <tool id="ip_points_to_binaryimage" name="Convert point coordinates to binary image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
     <description></description>
     <macros>
+        <import>bmcv.xml</import>
         <token name="@TOOL_VERSION@">0.2</token>
         <token name="@VERSION_SUFFIX@">2</token>
     </macros>

From 53ab3de55eb5befe0cef3c6273e65435a3edc02a Mon Sep 17 00:00:00 2001
From: Leonid Kostrykin <void@evoid.de>
Date: Thu, 14 Mar 2024 12:20:29 +0100
Subject: [PATCH 4/6] Fix creators

---
 macros/creators/bmcv.xml                        | 6 ++++--
 tools/points2binaryimage/points2binaryimage.xml | 1 +
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/macros/creators/bmcv.xml b/macros/creators/bmcv.xml
index 2f9b13f5..eedbcc55 100644
--- a/macros/creators/bmcv.xml
+++ b/macros/creators/bmcv.xml
@@ -1,5 +1,7 @@
 <macros>
     <xml name="creator">
-        <organization name="Biomedical Computer Vision Group" alternateName="BMCV" url="http://www.bioquant.uni-heidelberg.de/research/groups/biomedical_computer_vision.html" />
+        <creator>
+            <organization name="Biomedical Computer Vision Group" alternateName="BMCV" url="http://www.bioquant.uni-heidelberg.de/research/groups/biomedical_computer_vision.html" />
+        </creator>
     </xml>
-</macros>
\ No newline at end of file
+</macros>
diff --git a/tools/points2binaryimage/points2binaryimage.xml b/tools/points2binaryimage/points2binaryimage.xml
index c869df81..d96f4034 100644
--- a/tools/points2binaryimage/points2binaryimage.xml
+++ b/tools/points2binaryimage/points2binaryimage.xml
@@ -5,6 +5,7 @@
         <token name="@TOOL_VERSION@">0.2</token>
         <token name="@VERSION_SUFFIX@">2</token>
     </macros>
+    <expand macro="creator" />
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>
     </edam_operations>

From 53ddd7fbaa13a41e96409192da1cf37af918d610 Mon Sep 17 00:00:00 2001
From: Leonid Kostrykin <void@evoid.de>
Date: Thu, 14 Mar 2024 12:38:02 +0100
Subject: [PATCH 5/6] Update creators

---
 macros/creators/bmcv.xml                        | 6 ++----
 tools/points2binaryimage/points2binaryimage.xml | 4 +++-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/macros/creators/bmcv.xml b/macros/creators/bmcv.xml
index eedbcc55..66716ee4 100644
--- a/macros/creators/bmcv.xml
+++ b/macros/creators/bmcv.xml
@@ -1,7 +1,5 @@
 <macros>
-    <xml name="creator">
-        <creator>
-            <organization name="Biomedical Computer Vision Group" alternateName="BMCV" url="http://www.bioquant.uni-heidelberg.de/research/groups/biomedical_computer_vision.html" />
-        </creator>
+    <xml name="creators/bmcv">
+        <organization name="Biomedical Computer Vision Group" alternateName="BMCV" url="http://www.bioquant.uni-heidelberg.de/research/groups/biomedical_computer_vision.html" />
     </xml>
 </macros>
diff --git a/tools/points2binaryimage/points2binaryimage.xml b/tools/points2binaryimage/points2binaryimage.xml
index d96f4034..0380e6ab 100644
--- a/tools/points2binaryimage/points2binaryimage.xml
+++ b/tools/points2binaryimage/points2binaryimage.xml
@@ -5,7 +5,9 @@
         <token name="@TOOL_VERSION@">0.2</token>
         <token name="@VERSION_SUFFIX@">2</token>
     </macros>
-    <expand macro="creator" />
+    <creator>
+        <expand macro="creators/bmcv" />
+    </creator>
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>
     </edam_operations>

From 403ec07e95bc2f9a42abbfda2c3c61b7eeda6408 Mon Sep 17 00:00:00 2001
From: Leonid Kostrykin <void@evoid.de>
Date: Thu, 14 Mar 2024 15:26:44 +0100
Subject: [PATCH 6/6] Add `<yield/>` tag

---
 macros/creators/bmcv.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/macros/creators/bmcv.xml b/macros/creators/bmcv.xml
index 66716ee4..0fdcfe84 100644
--- a/macros/creators/bmcv.xml
+++ b/macros/creators/bmcv.xml
@@ -1,5 +1,6 @@
 <macros>
     <xml name="creators/bmcv">
         <organization name="Biomedical Computer Vision Group" alternateName="BMCV" url="http://www.bioquant.uni-heidelberg.de/research/groups/biomedical_computer_vision.html" />
+        <yield />
     </xml>
 </macros>