From 07aba15c8f753d650fee9cdd455896a77086a615 Mon Sep 17 00:00:00 2001
From: Leonid Kostrykin <void@evoid.de>
Date: Thu, 17 Oct 2024 13:34:52 +0200
Subject: [PATCH] [skip ci] Fix `remote_repository_url` of
 `color_deconvolution` tool (#139)

* Fix `remote_repository_url` in .shed.yml

* Increment version

Also rename: color-deconvolution.xml -> color_deconvolution.xml

* Fix XML formatting

* Fix dependency versions and tests
---
 tools/color_deconvolution/.shed.yml           |   2 +-
 ...onvolution.xml => color_deconvolution.xml} |  51 +++++++++++-------
 tools/color_deconvolution/creators.xml        |   1 +
 .../test-data/galaxyIcon_noText.tiff          | Bin 0 -> 4172 bytes
 tools/color_deconvolution/tests.xml           |   1 +
 5 files changed, 34 insertions(+), 21 deletions(-)
 rename tools/color_deconvolution/{color-deconvolution.xml => color_deconvolution.xml} (69%)
 create mode 120000 tools/color_deconvolution/creators.xml
 create mode 100644 tools/color_deconvolution/test-data/galaxyIcon_noText.tiff
 create mode 120000 tools/color_deconvolution/tests.xml

diff --git a/tools/color_deconvolution/.shed.yml b/tools/color_deconvolution/.shed.yml
index 05dbe697..38e59e2d 100644
--- a/tools/color_deconvolution/.shed.yml
+++ b/tools/color_deconvolution/.shed.yml
@@ -5,4 +5,4 @@ long_description: This tools does color space transformation using preset transf
 name: color_deconvolution 
 owner: imgteam
 homepage_url: https://github.com/bmcv
-remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/
+remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/
diff --git a/tools/color_deconvolution/color-deconvolution.xml b/tools/color_deconvolution/color_deconvolution.xml
similarity index 69%
rename from tools/color_deconvolution/color-deconvolution.xml
rename to tools/color_deconvolution/color_deconvolution.xml
index a420542e..e16f2ebd 100644
--- a/tools/color_deconvolution/color-deconvolution.xml
+++ b/tools/color_deconvolution/color_deconvolution.xml
@@ -1,5 +1,14 @@
-<tool id="ip_color_deconvolution" name="Perform color decomposition" version="0.8-2"> 
+<tool id="ip_color_deconvolution" name="Perform color decomposition" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 
     <description></description>
+    <macros>
+        <import>creators.xml</import>
+        <import>tests.xml</import>
+        <token name="@TOOL_VERSION@">0.8</token>
+        <token name="@VERSION_SUFFIX@">2</token>
+    </macros>
+    <creator>
+        <expand macro="creators/bmcv"/>
+    </creator>
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>
     </edam_operations>
@@ -7,11 +16,11 @@
         <xref type="bio.tools">galaxy_image_analysis</xref>
     </xrefs>
     <requirements>
-        <requirement type="package" version="0.14.2">scikit-image</requirement>
-        <requirement type="package" version="4.0.0">pillow</requirement>
-        <requirement type="package" version="0.18.1">scikit-learn</requirement>
-        <requirement type="package" version="1.12">numpy</requirement>
-        <requirement type="package" version="0.15.1">tifffile</requirement>
+        <requirement type="package" version="0.24.0">scikit-image</requirement>
+        <requirement type="package" version="11.0.0">pillow</requirement>
+        <requirement type="package" version="1.5.2">scikit-learn</requirement>
+        <requirement type="package" version="2.1.2">numpy</requirement>
+        <requirement type="package" version="2024.9.20">tifffile</requirement>
     </requirements>
     <command detect_errors="aggressive">
         <![CDATA[ 
@@ -74,26 +83,28 @@
         <test>
             <param name="input" value="galaxyIcon_noText.png" />
             <param name="convtype" value="rgb2hsv" />
-            <output name="output" ftype="tiff" />
+            <expand macro="tests/intensity_image_diff" name="output" value="galaxyIcon_noText.tiff" ftype="tiff"/>
         </test>
     </tests>
     <help>
-    **What it does**
 
-    This tools performs several color deconvolution techniques.</help>
+        **What it does**
+
+        This tools performs several color deconvolution techniques.
+
+    </help>
     <citations>
       <citation type="doi">10.7717/peerj.453</citation>
       <citation type="bibtex">@inproceedings{sklearn_api,
-  author    = {Lars Buitinck and Gilles Louppe and Mathieu Blondel and
-               Fabian Pedregosa and Andreas Mueller and Olivier Grisel and
-               Vlad Niculae and Peter Prettenhofer and Alexandre Gramfort
-               and Jaques Grobler and Robert Layton and Jake VanderPlas and
-               Arnaud Joly and Brian Holt and Ga{\"{e}}l Varoquaux},
-  title     = {{API} design for machine learning software: experiences from the scikit-learn
-               project},
-  booktitle = {ECML PKDD Workshop: Languages for Data Mining and Machine Learning},
-  year      = {2013},
-  pages = {108--122},
-}</citation>
+            author = {Lars Buitinck and Gilles Louppe and Mathieu Blondel and
+                      Fabian Pedregosa and Andreas Mueller and Olivier Grisel and
+                      Vlad Niculae and Peter Prettenhofer and Alexandre Gramfort
+                      and Jaques Grobler and Robert Layton and Jake VanderPlas and
+                      Arnaud Joly and Brian Holt and Ga{\"{e}}l Varoquaux},
+            title = {{API} design for machine learning software: experiences from the scikit-learn project},
+            booktitle = {ECML PKDD Workshop: Languages for Data Mining and Machine Learning},
+            year = {2013},
+            pages = {108--122},
+        }</citation>
     </citations>
 </tool>
diff --git a/tools/color_deconvolution/creators.xml b/tools/color_deconvolution/creators.xml
new file mode 120000
index 00000000..5d2b71e0
--- /dev/null
+++ b/tools/color_deconvolution/creators.xml
@@ -0,0 +1 @@
+../../macros/creators.xml
\ No newline at end of file
diff --git a/tools/color_deconvolution/test-data/galaxyIcon_noText.tiff b/tools/color_deconvolution/test-data/galaxyIcon_noText.tiff
new file mode 100644
index 0000000000000000000000000000000000000000..f6bff729d5f1e5e6d4c6d679114ae29b21d260bf
GIT binary patch
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diff --git a/tools/color_deconvolution/tests.xml b/tools/color_deconvolution/tests.xml
new file mode 120000
index 00000000..e20d710a
--- /dev/null
+++ b/tools/color_deconvolution/tests.xml
@@ -0,0 +1 @@
+../../macros/tests.xml
\ No newline at end of file