--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/colorize_labels.xml	Tue Sep 24 17:30:11 2024 +0000
@@ -0,0 +1,100 @@
+<tool id="colorize_labels" name="Colorize label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
+    <description>with NetworkX</description>
+    <macros>
+        <import>creators.xml</import>
+        <import>tests.xml</import>
+        <token name="@TOOL_VERSION@">3.2.1</token>
+        <token name="@VERSION_SUFFIX@">3</token>
+    </macros>
+    <creator>
+        <expand macro="creators/bmcv" />
+    </creator>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">networkx</requirement>
+        <requirement type="package" version="1.22">numpy</requirement>
+        <requirement type="package" version="0.18.1">scikit-image</requirement>
+        <requirement type="package" version="0.1">giatools</requirement>
+    </requirements>
+    <command><![CDATA[
+    
+    ## Inputs
+    
+    python '$__tool_directory__/colorize_labels.py' '$input'
+    --radius $radius
+    --bg_label $bg_label
+    --bg_color '$bg_color'
+    
+    ## Outputs
+    
+    --output output.png
+    
+    ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="tiff,png" label="Input image (label map)" />
+        <param argument="--radius" type="integer" min="1" value="10" label="Radius of the neighborhood" help="Defines the neighborhood (in pixels) where labels are considered to be adjacent." />
+        <param argument="--bg_label" type="integer" value="0" label="Background label" />
+        <param argument="--bg_color" type="color" value="#000000" label="Background color"/>
+    </inputs>
+    <outputs>
+       <data format="png" name="output" from_work_dir="output.png" />
+    </outputs>
+    <tests>
+        <!-- int64 -->
+        <test>
+            <param name="input" value="input1.tif" />
+            <param name="radius" value="1" />
+            <param name="bg_label" value="0" />
+            <param name="bg_color" value="#5a5a5a" />
+            <expand macro="tests/intensity_image_diff" name="output" value="output1.png" ftype="png">
+                <has_image_channels channels="3"/>
+            </expand>
+        </test>
+        <!-- uint8 -->
+        <test>
+            <param name="input" value="input2.tif" />
+            <param name="radius" value="10" />
+            <param name="bg_label" value="0" />
+            <param name="bg_color" value="#ffffff" />
+            <expand macro="tests/intensity_image_diff" name="output" value="output2.png" ftype="png">
+                <has_image_channels channels="3"/>
+            </expand>
+        </test>
+        <!-- uint16 -->
+        <test>
+            <param name="input" value="input3.tif" />
+            <param name="radius" value="100" />
+            <param name="bg_label" value="0" />
+            <param name="bg_color" value="#ffffff" />
+            <expand macro="tests/intensity_image_diff" name="output" value="output3.png" ftype="png">
+                <has_image_channels channels="3"/>
+            </expand>
+        </test>
+    </tests>
+    <help>
+
+        **Colorizes a 2-D label map for visualization using greedy coloring.**
+
+        Label maps are produced by segmentation and other image analysis steps.
+        Direct inspection of label maps can be difficult,
+        because labels usually correspond to gray values which are difficult to
+        distinguish visually from each other and from the image background.
+        To facilitate the visual inspection of label maps, this tools converts
+        label maps to color images, by assigning each label a unique color.
+
+    </help>
+    <citations>
+        <citation type="bibtex">
+        @inproceedings{networkx,
+          author = {Hagberg, Aric A. and Schult, Daniel A. and Swart, Pieter J.},
+          title = {Exploring network structure, dynamics, and function using {NetworkX}},
+          booktitle = {Proc. of the 7th Python in Science Conference (SciPy 2008)},
+          pages = {11--15},
+          year = {2008},
+        }
+        </citation>
+    </citations>
+</tool>