--- a/binary2label.xml	Wed Dec 18 09:56:41 2019 +0000
+++ b/binary2label.xml	Mon May 12 08:15:32 2025 +0000
@@ -1,30 +1,83 @@
-<tool id="ip_binary_to_labelimage" name="Binary 2 Label" version="0.4"> 
-    <description>Converts Binary to Label Image</description>
+<tool id="ip_binary_to_labelimage" name="Convert binary image to label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description></description>
+    <macros>
+        <import>creators.xml</import>
+        <token name="@TOOL_VERSION@">0.6</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <creator>
+        <expand macro="creators/bmcv"/>
+    </creator>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">galaxy_image_analysis</xref>
+    </xrefs>
     <requirements>
-        <requirement type="package" version="0.12.3">scikit-image</requirement> 
-        <requirement type="package" version="0.15.1">tifffile</requirement>
+        <requirement type="package" version="0.4.0">giatools</requirement>
+        <requirement type="package" version="1.12.0">scipy</requirement>
     </requirements>
     <command detect_errors="aggressive">
         <![CDATA[
-        python '$__tool_directory__/binary2label.py' '$input' '$output'
+        #if str($mode.mode_selector) == 'cca':
+            python '$__tool_directory__/binary2label.py' '$input' '$output'
+        #elif str($mode.mode_selector) == 'watershed':
+            python '$__tool_directory__/2d_split_binaryimage_by_watershed.py' '$input' '$output' $min_distance
+        #end if
         ]]>
     </command>
     <inputs>
-        <param name="input" type="data" format="tiff,png,jpg,bmp" label="Binary Image File"/>
+        <param name="input" type="data" format="tiff,png,jpg,bmp" label="Binary image"/>
+        <conditional name="mode">
+            <param name="mode_selector" type="select" label="Mode">
+                <option value="cca" selected="true">Connected component analysis</option>
+                <option value="watershed">Watershed transform</option>
+            </param>
+            <when value="cca">
+            </when>
+            <when value="watershed">
+                <param name="min_distance" type="integer" min="0" value="5" label="Minimum distance between two objects" />
+            </when>
+        </conditional>
     </inputs>
     <outputs>
         <data format="tiff" name="output"/>
     </outputs>
     <tests>
         <test>
-            <param name="input" value="galaxyIcon_noText.tif" />
-            <output name="output" value="label.tif" ftype="tiff" compare="sim_size"/>
+            <param name="input" value="galaxyIcon_noText.tiff" />
+            <conditional name="mode">
+                <param name="mode_selector" value="cca" />
+            </conditional>
+            <output name="output" value="label.tiff" ftype="tiff" compare="image_diff"/>
+        </test>
+        <test>
+            <param name="input" value="in.tiff"/>
+            <conditional name="mode">
+                <param name="mode_selector" value="watershed" />
+                <param name="min_distance" value="10" />
+            </conditional>
+            <output name="output" value="out.tiff" ftype="tiff" compare="image_diff"/>
+        </test>
+        <test>
+            <param name="input" value="uint8_z12_x11_y10.tiff"/>
+            <conditional name="mode">
+                <param name="mode_selector" value="cca" />
+            </conditional>
+            <output name="output" value="uint8_z12_x11_y10-output.tiff" ftype="tiff" compare="image_diff">
+                <assert_contents>
+                    <has_image_width width="11"/>
+                    <has_image_height height="10"/>
+                    <has_image_depth depth="12"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help>
-    **What it does**
+    This tool assigns each object a unique label.
 
-    This tool assigns every object an own grey value.
+    Individual objects are determined using connected component analysis, or distance transform and watershed.
     </help>
     <citations>
         <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>