--- a/imagej2_skeletonize3d.xml	Sun Nov 05 14:26:52 2023 +0000
+++ b/imagej2_skeletonize3d.xml	Wed Sep 25 16:14:34 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="imagej2_skeletonize3d" name="Skeletonize" version="@WRAPPER_VERSION@.2">
+<tool id="imagej2_skeletonize3d" name="Skeletonize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description>with ImageJ2</description>
     <macros>
         <import>imagej2_macros.xml</import>
@@ -13,26 +13,18 @@
     <expand macro="fiji_requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 #import os
-#set error_log = 'output_log.txt'
-touch '$error_log' &&
 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
-#set input_with_ext = '.'.join([input_sans_ext, $input.ext])
+#set input_with_ext = './' + '.'.join([input_sans_ext, $input.ext])
 ln -s '$input.file_name' '$input_with_ext' &&
 #set output_filename = '.'.join(['output', $input.ext])
 touch '$output_filename' &&
 ImageJ --ij2 --headless --debug
 --jython '$__tool_directory__/imagej2_skeletonize3d_jython_script.py'
-'$error_log'
 '$input_with_ext'
 '$black_background'
 '$output_filename'
 '$input.ext'
-&>'$error_log';
-if [[ $? -ne 0 ]]; then
-    cat '$error_log' >&2;
-else
-    mv '$output_filename' '$output';
-fi
+&& mv '$output_filename' '$output';
 ]]></command>
     <inputs>
         <expand macro="param_input"/>
@@ -44,11 +36,11 @@
     <tests>
         <test>
             <param name="input" value="blobs.gif"/>
-            <output name="output" file="skeletonized_blobs.gif" compare="sim_size"/>
+            <output name="output" file="skeletonized_blobs.gif" compare="image_diff"/>
         </test>
         <test>
             <param name="input" value="clown.jpg"/>
-            <output name="output" file="skeletonized_clown.jpg" compare="sim_size"/>
+            <output name="output" file="skeletonized_clown.jpg" compare="image_diff"/>
         </test>
     </tests>
     <help>