--- a/imagej2_bunwarpj_align.xml	Sun Nov 05 10:51:33 2023 +0000
+++ b/imagej2_bunwarpj_align.xml	Wed Sep 25 15:56:56 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="imagej2_bunwarpj_align" name="Align two images" version="@WRAPPER_VERSION@.1">
+<tool id="imagej2_bunwarpj_align" name="Align two images" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description>with ImageJ2</description>
     <macros>
         <import>imagej2_macros.xml</import>
@@ -20,10 +20,10 @@
 #set source_out_suffix = '.' + str($source_out_datatype)
 #set target_out_suffix = '.' + str($target_out_datatype)
 #set source_image_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0]
-#set source_image_with_ext = '.'.join([$source_image_sans_ext, $source_image.ext])
+#set source_image_with_ext = './' + '.'.join([$source_image_sans_ext, $source_image.ext])
 ln -s '$source_image.file_name' '$source_image_with_ext';
 #set target_image_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0]
-#set target_image_with_ext = '.'.join([$target_image_sans_ext, $target_image.ext])
+#set target_image_with_ext = './' + '.'.join([$target_image_sans_ext, $target_image.ext])
 ln -s '$target_image.file_name' '$target_image_with_ext';
 
 #set save_transformation = str($advanced_options_cond.advanced_options) == 'save_transformation'
@@ -33,11 +33,11 @@
 
 #if str($align_with_mask_cond.align_with_mask) == 'yes':
     #set source_mask_sans_ext = $os.path.splitext($os.path.basename($align_with_mask_cond.source_mask.file_name))[0]
-    #set source_mask_with_ext = '.'.join([$source_mask_sans_ext, $source_mask.ext])
+    #set source_mask_with_ext =  './' + '.'.join([$source_mask_sans_ext, $source_mask.ext])
     #set source_mask = $source_mask_with_ext
     ln -s '$align_with_mask_cond.source_mask.file_name' '$source_mask_with_ext';
     #set target_mask_sans_ext = $os.path.splitext($os.path.basename($align_with_mask_cond.target_mask.file_name))[0]
-    #set target_mask_with_ext = '.'.join([$target_mask_sans_ext, $target_mask.ext])
+    #set target_mask_with_ext =  './' + '.'.join([$target_mask_sans_ext, $target_mask.ext])
     #set target_mask = $target_mask_with_ext
     ln -s '$align_with_mask_cond.target_mask.file_name' '$target_mask_with_ext';
 #else:
@@ -65,7 +65,8 @@
 touch '$tmp_source_out_transf_name';
 
 ## Align the two images using bUnwarpJ.
-bunwarpj -align
+## The option -XX:ActiveProcessorCount="1" was set in version 20231211 to ensure reproducibility
+bunwarpj -XX:ActiveProcessorCount="1" -align
 '$target_image_with_ext'
 '$target_mask'
 '$source_image_with_ext'
@@ -97,14 +98,10 @@
 #if $save_transformation:
     '-save_transformation'
 #end if
-&>'$error_log';
 #if $save_transformation:
-    mv '$tmp_source_out_transf_name' '$source_trans_out';
-    mv '$tmp_target_out_transf_name' '$target_trans_out';
+    && mv '$tmp_source_out_transf_name' '$source_trans_out'
+    && mv '$tmp_target_out_transf_name' '$target_trans_out';
 #end if
-if [[ $? -ne 0 ]]; then
-    cat '$error_log' >&2;
-fi
 ]]></command>
     <inputs>
         <expand macro="param_target_image"/>
@@ -207,32 +204,32 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <!-- Align two images without landmarks or mask and not saving transformation matrices -->
             <expand macro="test_target_source_images"/>
             <param name="max_subsamp_fact" value="1"/>
-            <output name="source_out" file="registered_source1.png" compare="sim_size"/>
-            <output name="target_out" file="registered_target1.png" compare="sim_size"/>
+            <output name="source_out" file="registered_source1_forced1cpu.png" compare="image_diff"/>
+            <output name="target_out" file="registered_target1_forced1cpu.png" compare="image_diff"/>
         </test>
-        <test>
+        <test expect_num_outputs="4">
             <!-- Align two images without landmarks or mask, but saving transformation matrices -->
             <expand macro="test_target_source_images"/>
             <param name="max_subsamp_fact" value="1"/>
             <param name="advanced_options" value="save_transformation"/>
-            <output name="source_out" file="registered_source1.png" compare="sim_size"/>
-            <output name="target_out" file="registered_target1.png" compare="sim_size"/>
+            <output name="source_out" file="registered_source1_forced1cpu.png" compare="image_diff"/>
+            <output name="target_out" file="registered_target1_forced1cpu.png" compare="image_diff"/>
             <output name="source_trans_out" file="source_elastic_transformation_out.txt" compare="contains"/>
             <output name="target_trans_out" file="target_elastic_transformation_out.txt" compare="contains"/>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <!-- Align two images without landmarks but with mask, not saving transformation matrices -->
             <expand macro="test_target_source_images"/>
             <param name="align_with_mask" value="yes"/>
             <param name="target_mask" value="mask_white.png"/>
             <param name="source_mask" value="mask_ramp.gif"/>
             <param name="max_subsamp_fact" value="1"/>
-            <output name="source_out" file="registered_source2.png" compare="sim_size"/>
-            <output name="target_out" file="registered_target2.png" compare="sim_size"/>
+            <output name="source_out" file="registered_source2_forced1cpu.png" compare="image_diff"/>
+            <output name="target_out" file="registered_target2_forced1cpu.png" compare="image_diff"/>
         </test>
     </tests>
     <help>