diff imagej2_find_maxima.xml @ 3:4409f9eb9433 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56

--- a/imagej2_find_maxima.xml	Sun Nov 05 14:19:21 2023 +0000
+++ b/imagej2_find_maxima.xml	Wed Sep 25 15:58:30 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="imagej2_find_maxima" name="Find maxima" version="@WRAPPER_VERSION@.2">
+<tool id="imagej2_find_maxima" name="Find maxima" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description>with ImageJ2</description>
     <macros>
         <import>imagej2_macros.xml</import>
@@ -13,9 +13,8 @@
     <expand macro="fiji_requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 #import os
-#set error_log = 'output_log.txt'
 #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' '$input_with_ext' &&
 #if str($output_type) == 'List' or str($output_type) == 'Count':
     #set list_or_count = True
@@ -24,10 +23,8 @@
     touch '$output_filename' &&
     #set list_or_count = False
 #end if
-touch '$error_log' &&
 ImageJ --ij2 --headless --debug
 --jython '$__tool_directory__/imagej2_find_maxima_jython_script.py'
-'$error_log'
 '$input_with_ext'
 '$scale_when_converting'
 '$weighted_rgb_conversions'
@@ -42,16 +39,11 @@
     '$output_filename'
     '$input.ext'
 #end if
-&>'$error_log';
-if [[ $? -ne 0 ]]; then
-    cat '$error_log' >&2;
-else
-    #if $list_or_count:
-        mv '$results' '$output';
-    #else:
-        mv '$output_filename' '$output';
-    #end if
-fi
+#if $list_or_count
+    && mv '$results' '$output';
+#else
+    && mv '$output_filename' '$output';
+#end if
 ]]></command>
     <inputs>
         <expand macro="param_input"/>
@@ -89,27 +81,28 @@
         <data name="output" format_source="input">
             <filter>output_type != "List" and output_type != "Count"</filter>
         </data>
+        <!-- see comment at output_type parameter
         <data name="results" format="tabular">
             <filter>output_type == "List" or output_type == "Count"</filter>
-        </data>
+        </data> -->
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input" value="blobs.gif"/>
-            <output name="output" file="blobs_single_points.gif" compare="sim_size"/>
+            <output name="output" file="blobs_single_points.gif" compare="image_diff"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input" value="blobs.gif"/>
             <param name="noise_tolerance" value="13"/>
             <param name="output_type" value="Maxima_Within_Tolerance"/>
-            <output name="output" file="blobs_tolerance.gif" compare="sim_size"/>
+            <output name="output" file="blobs_tolerance.gif" compare="image_diff"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input" value="blobs.gif"/>
             <param name="noise_tolerance" value="16"/>
             <param name="output_type" value="Segmented_Particles"/>
             <param name="exclude_edge_maxima" value="yes"/>
-            <output name="output" file="blobs_segmented.gif" compare="sim_size"/>
+            <output name="output" file="blobs_segmented.gif" compare="image_diff"/>
         </test>
         <!--
         This version of Fiji does not produce the same resultsTable