diff imagej2_binary_to_edm.xml @ 3:91b8f4730a93 draft default tip

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

--- a/imagej2_binary_to_edm.xml	Sun Nov 05 14:23:08 2023 +0000
+++ b/imagej2_binary_to_edm.xml	Wed Sep 25 16:07:20 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="imagej2_binary_to_edm" name="Convert binary image to EDM" version="@WRAPPER_VERSION@.2">
+<tool id="imagej2_binary_to_edm" name="Convert binary image to EDM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description>with ImageJ2</description>
     <macros>
         <import>imagej2_macros.xml</import>
@@ -13,16 +13,13 @@
     <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' &&
 #set output_filename = '.'.join(['output', $input.ext])
 touch '$output_filename' &&
-touch '$error_log' &&
 ImageJ --ij2 --headless --debug
 --jython '$__tool_directory__/imagej2_binary_to_edm_jython_script.py'
-'$error_log'
 '$input_with_ext'
 $iterations
 $count
@@ -30,12 +27,7 @@
 '$pad_edges_when_eroding'
 '$output_filename'
 '$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"/>
@@ -49,7 +41,7 @@
             <param name="input" value="blobs.gif"/>
             <param name="iterations" value="1"/>
             <param name="count" value="1"/>
-            <output name="output" file="blobs_edm.gif" compare="sim_size"/>
+            <output name="output" file="blobs_edm.gif" compare="image_diff" metric="iou" />
         </test>
         <test>
             <param name="input" value="blobs.gif"/>
@@ -57,7 +49,7 @@
             <param name="count" value="3"/>
             <param name="black_background" value="yes"/>
             <param name="pad_edges_when_eroding" value="yes"/>
-            <output name="output" file="blobs_black_edm.gif" compare="sim_size"/>
+            <output name="output" file="blobs_black_edm.gif" compare="image_diff" metric="iou" />
         </test>
     </tests>
     <help>