Mercurial > repos > imgteam > imagej2_analyze_skeleton

diff imagej2_analyze_skeleton.xml @ 3:50f2b961b192 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author imgteam
date Wed, 25 Sep 2024 16:09:42 +0000
parents bdee06a1bcfa
children
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--- a/imagej2_analyze_skeleton.xml	Sun Nov 05 14:21:17 2023 +0000
+++ b/imagej2_analyze_skeleton.xml	Wed Sep 25 16:09:42 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="imagej2_analyze_skeleton" name="Analyze skeleton" version="@WRAPPER_VERSION@.1">
+<tool id="imagej2_analyze_skeleton" name="Analyze skeleton" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description>with ImageJ2</description>
     <macros>
         <import>imagej2_macros.xml</import>
@@ -13,13 +13,11 @@
     <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' '$input_with_ext' &&
 ImageJ --ij2 --headless --debug
 --jython '$__tool_directory__/imagej2_analyze_skeleton_jython_script.py'
-'$error_log'
 '$input_with_ext'
 '$black_background'
 '$prune_cycle_method'
@@ -27,10 +25,6 @@
 '$calculate_largest_shortest_path'
 'no'
 '$output'
-&>'$error_log';
-if [[ $? -ne 0 ]]; then
-    cat '$error_log' >&2;
-fi
 ]]></command>
     <inputs>
         <expand macro="param_input"/>