diff imagej2_bunwarpj_compare_raw.xml @ 3:b0da913f048e draft default tip

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

--- a/imagej2_bunwarpj_compare_raw.xml	Sun Nov 05 14:20:02 2023 +0000
+++ b/imagej2_bunwarpj_compare_raw.xml	Wed Sep 25 15:59:18 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="imagej2_bunwarpj_compare_raw" name="Compare two raw deformations" version="@WRAPPER_VERSION@.1">
+<tool id="imagej2_bunwarpj_compare_raw" name="Compare two raw deformations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description>with ImageJ2</description>
     <macros>
         <import>imagej2_macros.xml</import>
@@ -15,22 +15,18 @@
 #import os
 #set output_log = 'output_log.txt'
 #set source_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0]
-#set source_with_ext = '.'.join([source_sans_ext, $source_image.ext])
+#set source_with_ext = './' + '.'.join([source_sans_ext, $source_image.ext])
 ln -s '$source_image.file_name' '$source_with_ext' &&
 #set target_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0]
-#set target_with_ext = '.'.join([target_sans_ext, $target_image.ext])
+#set target_with_ext = './' + '.'.join([target_sans_ext, $target_image.ext])
 ln -s '$target_image.file_name' '$target_with_ext' &&
 bunwarpj -compare_raw
 '$target_with_ext'
 '$source_with_ext'
 '$target_raw_transformation'
 '$source_raw_transformation'
-&>'$output_log';
-if [[ $? -ne 0 ]]; then
-    cat '$output_log' >&2;
-else
-    grep -Po 'Warping index = \K[^ ]+' '$output_log' > '$output';
-fi
+2>&1 | tee '$output_log'
+&& grep -Po 'Warping index = \K[^ ]+' '$output_log' > '$output'
 ]]></command>
     <inputs>
         <expand macro="param_target_image"/>