Mercurial > repos > imgteam > imagej2_bunwarpj_compare_elastic_raw
diff imagej2_bunwarpj_compare_elastic_raw.xml @ 3:da91b5eaf92d draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
| author | imgteam |
|---|---|
| date | Wed, 25 Sep 2024 16:16:58 +0000 |
| parents | 3d5f59603e13 |
| children |
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--- a/imagej2_bunwarpj_compare_elastic_raw.xml Sun Nov 05 10:56:36 2023 +0000 +++ b/imagej2_bunwarpj_compare_elastic_raw.xml Wed Sep 25 16:16:58 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="imagej2_bunwarpj_compare_elastic_raw" name="Compare elastic and raw deformation" version="@WRAPPER_VERSION@.1"> +<tool id="imagej2_bunwarpj_compare_elastic_raw" name="Compare elastic and raw deformation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> <description>with ImageJ2</description> <macros> <import>imagej2_macros.xml</import> @@ -15,10 +15,10 @@ #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' '$target_with_ext' && bunwarpj -compare_elastic_raw '$target_with_ext' @@ -26,12 +26,8 @@ '$target_elastic_transformation' '$source_raw_transformation' '$output' -&>'$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"/>