Mercurial > repos > imgteam > imagej2_shadows
diff imagej2_shadows.xml @ 3:f7ae316b00e4 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 16:02:30 +0000 |
| parents | f3c9192bd0b9 |
| children |
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--- a/imagej2_shadows.xml Sun Nov 05 14:20:40 2023 +0000 +++ b/imagej2_shadows.xml Wed Sep 25 16:02:30 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="imagej2_shadows" name="Add shadow effect" version="@WRAPPER_VERSION@.2"> +<tool id="imagej2_shadows" name="Add shadow effect" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> <description>with ImageJ2</description> <macros> <import>imagej2_macros.xml</import> @@ -13,26 +13,18 @@ <expand macro="fiji_requirements"/> <command detect_errors="exit_code"><![CDATA[ #import os -#set error_log = 'output_log.txt' -touch '$error_log' && #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' && ImageJ --ij2 --headless --debug --jython '$__tool_directory__/imagej2_shadows_jython_script.py' -'$error_log' '$input_with_ext' '$direction' '$output_filename' '$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"/> @@ -54,7 +46,7 @@ <test> <param name="input" value="blobs.gif"/> <param name="direction" value="Northwest"/> - <output name="output" file="blobs_northwest.gif" compare="sim_size"/> + <output name="output" file="blobs_northwest.gif" compare="image_diff"/> </test> </tests> <help>