Mercurial > repos > imgteam > imagej2_binary_to_edm
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
| author | imgteam |
|---|---|
| date | Wed, 25 Sep 2024 16:07:20 +0000 |
| parents | 182994b12622 |
| children |
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--- 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>