Mercurial > repos > imgteam > imagej2_smooth
view imagej2_smooth.xml @ 3:c11777ffe5b1 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author | imgteam |
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date | Wed, 25 Sep 2024 16:05:45 +0000 |
parents | 6d7dd2194b4c |
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<tool id="imagej2_smooth" name="Smooth image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> <description>with ImageJ2</description> <macros> <import>imagej2_macros.xml</import> </macros> <edam_operations> <edam_operation>operation_3443</edam_operation> </edam_operations> <xrefs> <xref type="bio.tools">imagej</xref> <xref type="biii">imagej2</xref> </xrefs> <expand macro="fiji_requirements"/> <command detect_errors="exit_code"><![CDATA[ #import os #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0] #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 '$__tool_directory__/imagej2_smooth_jython_script.py' '$input_with_ext' '$output_filename' '$input.ext' && mv '$output_filename' '$output'; ]]></command> <inputs> <expand macro="param_input"/> </inputs> <outputs> <data name="output" format_source="input"/> </outputs> <tests> <test> <param name="input" value="blobs.gif"/> <output name="output" file="blobs_smooth.gif" compare="image_diff"/> </test> </tests> <help> **What it does** <![CDATA[ Blurs the image by replacing each pixel with the average of its 3x3 neighborhood. ]]> </help> <expand macro="fiji_headless_citations"/> </tool>