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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 16:08:55 +0000 |
parents | fa64e8aed5a5 |
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<tool id="imagej2_bunwarpj_adapt_transform" name="Adapt an elastic transformation" 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 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, $source_image.ext]) ln -s '$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, $target_image.ext]) ln -s '$target_image.file_name' '$target_with_ext' && bunwarpj -adapt_transform '$target_with_ext' '$source_with_ext' '$input_elastic_transformation' '$output' $image_size_factor ]]></command> <inputs> <expand macro="param_target_image"/> <expand macro="param_source_image"/> <param format="txt" name="input_elastic_transformation" type="data" label="Target inverse transformation"/> <param name="image_size_factor" type="float" value="2.0" label="Image size factor" help="Must be a positive or negative power of 2 (0.25, 0.5, 2, 4, 8, etc)"/> </inputs> <outputs> <data name="output" format="txt"/> </outputs> <tests> <test> <expand macro="test_target_source_images"/> <param name="input_elastic_transformation" value="source_elastic_transformation.txt"/> <output name="output" file="adapted_transformation.txt" ftype="txt"/> </test> </tests> <help> **What it does** <![CDATA[ Transforms the coefficients of an elastic transformation according to a real image factor. This is useful, for example, for very large images, where sub-sampled versions of the image (e.g., 4 times smaller) can be registered with the resulting transformations adapted to the smaller image size (image factor = 4) so they can be applied to the high resolution images. ]]> </help> <expand macro="bunwarpj_citations"/> </tool>