Mercurial > repos > imgteam > imagej2_bunwarpj_compose_raw_elastic
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author | imgteam |
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date | Sun, 05 Nov 2023 14:23:45 +0000 |
parents | 8d357579e407 |
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<tool id="imagej2_bunwarpj_compose_raw_elastic" name="Compose a raw and an elastic transformation" version="@WRAPPER_VERSION@.1"> <description>into a raw transformation with bUnwarpJ</description> <macros> <import>imagej2_macros.xml</import> </macros> <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' '$target_with_ext' && bunwarpj -compose_raw_elastic '$target_with_ext' '$source_with_ext' '$target_raw_transformation' '$source_elastic_transformation' '$output' &>'$output_log'; if [[ $? -ne 0 ]]; then cat '$output_log' >&2; fi ]]></command> <inputs> <expand macro="param_target_image"/> <expand macro="param_source_image"/> <param format="txt" name="target_raw_transformation" type="data" label="Target inverse transformation"/> <param format="txt" name="source_elastic_transformation" type="data" label="Source direct transformation"/> </inputs> <outputs> <data name="output" format="txt"/> </outputs> <tests> <test> <expand macro="test_target_source_images"/> <param name="target_raw_transformation" value="target_raw_transformation.txt"/> <param name="source_elastic_transformation" value="source_elastic_transformation.txt"/> <output name="output" file="composed_raw_elastic_transformation.txt" compare="contains"/> </test> </tests> <help> **What it does** <![CDATA[ Composes one raw transformation and one elastic transformation into a raw transformation. ]]> </help> <expand macro="bunwarpj_citations"/> </tool>