Mercurial > repos > imgteam > imagej2_bunwarpj_convert_to_raw
view imagej2_bunwarpj_convert_to_raw.xml @ 2:0cdd96322600 draft default tip
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 11:00:42 +0000 |
parents | 7f9840d3b7e7 |
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<tool id="imagej2_bunwarpj_convert_to_raw" name="Convert elastic transformation to raw" version="@WRAPPER_VERSION@.1"> <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' '$target_with_ext' && bunwarpj -convert_to_raw '$target_with_ext' '$source_with_ext' '$elastic_transformation' '$raw_transformation' &>'$output_log'; if [[ $? -ne 0 ]]; then cat '$output_log' >&2; fi ]]></command> <inputs> <expand macro="param_target_image"/> <expand macro="param_source_image"/> <!-- Support for a bUnwarpJ elastic transformation datatype should be added to Galaxy --> <param format="txt" name="elastic_transformation" type="data" label="Elastic transformation" help="As saved by bUnwarpJ in elastic format"/> </inputs> <outputs> <!-- Support for a bUnwarpJ raw transformation datatype should be added to Galaxy --> <data name="raw_transformation" format="txt"/> </outputs> <tests> <test> <expand macro="test_target_source_images"/> <param name="elastic_transformation" value="source_elastic_transformation.txt" ftype="txt"/> <output name="raw_transformation" file="source_raw_transformation.txt" ftype="txt"/> </test> </tests> <help> **What it does** <![CDATA[ Converts an elastic (i.e., B-spline ) transformation file into a raw transformation file. The elastic transformation file must be in the same format as the files created with the **Save Transformation** option in the **Align two images with bUnwarpJ** tool. ]]> </help> <expand macro="bunwarpj_citations"/> </tool>