Mercurial > repos > imgteam > imagej2_bunwarpj_raw_transform
view imagej2_bunwarpj_raw_transform.xml @ 0:95b7592729e2 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author | imgteam |
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date | Tue, 17 Sep 2019 17:03:42 -0400 |
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children | aa4a5a8c4cfd |
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<?xml version='1.0' encoding='UTF-8'?> <tool id="imagej2_bunwarpj_raw_transform" name="Apply raw transformation" version="@WRAPPER_VERSION@.0"> <description>with bUnwarpJ</description> <macros> <import>imagej2_macros.xml</import> </macros> <expand macro="fiji_requirements" /> <command> <![CDATA[ python $__tool_directory__/imagej2_bunwarpj_raw_transform.py --target_image "$target_image" --target_image_format $target_image.ext --source_image "$source_image" --source_image_format $source_image.ext --raw_transformation $raw_transformation --source_out "$source_out" --source_out_datatype $source_out_datatype --jython_script $__tool_directory__/imagej2_bunwarpj_raw_transform_jython_script.py ]]> </command> <inputs> <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/> <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/> <!-- Support for a bUnwarpJ raw transformation datatype should be added to Galaxy --> <param format="txt" name="raw_transformation" type="data" label="Elastic transformation" help="As saved by bUnwarpJ in raw format"/> <param name="source_out_datatype" type="select" label="Save registered source image as format"> <expand macro="image_datatypes" /> </param> </inputs> <outputs> <data name="source_out" format="png" label="${tool.name} on ${on_string}: Registered source image"> <actions> <action type="format"> <option type="from_param" name="source_out_datatype" /> </action> </actions> </data> </outputs> <tests> <test> <param name="target_image" value="dotblot.jpg" /> <param name="source_image" value="blobs.gif" /> <param name="raw_transformation" value="source_raw_transformation.txt" /> <param name="source_out_datatype" value="png" /> <output name="source_out" file="raw_trans_registered_source1.png" compare="sim_size" /> </test> </tests> <help> **What it does** <![CDATA[ Applies a raw transformation to an image, producing another image which is deformed according to the transformation. The transformation file must be in the same format as the files created with the **Convert elastic transformation to raw with bUnwarpJ** tool. ]]> </help> <expand macro="bunwarpj_citations" /> </tool>