Mercurial > repos > imgteam > imagej2_bunwarpj_elastic_transform
diff imagej2_bunwarpj_elastic_transform.xml @ 0:301f24849032 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author | imgteam |
---|---|
date | Tue, 17 Sep 2019 17:10:48 -0400 |
parents | |
children | 39b2bc251b2f |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_bunwarpj_elastic_transform.xml Tue Sep 17 17:10:48 2019 -0400 @@ -0,0 +1,61 @@ +<?xml version='1.0' encoding='UTF-8'?> +<tool id="imagej2_bunwarpj_elastic_transform" name="Apply elastic transformation" version="@WRAPPER_VERSION@.0"> + <description>with bUnwarpJ</description> + <macros> + <import>imagej2_macros.xml</import> + </macros> + <expand macro="fiji_requirements" /> + <command> +<![CDATA[ + python $__tool_directory__/imagej2_bunwarpj_elastic_transform.py + --target_image "$target_image" + --target_image_format $target_image.ext + --source_image "$source_image" + --source_image_format $source_image.ext + --elastic_transformation $elastic_transformation + --source_out "$source_out" + --source_out_datatype $source_out_datatype + --jython_script $__tool_directory__/imagej2_bunwarpj_elastic_transform_jython_script.py +]]> + </command> + <inputs> + <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/> + <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/> + <!-- Support for a bUnwarpJ elastic transformation datatype should be added to Galaxy --> + <param format="txt" name="elastic_transformation" type="data" label="Elastic transformation" help="As saved by bUnwarpJ in elastic format"/> + <param name="source_out_datatype" type="select" label="Save registered source image as format"> + <expand macro="image_datatypes" /> + </param> + </inputs> + <outputs> + <data name="source_out" format="png" label="${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="elastic_transformation" value="blobs_direct_transf.txt" /> + <param name="source_out_datatype" value="png" /> + <output name="source_out" file="elastic_trans_registered_source1.png" compare="sim_size" /> + </test> + </tests> + <help> +**What it does** + +<![CDATA[ +Applies an elastic transformation to an image, producing another image which is elastically +deformed according to the transformation. The 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>