Mercurial > repos > imgteam > imagej2_bunwarpj_convert_to_raw
comparison imagej2_bunwarpj_convert_to_raw.xml @ 0:95fb6fa70c2f 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 17:06:56 -0400 |
| parents | |
| children | 7f9840d3b7e7 |
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| -1:000000000000 | 0:95fb6fa70c2f |
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| 1 <?xml version='1.0' encoding='UTF-8'?> | |
| 2 <tool id="imagej2_bunwarpj_convert_to_raw" name="Convert elastic transformation to raw" version="@WRAPPER_VERSION@.0"> | |
| 3 <description>with bUnwarpJ</description> | |
| 4 <macros> | |
| 5 <import>imagej2_macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="fiji_requirements" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 python $__tool_directory__/imagej2_bunwarpj_convert_to_raw.py | |
| 11 --target_image "$target_image" | |
| 12 --target_image_format $target_image.ext | |
| 13 --source_image "$source_image" | |
| 14 --source_image_format $source_image.ext | |
| 15 --elastic_transformation "$elastic_transformation" | |
| 16 --raw_transformation "$raw_transformation" | |
| 17 ]]> | |
| 18 </command> | |
| 19 <inputs> | |
| 20 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/> | |
| 21 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/> | |
| 22 <!-- Support for a bUnwarpJ elastic transformation datatype should be added to Galaxy --> | |
| 23 <param format="txt" name="elastic_transformation" type="data" label="Elastic transformation" help="As saved by bUnwarpJ in elastic format"/> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <!-- Support for a bUnwarpJ raw transformation datatype should be added to Galaxy --> | |
| 27 <data name="raw_transformation" format="txt" label="${tool.name} on ${on_string}: Raw transformation" /> | |
| 28 </outputs> | |
| 29 <tests> | |
| 30 <test> | |
| 31 <param name="target_image" value="dotblot.jpg" /> | |
| 32 <param name="source_image" value="blobs.gif" /> | |
| 33 <param name="elastic_transformation" value="source_elastic_transformation.txt" ftype="txt" /> | |
| 34 <output name="raw_transformation" file="source_raw_transformation.txt" ftype="txt" /> | |
| 35 </test> | |
| 36 </tests> | |
| 37 <help> | |
| 38 **What it does** | |
| 39 | |
| 40 <![CDATA[ | |
| 41 Converts an elastic (i.e., B-spline ) transformation file into a raw transformation file. The elastic | |
| 42 transformation file must be in the same format as the files created with the **Save Transformation** | |
| 43 option in the **Align two images with bUnwarpJ** tool. | |
| 44 | |
| 45 ]]> | |
| 46 | |
| 47 </help> | |
| 48 <expand macro="bunwarpj_citations" /> | |
| 49 </tool> |