Mercurial > repos > imgteam > imagej2_bunwarpj_elastic_transform

comparison imagej2_bunwarpj_elastic_transform.xml @ 0:301f24849032 draft

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"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
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="imagej2_bunwarpj_elastic_transform" name="Apply elastic transformation" 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 $__tool_directory__/imagej2_bunwarpj_elastic_transform.py
11 --target_image "$target_image"
12 --target_image_format $target_image.ext
13 --source_image "$source_image"
14 --source_image_format $source_image.ext
15 --elastic_transformation $elastic_transformation
16 --source_out "$source_out"
17 --source_out_datatype $source_out_datatype
18 --jython_script $__tool_directory__/imagej2_bunwarpj_elastic_transform_jython_script.py
19 ]]>
20 </command>
21 <inputs>
22 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/>
23 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/>
24 <!-- Support for a bUnwarpJ elastic transformation datatype should be added to Galaxy -->
25 <param format="txt" name="elastic_transformation" type="data" label="Elastic transformation" help="As saved by bUnwarpJ in elastic format"/>
26 <param name="source_out_datatype" type="select" label="Save registered source image as format">
27 <expand macro="image_datatypes" />
28 </param>
29 </inputs>
30 <outputs>
31 <data name="source_out" format="png" label="${tool.name} on ${on_string}: Registered source image">
32 <actions>
33 <action type="format">
34 <option type="from_param" name="source_out_datatype" />
35 </action>
36 </actions>
37 </data>
38 </outputs>
39 <tests>
40 <test>
41 <param name="target_image" value="dotblot.jpg" />
42 <param name="source_image" value="blobs.gif" />
43 <param name="elastic_transformation" value="blobs_direct_transf.txt" />
44 <param name="source_out_datatype" value="png" />
45 <output name="source_out" file="elastic_trans_registered_source1.png" compare="sim_size" />
46 </test>
47 </tests>
48 <help>
49 **What it does**
50
51 <![CDATA[
52 Applies an elastic transformation to an image, producing another image which is elastically
53 deformed according to the transformation. The transformation file must be in the same format
54 as the files created with the **Save Transformation** option in the **Align two images with bUnwarpJ**
55 tool.
56
57 ]]>
58
59 </help>
60 <expand macro="bunwarpj_citations" />
61 </tool>