Mercurial > repos > imgteam > imagej2_bunwarpj_raw_transform

comparison imagej2_bunwarpj_raw_transform.xml @ 0:95b7592729e2 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 17:03:42 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="imagej2_bunwarpj_raw_transform" name="Apply raw 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 $__tool_directory__/imagej2_bunwarpj_raw_transform.py
11 --target_image "$target_image"
12 --target_image_format $target_image.ext
13 --source_image "$source_image"
14 --source_image_format $source_image.ext
15 --raw_transformation $raw_transformation
16 --source_out "$source_out"
17 --source_out_datatype $source_out_datatype
18 --jython_script $__tool_directory__/imagej2_bunwarpj_raw_transform_jython_script.py
19 ]]>
20 </command>
21 <inputs>
22 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/>
23 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/>
24 <!-- Support for a bUnwarpJ raw transformation datatype should be added to Galaxy -->
25 <param format="txt" name="raw_transformation" type="data" label="Elastic transformation" help="As saved by bUnwarpJ in raw format"/>
26 <param name="source_out_datatype" type="select" label="Save registered source image as format">
27 <expand macro="image_datatypes" />
28 </param>
29 </inputs>
30 <outputs>
31 <data name="source_out" format="png" label="${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="raw_transformation" value="source_raw_transformation.txt" />
44 <param name="source_out_datatype" value="png" />
45 <output name="source_out" file="raw_trans_registered_source1.png" compare="sim_size" />
46 </test>
47 </tests>
48 <help>
49 **What it does**
50
51 <![CDATA[
52 Applies a raw transformation to an image, producing another image which is deformed according
53 to the transformation. The transformation file must be in the same format as the files created
54 with the **Convert elastic transformation to raw with bUnwarpJ** tool.
55
56 ]]>
57
58 </help>
59 <expand macro="bunwarpj_citations" />
60 </tool>