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comparison imagej2_bunwarpj_elastic_transform.xml @ 3:f72f8e6787cd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author imgteam
date Wed, 25 Sep 2024 16:01:42 +0000
parents 55bf135d6b0c
children
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2:55bf135d6b0c 3:f72f8e6787cd
1 <tool id="imagej2_bunwarpj_elastic_transform" name="Apply elastic transformation" version="@WRAPPER_VERSION@.2"> 1 <tool id="imagej2_bunwarpj_elastic_transform" name="Apply elastic transformation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
2 <description>with ImageJ</description> 2 <description>with ImageJ</description>
3 <macros> 3 <macros>
4 <import>imagej2_macros.xml</import> 4 <import>imagej2_macros.xml</import>
5 </macros> 5 </macros>
6 <edam_operations> 6 <edam_operations>
16 #set error_log = 'output_log.txt' 16 #set error_log = 'output_log.txt'
17 touch '$error_log' && 17 touch '$error_log' &&
18 18
19 ## ImageJ2 requires file extensions to be valid image data types. 19 ## ImageJ2 requires file extensions to be valid image data types.
20 #set source_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0] 20 #set source_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0]
21 #set source_with_ext = '.'.join([source_sans_ext, $source_image.ext]) 21 #set source_with_ext = './' + '.'.join([source_sans_ext, $source_image.ext])
22 ln -s '$source_image.file_name' '$source_with_ext' && 22 ln -s '$source_image.file_name' '$source_with_ext' &&
23 #set target_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0] 23 #set target_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0]
24 #set target_with_ext = '.'.join([target_sans_ext, $target_image.ext]) 24 #set target_with_ext = './' + '.'.join([target_sans_ext, $target_image.ext])
25 ln -s '$target_image.file_name' '$target_with_ext' && 25 ln -s '$target_image.file_name' '$target_with_ext' &&
26 26
27 bunwarpj -elastic_transform 27 bunwarpj -elastic_transform
28 '$target_with_ext' 28 '$target_with_ext'
29 '$source_with_ext' 29 '$source_with_ext'
30 '$elastic_transformation' 30 '$elastic_transformation'
31 '$source_out' 31 '$source_out'
32 &>'$error_log';
33 if [[ $? -ne 0 ]]; then
34 cat '$error_log' >&2;
35 fi
36 ]]></command> 32 ]]></command>
37 <inputs> 33 <inputs>
38 <expand macro="param_target_image"/> 34 <expand macro="param_target_image"/>
39 <expand macro="param_source_image"/> 35 <expand macro="param_source_image"/>
40 <!-- Support for a bUnwarpJ elastic transformation datatype should be added to Galaxy --> 36 <!-- Support for a bUnwarpJ elastic transformation datatype should be added to Galaxy -->
54 </outputs> 50 </outputs>
55 <tests> 51 <tests>
56 <test> 52 <test>
57 <expand macro="test_target_source_images"/> 53 <expand macro="test_target_source_images"/>
58 <param name="elastic_transformation" value="blobs_direct_transf.txt"/> 54 <param name="elastic_transformation" value="blobs_direct_transf.txt"/>
59 <output name="source_out" file="elastic_trans_registered_source1.png" compare="sim_size"/> 55 <output name="source_out" file="elastic_trans_registered_source1.png" compare="image_diff"/>
60 </test> 56 </test>
61 </tests> 57 </tests>
62 <help> 58 <help>
63 **What it does** 59 **What it does**
64 60