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comparison imagej2_bunwarpj_raw_transform.xml @ 3:69e951528a0b 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 16:04:07 +0000
parents eabdcf6ad900
children
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2:eabdcf6ad900 3:69e951528a0b
1 <tool id="imagej2_bunwarpj_raw_transform" name="Apply raw transformation" version="@WRAPPER_VERSION@.2"> 1 <tool id="imagej2_bunwarpj_raw_transform" name="Apply raw transformation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
2 <description>with ImageJ2</description> 2 <description>with ImageJ2</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' '$target_with_ext' &&
26 26
27 bunwarpj -raw_transform 27 bunwarpj -raw_transform
28 '$target_with_ext' 28 '$target_with_ext'
29 '$source_with_ext' 29 '$source_with_ext'
30 '$raw_transformation' 30 '$raw_transformation'
31 '$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 raw transformation datatype should be added to Galaxy --> 36 <!-- Support for a bUnwarpJ raw transformation datatype should be added to Galaxy -->
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="raw_transformation" value="source_raw_transformation.txt"/> 54 <param name="raw_transformation" value="source_raw_transformation.txt"/>
59 <param name="source_out_datatype" value="png"/> 55 <param name="source_out_datatype" value="png"/>
60 <output name="source_out" file="raw_trans_registered_source1.png" compare="sim_size"/> 56 <output name="source_out" file="raw_trans_registered_source1.png" compare="image_diff"/>
61 </test> 57 </test>
62 </tests> 58 </tests>
63 <help> 59 <help>
64 **What it does** 60 **What it does**
65 61