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comparison imagej2_skeletonize3d.xml @ 3:5f5b7185bc16 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 16:14:34 +0000
parents 49b5288dcd8c
children
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2:49b5288dcd8c 3:5f5b7185bc16
1 <tool id="imagej2_skeletonize3d" name="Skeletonize" version="@WRAPPER_VERSION@.2"> 1 <tool id="imagej2_skeletonize3d" name="Skeletonize" 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>
11 <xref type="biii">imagej2</xref> 11 <xref type="biii">imagej2</xref>
12 </xrefs> 12 </xrefs>
13 <expand macro="fiji_requirements"/> 13 <expand macro="fiji_requirements"/>
14 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
15 #import os 15 #import os
16 #set error_log = 'output_log.txt'
17 touch '$error_log' &&
18 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0] 16 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
19 #set input_with_ext = '.'.join([input_sans_ext, $input.ext]) 17 #set input_with_ext = './' + '.'.join([input_sans_ext, $input.ext])
20 ln -s '$input.file_name' '$input_with_ext' && 18 ln -s '$input.file_name' '$input_with_ext' &&
21 #set output_filename = '.'.join(['output', $input.ext]) 19 #set output_filename = '.'.join(['output', $input.ext])
22 touch '$output_filename' && 20 touch '$output_filename' &&
23 ImageJ --ij2 --headless --debug 21 ImageJ --ij2 --headless --debug
24 --jython '$__tool_directory__/imagej2_skeletonize3d_jython_script.py' 22 --jython '$__tool_directory__/imagej2_skeletonize3d_jython_script.py'
25 '$error_log'
26 '$input_with_ext' 23 '$input_with_ext'
27 '$black_background' 24 '$black_background'
28 '$output_filename' 25 '$output_filename'
29 '$input.ext' 26 '$input.ext'
30 &>'$error_log'; 27 && mv '$output_filename' '$output';
31 if [[ $? -ne 0 ]]; then
32 cat '$error_log' >&2;
33 else
34 mv '$output_filename' '$output';
35 fi
36 ]]></command> 28 ]]></command>
37 <inputs> 29 <inputs>
38 <expand macro="param_input"/> 30 <expand macro="param_input"/>
39 <expand macro="black_background_param"/> 31 <expand macro="black_background_param"/>
40 </inputs> 32 </inputs>
42 <data name="output" format_source="input" label="${tool.name} on ${on_string}"/> 34 <data name="output" format_source="input" label="${tool.name} on ${on_string}"/>
43 </outputs> 35 </outputs>
44 <tests> 36 <tests>
45 <test> 37 <test>
46 <param name="input" value="blobs.gif"/> 38 <param name="input" value="blobs.gif"/>
47 <output name="output" file="skeletonized_blobs.gif" compare="sim_size"/> 39 <output name="output" file="skeletonized_blobs.gif" compare="image_diff"/>
48 </test> 40 </test>
49 <test> 41 <test>
50 <param name="input" value="clown.jpg"/> 42 <param name="input" value="clown.jpg"/>
51 <output name="output" file="skeletonized_clown.jpg" compare="sim_size"/> 43 <output name="output" file="skeletonized_clown.jpg" compare="image_diff"/>
52 </test> 44 </test>
53 </tests> 45 </tests>
54 <help> 46 <help>
55 47
56 .. class:: warningmark 48 .. class:: warningmark