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comparison imagej2_make_binary.xml @ 3:1cf9771e0e53 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 16:12:59 +0000
parents d3e8ef83f3bf
children
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2:d3e8ef83f3bf 3:1cf9771e0e53
1 <tool id="imagej2_make_binary" name="Convert to binary" version="@WRAPPER_VERSION@.1"> 1 <tool id="imagej2_make_binary" name="Convert to binary" 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 #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]
18 #set input_with_ext = '.'.join([input_sans_ext, $input.ext]) 17 #set input_with_ext = './' + '.'.join([input_sans_ext, $input.ext])
19 ln -s '$input.file_name' '$input_with_ext' && 18 ln -s '$input.file_name' '$input_with_ext' &&
20 #set output_filename = '.'.join(['output', $input.ext]) 19 #set output_filename = '.'.join(['output', $input.ext])
21 touch '$output_filename' && 20 touch '$output_filename' &&
22 touch '$error_log' &&
23 ImageJ --ij2 --headless --debug 21 ImageJ --ij2 --headless --debug
24 --jython '$__tool_directory__/imagej2_make_binary_jython_script.py' 22 --jython '$__tool_directory__/imagej2_make_binary_jython_script.py'
25 '$error_log'
26 '$input_with_ext' 23 '$input_with_ext'
27 $iterations 24 $iterations
28 $count 25 $count
29 '$black_background' 26 '$black_background'
30 '$pad_edges_when_eroding' 27 '$pad_edges_when_eroding'
31 '$output_filename' 28 '$output_filename'
32 '$input.ext' 29 '$input.ext'
33 &>'$error_log'; 30 && mv '$output_filename' '$output'
34 if [[ $? -ne 0 ]]; then
35 cat '$error_log' >&2;
36 else
37 mv '$output_filename' '$output';
38 fi
39 ]]></command> 31 ]]></command>
40 <inputs> 32 <inputs>
41 <expand macro="param_input"/> 33 <expand macro="param_input"/>
42 <expand macro="make_binary_params"/> 34 <expand macro="make_binary_params"/>
43 </inputs> 35 </inputs>
45 <data name="output" format_source="input"/> 37 <data name="output" format_source="input"/>
46 </outputs> 38 </outputs>
47 <tests> 39 <tests>
48 <test> 40 <test>
49 <param name="input" value="clown.jpg"/> 41 <param name="input" value="clown.jpg"/>
50 <output name="output" file="clown_binary.jpg" compare="sim_size"/> 42 <!-- It seems that metric iou does not work for this test -->
43 <output name="output" file="clown_binary.jpg" compare="image_diff" />
51 </test> 44 </test>
52 </tests> 45 </tests>
53 <help> 46 <help>
54 **What it does** 47 **What it does**
55 48