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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 16:09:42 +0000
parents bdee06a1bcfa
children
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2:bdee06a1bcfa 3:50f2b961b192
1 <tool id="imagej2_analyze_skeleton" name="Analyze skeleton" version="@WRAPPER_VERSION@.1"> 1 <tool id="imagej2_analyze_skeleton" name="Analyze skeleton" 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' '$input_with_ext' &&
20 ImageJ --ij2 --headless --debug 19 ImageJ --ij2 --headless --debug
21 --jython '$__tool_directory__/imagej2_analyze_skeleton_jython_script.py' 20 --jython '$__tool_directory__/imagej2_analyze_skeleton_jython_script.py'
22 '$error_log'
23 '$input_with_ext' 21 '$input_with_ext'
24 '$black_background' 22 '$black_background'
25 '$prune_cycle_method' 23 '$prune_cycle_method'
26 '$prune_ends' 24 '$prune_ends'
27 '$calculate_largest_shortest_path' 25 '$calculate_largest_shortest_path'
28 'no' 26 'no'
29 '$output' 27 '$output'
30 &>'$error_log';
31 if [[ $? -ne 0 ]]; then
32 cat '$error_log' >&2;
33 fi
34 ]]></command> 28 ]]></command>
35 <inputs> 29 <inputs>
36 <expand macro="param_input"/> 30 <expand macro="param_input"/>
37 <expand macro="black_background_param"/> 31 <expand macro="black_background_param"/>
38 <param name="prune_cycle_method" type="select" label="Prune cycle method"> 32 <param name="prune_cycle_method" type="select" label="Prune cycle method">