Mercurial > repos > imgteam > imagej2_analyze_skeleton

comparison imagej2_analyze_skeleton.xml @ 1:3272e0439968 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author imgteam
date Mon, 28 Sep 2020 16:52:29 +0000
parents bb84f130a4e1
children bdee06a1bcfa
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0:bb84f130a4e1 1:3272e0439968
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="imagej2_analyze_skeleton" name="Analyze skeleton" version="@WRAPPER_VERSION@.0"> 1 <tool id="imagej2_analyze_skeleton" name="Analyze skeleton" version="@WRAPPER_VERSION@.0">
3 <description></description> 2 <description></description>
4 <macros> 3 <macros>
5 <import>imagej2_macros.xml</import> 4 <import>imagej2_macros.xml</import>
6 </macros> 5 </macros>
7 <expand macro="fiji_requirements" /> 6 <expand macro="fiji_requirements"/>
8 <command> 7 <command detect_errors="exit_code"><![CDATA[
9 <![CDATA[ 8 #import os
10 python $__tool_directory__/imagej2_analyze_skeleton.py 9 #set error_log = 'output_log.txt'
11 --input "$input" 10 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
12 --input_datatype $input.ext 11 #set input_with_ext = '.'.join([input_sans_ext, $input.ext])
13 --black_background $black_background 12 ln -s '$input.file_name' '$input_with_ext' &&
14 --prune_cycle_method $prune_cycle_method 13 ImageJ --ij2 --headless --debug
15 --prune_ends $prune_ends 14 --jython '$__tool_directory__/imagej2_analyze_skeleton_jython_script.py'
16 --calculate_largest_shortest_path $calculate_largest_shortest_path 15 '$error_log'
17 ##TODO: seel below--show_detailed_info $show_detailed_info 16 '$input_with_ext'
18 --jython_script $__tool_directory__/imagej2_analyze_skeleton_jython_script.py 17 '$black_background'
19 --output "$output" 18 '$prune_cycle_method'
20 ]]> 19 '$prune_ends'
21 </command> 20 '$calculate_largest_shortest_path'
21 'no'
22 '$output'
23 &>'$error_log';
24 if [[ $? -ne 0 ]]; then
25 cat '$error_log' >&2;
26 fi
27 ]]></command>
22 <inputs> 28 <inputs>
23 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select grayscale image"/> 29 <expand macro="param_input"/>
24 <expand macro="black_background_param" /> 30 <expand macro="black_background_param"/>
25 <param name="prune_cycle_method" type="select" label="Prune cycle method"> 31 <param name="prune_cycle_method" type="select" label="Prune cycle method">
26 <option value="none" selected="True">None</option> 32 <option value="none" selected="True">None</option>
27 <option value="shortest_branch">Shortest branch</option> 33 <option value="shortest_branch">Shortest branch</option>
28 <option value="lowest_intensity_voxel">Lowest intensity voxel</option> 34 <option value="lowest_intensity_voxel">Lowest intensity voxel</option>
29 <option value="lowest_intensity_branch">Lowest intensity branch</option> 35 <option value="lowest_intensity_branch">Lowest intensity branch</option>
43 <option value="yes">Yes</option> 49 <option value="yes">Yes</option>
44 </param> 50 </param>
45 --> 51 -->
46 </inputs> 52 </inputs>
47 <outputs> 53 <outputs>
48 <data name="output" format="tabular" label="${tool.name} on ${on_string}" /> 54 <data name="output" format="tabular"/>
49 </outputs> 55 </outputs>
50 <tests> 56 <tests>
51 <test> 57 <test>
52 <param name="input" value="skeletonized_blobs.gif" /> 58 <param name="input" value="skeletonized_blobs.gif"/>
53 <param name="input_datatype" value="gif" /> 59 <output name="output" file="basic.tabular" ftype="tabular"/>
54 <output name="output" file="basic.tabular" ftype="tabular" />
55 </test> 60 </test>
56 <test> 61 <test>
57 <param name="input" value="skeletonized_clown.jpg" /> 62 <param name="input" value="skeletonized_clown.jpg"/>
58 <param name="input_datatype" value="jpg" /> 63 <param name="prune_cycle_method" value="shortest_branch"/>
59 <param name="prune_cycle_method" value="shortest_branch" /> 64 <output name="output" file="shortest_branch_basic.tabular" ftype="tabular"/>
60 <output name="output" file="shortest_branch_basic.tabular" ftype="tabular" />
61 </test> 65 </test>
62 <test> 66 <test>
63 <param name="input" value="skeletonized_blobs.gif" /> 67 <param name="input" value="skeletonized_blobs.gif"/>
64 <param name="input_datatype" value="gif" /> 68 <param name="calculate_largest_shortest_path" value="yes"/>
65 <param name="calculate_largest_shortest_path" value="yes" /> 69 <output name="output" file="largest_shortest_path_basic.tabular" ftype="tabular"/>
66 <output name="output" file="largest_shortest_path_basic.tabular" ftype="tabular" />
67 </test> 70 </test>
68 <test> 71 <test>
69 <!-- TODO: Change this test and the following test to set "show_detailed_info" 72 <param name="input" value="skeletonized_clown.jpg"/>
70 to "yes" when the tool has been enhanced to use the future "Display labeled skeletons" 73 <param name="prune_cycle_method" value="shortest_branch"/>
71 option. See http://fiji.sc/AnalyzeSkeleton. --> 74 <param name="calculate_largest_shortest_path" value="yes"/>
72 <param name="input" value="skeletonized_blobs.gif" /> 75 <output name="output" file="shortest_branch_all_yes.tabular" ftype="tabular"/>
73 <param name="input_datatype" value="gif" />
74 <!-- <param name="show_detailed_info" value="yes" /> -->
75 <output name="output" file="detailed.tabular" ftype="tabular" />
76 </test>
77 <test>
78 <param name="input" value="skeletonized_clown.jpg" />
79 <param name="input_datatype" value="jpg" />
80 <param name="prune_cycle_method" value="shortest_branch" />
81 <param name="calculate_largest_shortest_path" value="yes" />
82 <!-- <param name="show_detailed_info" value="yes" /> -->
83 <output name="output" file="shortest_branch_all_yes.tabular" ftype="tabular" />
84 </test> 76 </test>
85 </tests> 77 </tests>
86 <help> 78 <help>
87 79
88 .. class:: warningmark 80 .. class:: warningmark