Mercurial > repos > imgteam > imagej2_adjust_threshold_binary

comparison imagej2_adjust_threshold_binary.xml @ 1:29a4d422f32a 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 16:41:15 +0000
parents f1ba33cd9edf
children da29019170f1
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0:f1ba33cd9edf 1:29a4d422f32a
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="imagej2_adjust_threshold_binary" name="Adjust threshold" version="@WRAPPER_VERSION@.0"> 1 <tool id="imagej2_adjust_threshold_binary" name="Adjust threshold" version="@WRAPPER_VERSION@.0">
3 <description>of binary image</description> 2 <description>of binary image</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 $__tool_directory__/imagej2_adjust_threshold_binary.py 9 #set error_log = 'output_log.txt'
11 --input "$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 --threshold_min $threshold_min 12 ln -s '$input.file_name' '$input_with_ext' &&
14 --threshold_max $threshold_max 13 #set output_filename = '.'.join(['output', $input.ext])
15 --method $method 14 touch '$output_filename' &&
16 --display $display 15 touch '$error_log' &&
17 --black_background $black_background 16 ImageJ --ij2 --headless --debug
18 --stack_histogram $stack_histogram 17 --jython '$__tool_directory__/imagej2_adjust_threshold_binary_jython_script.py'
19 --jython_script $__tool_directory__/imagej2_adjust_threshold_binary_jython_script.py 18 '$error_log'
20 --output_datatype $output.ext 19 '$input_with_ext'
21 --output "$output" 20 $threshold_min
22 ]]> 21 $threshold_max
23 </command> 22 '$method'
23 '$display'
24 '$black_background'
25 '$stack_histogram'
26 '$output_filename'
27 '$input.ext'
28 &>'$error_log';
29 if [[ $? -ne 0 ]]; then
30 cat '$error_log' >&2;
31 else
32 mv '$output_filename' '$output';
33 fi
34 ]]></command>
24 <inputs> 35 <inputs>
25 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/> 36 <expand macro="param_input"/>
26 <param name="threshold_min" type="float" value="0" min="0" max="255" label="Minimum threshold value" /> 37 <param name="threshold_min" type="float" value="0" min="0" max="255" label="Minimum threshold value"/>
27 <param name="threshold_max" type="float" value="0" min="0" max="255" label="Maximum threshold value" /> 38 <param name="threshold_max" type="float" value="0" min="0" max="255" label="Maximum threshold value"/>
28 <param name="method" type="select" label="Method" help="The Default method is the modified IsoData algorithm."> 39 <param name="method" type="select" label="Method" help="The Default method is the modified IsoData algorithm.">
29 <option value="Default" selected="True">Default</option> 40 <option value="Default" selected="True">Default</option>
30 <option value="Huang">Huang</option> 41 <option value="Huang">Huang</option>
31 <option value="Intermodes">Intermodes</option> 42 <option value="Intermodes">Intermodes</option>
32 <option value="IsoData">IsoData</option> 43 <option value="IsoData">IsoData</option>
56 <option value="no" selected="True">No</option> 67 <option value="no" selected="True">No</option>
57 <option value="yes">Yes</option> 68 <option value="yes">Yes</option>
58 </param> 69 </param>
59 </inputs> 70 </inputs>
60 <outputs> 71 <outputs>
61 <data name="output" format_source="input" label="${tool.name} on ${on_string}"/> 72 <data name="output" format_source="input"/>
62 </outputs> 73 </outputs>
63 <tests> 74 <tests>
64 <test> 75 <test>
65 <param name="input" value="blobs.gif" /> 76 <param name="input" value="blobs.gif"/>
66 <param name="output_datatype" value="gif" /> 77 <param name="output_datatype" value="gif"/>
67 <param name="threshold_min" value="0.0" /> 78 <param name="threshold_min" value="0.0"/>
68 <param name="threshold_max" value="129.0" /> 79 <param name="threshold_max" value="129.0"/>
69 <param name="method" value="Default" /> 80 <param name="method" value="Default"/>
70 <param name="display" value="red" /> 81 <param name="display" value="red"/>
71 <param name="black_background" value="no" /> 82 <param name="black_background" value="no"/>
72 <param name="stack_histogram" value="no" /> 83 <param name="stack_histogram" value="no"/>
73 <output name="output" file="blobs_threshold_default.gif" compare="sim_size" /> 84 <output name="output" file="blobs_threshold_default.gif" compare="sim_size"/>
74 </test> 85 </test>
75 <test> 86 <test>
76 <param name="input" value="blobs.gif" /> 87 <param name="input" value="blobs.gif"/>
77 <param name="output_datatype" value="gif" /> 88 <param name="output_datatype" value="gif"/>
78 <param name="threshold_min" value="118.0" /> 89 <param name="threshold_min" value="118.0"/>
79 <param name="threshold_max" value="255.0" /> 90 <param name="threshold_max" value="255.0"/>
80 <param name="method" value="IJ_IsoData" /> 91 <param name="method" value="IJ_IsoData"/>
81 <param name="display" value="over_under" /> 92 <param name="display" value="over_under"/>
82 <param name="black_background" value="no" /> 93 <param name="black_background" value="no"/>
83 <param name="stack_histogram" value="no" /> 94 <param name="stack_histogram" value="no"/>
84 <output name="output" file="blobs_threshold_ijiso.gif" compare="sim_size" /> 95 <output name="output" file="blobs_threshold_ijiso.gif" compare="sim_size"/>
85 </test> 96 </test>
86 <test> 97 <test>
87 <param name="input" value="blobs.gif" /> 98 <param name="input" value="blobs.gif"/>
88 <param name="output_datatype" value="gif" /> 99 <param name="output_datatype" value="gif"/>
89 <param name="threshold_min" value="72.0" /> 100 <param name="threshold_min" value="72.0"/>
90 <param name="threshold_max" value="255.0" /> 101 <param name="threshold_max" value="255.0"/>
91 <param name="method" value="Huang" /> 102 <param name="method" value="Huang"/>
92 <param name="display" value="bw" /> 103 <param name="display" value="bw"/>
93 <param name="black_background" value="yes" /> 104 <param name="black_background" value="yes"/>
94 <param name="stack_histogram" value="no" /> 105 <param name="stack_histogram" value="no"/>
95 <output name="output" file="blobs_threshold_huang_dark.gif" compare="sim_size" /> 106 <output name="output" file="blobs_threshold_huang_dark.gif" compare="sim_size"/>
96 </test> 107 </test>
97 </tests> 108 </tests>
98 <help> 109 <help>
99 110
100 @requires_binary_input@ 111 @requires_binary_input@
111 - **Black background** - Select **yes** when features are lighter than the background. 122 - **Black background** - Select **yes** when features are lighter than the background.
112 - **Stack histogram**  Select **yes** to first compute the histogram of the whole stack (or hyperstack) and then compute the threshold based on that histogram. As such, all slices are binarized using the single computed value. If unchecked, the threshold of each slice is computed separately. 123 - **Stack histogram**  Select **yes** to first compute the histogram of the whole stack (or hyperstack) and then compute the threshold based on that histogram. As such, all slices are binarized using the single computed value. If unchecked, the threshold of each slice is computed separately.
113 ]]> 124 ]]>
114 125
115 </help> 126 </help>
116 <expand macro="fiji_headless_citations" /> 127 <expand macro="fiji_headless_citations"/>
117 </tool> 128 </tool>