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comparison imagej2_analyze_particles_binary.xml @ 3:862af85a50ec 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 16:13:47 +0000
parents ae4ae9c5c56c
children
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2:ae4ae9c5c56c 3:862af85a50ec
1 <tool id="imagej2_analyze_particles_binary" name="Analyze particles" version="@WRAPPER_VERSION@.1"> 1 <tool id="imagej2_analyze_particles_binary" name="Analyze particles" 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>
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 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]
17 #set input_with_ext = '.'.join([input_sans_ext, $input.ext]) 17 #set input_with_ext = './' + '.'.join([input_sans_ext, $input.ext])
18 ln -s '$input.file_name' '$input_with_ext' && 18 ln -s '$input.file_name' '$input_with_ext' &&
19 #set output_log = 'output_log.txt'
20 touch '$output_log' &&
21 #if str($show) == 'Nothing': 19 #if str($show) == 'Nothing':
22 #set display_results = 'yes' 20 #set display_results = 'yes'
23 #set all_results = 'yes'
24 #set output_filename = '' 21 #set output_filename = ''
25 #set output_datatype = '' 22 #set output_datatype = ''
26 #set results_filename = $results 23 #set results_filename = $results
27 #else: 24 #else:
28 #set display_results = $display_results_cond.display_results 25 #set display_results = $display_results
29 #set all_results = $display_results_cond.all_results
30 #set output_filename = '.'.join(['output', $input.ext]) 26 #set output_filename = '.'.join(['output', $input.ext])
31 #set output_datatype = $input.ext 27 #set output_datatype = $input.ext
32 touch '$output_filename' && 28 touch '$output_filename' &&
33 #if str($display_results_cond.display_results) == 'yes': 29 #if str($display_results) == 'yes':
34 #set results_filename = $results 30 #set results_filename = $results
35 #else: 31 #else:
36 #set results_filename = '' 32 #set results_filename = ''
37 #end if 33 #end if
38 #end if 34 #end if
35 #if str($export_rois) == 'true':
36 #set rois_filename = $rois
37 #else:
38 #set rois_filename = ''
39 #end if
39 ImageJ --ij2 --headless --debug 40 ImageJ --ij2 --headless --debug
40 --jython '$__tool_directory__/imagej2_analyze_particles_binary_jython_script.py' 41 --jython '$__tool_directory__/imagej2_analyze_particles_binary_jython_script.py'
41 '$output_log' 42 '$rois_filename'
42 '$input' 43 '$input'
43 '$black_background' 44 '$black_background'
44 '$size' 45 '$size'
45 $circularity_min 46 $circularity_min
46 $circularity_max 47 $circularity_max
47 '$show' 48 '$show'
48 '$display_results' 49 '$display_results'
49 '$all_results'
50 '$exclude_edges' 50 '$exclude_edges'
51 '$include_holes' 51 '$include_holes'
52 '$output_filename' 52 '$output_filename'
53 '$output_datatype' 53 '$output_datatype'
54 '$results_filename' 54 '$results_filename'
55 &>'$output_log';
56 #if str($output_filename) != '': 55 #if str($output_filename) != '':
57 if [[ $? -ne 0 ]]; then 56 && mv '$output_filename' '$output';
58 cat '$output_log' >&2;
59 else
60 mv '$output_filename' '$output';
61 fi
62 #else:
63 if [[ $? -ne 0 ]]; then
64 cat '$output_log' >&2;
65 fi
66 #end if 57 #end if
67 ]]></command> 58 ]]></command>
68 <inputs> 59 <inputs>
69 <expand macro="param_input"/> 60 <expand macro="param_input"/>
70 <expand macro="black_background_param"/> 61 <expand macro="black_background_param"/>
79 <option value="Outlines" selected="True">Outlines</option> 70 <option value="Outlines" selected="True">Outlines</option>
80 <option value="Bare_Outlines">Bare Outlines</option> 71 <option value="Bare_Outlines">Bare Outlines</option>
81 <option value="Ellipses">Ellipses</option> 72 <option value="Ellipses">Ellipses</option>
82 <option value="Masks">Masks</option> 73 <option value="Masks">Masks</option>
83 <option value="Count_Masks">Count Masks</option> 74 <option value="Count_Masks">Count Masks</option>
75 <option value="Overlay">Overlay</option>
76 <option value="Overlay_Masks">Overlay Masks</option>
84 <option value="Nothing">Nothing</option> 77 <option value="Nothing">Nothing</option>
85 </param> 78 </param>
86 <conditional name="display_results_cond"> 79 <param name="display_results" type="select" label="Display results">
87 <param name="display_results" type="select" label="Display results"> 80 <option value="no" selected="True">No</option>
88 <option value="no" selected="True">No</option> 81 <option value="yes">Yes</option>
89 <option value="yes">Yes</option> 82 </param>
90 </param>
91 <when value="no">
92 <param name="all_results" type="hidden" value="no"/>
93 </when>
94 <when value="yes">
95 <param name="all_results" type="select" label="All results?" help="If no, only summary displayed.">
96 <option value="yes" selected="True">Yes</option>
97 <option value="no">No</option>
98 </param>
99 </when>
100 </conditional>
101 <param name="exclude_edges" type="select" label="Exclude on edges?"> 83 <param name="exclude_edges" type="select" label="Exclude on edges?">
102 <option value="no" selected="True">No</option> 84 <option value="no" selected="True">No</option>
103 <option value="yes">Yes</option> 85 <option value="yes">Yes</option>
104 </param> 86 </param>
105 <param name="include_holes" type="select" label="Include holes?"> 87 <param name="include_holes" type="select" label="Include holes?">
106 <option value="no" selected="True">No</option> 88 <option value="no" selected="True">No</option>
107 <option value="yes">Yes</option> 89 <option value="yes">Yes</option>
108 </param> 90 </param>
91 <param name="export_rois" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Export particles outlines coordinates" help="Exports particles coordinates as a tabular file, which can be imported as ROIs in OMERO." />
109 </inputs> 92 </inputs>
110 <outputs> 93 <outputs>
111 <data name="output" format_source="input"> 94 <data name="output" format_source="input">
112 <filter>show != "Nothing"</filter> 95 <filter>show != "Nothing"</filter>
113 </data> 96 </data>
114 <data format="tabular" name="results" label="${tool.name} (results) on ${on_string}"> 97 <data format="tabular" name="results" label="${tool.name} (results) on ${on_string}">
115 <filter>show == "Nothing" or display_results_cond['display_results'] == "yes"</filter> 98 <filter>show == "Nothing" or display_results == "yes"</filter>
99 </data>
100 <data format="tabular" name="rois" label="${tool.name} (particles coordinates) on ${on_string}">
101 <filter>export_rois</filter>
116 </data> 102 </data>
117 </outputs> 103 </outputs>
118 <tests> 104 <tests>
119 <test> 105 <test expect_num_outputs="1">
120 <param name="input" value="blobs.gif"/> 106 <param name="input" value="blobs.gif"/>
121 <param name="show" value="Nothing"/> 107 <param name="show" value="Nothing"/>
122 <output name="output" file="analyze_particles_nothing.tabular"/> 108 <output name="results" file="analyze_particles_nothing.tabular"/>
123 </test> 109 </test>
124 <test> 110 <test expect_num_outputs="1">
125 <param name="input" value="blobs.gif"/> 111 <param name="input" value="blobs.gif"/>
126 <param name="show" value="Outlines"/> 112 <param name="show" value="Outlines"/>
127 <output name="output" file="analyze_particles_outlines.gif" compare="sim_size"/> 113 <output name="output" file="analyze_particles_outlines.gif" compare="image_diff"/>
128 </test> 114 </test>
129 <test> 115 <test expect_num_outputs="1">
130 <param name="input" value="blobs.gif"/> 116 <param name="input" value="blobs.gif"/>
131 <param name="show" value="Masks"/> 117 <param name="show" value="Bare_Outlines"/>
132 <param name="exclude_edges" value="yes"/> 118 <param name="exclude_edges" value="yes"/>
133 <param name="include_holes" value="yes"/> 119 <param name="include_holes" value="yes"/>
134 <output name="output" file="analyze_particles_masks.gif" compare="sim_size"/> 120 <output name="output" file="analyze_particles_bareoutlines.gif" compare="image_diff" metric="iou"/>
121 </test>
122 <test expect_num_outputs="3">
123 <param name="input" value="blobs.gif"/>
124 <param name="show" value="Overlay_Masks"/>
125 <param name="display_results" value="yes"/>
126 <param name="export_rois" value="true"/>
127 <output name="output" file="analyze_particles_overlaymasks.gif" compare="image_diff"/>
128 <output name="results" file="analyze_particles_nothing.tabular"/>
129 <output name="rois" file="analyze_particles_rois.tabular"/>
130 </test>
131 <test expect_num_outputs="3">
132 <param name="input" value="confocal-series-first-channel_threshold_default.tiff"/>
133 <param name="black_background" value="yes"/>
134 <param name="show" value="Overlay_Masks"/>
135 <param name="display_results" value="yes"/>
136 <param name="export_rois" value="true"/>
137 <output name="output" file="confocal-series-first-channel_threshold_default_overlay_mask.tiff" compare="sim_size"/>
138 <output name="results" file="confocal_analyze_particles.tabular"/>
139 <output name="rois" file="confocal_analyze_particles_rois.tabular"/>
135 </test> 140 </test>
136 </tests> 141 </tests>
137 <help> 142 <help>
138 .. class:: warningmark 143 .. class:: warningmark
139 144