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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
author imgteam
date Wed, 17 Dec 2025 11:20:49 +0000
parents b688b58d40a7
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3:f4bcb0207519 4:a4bc9dfde846
1 <tool id="ip_2d_feature_extraction" name="2D Feature Extraction" version="0.1.1"> 1 <tool id="ip_2d_feature_extraction" name="Extract image features" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description>Feature Extraction</description> 2 <description>with scikit-image</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.23.4">pandas</requirement> 4 <import>creators.xml</import>
5 <requirement type="package" version="0.14.2">scikit-image</requirement> 5 <token name="@TOOL_VERSION@">0.18.1</token>
6 <requirement type="package" version="1.15.4">numpy</requirement> 6 <token name="@VERSION_SUFFIX@">0</token>
7 <requirement type="package" version="0.15.1">tifffile</requirement> 7 </macros>
8 <creator>
9 <expand macro="creators/bmcv"/>
10 </creator>
11 <edam_operations>
12 <edam_operation>operation_3443</edam_operation>
13 </edam_operations>
14 <xrefs>
15 <xref type="bio.tools">scikit-image</xref>
16 <xref type="biii">scikit-image</xref>
17 </xrefs>
18 <requirements>
19 <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
20 <requirement type="package" version="2.2.2">pandas</requirement>
21 <requirement type="package" version="1.23.3">numpy</requirement>
22 <requirement type="package" version="2020.10.1">tifffile</requirement>
23 <requirement type="package" version="0.1">giatools</requirement>
8 </requirements> 24 </requirements>
9 <command detect_errors="aggressive"> 25 <command detect_errors="aggressive">
10 <![CDATA[ 26 <![CDATA[
11 python '$__tool_directory__/2d_feature_extraction.py' 27 python '$__tool_directory__/2d_feature_extraction.py'
12 #if $feature_options['features'] == 'all' 28 #if $feature_options['features'] == 'all'
19 #end if 35 #end if
20 '$input_label' '$output' 36 '$input_label' '$output'
21 ]]> 37 ]]>
22 </command> 38 </command>
23 <inputs> 39 <inputs>
24 <param name="input_label" type="data" format="tiff" label="Label file" /> 40 <param name="input_label" type="data" format="tiff,png" label="Label map"/>
25 <conditional name="use_raw_option"> 41 <conditional name="use_raw_option">
26 <param label="Use original image to compute additional features" name="use_raw" type="select"> 42 <param label="Use the intensity image to compute additional features" name="use_raw" type="select">
27 <option selected="True" value="no_original">No original image</option> 43 <option selected="True" value="no_original">No intensity image</option>
28 <option value="raw_image">Use original image</option> 44 <option value="raw_image">Use intensity image</option>
29 </param> 45 </param>
30 <when value="no_original"></when> 46 <when value="no_original"/>
31 <when value="raw_image"> 47 <when value="raw_image">
32 <param name="input_raw" type="data" format="tiff" label="Original image file" /> 48 <param name="input_raw" type="data" format="tiff,png" label="Intensity image"/>
33 </when> 49 </when>
34 </conditional> 50 </conditional>
35 <conditional name="feature_options"> 51 <conditional name="feature_options">
36 <param label="Select features to compute" name="features" type="select"> 52 <param label="Select features to compute" name="features" type="select">
37 <option selected="True" value="all">All features</option> 53 <option selected="True" value="all">All features</option>
38 <option value="select">Select features</option> 54 <option value="select">Select features</option>
39 </param> 55 </param>
40 <when value="all"> </when> 56 <when value="all"> </when>
41 <when value="select"> 57 <when value="select">
42 <param name="selected_features" type="select" label="Available features" multiple="true" display="checkboxes"> 58 <param name="selected_features" type="select" label="Available features" multiple="true" display="checkboxes">
43 <option value="--label">Add label id of label image</option> 59 <option value="--label">Label from the label map</option>
44 <option value="--patches">Patches (requires original image)</option> 60 <option value="--patches">Patches (requires original image)</option>
45 <option value="--max_intensity">Max Intensity (requires original image)</option> 61 <option value="--max_intensity">Max Intensity (requires original image)</option>
46 <option value="--mean_intensity">Mean Intensity (requires original image)</option> 62 <option value="--mean_intensity">Mean Intensity (requires original image)</option>
47 <option value="--min_intensity">Minimum Intensity (requires original image)</option> 63 <option value="--min_intensity">Minimum Intensity (requires original image)</option>
48 <option value="--moments_hu">Moments Hu</option> 64 <option value="--moments_hu">Moments Hu</option>
49 <option value="--centroid">Centroid</option> 65 <option value="--centroid">Centroid</option>
50 <option value="--bbox">Bounding Box</option> 66 <option value="--bbox">Bounding box</option>
51 <option value="--area">Area</option> 67 <option value="--area">Area</option>
52 <option value="--filled_area">Filled Area</option> 68 <option value="--filled_area">Filled area</option>
53 <option value="--convex_area">Convex Area</option> 69 <option value="--convex_area">Convex area</option>
54 <option value="--perimeter">Perimeter</option> 70 <option value="--perimeter">Perimeter</option>
55 <option value="--extent">Extent</option> 71 <option value="--extent">Extent</option>
56 <option value="--eccentricity">Eccentricity</option> 72 <option value="--eccentricity">Eccentricity</option>
57 <option value="--equivalent_diameter">Equivalent Diameter</option> 73 <option value="--equivalent_diameter">Equivalent diameter</option>
58 <option value="--euler_number">Euler Number</option> 74 <option value="--euler_number">Euler number</option>
59 <option value="--inertia_tensor_eigvals">Inertia Tensor Eigenvalues</option> 75 <option value="--inertia_tensor_eigvals">Inertia tensor eigenvalues</option>
60 <option value="--major_axis_length">Major Axis Length</option> 76 <option value="--major_axis_length">Major axis length</option>
61 <option value="--minor_axis_length">Minor Axis Length</option> 77 <option value="--minor_axis_length">Minor axis length</option>
62 <option value="--orientation">Orientation</option> 78 <option value="--orientation">Orientation</option>
63 <option value="--solidity">Solidity</option> 79 <option value="--solidity">Solidity</option>
64 <option value="--moments">Moments</option> 80 <option value="--moments">Moments</option>
65 <option value="--convexity">Convexity</option> 81 <option value="--convexity">Convexity</option>
66 </param> 82 </param>
67 </when> 83 </when>
68 </conditional> 84 </conditional>
69 </inputs> 85 </inputs>
70 <outputs> 86 <outputs>
71 <data format="tabular" name="output" /> 87 <data format="tabular" name="output"/>
72 </outputs> 88 </outputs>
73 <tests> 89 <tests>
74 <test> 90 <test>
75 <param name="input_label" value="input.tiff"/> 91 <param name="input_label" value="input.tiff" ftype="tiff"/>
76 <param name="features" value="select"/> 92 <conditional name="feature_options">
77 <param name="selected_features" value="--area"/> 93 <param name="features" value="select"/>
94 <param name="selected_features" value="--label,--area"/>
95 </conditional>
78 <output name="output" ftype="tabular" value="out.tsv"/> 96 <output name="output" ftype="tabular" value="out.tsv"/>
79 </test> 97 </test>
80 </tests> 98 </tests>
81 <help> 99 <help>
82 **What it does**
83 100
84 This tool computes several features of a 2D label image and optionally more features using the original image. 101 **Computes features of a label map.**
102
103 The computed features are computed based solely on the properties of the labels in the label map,
104 or, optionally, by also taking the intensities from a corresponding intensity image into account.
105
106 The label map must be a 2-D or 3-D single-channel image.
107
85 </help> 108 </help>
86 <citations> 109 <citations>
87 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 110 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
88 </citations> 111 </citations>
89 </tool> 112 </tool>