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comparison 2d_feature_extraction.xml @ 5:2436a8807ad1 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:23:23 +0000
parents 0a53256b48c6
children 5bc8cdc17fd0
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4:0a53256b48c6 5:2436a8807ad1
1 <tool id="ip_2d_feature_extraction" name="Extract 2D features" version="0.1.1-2"> 1 <tool id="ip_2d_feature_extraction" name="Extract image features" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description>with scikit-image</description> 2 <description>with scikit-image</description>
3 <macros>
4 <import>creators.xml</import>
5 <token name="@TOOL_VERSION@">0.14.2</token>
6 <token name="@VERSION_SUFFIX@">0</token>
7 </macros>
8 <creator>
9 <expand macro="creators/bmcv" />
10 </creator>
3 <edam_operations> 11 <edam_operations>
4 <edam_operation>operation_3443</edam_operation> 12 <edam_operation>operation_3443</edam_operation>
5 </edam_operations> 13 </edam_operations>
6 <xrefs> 14 <xrefs>
7 <xref type="bio.tools">scikit-image</xref> 15 <xref type="bio.tools">scikit-image</xref>
8 <xref type="biii">scikit-image</xref> 16 <xref type="biii">scikit-image</xref>
9 </xrefs> 17 </xrefs>
10 <requirements> 18 <requirements>
19 <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
11 <requirement type="package" version="0.23.4">pandas</requirement> 20 <requirement type="package" version="0.23.4">pandas</requirement>
12 <requirement type="package" version="0.14.2">scikit-image</requirement>
13 <requirement type="package" version="1.15.4">numpy</requirement> 21 <requirement type="package" version="1.15.4">numpy</requirement>
14 <requirement type="package" version="0.15.1">tifffile</requirement> 22 <requirement type="package" version="0.15.1">tifffile</requirement>
15 </requirements> 23 </requirements>
16 <command detect_errors="aggressive"> 24 <command detect_errors="aggressive">
17 <![CDATA[ 25 <![CDATA[
26 #end if 34 #end if
27 '$input_label' '$output' 35 '$input_label' '$output'
28 ]]> 36 ]]>
29 </command> 37 </command>
30 <inputs> 38 <inputs>
31 <param name="input_label" type="data" format="tiff" label="Label file" /> 39 <param name="input_label" type="data" format="tiff,png" label="Label map" />
32 <conditional name="use_raw_option"> 40 <conditional name="use_raw_option">
33 <param label="Use original image to compute additional features" name="use_raw" type="select"> 41 <param label="Use the intensity image to compute additional features" name="use_raw" type="select">
34 <option selected="True" value="no_original">No original image</option> 42 <option selected="True" value="no_original">No intensity image</option>
35 <option value="raw_image">Use original image</option> 43 <option value="raw_image">Use intensity image</option>
36 </param> 44 </param>
37 <when value="no_original"></when> 45 <when value="no_original"></when>
38 <when value="raw_image"> 46 <when value="raw_image">
39 <param name="input_raw" type="data" format="tiff" label="Original image file" /> 47 <param name="input_raw" type="data" format="tiff,png" label="Intensity image" />
40 </when> 48 </when>
41 </conditional> 49 </conditional>
42 <conditional name="feature_options"> 50 <conditional name="feature_options">
43 <param label="Select features to compute" name="features" type="select"> 51 <param label="Select features to compute" name="features" type="select">
44 <option selected="True" value="all">All features</option> 52 <option selected="True" value="all">All features</option>
45 <option value="select">Select features</option> 53 <option value="select">Select features</option>
46 </param> 54 </param>
47 <when value="all"> </when> 55 <when value="all"> </when>
48 <when value="select"> 56 <when value="select">
49 <param name="selected_features" type="select" label="Available features" multiple="true" display="checkboxes"> 57 <param name="selected_features" type="select" label="Available features" multiple="true" display="checkboxes">
50 <option value="--label">Add label id of label image</option> 58 <option value="--label">Label from the label map</option>
51 <option value="--patches">Patches (requires original image)</option> 59 <option value="--patches">Patches (requires original image)</option>
52 <option value="--max_intensity">Max Intensity (requires original image)</option> 60 <option value="--max_intensity">Max Intensity (requires original image)</option>
53 <option value="--mean_intensity">Mean Intensity (requires original image)</option> 61 <option value="--mean_intensity">Mean Intensity (requires original image)</option>
54 <option value="--min_intensity">Minimum Intensity (requires original image)</option> 62 <option value="--min_intensity">Minimum Intensity (requires original image)</option>
55 <option value="--moments_hu">Moments Hu</option> 63 <option value="--moments_hu">Moments Hu</option>
56 <option value="--centroid">Centroid</option> 64 <option value="--centroid">Centroid</option>
57 <option value="--bbox">Bounding Box</option> 65 <option value="--bbox">Bounding box</option>
58 <option value="--area">Area</option> 66 <option value="--area">Area</option>
59 <option value="--filled_area">Filled Area</option> 67 <option value="--filled_area">Filled area</option>
60 <option value="--convex_area">Convex Area</option> 68 <option value="--convex_area">Convex area</option>
61 <option value="--perimeter">Perimeter</option> 69 <option value="--perimeter">Perimeter</option>
62 <option value="--extent">Extent</option> 70 <option value="--extent">Extent</option>
63 <option value="--eccentricity">Eccentricity</option> 71 <option value="--eccentricity">Eccentricity</option>
64 <option value="--equivalent_diameter">Equivalent Diameter</option> 72 <option value="--equivalent_diameter">Equivalent diameter</option>
65 <option value="--euler_number">Euler Number</option> 73 <option value="--euler_number">Euler number</option>
66 <option value="--inertia_tensor_eigvals">Inertia Tensor Eigenvalues</option> 74 <option value="--inertia_tensor_eigvals">Inertia tensor eigenvalues</option>
67 <option value="--major_axis_length">Major Axis Length</option> 75 <option value="--major_axis_length">Major axis length</option>
68 <option value="--minor_axis_length">Minor Axis Length</option> 76 <option value="--minor_axis_length">Minor axis length</option>
69 <option value="--orientation">Orientation</option> 77 <option value="--orientation">Orientation</option>
70 <option value="--solidity">Solidity</option> 78 <option value="--solidity">Solidity</option>
71 <option value="--moments">Moments</option> 79 <option value="--moments">Moments</option>
72 <option value="--convexity">Convexity</option> 80 <option value="--convexity">Convexity</option>
73 </param> 81 </param>
79 </outputs> 87 </outputs>
80 <tests> 88 <tests>
81 <test> 89 <test>
82 <param name="input_label" value="input.tiff"/> 90 <param name="input_label" value="input.tiff"/>
83 <param name="features" value="select"/> 91 <param name="features" value="select"/>
84 <param name="selected_features" value="--area"/> 92 <param name="selected_features" value="--label,--area"/>
85 <output name="output" ftype="tabular" value="out.tsv"/> 93 <output name="output" ftype="tabular" value="out.tsv"/>
86 </test> 94 </test>
87 </tests> 95 </tests>
88 <help> 96 <help>
89 **What it does**
90 97
91 This tool computes several features of a 2D label image and optionally more features using the original image. 98 **Computes features of a label map.**
99
100 The computed features are computed based solely on the properties of the labels in the label map,
101 or, optionally, by also taking the intensities from a corresponding intensity image into account.
102
103 The label map must be a 2-D or 3-D single-channel image.
104
92 </help> 105 </help>
93 <citations> 106 <citations>
94 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 107 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
95 </citations> 108 </citations>
96 </tool> 109 </tool>