Mercurial > repos > thomaswollmann > 2d_feature_extraction
comparison 2d_feature_extraction.xml @ 0:4d6e6901df43 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit d93e1dd276027cfc3fb518236110395a23d96f66
author | thomaswollmann |
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date | Wed, 16 Jan 2019 15:32:39 -0500 |
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1 <?xml version="1.0"?> | |
2 <tool name="2D Feature Extraction" id="ip_2d_feature_extraction" version="0.0.8"> | |
3 <description>Feature Extraction</description> | |
4 <requirements> | |
5 <requirement type="package" version="0.23.4">pandas</requirement> | |
6 <requirement type="package" version="0.14.0">scikit-image</requirement> | |
7 <requirement type="package" version="1.15.4">numpy</requirement> | |
8 <requirement type="package" version="0.15.1">tifffile</requirement> | |
9 </requirements> | |
10 <command> | |
11 <![CDATA[ | |
12 python '$__tool_directory__/2d_feature_extraction.py' | |
13 #if $feature_options['features'] == 'all' | |
14 --all | |
15 #else if $feature_options['features'] == 'select' | |
16 ${' '.join(str( $feature_options['selected_features'] ).split(','))} | |
17 #end if | |
18 #if $use_raw_option['use_raw'] == 'raw_image' | |
19 --raw '$input_raw' | |
20 #end if | |
21 '$input_label' '$output' | |
22 ]]> | |
23 </command> | |
24 <inputs> | |
25 <param name="input_label" type="data" format="tiff" label="Label file" /> | |
26 <conditional name="use_raw_option"> | |
27 <param label="Use original image to compute additional features" name="use_raw" type="select"> | |
28 <option selected="True" value="no_original">No original image</option> | |
29 <option value="raw_image">Use original image</option> | |
30 </param> | |
31 <when value="no_original"> </when> | |
32 <when value="raw_image"> | |
33 <param name="input_raw" type="data" format="tiff" label="Original image file" /> | |
34 </when> | |
35 </conditional> | |
36 <conditional name="feature_options"> | |
37 <param label="Select features to compute" name="features" type="select"> | |
38 <option selected="True" value="all">All features</option> | |
39 <option value="select">Select features</option> | |
40 </param> | |
41 <when value="all"> </when> | |
42 <when value="select"> | |
43 <param name="selected_features" type="select" label="Available features" multiple="true" display="checkboxes"> | |
44 <option value="--label">Add label id of label image</option> | |
45 <option value="--patches">Patches (requires original image)</option> | |
46 <option value="--max_intensity">Max Intensity (requires original image)</option> | |
47 <option value="--mean_intensity">Mean Intensity (requires original image)</option> | |
48 <option value="--min_intensity">Minimum Intensity (requires original image)</option> | |
49 <option value="--moments_hu">Moments Hu</option> | |
50 <option value="--centroid">Centroid</option> | |
51 <option value="--bbox">Bounding Box</option> | |
52 <option value="--area">Area</option> | |
53 <option value="--filled_area">Filled Area</option> | |
54 <option value="--convex_area">Convex Area</option> | |
55 <option value="--perimeter">Perimeter</option> | |
56 <option value="--extent">Extent</option> | |
57 <option value="--eccentricity">Eccentricity</option> | |
58 <option value="--equivalent_diameter">Equivalent Diameter</option> | |
59 <option value="--euler_number">Euler Number</option> | |
60 <option value="--inertia_tensor_eigvals">Inertia Tensor Eigenvalues</option> | |
61 <option value="--major_axis_length">Major Axis Length</option> | |
62 <option value="--minor_axis_length">Minor Axis Length</option> | |
63 <option value="--orientation">Orientation</option> | |
64 <option value="--solidity">Solidity</option> | |
65 <option value="--moments">Moments</option> | |
66 <option value="--convexity">Convexity</option> | |
67 </param> | |
68 </when> | |
69 </conditional> | |
70 </inputs> | |
71 <outputs> | |
72 <data format="tabular" name="output" /> | |
73 </outputs> | |
74 <tests> | |
75 <test> | |
76 <param name="input_label" value="input.tiff"/> | |
77 <param name="features" value="select"/> | |
78 <param name="selected_features" value="--area"/> | |
79 <output name="output" ftype="tabular" value="out.csv"/> | |
80 </test> | |
81 </tests> | |
82 <help> | |
83 This tool computes several features of a 2D label image and optionally more features using the original image. | |
84 </help> | |
85 <citations> | |
86 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> | |
87 </citations> | |
88 </tool> |