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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit d93e1dd276027cfc3fb518236110395a23d96f66
author thomaswollmann
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>