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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:28:26 -0500
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1 <tool id="ip_2d_feature_extraction" name="2D Feature Extraction" version="0.0.8">
2 <description>Feature Extraction</description>
3 <requirements>
4 <requirement type="package" version="0.23.4">pandas</requirement>
5 <requirement type="package" version="0.14.2">scikit-image</requirement>
6 <requirement type="package" version="1.15.4">numpy</requirement>
7 <requirement type="package" version="0.15.1">tifffile</requirement>
8 </requirements>
9 <command>
10 <![CDATA[
11 python '$__tool_directory__/2d_feature_extraction.py'
12 #if $feature_options['features'] == 'all'
13 --all
14 #else if $feature_options['features'] == 'select'
15 ${' '.join(str( $feature_options['selected_features'] ).split(','))}
16 #end if
17 #if $use_raw_option['use_raw'] == 'raw_image'
18 --raw '$input_raw'
19 #end if
20 '$input_label' '$output'
21 ]]>
22 </command>
23 <inputs>
24 <param name="input_label" type="data" format="tiff" label="Label file" />
25 <conditional name="use_raw_option">
26 <param label="Use original image to compute additional features" name="use_raw" type="select">
27 <option selected="True" value="no_original">No original image</option>
28 <option value="raw_image">Use original image</option>
29 </param>
30 <when value="no_original"></when>
31 <when value="raw_image">
32 <param name="input_raw" type="data" format="tiff" label="Original image file" />
33 </when>
34 </conditional>
35 <conditional name="feature_options">
36 <param label="Select features to compute" name="features" type="select">
37 <option selected="True" value="all">All features</option>
38 <option value="select">Select features</option>
39 </param>
40 <when value="all"> </when>
41 <when value="select">
42 <param name="selected_features" type="select" label="Available features" multiple="true" display="checkboxes">
43 <option value="--label">Add label id of label image</option>
44 <option value="--patches">Patches (requires original image)</option>
45 <option value="--max_intensity">Max Intensity (requires original image)</option>
46 <option value="--mean_intensity">Mean Intensity (requires original image)</option>
47 <option value="--min_intensity">Minimum Intensity (requires original image)</option>
48 <option value="--moments_hu">Moments Hu</option>
49 <option value="--centroid">Centroid</option>
50 <option value="--bbox">Bounding Box</option>
51 <option value="--area">Area</option>
52 <option value="--filled_area">Filled Area</option>
53 <option value="--convex_area">Convex Area</option>
54 <option value="--perimeter">Perimeter</option>
55 <option value="--extent">Extent</option>
56 <option value="--eccentricity">Eccentricity</option>
57 <option value="--equivalent_diameter">Equivalent Diameter</option>
58 <option value="--euler_number">Euler Number</option>
59 <option value="--inertia_tensor_eigvals">Inertia Tensor Eigenvalues</option>
60 <option value="--major_axis_length">Major Axis Length</option>
61 <option value="--minor_axis_length">Minor Axis Length</option>
62 <option value="--orientation">Orientation</option>
63 <option value="--solidity">Solidity</option>
64 <option value="--moments">Moments</option>
65 <option value="--convexity">Convexity</option>
66 </param>
67 </when>
68 </conditional>
69 </inputs>
70 <outputs>
71 <data format="tabular" name="output" />
72 </outputs>
73 <tests>
74 <test>
75 <param name="input_label" value="input.tiff"/>
76 <param name="features" value="select"/>
77 <param name="selected_features" value="--area"/>
78 <output name="output" ftype="tabular" value="out.tsv"/>
79 </test>
80 </tests>
81 <help>
82 **What it does**
83
84 This tool computes several features of a 2D label image and optionally more features using the original image.
85 </help>
86 <citations>
87 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
88 </citations>
89 </tool>