Mercurial > repos > imgteam > 2d_feature_extraction

annotate 2d_feature_extraction.xml @ 4:0a53256b48c6 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
author imgteam
date Fri, 10 Nov 2023 14:23:12 +0000
parents 6fdb3542a406
children 2436a8807ad1
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4
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1 <tool id="ip_2d_feature_extraction" name="Extract 2D features" version="0.1.1-2">
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2 <description>with scikit-image</description>
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3 <edam_operations>
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4 <edam_operation>operation_3443</edam_operation>
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5 </edam_operations>
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6 <xrefs>
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7 <xref type="bio.tools">scikit-image</xref>
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8 <xref type="biii">scikit-image</xref>
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9 </xrefs>
2
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10 <requirements>
0
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11 <requirement type="package" version="0.23.4">pandas</requirement>
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12 <requirement type="package" version="0.14.2">scikit-image</requirement>
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13 <requirement type="package" version="1.15.4">numpy</requirement>
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14 <requirement type="package" version="0.15.1">tifffile</requirement>
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15 </requirements>
2
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16 <command detect_errors="aggressive">
0
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17 <![CDATA[
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18 python '$__tool_directory__/2d_feature_extraction.py'
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19 #if $feature_options['features'] == 'all'
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20 --all
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21 #else if $feature_options['features'] == 'select'
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22 ${' '.join(str( $feature_options['selected_features'] ).split(','))}
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23 #end if
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24 #if $use_raw_option['use_raw'] == 'raw_image'
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25 --raw '$input_raw'
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26 #end if
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27 '$input_label' '$output'
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28 ]]>
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29 </command>
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30 <inputs>
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31 <param name="input_label" type="data" format="tiff" label="Label file" />
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32 <conditional name="use_raw_option">
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33 <param label="Use original image to compute additional features" name="use_raw" type="select">
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34 <option selected="True" value="no_original">No original image</option>
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35 <option value="raw_image">Use original image</option>
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36 </param>
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37 <when value="no_original"></when>
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38 <when value="raw_image">
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39 <param name="input_raw" type="data" format="tiff" label="Original image file" />
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40 </when>
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41 </conditional>
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42 <conditional name="feature_options">
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43 <param label="Select features to compute" name="features" type="select">
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44 <option selected="True" value="all">All features</option>
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45 <option value="select">Select features</option>
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46 </param>
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47 <when value="all"> </when>
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48 <when value="select">
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49 <param name="selected_features" type="select" label="Available features" multiple="true" display="checkboxes">
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50 <option value="--label">Add label id of label image</option>
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51 <option value="--patches">Patches (requires original image)</option>
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52 <option value="--max_intensity">Max Intensity (requires original image)</option>
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53 <option value="--mean_intensity">Mean Intensity (requires original image)</option>
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54 <option value="--min_intensity">Minimum Intensity (requires original image)</option>
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55 <option value="--moments_hu">Moments Hu</option>
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56 <option value="--centroid">Centroid</option>
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57 <option value="--bbox">Bounding Box</option>
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58 <option value="--area">Area</option>
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59 <option value="--filled_area">Filled Area</option>
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60 <option value="--convex_area">Convex Area</option>
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61 <option value="--perimeter">Perimeter</option>
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62 <option value="--extent">Extent</option>
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63 <option value="--eccentricity">Eccentricity</option>
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64 <option value="--equivalent_diameter">Equivalent Diameter</option>
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65 <option value="--euler_number">Euler Number</option>
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66 <option value="--inertia_tensor_eigvals">Inertia Tensor Eigenvalues</option>
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67 <option value="--major_axis_length">Major Axis Length</option>
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68 <option value="--minor_axis_length">Minor Axis Length</option>
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69 <option value="--orientation">Orientation</option>
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70 <option value="--solidity">Solidity</option>
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71 <option value="--moments">Moments</option>
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72 <option value="--convexity">Convexity</option>
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73 </param>
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74 </when>
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75 </conditional>
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76 </inputs>
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77 <outputs>
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78 <data format="tabular" name="output" />
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79 </outputs>
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80 <tests>
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81 <test>
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82 <param name="input_label" value="input.tiff"/>
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83 <param name="features" value="select"/>
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84 <param name="selected_features" value="--area"/>
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85 <output name="output" ftype="tabular" value="out.tsv"/>
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86 </test>
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87 </tests>
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88 <help>
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89 **What it does**
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90
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91 This tool computes several features of a 2D label image and optionally more features using the original image.
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92 </help>
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93 <citations>
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94 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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95 </citations>
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96 </tool>