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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
author imgteam
date Wed, 24 Apr 2024 08:11:39 +0000
parents 2436a8807ad1
children
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2436a8807ad1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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1 <tool id="ip_2d_feature_extraction" name="Extract image features" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description>with scikit-image</description>
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3 <macros>
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4 <import>creators.xml</import>
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5 <token name="@TOOL_VERSION@">0.18.1</token>
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6 <token name="@VERSION_SUFFIX@">0</token>
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7 </macros>
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8 <creator>
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9 <expand macro="creators/bmcv" />
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10 </creator>
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11 <edam_operations>
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12 <edam_operation>operation_3443</edam_operation>
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13 </edam_operations>
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14 <xrefs>
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15 <xref type="bio.tools">scikit-image</xref>
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16 <xref type="biii">scikit-image</xref>
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17 </xrefs>
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18 <requirements>
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19 <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
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20 <requirement type="package" version="2.2.2">pandas</requirement>
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21 <requirement type="package" version="1.23.3">numpy</requirement>
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22 <requirement type="package" version="2020.10.1">tifffile</requirement>
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23 <requirement type="package" version="0.1">giatools</requirement>
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24 </requirements>
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25 <command detect_errors="aggressive">
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26 <![CDATA[
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27 python '$__tool_directory__/2d_feature_extraction.py'
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28 #if $feature_options['features'] == 'all'
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29 --all
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30 #else if $feature_options['features'] == 'select'
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31 ${' '.join(str( $feature_options['selected_features'] ).split(','))}
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32 #end if
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33 #if $use_raw_option['use_raw'] == 'raw_image'
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34 --raw '$input_raw'
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35 #end if
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36 '$input_label' '$output'
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37 ]]>
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38 </command>
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39 <inputs>
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40 <param name="input_label" type="data" format="tiff,png" label="Label map" />
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41 <conditional name="use_raw_option">
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42 <param label="Use the intensity image to compute additional features" name="use_raw" type="select">
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43 <option selected="True" value="no_original">No intensity image</option>
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44 <option value="raw_image">Use intensity image</option>
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45 </param>
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46 <when value="no_original"></when>
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47 <when value="raw_image">
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48 <param name="input_raw" type="data" format="tiff,png" label="Intensity image" />
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49 </when>
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50 </conditional>
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51 <conditional name="feature_options">
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52 <param label="Select features to compute" name="features" type="select">
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53 <option selected="True" value="all">All features</option>
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54 <option value="select">Select features</option>
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55 </param>
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56 <when value="all"> </when>
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57 <when value="select">
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58 <param name="selected_features" type="select" label="Available features" multiple="true" display="checkboxes">
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59 <option value="--label">Label from the label map</option>
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60 <option value="--patches">Patches (requires original image)</option>
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61 <option value="--max_intensity">Max Intensity (requires original image)</option>
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62 <option value="--mean_intensity">Mean Intensity (requires original image)</option>
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63 <option value="--min_intensity">Minimum Intensity (requires original image)</option>
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64 <option value="--moments_hu">Moments Hu</option>
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65 <option value="--centroid">Centroid</option>
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66 <option value="--bbox">Bounding box</option>
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67 <option value="--area">Area</option>
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68 <option value="--filled_area">Filled area</option>
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69 <option value="--convex_area">Convex area</option>
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70 <option value="--perimeter">Perimeter</option>
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71 <option value="--extent">Extent</option>
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72 <option value="--eccentricity">Eccentricity</option>
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73 <option value="--equivalent_diameter">Equivalent diameter</option>
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74 <option value="--euler_number">Euler number</option>
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75 <option value="--inertia_tensor_eigvals">Inertia tensor eigenvalues</option>
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76 <option value="--major_axis_length">Major axis length</option>
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77 <option value="--minor_axis_length">Minor axis length</option>
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78 <option value="--orientation">Orientation</option>
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79 <option value="--solidity">Solidity</option>
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80 <option value="--moments">Moments</option>
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81 <option value="--convexity">Convexity</option>
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82 </param>
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83 </when>
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84 </conditional>
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85 </inputs>
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86 <outputs>
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87 <data format="tabular" name="output" />
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88 </outputs>
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89 <tests>
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90 <test>
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91 <param name="input_label" value="input.tiff"/>
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92 <param name="features" value="select"/>
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93 <param name="selected_features" value="--label,--area"/>
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94 <output name="output" ftype="tabular" value="out.tsv"/>
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95 </test>
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96 </tests>
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97 <help>
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98
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99 **Computes features of a label map.**
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100
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101 The computed features are computed based solely on the properties of the labels in the label map,
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102 or, optionally, by also taking the intensities from a corresponding intensity image into account.
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103
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104 The label map must be a 2-D or 3-D single-channel image.
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105
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106 </help>
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107 <citations>
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108 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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109 </citations>
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110 </tool>