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annotate 2d_feature_extraction.xml @ 3:5791a7f65275 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author imgteam
date Wed, 18 Dec 2019 05:00:56 -0500
parents 6fdb3542a406
children 0a53256b48c6
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1 <tool id="ip_2d_feature_extraction" name="2D Feature Extraction" version="0.1.1">
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2 <description>Feature Extraction</description>
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3 <requirements>
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4 <requirement type="package" version="0.23.4">pandas</requirement>
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5 <requirement type="package" version="0.14.2">scikit-image</requirement>
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6 <requirement type="package" version="1.15.4">numpy</requirement>
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7 <requirement type="package" version="0.15.1">tifffile</requirement>
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8 </requirements>
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9 <command detect_errors="aggressive">
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10 <![CDATA[
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11 python '$__tool_directory__/2d_feature_extraction.py'
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12 #if $feature_options['features'] == 'all'
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13 --all
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14 #else if $feature_options['features'] == 'select'
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15 ${' '.join(str( $feature_options['selected_features'] ).split(','))}
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16 #end if
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17 #if $use_raw_option['use_raw'] == 'raw_image'
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18 --raw '$input_raw'
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19 #end if
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20 '$input_label' '$output'
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21 ]]>
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22 </command>
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23 <inputs>
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24 <param name="input_label" type="data" format="tiff" label="Label file" />
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25 <conditional name="use_raw_option">
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26 <param label="Use original image to compute additional features" name="use_raw" type="select">
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27 <option selected="True" value="no_original">No original image</option>
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28 <option value="raw_image">Use original image</option>
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29 </param>
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30 <when value="no_original"></when>
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31 <when value="raw_image">
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32 <param name="input_raw" type="data" format="tiff" label="Original image file" />
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33 </when>
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34 </conditional>
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35 <conditional name="feature_options">
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36 <param label="Select features to compute" name="features" type="select">
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37 <option selected="True" value="all">All features</option>
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38 <option value="select">Select features</option>
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39 </param>
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40 <when value="all"> </when>
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41 <when value="select">
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42 <param name="selected_features" type="select" label="Available features" multiple="true" display="checkboxes">
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43 <option value="--label">Add label id of label image</option>
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44 <option value="--patches">Patches (requires original image)</option>
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45 <option value="--max_intensity">Max Intensity (requires original image)</option>
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46 <option value="--mean_intensity">Mean Intensity (requires original image)</option>
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47 <option value="--min_intensity">Minimum Intensity (requires original image)</option>
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48 <option value="--moments_hu">Moments Hu</option>
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49 <option value="--centroid">Centroid</option>
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50 <option value="--bbox">Bounding Box</option>
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51 <option value="--area">Area</option>
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52 <option value="--filled_area">Filled Area</option>
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53 <option value="--convex_area">Convex Area</option>
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54 <option value="--perimeter">Perimeter</option>
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55 <option value="--extent">Extent</option>
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56 <option value="--eccentricity">Eccentricity</option>
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57 <option value="--equivalent_diameter">Equivalent Diameter</option>
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58 <option value="--euler_number">Euler Number</option>
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59 <option value="--inertia_tensor_eigvals">Inertia Tensor Eigenvalues</option>
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60 <option value="--major_axis_length">Major Axis Length</option>
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61 <option value="--minor_axis_length">Minor Axis Length</option>
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62 <option value="--orientation">Orientation</option>
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63 <option value="--solidity">Solidity</option>
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64 <option value="--moments">Moments</option>
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65 <option value="--convexity">Convexity</option>
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66 </param>
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67 </when>
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68 </conditional>
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69 </inputs>
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70 <outputs>
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71 <data format="tabular" name="output" />
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72 </outputs>
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73 <tests>
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74 <test>
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75 <param name="input_label" value="input.tiff"/>
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76 <param name="features" value="select"/>
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77 <param name="selected_features" value="--area"/>
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78 <output name="output" ftype="tabular" value="out.tsv"/>
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79 </test>
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80 </tests>
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81 <help>
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82 **What it does**
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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83
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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84 This tool computes several features of a 2D label image and optionally more features using the original image.
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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85 </help>
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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86 <citations>
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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87 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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88 </citations>
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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89 </tool>