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annotate segmetrics.xml @ 3:c496306c1cba draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit baee438adb94f6e8b6c3e45e8413c36f9d1dadee
author imgteam
date Sat, 08 Oct 2022 21:54:40 +0000
parents 3a7310406943
children 7989264b5780
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c496306c1cba planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit baee438adb94f6e8b6c3e45e8413c36f9d1dadee
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1 <tool id="ip_segmetrics" name="SegMetrics" version="0.11.3-2" profile="20.05">
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2 <description>image segmentation and object detection performance measures</description>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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3 <requirements>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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4 <requirement type="package" version="0.11.3">segmetrics</requirement>
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5 <requirement type="package" version="0.18.1">scikit-image</requirement>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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6 </requirements>
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7 <command detect_errors="aggressive">
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8 <![CDATA[
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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9 python '$__tool_directory__/run-segmetrics.py'
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10 '$input_seg'
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11 '$input_gt'
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c496306c1cba planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit baee438adb94f6e8b6c3e45e8413c36f9d1dadee
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12 ./results.tsv
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13 $unzip
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14 $is_seg_unique
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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15 $is_gt_unique
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16 $measures.dice
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17 $measures.seg
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18 $measures.jc
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19 $measures.ji
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20 $measures.ri
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21 $measures.ari
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22 $measures.hsd_sym
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23 $measures.hsd_e2a
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24 $measures.hsd_a2e
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25 $measures.nsd
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26 $measures.o_hsd_sym
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27 $measures.o_hsd_e2a
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28 $measures.o_hsd_a2e
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29 $measures.o_nsd
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30 $measures.fs
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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31 $measures.fm
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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32 $measures.fp
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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33 $measures.fn
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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34 ]]>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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35 </command>
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36 <inputs>
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37
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38 <param name="input_seg" type="data" format="tiff,png,zip" label="Segmented images" />
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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39 <param name="input_gt" type="data" format="tiff,png,zip" label="Ground truth images" />
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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40
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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41 <param name="unzip" type="boolean" checked="false" truevalue="-unzip" falsevalue="" label="Unzip" />
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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42
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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43 <param name="is_seg_unique" type="boolean" checked="false" truevalue="-seg_unique" falsevalue="" label="Segmentation is uniquely labeled" />
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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44 <param name="is_gt_unique" type="boolean" checked="false" truevalue="-gt_unique" falsevalue="" label="Ground truth is uniquely labeled" />
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45
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46 <section name="measures" title="Performance measures" >
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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47 <param name="dice" type="boolean" checked="true" truevalue="-measure-dice" falsevalue="" label="Dice" />
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48 <param name="seg" type="boolean" checked="true" truevalue="-measure-seg" falsevalue="" label="SEG" />
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49 <param name="jc" type="boolean" checked="false" truevalue="-measure-jc" falsevalue="" label="Jaccard coefficient" />
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50 <param name="ji" type="boolean" checked="true" truevalue="-measure-ji" falsevalue="" label="Jaccard index" />
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51 <param name="ri" type="boolean" checked="false" truevalue="-measure-ri" falsevalue="" label="Rand index" />
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52 <param name="ari" type="boolean" checked="false" truevalue="-measure-ari" falsevalue="" label="Adjusted Rand index" />
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53 <param name="hsd_sym" type="boolean" checked="false" truevalue="-measure-hsd_sym" falsevalue="" label="Hausdorff distance (symmetric)" />
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54 <param name="hsd_e2a" type="boolean" checked="false" truevalue="-measure-hsd_e2a" falsevalue="" label="Hausdorff distance (ground truth to segmented)" />
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55 <param name="hsd_a2e" type="boolean" checked="false" truevalue="-measure-hsd_a2e" falsevalue="" label="Hausdorff distance (segmented to ground truth)" />
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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56 <param name="nsd" type="boolean" checked="false" truevalue="-measure-nsd" falsevalue="" label="Normalized sum of distances" />
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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57 <param name="o_hsd_sym" type="boolean" checked="true" truevalue="-measure-o_hsd_sym" falsevalue="" label="Object-based Hausdorff distance (symmetric)" />
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58 <param name="o_hsd_e2a" type="boolean" checked="false" truevalue="-measure-o_hsd_e2a" falsevalue="" label="Object-based Hausdorff distance (ground truth to segmented)" />
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59 <param name="o_hsd_a2e" type="boolean" checked="false" truevalue="-measure-o_hsd_a2e" falsevalue="" label="Object-based Hausdorff distance (segmented to ground truth)" />
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60 <param name="o_nsd" type="boolean" checked="true" truevalue="-measure-o_nsd" falsevalue="" label="Object-based normalized sum of distances" />
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61 <param name="fs" type="boolean" checked="true" truevalue="-measure-fs" falsevalue="" label="Falsely split objects per image" />
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62 <param name="fm" type="boolean" checked="true" truevalue="-measure-fm" falsevalue="" label="Falsely merged objects per image" />
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63 <param name="fp" type="boolean" checked="true" truevalue="-measure-fp" falsevalue="" label="Spurious objects per image" />
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64 <param name="fn" type="boolean" checked="true" truevalue="-measure-fn" falsevalue="" label="Missing objects per image" />
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65 </section>
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66
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67 </inputs>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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68 <outputs>
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c496306c1cba planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit baee438adb94f6e8b6c3e45e8413c36f9d1dadee
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69 <data format="tsv" name="results" from_work_dir="results.tsv" />
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70 </outputs>
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71 <tests>
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72 <test>
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73 <param name="input_seg" value="input2.png"/>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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74 <param name="input_gt" value="input1.png"/>
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75 <output name="results" value="results1.tsv" ftype="tsv" compare="diff"/>
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76 <param name="is_seg_unique" value="True"/>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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77 <param name="is_gt_unique" value="True"/>
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78 </test>
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79 <test>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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80 <param name="input_seg" value="input1.zip"/>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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81 <param name="input_gt" value="input2.zip"/>
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82 <output name="results" value="results2.tsv" ftype="tsv" compare="diff"/>
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83 <param name="is_seg_unique" value="True"/>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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84 <param name="is_gt_unique" value="True"/>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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85 <param name="unzip" value="True"/>
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86 </test>
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87 </tests>
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88 <help>
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89 This tool permits the computation of image segmentation and object detection performance measures for 2-D image data.
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90
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91 You can either use a pair of individual input images (a segmented and a ground truth image), or a pair of ZIP archives which contain the segmented and the correspondiong ground truth images. When using a pair of individual images, remember to turn off the "Unzip" option. When using ZIP archives, turn it on instead and make sure that the directory structure is the same for the segmented and the ground truth images. Correspondences are estbalished based on the file names, which should be *identical* for a pair of corresponding images.
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92
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93 If all objects within your segmented images are *uniquely* labeled, you can turn on the "Segmentation is uniquely labeled" switch to speed up the computations. Leave it off otherwise, or if you are unsure. The same accounts for the "Ground truth is uniquely labeled" switch and your ground turth image data.
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94 </help>
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95 <citations>
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96 <citation type="doi">10.1093/bioinformatics/btu080</citation>
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97 <citation type="doi">10.1109/ISBI.2009.5193098</citation>
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98 <citation type="doi">10.1109/ICIP.2003.1246871</citation>
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99 </citations>
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100 </tool>