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annotate segmetrics.xml @ 0:0729657d9e4e draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
author imgteam
date Fri, 07 Oct 2022 22:05:59 +0000
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children 3a7310406943
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0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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1 <tool id="ip_segmetrics" name="SegMetrics" version="0.11.3" profile="20.05">
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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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>
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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 '$__tool_directory__/run-segmetrics.py'
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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10 '$input_seg'
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11 '$input_gt'
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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12 ./results.csv
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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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
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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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
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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
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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>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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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)" />
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56 <param name="nsd" type="boolean" checked="false" truevalue="-measure-nsd" falsevalue="" label="Normalized sum of distances" />
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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>
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68 <outputs>
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69 <data format="csv" name="results" from_work_dir="results.csv" />
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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"/>
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74 <param name="input_gt" value="input1.png"/>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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75 <output name="results" value="results1.csv" ftype="csv" 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>
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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"/>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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82 <output name="results" value="results2.csv" ftype="csv" compare="diff"/>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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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"/>
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85 <param name="unzip" value="True"/>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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86 </test>
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87 </tests>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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88 <help>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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89 Image segmentation and object detection performance measures for 2-D image data.
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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90 </help>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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91 <citations>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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92 <citation type="doi">10.1093/bioinformatics/btu080</citation>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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93 <citation type="doi">10.1109/ISBI.2009.5193098</citation>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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94 <citation type="doi">10.1109/ICIP.2003.1246871</citation>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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95 </citations>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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96 </tool>