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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
author imgteam
date Tue, 20 Jun 2023 21:40:19 +0000
parents 48dcf95aebc7
children
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ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
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1 <tool id="ip_segmetrics" name="SegMetrics" version="1.4.0-1" profile="20.05">
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2 <description>image segmentation and object detection performance measures</description>
6cbb36364b82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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3 <requirements>
4
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4 <requirement type="package" version="1.4">segmetrics</requirement>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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5 <requirement type="package" version="0.23.4">pandas</requirement>
0
6cbb36364b82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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6 </requirements>
6cbb36364b82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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7 <command detect_errors="aggressive">
6cbb36364b82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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8 <![CDATA[
6cbb36364b82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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9 python '$__tool_directory__/run-segmetrics.py'
6cbb36364b82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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10 '$input_seg'
6cbb36364b82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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11 '$input_gt'
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12 ./results.tsv
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13 $unzip
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14 $is_seg_unique
6cbb36364b82 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 #for $m in $measures
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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17 #set $kwargs = ''
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18 #set $suffix = ''
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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19 #set $is_distance = False
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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20 #if str($m.measure_type.measure_type_selector) == 'ISBIScore':
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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21 #set $kwargs = 'min_ref_size=' + str($m.measure_type.min_ref_size) + ', '
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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22 #elif str($m.measure_type.measure_type_selector) == 'Hausdorff':
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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23 #set $kwargs = 'mode="' + str($m.measure_type.mode) + '", quantile=' + str($m.measure_type.quantile) + ', '
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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24 #set $is_distance = True
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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25 #elif str($m.measure_type.measure_type_selector) == 'NSD':
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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26 #set $is_distance = True
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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27 #end if
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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28 #if $is_distance:
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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29 #if $m.measure_type.object_based:
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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30 #set $suffix = '.object_based()'
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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31 #end if
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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32 #end if
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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33 #if str($m.measure_type.aggregation) != '':
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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34 #set $kwargs = 'aggregation="' + str($m.measure_type.aggregation) + '", ' + $kwargs
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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35 #end if
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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36 'sm.${m.measure_type.measure_type_selector}(${kwargs})${suffix}'
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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37 #end for
0
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38 ]]>
6cbb36364b82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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39 </command>
6cbb36364b82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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40 <inputs>
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41
6cbb36364b82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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42 <param name="input_seg" type="data" format="tiff,png,zip" label="Segmented images" />
6cbb36364b82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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43 <param name="input_gt" type="data" format="tiff,png,zip" label="Ground truth images" />
6cbb36364b82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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44
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45 <param name="unzip" type="boolean" checked="false" truevalue="-unzip" falsevalue="" label="Unzip" />
6cbb36364b82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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46
6cbb36364b82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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47 <param name="is_seg_unique" type="boolean" checked="false" truevalue="-seg_unique" falsevalue="" label="Segmentation is uniquely labeled" />
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48 <param name="is_gt_unique" type="boolean" checked="false" truevalue="-gt_unique" falsevalue="" label="Ground truth is uniquely labeled" />
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49
4
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50 <repeat name="measures" title="Performance measure(s)" min="1">
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51 <conditional name="measure_type">
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52 <param name="measure_type_selector" type="select" label="Type">
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53 <option value="Dice">Region-based / Dice</option>
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54 <option value="ISBIScore">Region-based / SEG</option>
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55 <option value="JaccardCoefficient">Region-based / Jaccard Coefficient</option>
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56 <option value="JaccardIndex">Region-based / Jaccard Index</option>
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57 <option value="RandIndex">Region-based / Rand Index</option>
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58 <option value="AdjustedRandIndex">Region-based / Adjusted Rand Index</option>
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59 <option value="Hausdorff">Contour-based / Hausdorff Distance</option>
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60 <option value="NSD">Contour-based / Normalized Sum of Distances</option>
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61 <option value="FalseSplit">Detection-based / Count Falsely Split Objects</option>
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62 <option value="FalseMerge">Detection-based / Count Falsely Merged Objects</option>
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63 <option value="FalsePositive">Detection-based / Count Spurious Objects</option>
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64 <option value="FalseNegative">Detection-based / Count Missing Objects</option>
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65 </param>
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66 <when value="Dice">
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67 <param name="aggregation" type="hidden" value="" />
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68 </when>
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69 <when value="ISBIScore">
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70 <param name="aggregation" type="hidden" value="" />
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71 <param name="min_ref_size" type="integer" value="1" label="Minimum size of ground truth objects (in pixels)" help="Ground truth objects smaller than this value (in pixels) are skipped. It is reasonable to set this value to 2 so that objects of a single pixel in size are skipped, since such objects obviously correspond to misannotations which distort the performance evaluation. However, for compatibility to the official implementation, the value is set to 1 by default so all ground truth objects are included."/>
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72 </when>
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73 <when value="JaccardCoefficient">
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74 <param name="aggregation" type="hidden" value="" />
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75 </when>
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76 <when value="JaccardIndex">
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77 <param name="aggregation" type="hidden" value="" />
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78 </when>
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79 <when value="RandIndex">
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80 <param name="aggregation" type="hidden" value="" />
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81 </when>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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82 <when value="AdjustedRandIndex">
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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83 <param name="aggregation" type="hidden" value="" />
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84 </when>
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85 <when value="Hausdorff">
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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86 <param name="aggregation" type="hidden" value="" />
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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87 <param name="mode" type="select" label="Direction">
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88 <option value="a2e">Actual (segmentation result) to expected (ground truth)</option>
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89 <option value="e2a">Expected (ground truth) to actual (segmentation result)</option>
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90 <option value="sym" selected="true">Symmetric (maximum of the two)</option>
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91 </param>
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92 <param name="quantile" type="float" min="0" max="1" value="1" label="Quantile" help="Must be between 0 and 1. If set to 1, then the implementaiton corresponds to the Hausdorff distance described by Bamford (2003). Any other value corresponds to the quantile method described by Rucklidge (1997)." />
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93 <param name="object_based" type="boolean" label="Object-based" help="Object correspondances between the segmented and the ground truth objects are established on a many-to-many basis, so that the resulting distances are minimal." />
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94 </when>
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95 <when value="NSD">
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96 <param name="aggregation" type="hidden" value="" />
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97 <param name="object_based" type="boolean" label="Object-based" help="Object correspondances between the segmented and the ground truth objects are established on a many-to-many basis, so that the resulting distances are minimal." />
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98 </when>
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99 <when value="FalseSplit">
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100 <param name="aggregation" type="select" label="Aggregation">
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101 <option value="mean" selected="true">Mean per Image</option>
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102 <option value="sum">Sum over all images</option>
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103 <option value="obj-mean">Proportion w.r.t. ground truth objects</option>
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104 </param>
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105 </when>
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106 <when value="FalseMerge">
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107 <param name="aggregation" type="select" label="Aggregation">
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108 <option value="mean" selected="true">Mean per Image</option>
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109 <option value="sum">Sum over all images</option>
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110 <option value="obj-mean">Proportion w.r.t. ground truth objects</option>
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111 </param>
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112 </when>
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113 <when value="FalsePositive">
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114 <param name="aggregation" type="select" label="Aggregation">
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115 <option value="mean" selected="true">Mean per Image</option>
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116 <option value="sum">Sum over all images</option>
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117 <option value="obj-mean">Proportion w.r.t. ground truth objects</option>
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118 </param>
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119 </when>
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120 <when value="FalseNegative">
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121 <param name="aggregation" type="select" label="Aggregation">
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122 <option value="mean" selected="true">Mean per Image</option>
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123 <option value="sum">Sum over all images</option>
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124 <option value="obj-mean">Proportion w.r.t. ground truth objects</option>
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125 </param>
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126 </when>
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127 </conditional>
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128 </repeat>
0
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129 </inputs>
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130 <outputs>
3
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131 <data format="tsv" name="results" from_work_dir="results.tsv" />
0
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132 </outputs>
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133 <tests>
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134 <test>
4
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135 <param name="input_seg" value="input1.png"/>
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136 <param name="input_gt" value="input2.png"/>
3
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137 <output name="results" value="results1.tsv" ftype="tsv" compare="diff"/>
4
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138 <param name="is_seg_unique" value="true"/>
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139 <param name="is_gt_unique" value="true"/>
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140 <repeat name="measures">
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141 <conditional name="measure_type">
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142 <param name="measure_type_selector" value="Dice" />
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143 </conditional>
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144 </repeat>
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145 <repeat name="measures">
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146 <conditional name="measure_type">
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147 <param name="measure_type_selector" value="ISBIScore" />
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148 </conditional>
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149 </repeat>
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150 <repeat name="measures">
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151 <conditional name="measure_type">
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152 <param name="measure_type_selector" value="JaccardCoefficient" />
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153 </conditional>
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154 </repeat>
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155 <repeat name="measures">
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156 <conditional name="measure_type">
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157 <param name="measure_type_selector" value="JaccardIndex" />
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158 </conditional>
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159 </repeat>
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160 <repeat name="measures">
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161 <conditional name="measure_type">
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162 <param name="measure_type_selector" value="RandIndex" />
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163 </conditional>
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164 </repeat>
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165 <repeat name="measures">
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166 <conditional name="measure_type">
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167 <param name="measure_type_selector" value="AdjustedRandIndex" />
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168 </conditional>
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169 </repeat>
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170 <repeat name="measures">
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171 <conditional name="measure_type">
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172 <param name="measure_type_selector" value="Hausdorff" />
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173 </conditional>
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174 </repeat>
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175 <repeat name="measures">
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176 <conditional name="measure_type">
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177 <param name="measure_type_selector" value="Hausdorff" />
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178 <param name="quantile" value="0.9" />
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179 </conditional>
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180 </repeat>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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181 <repeat name="measures">
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182 <conditional name="measure_type">
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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183 <param name="measure_type_selector" value="Hausdorff" />
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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184 <param name="object_based" value="true" />
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185 </conditional>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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186 </repeat>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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187 <repeat name="measures">
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188 <conditional name="measure_type">
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189 <param name="measure_type_selector" value="NSD" />
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190 </conditional>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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191 </repeat>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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192 <repeat name="measures">
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193 <conditional name="measure_type">
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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194 <param name="measure_type_selector" value="NSD" />
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195 <param name="object_based" value="true" />
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196 </conditional>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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197 </repeat>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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198 <repeat name="measures">
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199 <conditional name="measure_type">
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200 <param name="measure_type_selector" value="FalseSplit" />
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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201 </conditional>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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202 </repeat>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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203 <repeat name="measures">
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204 <conditional name="measure_type">
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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205 <param name="measure_type_selector" value="FalseMerge" />
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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206 </conditional>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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207 </repeat>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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208 <repeat name="measures">
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209 <conditional name="measure_type">
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210 <param name="measure_type_selector" value="FalsePositive" />
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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211 </conditional>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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212 </repeat>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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213 <repeat name="measures">
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214 <conditional name="measure_type">
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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215 <param name="measure_type_selector" value="FalseNegative" />
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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216 </conditional>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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217 </repeat>
0
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218 </test>
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219 <test>
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220 <param name="input_seg" value="input1.zip"/>
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221 <param name="input_gt" value="input2.zip"/>
3
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222 <output name="results" value="results2.tsv" ftype="tsv" compare="diff"/>
4
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223 <param name="is_seg_unique" value="true"/>
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224 <param name="is_gt_unique" value="true"/>
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225 <param name="unzip" value="true"/>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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226 <repeat name="measures">
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227 <conditional name="measure_type">
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228 <param name="measure_type_selector" value="Dice" />
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229 </conditional>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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230 </repeat>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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231 <repeat name="measures">
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232 <conditional name="measure_type">
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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233 <param name="measure_type_selector" value="ISBIScore" />
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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234 </conditional>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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235 </repeat>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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236 <repeat name="measures">
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237 <conditional name="measure_type">
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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238 <param name="measure_type_selector" value="JaccardCoefficient" />
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239 </conditional>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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240 </repeat>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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241 <repeat name="measures">
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242 <conditional name="measure_type">
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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243 <param name="measure_type_selector" value="JaccardIndex" />
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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244 </conditional>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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245 </repeat>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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246 <repeat name="measures">
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247 <conditional name="measure_type">
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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248 <param name="measure_type_selector" value="RandIndex" />
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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249 </conditional>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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250 </repeat>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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251 <repeat name="measures">
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252 <conditional name="measure_type">
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253 <param name="measure_type_selector" value="AdjustedRandIndex" />
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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254 </conditional>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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255 </repeat>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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256 <repeat name="measures">
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257 <conditional name="measure_type">
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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258 <param name="measure_type_selector" value="Hausdorff" />
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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259 </conditional>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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260 </repeat>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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261 <repeat name="measures">
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262 <conditional name="measure_type">
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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263 <param name="measure_type_selector" value="Hausdorff" />
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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264 <param name="quantile" value="0.9" />
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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265 </conditional>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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266 </repeat>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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267 <repeat name="measures">
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268 <conditional name="measure_type">
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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269 <param name="measure_type_selector" value="Hausdorff" />
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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270 <param name="object_based" value="true" />
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271 </conditional>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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272 </repeat>
ef65ecafa3ef planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
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273 <repeat name="measures">
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274 <conditional name="measure_type">
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275 <param name="measure_type_selector" value="NSD" />
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276 </conditional>
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277 </repeat>
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278 <repeat name="measures">
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279 <conditional name="measure_type">
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280 <param name="measure_type_selector" value="NSD" />
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281 <param name="object_based" value="true" />
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282 </conditional>
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283 </repeat>
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284 <repeat name="measures">
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285 <conditional name="measure_type">
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286 <param name="measure_type_selector" value="FalseSplit" />
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287 </conditional>
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288 </repeat>
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289 <repeat name="measures">
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290 <conditional name="measure_type">
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291 <param name="measure_type_selector" value="FalseMerge" />
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292 </conditional>
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293 </repeat>
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294 <repeat name="measures">
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295 <conditional name="measure_type">
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296 <param name="measure_type_selector" value="FalsePositive" />
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297 </conditional>
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298 </repeat>
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299 <repeat name="measures">
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300 <conditional name="measure_type">
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301 <param name="measure_type_selector" value="FalseNegative" />
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302 </conditional>
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303 </repeat>
0
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304 </test>
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305 </tests>
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306 <help>
1
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307 This tool permits the computation of image segmentation and object detection performance measures for 2-D image data.
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308
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309 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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310
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311 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.
0
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312 </help>
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313 <citations>
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314 <citation type="doi">10.1093/bioinformatics/btu080</citation>
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315 <citation type="doi">10.1109/ISBI.2009.5193098</citation>
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316 <citation type="doi">10.1109/ICIP.2003.1246871</citation>
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317 <citation type="doi">10.1023/A:1007975324482</citation>
0
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318 </citations>
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319 </tool>