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comparison segmetrics.xml @ 5:ac55e2f4d9e3 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:12:16 +0000
parents 7989264b5780
children 462f49860277
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4:7989264b5780 5:ac55e2f4d9e3
1 <tool id="ip_segmetrics" name="SegMetrics" version="1.4.0-1" profile="20.05"> 1 <tool id="ip_segmetrics" name="Compute image segmentation and object detection performance measures" version="1.4.0-2" profile="20.05">
2 <description>image segmentation and object detection performance measures</description> 2 <description>with SegMetrics</description>
3 <requirements> 3 <edam_operations>
4 <edam_operation>operation_3443</edam_operation>
5 </edam_operations>
6 <requirements>
4 <requirement type="package" version="1.4">segmetrics</requirement> 7 <requirement type="package" version="1.4">segmetrics</requirement>
5 <requirement type="package" version="0.23.4">pandas</requirement> 8 <requirement type="package" version="0.23.4">pandas</requirement>
6 </requirements> 9 </requirements>
7 <command detect_errors="aggressive"> 10 <command detect_errors="aggressive">
8 <![CDATA[ 11 <![CDATA[
9 python '$__tool_directory__/run-segmetrics.py' 12 python '$__tool_directory__/run-segmetrics.py'
10 '$input_seg' 13 '$input_seg'
11 '$input_gt' 14 '$input_gt'
12 ./results.tsv 15 ./results.tsv
13 $unzip 16 $unzip
14 $is_seg_unique 17 $is_seg_unique
15 $is_gt_unique 18 $is_gt_unique
16 #for $m in $measures 19 #for $m in $measures
17 #set $kwargs = '' 20 #set $kwargs = ''
18 #set $suffix = '' 21 #set $suffix = ''
19 #set $is_distance = False 22 #set $is_distance = False
20 #if str($m.measure_type.measure_type_selector) == 'ISBIScore': 23 #if str($m.measure_type.measure_type_selector) == 'ISBIScore':
21 #set $kwargs = 'min_ref_size=' + str($m.measure_type.min_ref_size) + ', ' 24 #set $kwargs = 'min_ref_size=' + str($m.measure_type.min_ref_size) + ', '
22 #elif str($m.measure_type.measure_type_selector) == 'Hausdorff': 25 #elif str($m.measure_type.measure_type_selector) == 'Hausdorff':
23 #set $kwargs = 'mode="' + str($m.measure_type.mode) + '", quantile=' + str($m.measure_type.quantile) + ', ' 26 #set $kwargs = 'mode="' + str($m.measure_type.mode) + '", quantile=' + str($m.measure_type.quantile) + ', '
24 #set $is_distance = True 27 #set $is_distance = True
25 #elif str($m.measure_type.measure_type_selector) == 'NSD': 28 #elif str($m.measure_type.measure_type_selector) == 'NSD':
26 #set $is_distance = True 29 #set $is_distance = True
27 #end if 30 #end if
28 #if $is_distance: 31 #if $is_distance:
29 #if $m.measure_type.object_based: 32 #if $m.measure_type.object_based:
30 #set $suffix = '.object_based()' 33 #set $suffix = '.object_based()'
31 #end if 34 #end if
32 #end if 35 #end if
33 #if str($m.measure_type.aggregation) != '': 36 #if str($m.measure_type.aggregation) != '':
34 #set $kwargs = 'aggregation="' + str($m.measure_type.aggregation) + '", ' + $kwargs 37 #set $kwargs = 'aggregation="' + str($m.measure_type.aggregation) + '", ' + $kwargs
35 #end if 38 #end if
36 'sm.${m.measure_type.measure_type_selector}(${kwargs})${suffix}' 39 'sm.${m.measure_type.measure_type_selector}(${kwargs})${suffix}'
37 #end for 40 #end for
38 ]]> 41 ]]>
39 </command> 42 </command>
40 <inputs> 43 <inputs>
41 44
42 <param name="input_seg" type="data" format="tiff,png,zip" label="Segmented images" /> 45 <param name="input_seg" type="data" format="tiff,png,zip" label="Segmented images" />
43 <param name="input_gt" type="data" format="tiff,png,zip" label="Ground truth images" /> 46 <param name="input_gt" type="data" format="tiff,png,zip" label="Ground truth images" />
44 47
45 <param name="unzip" type="boolean" checked="false" truevalue="-unzip" falsevalue="" label="Unzip" /> 48 <param name="unzip" type="boolean" checked="false" truevalue="-unzip" falsevalue="" label="Unzip" />