Mercurial > repos > imgteam > segmetrics

annotate segmetrics.xml @ 8:4512751bccca draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:26:32 +0000
parents b6e88e7bf2fa
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
462f49860277 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 1db841fd5b650baafe7484d17b55b6035bf1ae10
imgteam
parents: 5
diff changeset
1 <tool id="ip_segmetrics" name="Compute image segmentation and object detection performance measures" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
5
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
2 <description>with SegMetrics</description>
6
462f49860277 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 1db841fd5b650baafe7484d17b55b6035bf1ae10
imgteam
parents: 5
diff changeset
3 <macros>
8
4512751bccca planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 7
diff changeset
4 <import>creators.xml</import>
6
462f49860277 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 1db841fd5b650baafe7484d17b55b6035bf1ae10
imgteam
parents: 5
diff changeset
5 <token name="@TOOL_VERSION@">1.4</token>
8
4512751bccca planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 7
diff changeset
6 <token name="@VERSION_SUFFIX@">5</token>
6
462f49860277 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 1db841fd5b650baafe7484d17b55b6035bf1ae10
imgteam
parents: 5
diff changeset
7 </macros>
8
4512751bccca planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 7
diff changeset
8 <creator>
4512751bccca planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 7
diff changeset
9 <expand macro="creators/bmcv"/>
4512751bccca planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 7
diff changeset
10 </creator>
5
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
11 <edam_operations>
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
12 <edam_operation>operation_3443</edam_operation>
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
13 </edam_operations>
7
b6e88e7bf2fa planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 6
diff changeset
14 <xrefs>
b6e88e7bf2fa planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 6
diff changeset
15 <xref type="bio.tools">segmetrics</xref>
b6e88e7bf2fa planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 6
diff changeset
16 <xref type="biii">segmetrics</xref>
b6e88e7bf2fa planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 6
diff changeset
17 </xrefs>
5
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
18 <requirements>
6
462f49860277 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 1db841fd5b650baafe7484d17b55b6035bf1ae10
imgteam
parents: 5
diff changeset
19 <requirement type="package" version="@TOOL_VERSION@">segmetrics</requirement>
4
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
20 <requirement type="package" version="0.23.4">pandas</requirement>
5
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
21 </requirements>
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
22 <command detect_errors="aggressive">
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
23 <![CDATA[
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
24 python '$__tool_directory__/run-segmetrics.py'
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
25 '$input_seg'
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
26 '$input_gt'
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
27 ./results.tsv
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
28 $unzip
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
29 $is_seg_unique
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
30 $is_gt_unique
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
31 #for $m in $measures
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
32 #set $kwargs = ''
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
33 #set $suffix = ''
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
34 #set $is_distance = False
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
35 #if str($m.measure_type.measure_type_selector) == 'ISBIScore':
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
36 #set $kwargs = 'min_ref_size=' + str($m.measure_type.min_ref_size) + ', '
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
37 #elif str($m.measure_type.measure_type_selector) == 'Hausdorff':
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
38 #set $kwargs = 'mode="' + str($m.measure_type.mode) + '", quantile=' + str($m.measure_type.quantile) + ', '
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
39 #set $is_distance = True
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
40 #elif str($m.measure_type.measure_type_selector) == 'NSD':
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
41 #set $is_distance = True
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
42 #end if
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
43 #if $is_distance:
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
44 #if $m.measure_type.object_based:
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
45 #set $suffix = '.object_based()'
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
46 #end if
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
47 #end if
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
48 #if str($m.measure_type.aggregation) != '':
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
49 #set $kwargs = 'aggregation="' + str($m.measure_type.aggregation) + '", ' + $kwargs
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
50 #end if
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
51 'sm.${m.measure_type.measure_type_selector}(${kwargs})${suffix}'
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
52 #end for
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
53 ]]>
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
54 </command>
ac55e2f4d9e3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 4
diff changeset
55 <inputs>
0
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
56
8
4512751bccca planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 7
diff changeset
57 <param name="input_seg" type="data" format="tiff,png,zip" label="Segmented image(s)" />
4512751bccca planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 7
diff changeset
58 <param name="input_gt" type="data" format="tiff,png,zip" label="Ground truth image(s)" />
0
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
59
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
60 <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
imgteam
parents:
diff changeset
61
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
62 <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
imgteam
parents:
diff changeset
63 <param name="is_gt_unique" type="boolean" checked="false" truevalue="-gt_unique" falsevalue="" label="Ground truth is uniquely labeled" />
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
64
4
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
65 <repeat name="measures" title="Performance measure(s)" min="1">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
66 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
67 <param name="measure_type_selector" type="select" label="Type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
68 <option value="Dice">Region-based / Dice</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
69 <option value="ISBIScore">Region-based / SEG</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
70 <option value="JaccardCoefficient">Region-based / Jaccard Coefficient</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
71 <option value="JaccardIndex">Region-based / Jaccard Index</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
72 <option value="RandIndex">Region-based / Rand Index</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
73 <option value="AdjustedRandIndex">Region-based / Adjusted Rand Index</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
74 <option value="Hausdorff">Contour-based / Hausdorff Distance</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
75 <option value="NSD">Contour-based / Normalized Sum of Distances</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
76 <option value="FalseSplit">Detection-based / Count Falsely Split Objects</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
77 <option value="FalseMerge">Detection-based / Count Falsely Merged Objects</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
78 <option value="FalsePositive">Detection-based / Count Spurious Objects</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
79 <option value="FalseNegative">Detection-based / Count Missing Objects</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
80 </param>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
81 <when value="Dice">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
82 <param name="aggregation" type="hidden" value="" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
83 </when>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
84 <when value="ISBIScore">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
85 <param name="aggregation" type="hidden" value="" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
86 <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."/>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
87 </when>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
88 <when value="JaccardCoefficient">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
89 <param name="aggregation" type="hidden" value="" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
90 </when>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
91 <when value="JaccardIndex">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
92 <param name="aggregation" type="hidden" value="" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
93 </when>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
94 <when value="RandIndex">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
95 <param name="aggregation" type="hidden" value="" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
96 </when>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
97 <when value="AdjustedRandIndex">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
98 <param name="aggregation" type="hidden" value="" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
99 </when>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
100 <when value="Hausdorff">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
101 <param name="aggregation" type="hidden" value="" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
102 <param name="mode" type="select" label="Direction">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
103 <option value="a2e">Actual (segmentation result) to expected (ground truth)</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
104 <option value="e2a">Expected (ground truth) to actual (segmentation result)</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
105 <option value="sym" selected="true">Symmetric (maximum of the two)</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
106 </param>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
107 <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)." />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
108 <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." />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
109 </when>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
110 <when value="NSD">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
111 <param name="aggregation" type="hidden" value="" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
112 <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." />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
113 </when>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
114 <when value="FalseSplit">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
115 <param name="aggregation" type="select" label="Aggregation">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
116 <option value="mean" selected="true">Mean per Image</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
117 <option value="sum">Sum over all images</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
118 <option value="obj-mean">Proportion w.r.t. ground truth objects</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
119 </param>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
120 </when>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
121 <when value="FalseMerge">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
122 <param name="aggregation" type="select" label="Aggregation">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
123 <option value="mean" selected="true">Mean per Image</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
124 <option value="sum">Sum over all images</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
125 <option value="obj-mean">Proportion w.r.t. ground truth objects</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
126 </param>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
127 </when>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
128 <when value="FalsePositive">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
129 <param name="aggregation" type="select" label="Aggregation">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
130 <option value="mean" selected="true">Mean per Image</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
131 <option value="sum">Sum over all images</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
132 <option value="obj-mean">Proportion w.r.t. ground truth objects</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
133 </param>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
134 </when>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
135 <when value="FalseNegative">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
136 <param name="aggregation" type="select" label="Aggregation">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
137 <option value="mean" selected="true">Mean per Image</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
138 <option value="sum">Sum over all images</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
139 <option value="obj-mean">Proportion w.r.t. ground truth objects</option>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
140 </param>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
141 </when>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
142 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
143 </repeat>
0
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
144 </inputs>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
145 <outputs>
3
c496306c1cba planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit baee438adb94f6e8b6c3e45e8413c36f9d1dadee
imgteam
parents: 1
diff changeset
146 <data format="tsv" name="results" from_work_dir="results.tsv" />
0
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
147 </outputs>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
148 <tests>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
149 <test>
4
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
150 <param name="input_seg" value="input1.png"/>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
151 <param name="input_gt" value="input2.png"/>
3
c496306c1cba planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit baee438adb94f6e8b6c3e45e8413c36f9d1dadee
imgteam
parents: 1
diff changeset
152 <output name="results" value="results1.tsv" ftype="tsv" compare="diff"/>
4
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
153 <param name="is_seg_unique" value="true"/>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
154 <param name="is_gt_unique" value="true"/>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
155 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
156 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
157 <param name="measure_type_selector" value="Dice" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
158 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
159 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
160 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
161 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
162 <param name="measure_type_selector" value="ISBIScore" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
163 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
164 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
165 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
166 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
167 <param name="measure_type_selector" value="JaccardCoefficient" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
168 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
169 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
170 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
171 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
172 <param name="measure_type_selector" value="JaccardIndex" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
173 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
174 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
175 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
176 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
177 <param name="measure_type_selector" value="RandIndex" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
178 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
179 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
180 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
181 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
182 <param name="measure_type_selector" value="AdjustedRandIndex" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
183 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
184 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
185 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
186 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
187 <param name="measure_type_selector" value="Hausdorff" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
188 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
189 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
190 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
191 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
192 <param name="measure_type_selector" value="Hausdorff" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
193 <param name="quantile" value="0.9" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
194 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
195 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
196 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
197 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
198 <param name="measure_type_selector" value="Hausdorff" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
199 <param name="object_based" value="true" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
200 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
201 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
202 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
203 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
204 <param name="measure_type_selector" value="NSD" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
205 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
206 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
207 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
208 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
209 <param name="measure_type_selector" value="NSD" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
210 <param name="object_based" value="true" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
211 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
212 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
213 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
214 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
215 <param name="measure_type_selector" value="FalseSplit" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
216 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
217 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
218 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
219 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
220 <param name="measure_type_selector" value="FalseMerge" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
221 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
222 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
223 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
224 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
225 <param name="measure_type_selector" value="FalsePositive" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
226 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
227 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
228 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
229 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
230 <param name="measure_type_selector" value="FalseNegative" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
231 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
232 </repeat>
0
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
233 </test>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
234 <test>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
235 <param name="input_seg" value="input1.zip"/>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
236 <param name="input_gt" value="input2.zip"/>
3
c496306c1cba planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit baee438adb94f6e8b6c3e45e8413c36f9d1dadee
imgteam
parents: 1
diff changeset
237 <output name="results" value="results2.tsv" ftype="tsv" compare="diff"/>
4
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
238 <param name="is_seg_unique" value="true"/>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
239 <param name="is_gt_unique" value="true"/>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
240 <param name="unzip" value="true"/>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
241 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
242 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
243 <param name="measure_type_selector" value="Dice" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
244 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
245 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
246 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
247 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
248 <param name="measure_type_selector" value="ISBIScore" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
249 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
250 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
251 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
252 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
253 <param name="measure_type_selector" value="JaccardCoefficient" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
254 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
255 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
256 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
257 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
258 <param name="measure_type_selector" value="JaccardIndex" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
259 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
260 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
261 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
262 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
263 <param name="measure_type_selector" value="RandIndex" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
264 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
265 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
266 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
267 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
268 <param name="measure_type_selector" value="AdjustedRandIndex" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
269 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
270 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
271 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
272 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
273 <param name="measure_type_selector" value="Hausdorff" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
274 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
275 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
276 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
277 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
278 <param name="measure_type_selector" value="Hausdorff" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
279 <param name="quantile" value="0.9" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
280 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
281 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
282 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
283 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
284 <param name="measure_type_selector" value="Hausdorff" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
285 <param name="object_based" value="true" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
286 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
287 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
288 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
289 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
290 <param name="measure_type_selector" value="NSD" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
291 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
292 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
293 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
294 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
295 <param name="measure_type_selector" value="NSD" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
296 <param name="object_based" value="true" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
297 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
298 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
299 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
300 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
301 <param name="measure_type_selector" value="FalseSplit" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
302 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
303 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
304 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
305 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
306 <param name="measure_type_selector" value="FalseMerge" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
307 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
308 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
309 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
310 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
311 <param name="measure_type_selector" value="FalsePositive" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
312 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
313 </repeat>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
314 <repeat name="measures">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
315 <conditional name="measure_type">
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
316 <param name="measure_type_selector" value="FalseNegative" />
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
317 </conditional>
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
318 </repeat>
0
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
319 </test>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
320 </tests>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
321 <help>
8
4512751bccca planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 7
diff changeset
322
4512751bccca planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 7
diff changeset
323 **Computates image segmentation and object detection performance measures for 2-D image data.**
1
3a7310406943 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 288ebcb2217c2b0324392cdf74a143252121aa50
imgteam
parents: 0
diff changeset
324
3a7310406943 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 288ebcb2217c2b0324392cdf74a143252121aa50
imgteam
parents: 0
diff changeset
325 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.
3a7310406943 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 288ebcb2217c2b0324392cdf74a143252121aa50
imgteam
parents: 0
diff changeset
326
3a7310406943 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 288ebcb2217c2b0324392cdf74a143252121aa50
imgteam
parents: 0
diff changeset
327 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.
8
4512751bccca planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 7
diff changeset
328
0
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
329 </help>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
330 <citations>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
331 <citation type="doi">10.1093/bioinformatics/btu080</citation>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
332 <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
imgteam
parents:
diff changeset
333 <citation type="doi">10.1109/ICIP.2003.1246871</citation>
4
7989264b5780 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 075271cee9cb9c2625c04dbefd903cdea6e74724
imgteam
parents: 3
diff changeset
334 <citation type="doi">10.1023/A:1007975324482</citation>
0
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
335 </citations>
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
imgteam
parents:
diff changeset
336 </tool>