Mercurial > repos > imgteam > superdsm

annotate superdsm.xml @ 6:79ec3263686a 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/superdsm/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
author imgteam
date Wed, 24 Apr 2024 08:13:34 +0000
parents 9b4830300f3a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
1 <tool id="ip_superdsm" name="Perform segmentation using deformable shape models" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
2 <description>with SuperDSM</description>
3
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
3 <macros>
5
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
4 <import>creators.xml</import>
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
5 <import>tests.xml</import>
4
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
6 <token name="@TOOL_VERSION@">0.2.0</token>
6
79ec3263686a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
imgteam
parents: 5
diff changeset
7 <token name="@VERSION_SUFFIX@">1</token>
3
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
8 </macros>
5
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
9 <creator>
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
10 <expand macro="creators/bmcv"/>
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
11 </creator>
2
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
12 <edam_operations>
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
13 <edam_operation>operation_3443</edam_operation>
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
14 </edam_operations>
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
15 <xrefs>
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
16 <xref type="bio.tools">superdsm</xref>
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
17 <xref type="biii">superdsm</xref>
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
18 </xrefs>
4
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
19 <requirements>
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
20
5
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
21 <requirement type="package" version="@TOOL_VERSION@">superdsm</requirement>
6
79ec3263686a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
imgteam
parents: 5
diff changeset
22 <requirement type="package" version="0.1.1">giatools</requirement>
4
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
23
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
24 <!--
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
25 Pin the dependencies to specific versions for reproducibility:
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
26 https://github.com/BMCV/SuperDSM#dependency-version-considerations
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
27 -->
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
28 <requirement type="package" version="1.20">numpy</requirement>
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
29 <requirement type="package" version="1.6.3">scipy</requirement>
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
30 <requirement type="package" version="0.18.1">scikit-image</requirement>
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
31 <requirement type="package" version="1.2.6">cvxopt</requirement>
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
32 <requirement type="package" version="1.1.13">cvxpy</requirement>
0
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
diff changeset
33 <requirement type="package" version="1.6.0">ray-core</requirement>
4
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
34
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
35 <!--
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
36 2020.0 is the last version of MKL which supports the "MKL_DEBUG_CPU_TYPE" environment variable.
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
37 -->
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
38 <requirement type="package" version="2020.0">mkl</requirement>
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
39
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
40 <!--
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
41 Using MKL instead of other BLAS can significantly improve performance on some hardware:
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
42 https://stackoverflow.com/questions/62783262/why-is-numpy-with-ryzen-threadripper-so-much-slower-than-xeon
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
43
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
44 Pinning BLAS to version 1.0 is required for reproducibility:
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
45 https://github.com/BMCV/SuperDSM#dependency-version-considerations
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
46 -->
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
47 <requirement type="package" version="1.0=mkl">blas</requirement>
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
48
2
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
49 </requirements>
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
50 <command detect_errors="aggressive">
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
51 <![CDATA[
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
52 python '$__tool_directory__/run-superdsm.py'
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
53 '${dataset}'
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
54 \${GALAXY_SLOTS:-4}
3
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
55 #if 'masks' in $outputs:
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
56 --do-masks 'masks.png'
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
57 #end if
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
58 #if 'cfg' in $outputs:
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
59 --do-cfg 'cfg.tsv'
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
60 #end if
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
61 #if 'overlay' in $outputs:
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
62 --do-overlay 'overlay.png'
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
63 #if $seg_border.value % 2 == 1:
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
64 #set $seg_border = "%d" % ($seg_border.value + 1)
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
65 --do-overlay-border $seg_border
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
66 #else:
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
67 --do-overlay-border $seg_border
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
68 #end if
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
69 #end if
2
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
70 #if str($config.AF_scale) != '':
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
71 --AF_scale '${config.AF_scale}'
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
72 #end if
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
73 #if str($config.c2f_region_analysis_min_atom_radius) != '':
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
74 --c2f_region_analysis_min_atom_radius '${config.c2f_region_analysis_min_atom_radius}'
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
75 #end if
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
76 #if str($config.c2f_region_analysis_min_norm_energy_improvement) != '':
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
77 --c2f_region_analysis_min_norm_energy_improvement '${config.c2f_region_analysis_min_norm_energy_improvement}'
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
78 #end if
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
79 #if str($config.c2f_region_analysis_max_atom_norm_energy) != '':
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
80 --c2f_region_analysis_max_atom_norm_energy '${config.c2f_region_analysis_max_atom_norm_energy}'
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
81 #end if
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
82 #if str($config.c2f_region_analysis_max_cluster_marker_irregularity) != '':
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
83 --c2f_region_analysis_max_cluster_marker_irregularity '${config.c2f_region_analysis_max_cluster_marker_irregularity}'
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
84 #end if
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
85 #if str($config.dsm_alpha) != '':
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
86 --dsm_alpha '${config.dsm_alpha}'
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
87 #end if
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
88 #if str($config.dsm_AF_alpha) != '':
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
89 --dsm_AF_alpha '${config.dsm_AF_alpha}'
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
90 #end if
4
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
91 --global_energy_minimization_pruning '${global_energy_minimization_pruning}'
2
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
92 #if str($config.global_energy_minimization_beta) != '':
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
93 --global_energy_minimization_beta '${config.global_energy_minimization_beta}'
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
94 #end if
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
95 #if str($config.global_energy_minimization_AF_beta) != '':
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
96 --global_energy_minimization_AF_beta '${config.global_energy_minimization_AF_beta}'
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
97 #end if
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
98 #if str($config.postprocess_mask_max_distance) != '':
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
99 --postprocess_mask_max_distance '${config.postprocess_mask_max_distance}'
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
100 #end if
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
101 #if str($config.postprocess_mask_stdamp) != '':
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
102 --postprocess_mask_stdamp '${config.postprocess_mask_stdamp}'
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
103 #end if
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
104 #if str($config.postprocess_max_norm_energy) != '':
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
105 --postprocess_max_norm_energy '${config.postprocess_max_norm_energy}'
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
106 #end if
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
107 #if str($config.postprocess_min_contrast) != '':
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
108 --postprocess_min_contrast '${config.postprocess_min_contrast}'
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
109 #end if
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
110 #if str($config.postprocess_min_object_radius) != '':
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
111 --postprocess_min_object_radius '${config.postprocess_min_object_radius}'
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
112 #end if
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
113 ]]>
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
114 </command>
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
115 <environment_variables>
4
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
116
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
117 <!--
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
118 This enables accelerated CPU instruction sets on AMD hardware, does nothing in Intel hardware, thus no need to change this:
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
119 -->
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
120 <environment_variable name="MKL_DEBUG_CPU_TYPE">5</environment_variable>
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
121
2
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
122 </environment_variables>
244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
123 <inputs>
0
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
diff changeset
124 <param name="dataset" type="data" format="tiff,png" label="Dataset" />
4
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
125 <param argument="--global_energy_minimization_pruning" type="select" label="Graph pruning for global energy minimization" help="Exact graph pruning corresponds to the original algorithm, which provably yields globally optimal results. Robust graph pruning is more greedy and has a provably bounded approximation error. Depending on the data, this can be significantly faster than exact graph pruning, without degrading the segmentation or cluster splitting performance.">
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
126 <option value="exact">Exact graph pruning (Kostrykin and Rohr, TPAMI 2023)</option>
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
127 <option value="isbi24" selected="true">Robust graph pruning (Kostrykin and Rohr, ISBI 2024)</option>
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
128 </param>
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
129 <param name="outputs" type="select" label="Tool outputs" multiple="true" optional="false" help="Note that if neither a segmentation overlay nor a label map is created, segmentation and cluster splitting will not be performed. As a consequence, hyperparameters which are determined automatically during segmentation and cluster splitting will not be reported, even if &quot;Report all hyperparameters&quot; is selected.">
3
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
130 <option value="overlay" selected="true">Create a segmentation overlay</option>
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
131 <option value="masks">Create a label map (e.g., for further processing)</option>
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
132 <option value="cfg">Report all hyperparameters (manually set and automatically determined values)</option>
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
133 </param>
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
134 <param name="seg_border" type="integer" min="1" value="8" label="Width of the outlines (in pixels)" help="This parameter is only used for segmentation overlays (see above)." />
0
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
diff changeset
135 <section name="config" title="Hyperparameters" expanded="false">
1
700ae37e5c69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 7db4b765fa5a1f526cc94cd1f65d963d1e047b27
imgteam
parents: 0
diff changeset
136 <param argument="--AF_scale" optional="true" type="float" value="" min="0" label="scale Οƒ" help="The scale of the objects to be segmented. Leave empty to use the automatically determined value." />
700ae37e5c69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 7db4b765fa5a1f526cc94cd1f65d963d1e047b27
imgteam
parents: 0
diff changeset
137 <param argument="--c2f_region_analysis_min_atom_radius" optional="true" type="float" value="" min="0" label="min_atom_radius" help="No region determined by the Coarse-to-fine region analysis scheme is smaller than a circle of this radius (in terms of the surface area). Leave empty to use the automatically determined value." />
700ae37e5c69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 7db4b765fa5a1f526cc94cd1f65d963d1e047b27
imgteam
parents: 0
diff changeset
138 <param argument="--c2f_region_analysis_min_norm_energy_improvement" type="float" value="0.1" min="0" label="min_norm_energy_improvement" help="Each split performed during the computation of the atomic image regions must improve the normalized energy π‘Ÿ(πœ”) of an image region πœ” by at least this factor. Given that an image region is split into the sub-regions πœ”β‚, πœ”β‚‚, the improvement of the split is defined by the fraction max{π‘Ÿ(πœ”)₁, π‘Ÿ(πœ”β‚‚)} / π‘Ÿ(πœ”β‚ βˆͺ πœ”β‚‚). Lower values of the fraction correspond to better improvements." />
700ae37e5c69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 7db4b765fa5a1f526cc94cd1f65d963d1e047b27
imgteam
parents: 0
diff changeset
139 <param argument="--c2f_region_analysis_max_atom_norm_energy" type="float" value="0.05" min="0" label="max_norm_energy1" help="No atomic image region πœ” determined by the Coarse-to-fine region analysis has a normalized energy π‘Ÿ(πœ”) smaller than this value." />
700ae37e5c69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 7db4b765fa5a1f526cc94cd1f65d963d1e047b27
imgteam
parents: 0
diff changeset
140 <param argument="--c2f_region_analysis_max_cluster_marker_irregularity" type="float" value="0.2" min="0" label="max_pa_ratio" help="Threshold for the β€œirregularity” of image regions. Image regions with an β€œirregularity” higher than this value are masked as β€œempty” image regions and discarded from further considerations." />
700ae37e5c69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 7db4b765fa5a1f526cc94cd1f65d963d1e047b27
imgteam
parents: 0
diff changeset
141 <param argument="--dsm_alpha" type="float" value="" optional="true" min="0" label="regularization of the deformations 𝛼" help="Governs the regularization of the deformations. Increasing this value leads to a smoother segmentation result. Leave empty to use the automatically determined value." />
700ae37e5c69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 7db4b765fa5a1f526cc94cd1f65d963d1e047b27
imgteam
parents: 0
diff changeset
142 <param argument="--dsm_AF_alpha" type="float" value="0.0005" min="0" label="factor used for automatic computation of 𝛼" />
700ae37e5c69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 7db4b765fa5a1f526cc94cd1f65d963d1e047b27
imgteam
parents: 0
diff changeset
143 <param argument="--global_energy_minimization_beta" type="float" value="" optional="true" min="0" label="sparsity 𝛽" help="Increasing this value leads to a sparser segmentation result. Leave empty to use the automatically determined value." />
700ae37e5c69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 7db4b765fa5a1f526cc94cd1f65d963d1e047b27
imgteam
parents: 0
diff changeset
144 <param argument="--global_energy_minimization_AF_beta" type="float" value="0.66" min="0" label="factor used for automatic computation of 𝛽" />
700ae37e5c69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 7db4b765fa5a1f526cc94cd1f65d963d1e047b27
imgteam
parents: 0
diff changeset
145 <param argument="--postprocess_mask_max_distance" type="integer" value="1" min="0" label="mask_max_distance" help="Image points within this maximum distance of the boundary of the original segmentation mask are subject to refinement in post-processing. Image points further away from the boundary are neither added to nor removed from the segmentation mask." />
700ae37e5c69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 7db4b765fa5a1f526cc94cd1f65d963d1e047b27
imgteam
parents: 0
diff changeset
146 <param argument="--postprocess_mask_stdamp" type="float" value="2" min="0" label="mask_stdamp" help="An image point adjacent to the boundary of the original segmentation mask is added to the segmentation mask in post-processing, if its Gaussian-smoothed intensity is sufficiently similar to the mean intensity of the mask. The image point is removed otherwise. The lower the value set, the stricter the similarity must be." />
700ae37e5c69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 7db4b765fa5a1f526cc94cd1f65d963d1e047b27
imgteam
parents: 0
diff changeset
147 <param argument="--postprocess_max_norm_energy" type="float" value="0.2" label="max_norm_energy2" help="Objects with a normalized energy larger than this value are discarded in post-processing." />
700ae37e5c69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 7db4b765fa5a1f526cc94cd1f65d963d1e047b27
imgteam
parents: 0
diff changeset
148 <param argument="--postprocess_min_contrast" type="float" value="1.35" label="min_contrast" help="A segmented object is discarded in post-processing, if the contrast as defined above is below this threshold." />
700ae37e5c69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 7db4b765fa5a1f526cc94cd1f65d963d1e047b27
imgteam
parents: 0
diff changeset
149 <param argument="--postprocess_min_object_radius" type="float" value="0" label="min_object_radius" help="Objects smaller than a circle of this radius are discarded in post-processing (in terms of the surface area)." />
0
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
diff changeset
150 </section>
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
diff changeset
151 </inputs>
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
diff changeset
152 <outputs>
3
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
153 <data format="png" name="masks" from_work_dir="masks.png" label="${tool.name} on ${on_string}: masks">
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
154 <filter>'masks' in outputs</filter>
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
155 </data>
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
156 <data format="tsv" name="cfg" from_work_dir="cfg.tsv" label="${tool.name} on ${on_string}: cfg">
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
157 <filter>'cfg' in outputs</filter>
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
158 </data>
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
159 <data format="png" name="overlay" from_work_dir="overlay.png" label="${tool.name} on ${on_string}: overlay">
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
160 <filter>'overlay' in outputs</filter>
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
161 </data>
0
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
diff changeset
162 </outputs>
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
diff changeset
163 <tests>
3
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
164 <test expect_num_outputs="3">
0
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
diff changeset
165 <param name="dataset" value="BBBC033_C2_z28.png" />
4
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
166 <param name="global_energy_minimization_pruning" value="exact" />
3
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
167 <param name="outputs" value="overlay,masks,cfg" />
5
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
168 <expand macro="tests/intensity_image_diff" name="overlay" value="overlay.png" ftype="png"/>
4
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
169 <output name="cfg" value="cfg-full.tsv" ftype="tsv" compare="diff" />
5
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
170 <output name="masks" ftype="png">
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
171 <assert_contents>
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
172
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
173 <has_image_width width="1024"/>
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
174 <has_image_height height="1344"/>
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
175 <has_image_channels channels="1"/>
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
176 <has_image_n_labels n="16"/><!-- 15 objects plus the background -->
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
177
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
178 </assert_contents>
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
179 </output>
3
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
180 </test>
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
181 <test expect_num_outputs="1">
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
182 <param name="dataset" value="BBBC033_C2_z28.png" />
4
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
183 <param name="global_energy_minimization_pruning" value="exact" />
3
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
imgteam
parents: 2
diff changeset
184 <param name="outputs" value="cfg" />
4
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
185 <output name="cfg" value="cfg.tsv" ftype="tsv" compare="diff" />
0
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
diff changeset
186 </test>
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
diff changeset
187 </tests>
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
diff changeset
188 <help>
5
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
189
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
190 **Performs segmentation of 2-D fluorescence microscopy images using deformable shape models and superadditivity.**
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
191
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
192 SuperDSM is a globally optimal method for cell nuclei segmentation using deformable shape models and their inherent law of superadditivity.
0
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
diff changeset
193
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
diff changeset
194 You can either use an individual input image (PNG, TIF) or a collection of such images.
5
9b4830300f3a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 4
diff changeset
195
0
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
diff changeset
196 </help>
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
diff changeset
197 <citations>
4
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
198 <citation type="bibtex">
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
199 @inproceedings{kostrykin2024,
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
200 author = {Kostrykin, L. and Rohr, K.},
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
201 title = {Robust Graph Pruning for Efficient Segmentation and Cluster Splitting of Cell Nuclei using Deformable Shape Models},
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
202 booktitle = {Proc. IEEE International Symposium on Biomedical Imaging (ISBI'24)},
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
203 pages = {accepted for presentation},
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
204 year = {2024},
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
205 }
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
imgteam
parents: 3
diff changeset
206 </citation>
0
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
diff changeset
207 <citation type="doi">10.1109/TPAMI.2022.3185583</citation>
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
diff changeset
208 </citations>
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
diff changeset
209 </tool>