Mercurial > repos > imgteam > superdsm

comparison superdsm.xml @ 2:244f67290d28 draft

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 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:12:35 +0000
parents 700ae37e5c69
children 7fd8dba15bd3
comparison
equal deleted inserted replaced
1:700ae37e5c69 2:244f67290d28
1 <tool id="ip_superdsm" name="SuperDSM" version="0.1.3" profile="20.05"> 1 <tool id="ip_superdsm" name="Perform segmentation using deformable shape models" version="0.1.3+galaxy2" profile="20.05">
2 <description>globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images</description> 2 <description>with SuperDSM</description>
3 <requirements> 3 <edam_operations>
4 <edam_operation>operation_3443</edam_operation>
5 </edam_operations>
6 <xrefs>
7 <xref type="bio.tools">superdsm</xref>
8 <xref type="biii">superdsm</xref>
9 </xrefs>
10 <requirements>
4 <requirement type="package" version="0.1.3">superdsm</requirement> 11 <requirement type="package" version="0.1.3">superdsm</requirement>
5 <requirement type="package" version="1.6.0">ray-core</requirement> 12 <requirement type="package" version="1.6.0">ray-core</requirement>
6 <requirement type="package" version="0.18.1">scikit-image</requirement> 13 <requirement type="package" version="0.18.1">scikit-image</requirement>
7 </requirements> 14 <requirement type="package" version="2020.0">mkl</requirement><!-- this seems to be the last version of MKL which supports the "MKL_DEBUG_CPU_TYPE" environment variable -->
8 <command detect_errors="aggressive"> 15 <requirement type="package" version="*=mkl">blas</requirement><!-- using MKL instead of other BLAS can significantly improve performance on some hardware, cf. https://stackoverflow.com/questions/62783262/why-is-numpy-with-ryzen-threadripper-so-much-slower-than-xeon -->
9 <![CDATA[ 16 </requirements>
10 python '$__tool_directory__/run-superdsm.py' 17 <command detect_errors="aggressive">
11 '${dataset}' 18 <![CDATA[
12 'cfg.json' 19 python '$__tool_directory__/run-superdsm.py'
13 'masks.png' 20 '${dataset}'
14 'overlay.png' 21 'cfg.json'
15 $seg_border 22 'masks.png'
16 \${GALAXY_SLOTS:-4} 23 'overlay.png'
17 #if str($config.AF_scale) != '': 24 $seg_border
18 --AF_scale '${config.AF_scale}' 25 \${GALAXY_SLOTS:-4}
19 #end if 26 #if str($config.AF_scale) != '':
20 #if str($config.c2f_region_analysis_min_atom_radius) != '': 27 --AF_scale '${config.AF_scale}'
21 --c2f_region_analysis_min_atom_radius '${config.c2f_region_analysis_min_atom_radius}' 28 #end if
22 #end if 29 #if str($config.c2f_region_analysis_min_atom_radius) != '':
23 #if str($config.c2f_region_analysis_min_norm_energy_improvement) != '': 30 --c2f_region_analysis_min_atom_radius '${config.c2f_region_analysis_min_atom_radius}'
24 --c2f_region_analysis_min_norm_energy_improvement '${config.c2f_region_analysis_min_norm_energy_improvement}' 31 #end if
25 #end if 32 #if str($config.c2f_region_analysis_min_norm_energy_improvement) != '':
26 #if str($config.c2f_region_analysis_max_atom_norm_energy) != '': 33 --c2f_region_analysis_min_norm_energy_improvement '${config.c2f_region_analysis_min_norm_energy_improvement}'
27 --c2f_region_analysis_max_atom_norm_energy '${config.c2f_region_analysis_max_atom_norm_energy}' 34 #end if
28 #end if 35 #if str($config.c2f_region_analysis_max_atom_norm_energy) != '':
29 #if str($config.c2f_region_analysis_max_cluster_marker_irregularity) != '': 36 --c2f_region_analysis_max_atom_norm_energy '${config.c2f_region_analysis_max_atom_norm_energy}'
30 --c2f_region_analysis_max_cluster_marker_irregularity '${config.c2f_region_analysis_max_cluster_marker_irregularity}' 37 #end if
31 #end if 38 #if str($config.c2f_region_analysis_max_cluster_marker_irregularity) != '':
32 #if str($config.dsm_alpha) != '': 39 --c2f_region_analysis_max_cluster_marker_irregularity '${config.c2f_region_analysis_max_cluster_marker_irregularity}'
33 --dsm_alpha '${config.dsm_alpha}' 40 #end if
34 #end if 41 #if str($config.dsm_alpha) != '':
35 #if str($config.dsm_AF_alpha) != '': 42 --dsm_alpha '${config.dsm_alpha}'
36 --dsm_AF_alpha '${config.dsm_AF_alpha}' 43 #end if
37 #end if 44 #if str($config.dsm_AF_alpha) != '':
38 #if str($config.global_energy_minimization_beta) != '': 45 --dsm_AF_alpha '${config.dsm_AF_alpha}'
39 --global_energy_minimization_beta '${config.global_energy_minimization_beta}' 46 #end if
40 #end if 47 #if str($config.global_energy_minimization_beta) != '':
41 #if str($config.global_energy_minimization_AF_beta) != '': 48 --global_energy_minimization_beta '${config.global_energy_minimization_beta}'
42 --global_energy_minimization_AF_beta '${config.global_energy_minimization_AF_beta}' 49 #end if
43 #end if 50 #if str($config.global_energy_minimization_AF_beta) != '':
44 #if str($config.postprocess_mask_max_distance) != '': 51 --global_energy_minimization_AF_beta '${config.global_energy_minimization_AF_beta}'
45 --postprocess_mask_max_distance '${config.postprocess_mask_max_distance}' 52 #end if
46 #end if 53 #if str($config.postprocess_mask_max_distance) != '':
47 #if str($config.postprocess_mask_stdamp) != '': 54 --postprocess_mask_max_distance '${config.postprocess_mask_max_distance}'
48 --postprocess_mask_stdamp '${config.postprocess_mask_stdamp}' 55 #end if
49 #end if 56 #if str($config.postprocess_mask_stdamp) != '':
50 #if str($config.postprocess_max_norm_energy) != '': 57 --postprocess_mask_stdamp '${config.postprocess_mask_stdamp}'
51 --postprocess_max_norm_energy '${config.postprocess_max_norm_energy}' 58 #end if
52 #end if 59 #if str($config.postprocess_max_norm_energy) != '':
53 #if str($config.postprocess_min_contrast) != '': 60 --postprocess_max_norm_energy '${config.postprocess_max_norm_energy}'
54 --postprocess_min_contrast '${config.postprocess_min_contrast}' 61 #end if
55 #end if 62 #if str($config.postprocess_min_contrast) != '':
56 #if str($config.postprocess_min_object_radius) != '': 63 --postprocess_min_contrast '${config.postprocess_min_contrast}'
57 --postprocess_min_object_radius '${config.postprocess_min_object_radius}' 64 #end if
58 #end if 65 #if str($config.postprocess_min_object_radius) != '':
59 ]]> 66 --postprocess_min_object_radius '${config.postprocess_min_object_radius}'
60 </command> 67 #end if
61 <inputs> 68 ]]>
69 </command>
70 <environment_variables>
71 <environment_variable name="MKL_DEBUG_CPU_TYPE">5</environment_variable><!-- this enables accelerated CPU instruction sets on AMD hardware, does nothing in Intel hardware, thus no need to change this -->
72 </environment_variables>
73 <inputs>
62 <param name="dataset" type="data" format="tiff,png" label="Dataset" /> 74 <param name="dataset" type="data" format="tiff,png" label="Dataset" />
63 <param name="seg_border" type="integer" min="1" value="8" label="Width of the outlines (in pixels) of the segmentation results (overlays)" /> 75 <param name="seg_border" type="integer" min="1" value="8" label="Width of the outlines (in pixels) of the segmentation results (overlays)" />
64 <section name="config" title="Hyperparameters" expanded="false"> 76 <section name="config" title="Hyperparameters" expanded="false">
65 <param argument="--AF_scale" optional="true" type="float" value="" min="0" label="scale σ" help="The scale of the objects to be segmented. Leave empty to use the automatically determined value." /> 77 <param argument="--AF_scale" optional="true" type="float" value="" min="0" label="scale σ" help="The scale of the objects to be segmented. Leave empty to use the automatically determined value." />
66 <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." /> 78 <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." />