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comparison superdsm.xml @ 1:700ae37e5c69 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 7db4b765fa5a1f526cc94cd1f65d963d1e047b27
author imgteam
date Thu, 06 Jul 2023 00:01:18 +0000
parents 1b0fc671187f
children 244f67290d28
comparison
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0:1b0fc671187f 1:700ae37e5c69
1 <tool id="ip_superdsm" name="SuperDSM" version="0.1.2-1" profile="20.05"> 1 <tool id="ip_superdsm" name="SuperDSM" version="0.1.3" 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>globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.1.2">superdsm</requirement> 4 <requirement type="package" version="0.1.3">superdsm</requirement>
5 <requirement type="package" version="1.6.0">ray-core</requirement> 5 <requirement type="package" version="1.6.0">ray-core</requirement>
6 <requirement type="package" version="0.18.1">scikit-image</requirement> 6 <requirement type="package" version="0.18.1">scikit-image</requirement>
7 </requirements> 7 </requirements>
8 <command detect_errors="aggressive"> 8 <command detect_errors="aggressive">
9 <![CDATA[ 9 <![CDATA[
12 'cfg.json' 12 'cfg.json'
13 'masks.png' 13 'masks.png'
14 'overlay.png' 14 'overlay.png'
15 $seg_border 15 $seg_border
16 \${GALAXY_SLOTS:-4} 16 \${GALAXY_SLOTS:-4}
17 > stdout.txt 17 #if str($config.AF_scale) != '':
18 --AF_scale '${config.AF_scale}'
19 #end if
20 #if str($config.c2f_region_analysis_min_atom_radius) != '':
21 --c2f_region_analysis_min_atom_radius '${config.c2f_region_analysis_min_atom_radius}'
22 #end if
23 #if str($config.c2f_region_analysis_min_norm_energy_improvement) != '':
24 --c2f_region_analysis_min_norm_energy_improvement '${config.c2f_region_analysis_min_norm_energy_improvement}'
25 #end if
26 #if str($config.c2f_region_analysis_max_atom_norm_energy) != '':
27 --c2f_region_analysis_max_atom_norm_energy '${config.c2f_region_analysis_max_atom_norm_energy}'
28 #end if
29 #if str($config.c2f_region_analysis_max_cluster_marker_irregularity) != '':
30 --c2f_region_analysis_max_cluster_marker_irregularity '${config.c2f_region_analysis_max_cluster_marker_irregularity}'
31 #end if
32 #if str($config.dsm_alpha) != '':
33 --dsm_alpha '${config.dsm_alpha}'
34 #end if
35 #if str($config.dsm_AF_alpha) != '':
36 --dsm_AF_alpha '${config.dsm_AF_alpha}'
37 #end if
38 #if str($config.global_energy_minimization_beta) != '':
39 --global_energy_minimization_beta '${config.global_energy_minimization_beta}'
40 #end if
41 #if str($config.global_energy_minimization_AF_beta) != '':
42 --global_energy_minimization_AF_beta '${config.global_energy_minimization_AF_beta}'
43 #end if
44 #if str($config.postprocess_mask_max_distance) != '':
45 --postprocess_mask_max_distance '${config.postprocess_mask_max_distance}'
46 #end if
47 #if str($config.postprocess_mask_stdamp) != '':
48 --postprocess_mask_stdamp '${config.postprocess_mask_stdamp}'
49 #end if
50 #if str($config.postprocess_max_norm_energy) != '':
51 --postprocess_max_norm_energy '${config.postprocess_max_norm_energy}'
52 #end if
53 #if str($config.postprocess_min_contrast) != '':
54 --postprocess_min_contrast '${config.postprocess_min_contrast}'
55 #end if
56 #if str($config.postprocess_min_object_radius) != '':
57 --postprocess_min_object_radius '${config.postprocess_min_object_radius}'
58 #end if
18 ]]> 59 ]]>
19 </command> 60 </command>
20 <inputs> 61 <inputs>
21 <param name="dataset" type="data" format="tiff,png" label="Dataset" /> 62 <param name="dataset" type="data" format="tiff,png" label="Dataset" />
22 <param name="seg_border" type="integer" min="1" value="8" label="Width of the outlines (in pixels) of the segmentation results (overlays)" /> 63 <param name="seg_border" type="integer" min="1" value="8" label="Width of the outlines (in pixels) of the segmentation results (overlays)" />
23 <!--
24 <section name="config" title="Hyperparameters" expanded="false"> 64 <section name="config" title="Hyperparameters" expanded="false">
65 <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." />
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." />
67 <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." />
68 <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." />
69 <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." />
70 <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." />
71 <param argument="--dsm_AF_alpha" type="float" value="0.0005" min="0" label="factor used for automatic computation of 𝛼" />
72 <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." />
73 <param argument="--global_energy_minimization_AF_beta" type="float" value="0.66" min="0" label="factor used for automatic computation of 𝛽" />
74 <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." />
75 <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." />
76 <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." />
77 <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." />
78 <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)." />
25 </section> 79 </section>
26 -->
27 </inputs> 80 </inputs>
28 <outputs> 81 <outputs>
29 <data format="txt" name="stdout" from_work_dir="stdout.txt" label="${tool.name} on ${on_string}: stdout" />
30 <data format="json" name="cfg" from_work_dir="cfg.json" label="${tool.name} on ${on_string}: cfg" /> 82 <data format="json" name="cfg" from_work_dir="cfg.json" label="${tool.name} on ${on_string}: cfg" />
31 <data format="png" name="masks" from_work_dir="masks.png" label="${tool.name} on ${on_string}: masks" /> 83 <data format="png" name="masks" from_work_dir="masks.png" label="${tool.name} on ${on_string}: masks" />
32 <data format="png" name="overlay" from_work_dir="overlay.png" label="${tool.name} on ${on_string}: overlay" /> 84 <data format="png" name="overlay" from_work_dir="overlay.png" label="${tool.name} on ${on_string}: overlay" />
33 </outputs> 85 </outputs>
34 <tests> 86 <tests>