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comparison superdsm.xml @ 3:7fd8dba15bd3 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
author imgteam
date Thu, 16 Nov 2023 12:29:41 +0000
parents 244f67290d28
children dc5f72f6b1e9
comparison
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2:244f67290d28 3:7fd8dba15bd3
1 <tool id="ip_superdsm" name="Perform segmentation using deformable shape models" version="0.1.3+galaxy2" profile="20.05"> 1 <tool id="ip_superdsm" name="Perform segmentation using deformable shape models" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description>with SuperDSM</description> 2 <description>with SuperDSM</description>
3 <macros>
4 <token name="@TOOL_VERSION@">0.1.3</token>
5 <token name="@VERSION_SUFFIX@">3</token>
6 </macros>
3 <edam_operations> 7 <edam_operations>
4 <edam_operation>operation_3443</edam_operation> 8 <edam_operation>operation_3443</edam_operation>
5 </edam_operations> 9 </edam_operations>
6 <xrefs> 10 <xrefs>
7 <xref type="bio.tools">superdsm</xref> 11 <xref type="bio.tools">superdsm</xref>
16 </requirements> 20 </requirements>
17 <command detect_errors="aggressive"> 21 <command detect_errors="aggressive">
18 <![CDATA[ 22 <![CDATA[
19 python '$__tool_directory__/run-superdsm.py' 23 python '$__tool_directory__/run-superdsm.py'
20 '${dataset}' 24 '${dataset}'
21 'cfg.json'
22 'masks.png'
23 'overlay.png'
24 $seg_border
25 \${GALAXY_SLOTS:-4} 25 \${GALAXY_SLOTS:-4}
26 #if 'masks' in $outputs:
27 --do-masks 'masks.png'
28 #end if
29 #if 'cfg' in $outputs:
30 --do-cfg 'cfg.tsv'
31 #end if
32 #if 'overlay' in $outputs:
33 --do-overlay 'overlay.png'
34 #if $seg_border.value % 2 == 1:
35 #set $seg_border = "%d" % ($seg_border.value + 1)
36 --do-overlay-border $seg_border
37 #else:
38 --do-overlay-border $seg_border
39 #end if
40 #end if
26 #if str($config.AF_scale) != '': 41 #if str($config.AF_scale) != '':
27 --AF_scale '${config.AF_scale}' 42 --AF_scale '${config.AF_scale}'
28 #end if 43 #end if
29 #if str($config.c2f_region_analysis_min_atom_radius) != '': 44 #if str($config.c2f_region_analysis_min_atom_radius) != '':
30 --c2f_region_analysis_min_atom_radius '${config.c2f_region_analysis_min_atom_radius}' 45 --c2f_region_analysis_min_atom_radius '${config.c2f_region_analysis_min_atom_radius}'
70 <environment_variables> 85 <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 --> 86 <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> 87 </environment_variables>
73 <inputs> 88 <inputs>
74 <param name="dataset" type="data" format="tiff,png" label="Dataset" /> 89 <param name="dataset" type="data" format="tiff,png" label="Dataset" />
75 <param name="seg_border" type="integer" min="1" value="8" label="Width of the outlines (in pixels) of the segmentation results (overlays)" /> 90 <param name="outputs" type="select" label="Outputs" multiple="true" optional="false">
91 <option value="overlay" selected="true">Create a segmentation overlay</option>
92 <option value="masks">Create a label map (e.g., for further processing)</option>
93 <option value="cfg">Report all hyperparameters (manually set and automatically determined values)</option>
94 </param>
95 <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)." />
76 <section name="config" title="Hyperparameters" expanded="false"> 96 <section name="config" title="Hyperparameters" expanded="false">
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." /> 97 <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." />
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." /> 98 <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." />
79 <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 𝑟(𝜔) of an image region 𝜔 by at least this factor. Given that an image region is split into the sub-regions 𝜔₁, 𝜔₂, the improvement of the split is defined by the fraction max{𝑟(𝜔)₁, 𝑟(𝜔₂)} / 𝑟(𝜔₁ ∪ 𝜔₂). Lower values of the fraction correspond to better improvements." /> 99 <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 𝑟(𝜔) of an image region 𝜔 by at least this factor. Given that an image region is split into the sub-regions 𝜔₁, 𝜔₂, the improvement of the split is defined by the fraction max{𝑟(𝜔)₁, 𝑟(𝜔₂)} / 𝑟(𝜔₁ ∪ 𝜔₂). Lower values of the fraction correspond to better improvements." />
80 <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 𝜔 determined by the Coarse-to-fine region analysis has a normalized energy 𝑟(𝜔) smaller than this value." /> 100 <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 𝜔 determined by the Coarse-to-fine region analysis has a normalized energy 𝑟(𝜔) smaller than this value." />
89 <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." /> 109 <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." />
90 <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)." /> 110 <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)." />
91 </section> 111 </section>
92 </inputs> 112 </inputs>
93 <outputs> 113 <outputs>
94 <data format="json" name="cfg" from_work_dir="cfg.json" label="${tool.name} on ${on_string}: cfg" /> 114 <data format="png" name="masks" from_work_dir="masks.png" label="${tool.name} on ${on_string}: masks">
95 <data format="png" name="masks" from_work_dir="masks.png" label="${tool.name} on ${on_string}: masks" /> 115 <filter>'masks' in outputs</filter>
96 <data format="png" name="overlay" from_work_dir="overlay.png" label="${tool.name} on ${on_string}: overlay" /> 116 </data>
117 <data format="tsv" name="cfg" from_work_dir="cfg.tsv" label="${tool.name} on ${on_string}: cfg">
118 <filter>'cfg' in outputs</filter>
119 </data>
120 <data format="png" name="overlay" from_work_dir="overlay.png" label="${tool.name} on ${on_string}: overlay">
121 <filter>'overlay' in outputs</filter>
122 </data>
97 </outputs> 123 </outputs>
98 <tests> 124 <tests>
99 <test> 125 <test expect_num_outputs="3">
100 <param name="dataset" value="BBBC033_C2_z28.png" /> 126 <param name="dataset" value="BBBC033_C2_z28.png" />
127 <param name="outputs" value="overlay,masks,cfg" />
101 <output name="overlay" value="overlay.png" ftype="png" compare="sim_size" /> 128 <output name="overlay" value="overlay.png" ftype="png" compare="sim_size" />
129 <output name="cfg" value="cfg.tsv" ftype="tsv" compare="sim_size" />
130 </test>
131 <test expect_num_outputs="1">
132 <param name="dataset" value="BBBC033_C2_z28.png" />
133 <param name="outputs" value="cfg" />
134 <output name="cfg" value="cfg.tsv" ftype="tsv" compare="sim_size" />
102 </test> 135 </test>
103 </tests> 136 </tests>
104 <help> 137 <help>
105 This tool permits the segmentation of cell nuclei in 2-D fluorescence microscopy images. 138 This tool permits the segmentation of cell nuclei in 2-D fluorescence microscopy images.
106 139