Mercurial > repos > bgruening > vpt_segment

comparison vpt_segment.xml @ 1:ed28a1feba82 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1011b91cc4b13f365c51661bedb27a898b1bf817
author bgruening
date Mon, 26 May 2025 06:54:28 +0000
parents 5bd5f26279fd
children a88a1e78702e
comparison
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0:5bd5f26279fd 1:ed28a1feba82
80 #set $indices = ",".join([str(i) for i in range(len(str($vpt_config.experiment_properties.z_positions_um.value).split(",")))]) 80 #set $indices = ",".join([str(i) for i in range(len(str($vpt_config.experiment_properties.z_positions_um.value).split(",")))])
81 81
82 "all_z_indexes": [$indices], 82 "all_z_indexes": [$indices],
83 "z_positions_um": [$vpt_config.experiment_properties.z_positions_um] 83 "z_positions_um": [$vpt_config.experiment_properties.z_positions_um]
84 }, 84 },
85 #set $task_n = len($vpt_config.segmentation_tasks.segmentation_task) - 1
86 #for $i, $task in enumerate($vpt_config.segmentation_tasks.segmentation_task):
87 "segmentation_tasks": [ 85 "segmentation_tasks": [
86 #set $task_n = len($vpt_config.segmentation_tasks.segmentation_task) - 1
87 #for $i, $task in enumerate($vpt_config.segmentation_tasks.segmentation_task):
88 { 88 {
89 "task_id": $i, 89 "task_id": $i,
90 "segmentation_family": "Cellpose2", 90 "segmentation_family": "Cellpose2",
91 #if $task.entity_types_detected != "both": 91 #if $task.entity_types_detected != "both":
92 "entity_types_detected": ["$task.entity_types_detected"], 92 "entity_types_detected": ["$task.entity_types_detected"],
194 "polygon_parameters": { 194 "polygon_parameters": {
195 "simplification_tol": $task.polygon_parameters.simplification_tol, 195 "simplification_tol": $task.polygon_parameters.simplification_tol,
196 "smoothing_radius": $task.polygon_parameters.smoothing_radius, 196 "smoothing_radius": $task.polygon_parameters.smoothing_radius,
197 "minimum_final_area": $task.polygon_parameters.minimum_final_area 197 "minimum_final_area": $task.polygon_parameters.minimum_final_area
198 } 198 }
199 } 199 }#if $i != $task_n
200 ]#if $j != $task_n 200 ,
201 , 201 #end if
202 #end if 202 #end for
203 #end for 203 ],
204 "segmentation_task_fusion": { 204 "segmentation_task_fusion": {
205 "entity_fusion_strategy": "$segmentation_task_fusion.entity_fusion_strategy", 205 "entity_fusion_strategy": "$segmentation_task_fusion.entity_fusion_strategy",
206 "fused_polygon_postprocessing_parameters": { 206 "fused_polygon_postprocessing_parameters": {
207 "min_distance_between_entities": $segmentation_task_fusion.min_distance_between_entities, 207 "min_distance_between_entities": $segmentation_task_fusion.min_distance_between_entities,
208 "min_final_area": $segmentation_task_fusion.min_final_area 208 "min_final_area": $segmentation_task_fusion.min_final_area
246 <param argument="--entity_types_detected" type="select" label="Detect cell or nucleus?"> 246 <param argument="--entity_types_detected" type="select" label="Detect cell or nucleus?">
247 <option value="cell">cell</option> 247 <option value="cell">cell</option>
248 <option value="nucleus">nucleus</option> 248 <option value="nucleus">nucleus</option>
249 <option value="both">both</option> 249 <option value="both">both</option>
250 </param> 250 </param>
251 <param argument="--z_layers" type="text" value="" optional="true" label="Comma-separated list of z-index images to segment." help="2D segmentation is applied to all z-layers in the experiment by default without needing to explicitly specify the behavior."> 251 <param argument="--z_layers" type="text" value="3" optional="false" label="Comma-separated list of z-index images to segment.">
252 <expand macro="sanitize_digits"/> 252 <expand macro="sanitize_digits"/>
253 </param> 253 </param>
254 <section name="segmentation_properties" title="Segmentation properties"> 254 <section name="segmentation_properties" title="Segmentation properties">
255 <param argument="--model" type="select" label="Cellpose model"> 255 <param argument="--model" type="select" label="Cellpose model">
256 <option value="cyto2">cyto2</option> 256 <option value="cyto2">cyto2</option>
726 </assert_contents> 726 </assert_contents>
727 </element> 727 </element>
728 <element name="metrics"> 728 <element name="metrics">
729 <assert_contents> 729 <assert_contents>
730 <has_text_matching expression=",Cell count,Cell volume"/> 730 <has_text_matching expression=",Cell count,Cell volume"/>
731 <has_text_matching expression="All cells,618,1026.0,1005.3,649.1,621.0,94.2,106.0,64.6,33.8,0.0"/> 731 <has_text_matching expression="All cells,811,1588.0,1549.9,740.5,669.0,92.2,109.0,96.7,68.6,0.0"/>
732 <has_text_matching expression="Cells after filtering,563,1061.2,1025.9,710.8,666.0,102.3,107.0,64.4,31.8,0.03"/> 732 <has_text_matching expression="Cells after filtering,698,1711.6,1705.9,856.1,817.5,104.6,111.0,96.2,63.7,0.06"/>
733 </assert_contents> 733 </assert_contents>
734 </element> 734 </element>
735 <element name="sum_signals"> 735 <element name="sum_signals">
736 <assert_contents> 736 <assert_contents>
737 <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/> 737 <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/>
753 </element> 753 </element>
754 </output_collection> 754 </output_collection>
755 <output name="vpt_qc"> 755 <output name="vpt_qc">
756 <assert_contents> 756 <assert_contents>
757 <has_text text="VPT Segmentation Report (cyto2_2task)"/> 757 <has_text text="VPT Segmentation Report (cyto2_2task)"/>
758 <has_text text="Cell count: &lt;b class=&quot;summary__value&quot;&gt;618&lt;/b&gt;&lt;/p&gt;"/> 758 <has_text text="Cell count: &lt;b class=&quot;summary__value&quot;&gt;811&lt;/b&gt;&lt;/p&gt;"/>
759 <has_text text="Transcripts per cell - median: &lt;b class=&quot;summary__value&quot;&gt;621.0&lt;/b&gt;&lt;/p&gt;"/> 759 <has_text text="Transcripts per cell - median: &lt;b class=&quot;summary__value&quot;&gt;669.0&lt;/b&gt;&lt;/p&gt;"/>
760 </assert_contents> 760 </assert_contents>
761 </output> 761 </output>
762 <output_collection name="vpt_config_out" type="list"> 762 <output_collection name="vpt_config_out" type="list">
763 <element name="segmentation_specification"> 763 <element name="segmentation_specification">
764 <assert_contents> 764 <assert_contents>