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comparison vpt_segment.xml @ 3:0811613196a2 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1180d1e85b63beb3d2e7fd6e9c73b054a9348e7f
author bgruening
date Mon, 11 Aug 2025 08:53:09 +0000
parents a88a1e78702e
children
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2:a88a1e78702e 3:0811613196a2
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="creator" /> 7 <expand macro="creator" />
8 <required_files>
9 <include path="safetensors_convert_pytorch.py"/>
10 </required_files>
8 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
9 @CMD@ 12 @CMD@
10 ln -s '$detected_transcripts' 'input/detected_transcripts.csv' && 13 ln -s '$detected_transcripts' 'input/detected_transcripts.csv' &&
11 ln -s '$vpt_config_file' 'input/vpt_config_file.json' && 14 ln -s '$vpt_config_file' 'input/vpt_config_file.json' &&
15 #for $i, $task in enumerate($vpt_config.segmentation_tasks.segmentation_task):
16 #if $task.segmentation_properties.custom_weights:
17 ln -s '$task.segmentation_properties.custom_weights' 'input/model/custom_weights_${i}.safetensors' &&
18 python '$__tool_directory__/safetensors_convert_pytorch.py' --convert safe_pt -i 'input/model/custom_weights_${i}.safetensors' -o 'input/model/custom_weights_${i}.pth' &&
19 #end if
20 #end for
12 ### segmentation 21 ### segmentation
13 vpt 22 vpt
14 @COMMON_ARGS@ 23 @COMMON_ARGS@
15 run-segmentation 24 run-segmentation
16 --segmentation-algorithm 'input/vpt_config_file.json' 25 --segmentation-algorithm 'input/vpt_config_file.json'
103 #else: 112 #else:
104 "model": null, 113 "model": null,
105 #end if 114 #end if
106 "model_dimensions": "$task.segmentation_properties.model_dimensions", 115 "model_dimensions": "$task.segmentation_properties.model_dimensions",
107 #if $task.segmentation_properties.custom_weights: 116 #if $task.segmentation_properties.custom_weights:
108 "custom_weights": "$task.segmentation_properties.custom_weights", 117 "custom_weights": "input/model/custom_weights_${i}.pth",
109 #else: 118 #else:
110 "custom_weights": null, 119 "custom_weights": null,
111 #end if 120 #end if
112 "channel_map": { 121 "channel_map": {
113 #if $task.segmentation_properties.channel_map.channel_red_conditional.red != "None": 122 #if $task.segmentation_properties.channel_map.channel_red_conditional.red != "None":
349 </param> 358 </param>
350 <param argument="--model_dimensions" type="select" label="Model dimensions" help="2D applies the 2D Cellpose model to all z-planes specified in the z_layers list separately and the results are combined into a 3D output. 3D applies the native-3D Cellpose model to all z-planes specified in the z_layers list."> 359 <param argument="--model_dimensions" type="select" label="Model dimensions" help="2D applies the 2D Cellpose model to all z-planes specified in the z_layers list separately and the results are combined into a 3D output. 3D applies the native-3D Cellpose model to all z-planes specified in the z_layers list.">
351 <option value="2D">2D</option> 360 <option value="2D">2D</option>
352 <option value="3D">3D</option> 361 <option value="3D">3D</option>
353 </param> 362 </param>
354 <param argument="--custom_weights" type="data" format="data" optional="true" label="Custom Cellpose weights file"/> 363 <param argument="--custom_weights" type="data" format="safetensors" optional="true" label="Custom Cellpose weights file"/>
355 <section name="channel_map" title="Channel map" expanded="true" help="Specify the channel map for the segmentation task with the corresponding task input data"> 364 <section name="channel_map" title="Channel map" expanded="true" help="Specify the channel map for the segmentation task with the corresponding task input data">
356 <conditional name="channel_red_conditional"> 365 <conditional name="channel_red_conditional">
357 <param name="red" type="select" label="The stain that will be used for red channel"> 366 <param name="red" type="select" label="The stain that will be used for red channel">
358 <expand macro="channel_options_none"/> 367 <expand macro="channel_options_none"/>
359 </param> 368 </param>
551 </element> 560 </element>
552 <element name="cell_metadata"> 561 <element name="cell_metadata">
553 <assert_contents> 562 <assert_contents>
554 <has_text_matching expression="EntityID,fov,volume,center_x,center_y,min_x,min_y,max_x,max_y,anisotropy,transcript_count,perimeter_area_ratio,solidity"/> 563 <has_text_matching expression="EntityID,fov,volume,center_x,center_y,min_x,min_y,max_x,max_y,anisotropy,transcript_count,perimeter_area_ratio,solidity"/>
555 <has_text_matching expression=",752.854533232[0-9]+,315.600965641[0-9]+,5.50107977386[0-9]+,310.1669732237[0-9]+,"/> 564 <has_text_matching expression=",752.854533232[0-9]+,315.600965641[0-9]+,5.50107977386[0-9]+,310.1669732237[0-9]+,"/>
556 <has_text_matching expression=",416.540438981[0-9]+,68.7110642977[0-9]+,9.67291568732[0-9]+,64.4947481953[0-9]+,"/> 565 <has_text_matching expression=",777.13824141[0-9]+,70.4487975801[0-9]+,1.976992703078[0-9]+,65.5065863409[0-9]+,"/>
557 </assert_contents> 566 </assert_contents>
558 </element> 567 </element>
559 <element name="detected_transcripts"> 568 <element name="detected_transcripts">
560 <assert_contents> 569 <assert_contents>
561 <has_text_matching expression=",barcode_id,global_x,global_y,global_z,x,y,fov,gene,transcript_id,cell_id"/> 570 <has_text_matching expression=",barcode_id,global_x,global_y,global_z,x,y,fov,gene,transcript_id,cell_id"/>
562 <has_text_matching expression="86,10,285.00012,10.13364,0.0,816.0,153.0,0,AKAP11,ENST00000025301.3"/> 571 <has_text_matching expression="63,10,370.95007,5.520504,0.0,1611.833,110.285774,0,AKAP11,ENST00000025301.3"/>
563 <has_text_matching expression="229,10,274.95612,35.72964,0.0,723.0,390.0,0,AKAP11,ENST00000025301.3"/> 572 <has_text_matching expression="68,10,355.46716,6.4616404,0.0,1468.4725,119.0,0,AKAP11,ENST00000025301.3"/>
564 </assert_contents> 573 </assert_contents>
565 </element> 574 </element>
566 <element name="metrics"> 575 <element name="metrics">
567 <assert_contents> 576 <assert_contents>
568 <has_text_matching expression=",Cell count,Cell volume"/> 577 <has_text_matching expression=",Cell count,Cell volume"/>
569 <has_text_matching expression="All cells,814,1572.4,1533.3,735.8,654.0,92.1,108.0,96.4,68.2,0.0"/> 578 <has_n_lines n="3"/>
570 <has_text_matching expression="Cells after filtering,700,1694.1,1667.9,851.1,810.5,104.5,111.0,95.9,63.2,0.06"/>
571 </assert_contents> 579 </assert_contents>
572 </element> 580 </element>
573 <element name="sum_signals"> 581 <element name="sum_signals">
574 <assert_contents> 582 <assert_contents>
575 <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/> 583 <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/>
760 </assert_contents> 768 </assert_contents>
761 </element> 769 </element>
762 <element name="metrics"> 770 <element name="metrics">
763 <assert_contents> 771 <assert_contents>
764 <has_text_matching expression=",Cell count,Cell volume"/> 772 <has_text_matching expression=",Cell count,Cell volume"/>
765 <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"/> 773 <has_n_lines n="3"/>
766 <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"/>
767 </assert_contents> 774 </assert_contents>
768 </element> 775 </element>
769 <element name="sum_signals"> 776 <element name="sum_signals">
770 <assert_contents> 777 <assert_contents>
771 <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/> 778 <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/>
832 <param name="entity_types_detected" value="cell"/> 839 <param name="entity_types_detected" value="cell"/>
833 <param name="z_layers" value="3"/> 840 <param name="z_layers" value="3"/>
834 <section name="segmentation_properties"> 841 <section name="segmentation_properties">
835 <param name="model" value="null"/> 842 <param name="model" value="null"/>
836 <param name="model_dimensions" value="2D"/> 843 <param name="model_dimensions" value="2D"/>
837 <param name="custom_weights" location="https://zenodo.org/records/15319018/files/CP_20230830_093420"/> 844 <param name="custom_weights" location="https://zenodo.org/records/16784480/files/CP_20230830_093420.safetensors"/>
838 <section name="channel_map"> 845 <section name="channel_map">
839 <conditional name="channel_red_conditional"> 846 <conditional name="channel_red_conditional">
840 <param name="red" value="Cellbound1"/> 847 <param name="red" value="Cellbound1"/>
841 <conditional name="normalize_conditional"> 848 <conditional name="normalize_conditional">
842 <param name="normalize_select" value="Yes"/> 849 <param name="normalize_select" value="Yes"/>
903 </section> 910 </section>
904 <output_collection name="vpt_results" type="list"> 911 <output_collection name="vpt_results" type="list">
905 <element name="cell_by_gene"> 912 <element name="cell_by_gene">
906 <assert_contents> 913 <assert_contents>
907 <has_text_matching expression="cell,AKAP11,CBX5,CCDC113"/> 914 <has_text_matching expression="cell,AKAP11,CBX5,CCDC113"/>
908 <has_text_matching expression="6,11,4,0,5,2,1,0,1,2,1,2"/> 915 <has_text_matching expression="6,10,4,0,5,2,1,0,1,2"/>
909 <has_text_matching expression="0,1,0,0,0,0,1,0,0,4"/> 916 <has_text_matching expression="0,1,0,0,0,0,1,0,0,4,0"/>
910 </assert_contents> 917 </assert_contents>
911 </element> 918 </element>
912 <element name="cell_metadata"> 919 <element name="cell_metadata">
913 <assert_contents> 920 <assert_contents>
914 <has_text_matching expression="EntityID,fov,volume,center_x,center_y,min_x,min_y,max_x,max_y,anisotropy,transcript_count,perimeter_area_ratio,solidity"/> 921 <has_text_matching expression="EntityID,fov,volume,center_x,center_y,min_x,min_y,max_x,max_y,anisotropy,transcript_count,perimeter_area_ratio,solidity"/>
915 <has_text_matching expression="168.0683921161[0-9]+,246.3592447472[0-9]+,-1.507707574380[0-9]+,243.9322371166[0-9]+"/> 922 <has_text_matching expression="167.0695914980[0-9]+,246.371389688[0-9]+,-1.502969079760[0-9]+,243.9322371166[0-9]+"/>
916 <has_text_matching expression="1540.721726928[0-9]+,412.175889439[0-9]+,2.951632912099[0-9]+,404.3500198495[0-9]+"/> 923 <has_text_matching expression="1540.721726928[0-9]+,412.175889439[0-9]+,2.951632912099[0-9]+,404.3500198495[0-9]+"/>
917 </assert_contents> 924 </assert_contents>
918 </element> 925 </element>
919 <element name="detected_transcripts"> 926 <element name="detected_transcripts">
920 <assert_contents> 927 <assert_contents>
924 </assert_contents> 931 </assert_contents>
925 </element> 932 </element>
926 <element name="metrics"> 933 <element name="metrics">
927 <assert_contents> 934 <assert_contents>
928 <has_text_matching expression=",Cell count,Cell volume"/> 935 <has_text_matching expression=",Cell count,Cell volume"/>
929 <has_text_matching expression="All cells,93[0-9]+,121\d*(\.\d+)?,118\d*(\.\d+)?,60\d*(\.\d+)?,49\d*(\.\d+)?,7\d*(\.\d+)?,10\d*(\.\d+)?,9\d*(\.\d+)?,6\d*(\.\d+)?,0.0"/> 936 <has_n_lines n="3"/>
930 <has_text_matching expression="Cells after filtering,659,1532.9,1553.5,850.2,837.0,104.8,112.0,90.2,53.8,0.15"/>
931 </assert_contents> 937 </assert_contents>
932 </element> 938 </element>
933 <element name="sum_signals"> 939 <element name="sum_signals">
934 <assert_contents> 940 <assert_contents>
935 <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/> 941 <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/>
936 <has_text_matching expression="73446567.0,1605103.666715[0-9]+"/> 942 <has_text_matching expression="72859278.0,1502895.008866[0-9]+"/>
937 <has_text_matching expression="1642190888.0,16154095.44810[0-9]+"/> 943 <has_text_matching expression="1642190888.0,16154095.44810[0-9]+"/>
938 </assert_contents> 944 </assert_contents>
939 </element> 945 </element>
940 </output_collection> 946 </output_collection>
941 <output_collection name="vpt_boundaries" type="list"> 947 <output_collection name="vpt_boundaries" type="list">
970 <has_text_matching expression="0,1,2,3,4,5,6"/> 976 <has_text_matching expression="0,1,2,3,4,5,6"/>
971 <has_text_matching expression="Cellpose2"/> 977 <has_text_matching expression="Cellpose2"/>
972 <has_text_matching expression="null"/> 978 <has_text_matching expression="null"/>
973 <has_text_matching expression="CLAHE"/> 979 <has_text_matching expression="CLAHE"/>
974 <has_text_matching expression="harmonize"/> 980 <has_text_matching expression="harmonize"/>
981 <has_text_matching expression="input/model/custom_weights_0.pth"/>
975 </assert_contents> 982 </assert_contents>
976 </element> 983 </element>
977 </output_collection> 984 </output_collection>
978 <output name="vpt_log"> 985 <output name="vpt_log">
979 <assert_contents> 986 <assert_contents>