# HG changeset patch # User tduigou # Date 1680006941 0 # Node ID 5834e459771676ebf18df6a0df8bd056e646083f planemo upload for repository https://github.com/brsynth/icfree-ml commit e908694368c306390bc9253f81a9249ad988970d diff -r 000000000000 -r 5834e4597716 config/tool_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config/tool_conf.xml Tue Mar 28 12:35:41 2023 +0000 @@ -0,0 +1,6 @@ +
+ + + + +
diff -r 000000000000 -r 5834e4597716 converter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/converter.xml Tue Mar 28 12:35:41 2023 +0000 @@ -0,0 +1,61 @@ + + Convert concentration values into volume values. + + macros.xml + + + + + + + +
+ +
+ + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 5834e4597716 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Mar 28 12:35:41 2023 +0000 @@ -0,0 +1,33 @@ + + 2.1.1 + 0 + MIT + + + icfree + + + + + + + + + + + + + @unpublished{icfree + author = {Joan Hérisson, Yorgo El Moubayed}, + title = {{icfree}}, + url = {https://github.com/brsynth/icfree-ml/}, + } + + + + + + + + + diff -r 000000000000 -r 5834e4597716 test-data/converter_proCFPS_parameters.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/converter_proCFPS_parameters.tsv Tue Mar 28 12:35:41 2023 +0000 @@ -0,0 +1,17 @@ +Parameter maxValue stockConcentration deadVolume Ratios +Mg-glutamate 4 168 0 0.0 0.1 0.3 0.5 1.0 +k-glutamate 80 3360 0 +CoA 0.26 210 0 +3-PGA 30 1400 0 +NTP 1.5 630 0 +NAD 0.33 138.6 0 +Folinic acid 0.068 28.56 0 +Spermidine 1 420 0 +tRNA 0.2 84 0 +Amino acids 1.5 6 0 +CAMP 0.75 200 0 +Extract 30 300 2000 1 +HEPES 50 2100 0 1 +PEG 2 200 4000 1 +Promoter 10 300 0 1 +RBS 10 200 0 1 \ No newline at end of file diff -r 000000000000 -r 5834e4597716 test-data/converter_sampling_concentrations.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/converter_sampling_concentrations.tsv Tue Mar 28 12:35:41 2023 +0000 @@ -0,0 +1,101 @@ +Mg-glutamate k-glutamate CoA 3-PGA NTP NAD Folinic acid Spermidine tRNA Amino acids CAMP Extract HEPES PEG Promoter RBS +0.4 44.8 0.0 21.6 0.6 0.0 0.049 0.2 0.112 1.2 0.15 30.0 50.0 2.0 10.0 10.0 +4.0 32.0 0.104 6.0 0.3 0.264 0.014 0.56 0.08 0.3 0.6 30.0 50.0 2.0 10.0 10.0 +4.0 0.0 0.146 0.0 0.0 0.132 0.027 0.8 0.04 0.6 0.75 30.0 50.0 2.0 10.0 10.0 +0.0 32.0 0.052 6.0 1.08 0.132 0.054 0.0 0.144 1.5 0.6 30.0 50.0 2.0 10.0 10.0 +2.0 64.0 0.0 12.0 1.5 0.066 0.044 0.64 0.16 0.3 0.3 30.0 50.0 2.0 10.0 10.0 +0.4 80.0 0.0 30.0 0.84 0.066 0.038 0.4 0.0 1.2 0.48 30.0 50.0 2.0 10.0 10.0 +2.0 51.2 0.208 12.0 0.3 0.066 0.038 0.56 0.08 1.2 0.3 30.0 50.0 2.0 10.0 10.0 +2.0 32.0 0.104 24.0 1.5 0.33 0.014 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0.6 30.0 50.0 2.0 10.0 10.0 +2.0 16.0 0.208 30.0 1.5 0.066 0.044 0.56 0.04 0.3 0.15 30.0 50.0 2.0 10.0 10.0 +0.4 16.0 0.187 21.6 0.6 0.066 0.014 0.4 0.2 0.0 0.42 30.0 50.0 2.0 10.0 10.0 +4.0 51.2 0.104 6.0 1.2 0.238 0.0 0.2 0.04 0.0 0.42 30.0 50.0 2.0 10.0 10.0 diff -r 000000000000 -r 5834e4597716 test-data/converter_sampling_volumes.test-1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/converter_sampling_volumes.test-1.tsv Tue Mar 28 12:35:41 2023 +0000 @@ -0,0 +1,101 @@ +Mg-glutamate k-glutamate CoA 3-PGA NTP NAD Folinic acid Spermidine tRNA Amino acids CAMP Extract HEPES PEG Promoter RBS +2.5 12.5 2.5 15.0 0.0 0.0 2.5 0.0 2.5 200.0 0.0 100.0 25.0 10.0 32.5 50.0 +25.0 10.0 2.5 5.0 0.0 2.5 0.0 2.5 0.0 50.0 2.5 100.0 25.0 10.0 32.5 50.0 +25.0 0.0 2.5 0.0 0.0 0.0 0.0 2.5 0.0 100.0 5.0 100.0 25.0 10.0 32.5 50.0 +0.0 10.0 2.5 5.0 2.5 0.0 2.5 0.0 2.5 250.0 2.5 100.0 25.0 10.0 32.5 50.0 +12.5 20.0 2.5 7.5 2.5 0.0 2.5 2.5 2.5 50.0 2.5 100.0 25.0 10.0 32.5 50.0 +2.5 25.0 2.5 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5.0 2.5 2.5 0.0 0.0 0.0 0.0 2.5 100.0 25.0 10.0 32.5 50.0 diff -r 000000000000 -r 5834e4597716 test-data/converter_sampling_volumes.test-2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/converter_sampling_volumes.test-2.tsv Tue Mar 28 12:35:41 2023 +0000 @@ -0,0 +1,101 @@ +Mg-glutamate k-glutamate CoA 3-PGA NTP NAD Folinic acid Spermidine tRNA Amino acids CAMP Extract HEPES PEG Promoter RBS +0.0 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 20.0 2.5 10.0 2.5 2.5 2.5 5.0 +2.5 0.0 2.5 0.0 2.5 2.5 2.5 2.5 2.5 5.0 2.5 10.0 2.5 2.5 2.5 5.0 +2.5 0.0 2.5 0.0 2.5 2.5 2.5 2.5 2.5 10.0 2.5 10.0 2.5 2.5 2.5 5.0 +0.0 0.0 2.5 0.0 2.5 2.5 2.5 2.5 2.5 25.0 2.5 10.0 2.5 2.5 2.5 5.0 +0.0 2.5 2.5 0.0 2.5 2.5 2.5 2.5 2.5 5.0 2.5 10.0 2.5 2.5 2.5 5.0 +0.0 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 20.0 2.5 10.0 2.5 2.5 2.5 5.0 +0.0 2.5 2.5 0.0 2.5 2.5 2.5 2.5 2.5 20.0 2.5 10.0 2.5 2.5 2.5 5.0 +0.0 0.0 2.5 2.5 2.5 2.5 2.5 2.5 2.5 5.0 2.5 10.0 2.5 2.5 2.5 5.0 +0.0 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 15.0 2.5 10.0 2.5 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10.0 2.5 2.5 2.5 5.0 +0.0 0.0 2.5 0.0 2.5 2.5 2.5 2.5 2.5 5.0 2.5 10.0 2.5 2.5 2.5 5.0 +0.0 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 5.0 2.5 10.0 2.5 2.5 2.5 5.0 +0.0 2.5 2.5 0.0 2.5 2.5 2.5 2.5 2.5 5.0 2.5 10.0 2.5 2.5 2.5 5.0 +0.0 2.5 2.5 0.0 2.5 2.5 2.5 2.5 2.5 10.0 2.5 10.0 2.5 2.5 2.5 5.0 +0.0 2.5 2.5 0.0 2.5 2.5 2.5 2.5 2.5 20.0 2.5 10.0 2.5 2.5 2.5 5.0 +0.0 0.0 2.5 0.0 2.5 2.5 2.5 2.5 2.5 10.0 2.5 10.0 2.5 2.5 2.5 5.0 +0.0 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 25.0 2.5 10.0 2.5 2.5 2.5 5.0 +0.0 2.5 2.5 0.0 2.5 2.5 2.5 2.5 2.5 10.0 2.5 10.0 2.5 2.5 2.5 5.0 +0.0 0.0 2.5 2.5 2.5 2.5 2.5 2.5 2.5 25.0 2.5 10.0 2.5 2.5 2.5 5.0 +0.0 2.5 2.5 0.0 2.5 2.5 2.5 2.5 2.5 5.0 2.5 10.0 2.5 2.5 2.5 5.0 +0.0 0.0 2.5 0.0 2.5 2.5 2.5 2.5 2.5 10.0 2.5 10.0 2.5 2.5 2.5 5.0 +2.5 2.5 2.5 0.0 2.5 2.5 2.5 2.5 2.5 15.0 2.5 10.0 2.5 2.5 2.5 5.0 +2.5 0.0 2.5 0.0 2.5 2.5 2.5 2.5 2.5 15.0 2.5 10.0 2.5 2.5 2.5 5.0 +0.0 0.0 2.5 2.5 2.5 2.5 2.5 2.5 2.5 5.0 2.5 10.0 2.5 2.5 2.5 5.0 +0.0 0.0 2.5 2.5 2.5 2.5 2.5 2.5 2.5 0.0 2.5 10.0 2.5 2.5 2.5 5.0 +2.5 2.5 2.5 0.0 2.5 2.5 2.5 2.5 2.5 0.0 2.5 10.0 2.5 2.5 2.5 5.0 diff -r 000000000000 -r 5834e4597716 test-data/instructor_instructions.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/instructor_instructions.csv Tue Mar 28 12:35:41 2023 +0000 @@ -0,0 +1,1701 @@ +Source Plate Name,Source Plate Type,Source Well,Destination Plate Name,Destination Well,Transfer Volume,Sample ID +Source[1],384PP_AQ_GP3,A1,Destination[1],A1,0.4,Mg-glutamate +Source[1],384PP_AQ_GP3,A1,Destination[1],B1,4.0,Mg-glutamate +Source[1],384PP_AQ_GP3,A1,Destination[1],C1,4.0,Mg-glutamate +Source[1],384PP_AQ_GP3,A1,Destination[1],D1,0.0,Mg-glutamate +Source[1],384PP_AQ_GP3,A1,Destination[1],E1,2.0,Mg-glutamate +Source[1],384PP_AQ_GP3,A1,Destination[1],F1,0.4,Mg-glutamate +Source[1],384PP_AQ_GP3,A1,Destination[1],G1,2.0,Mg-glutamate +Source[1],384PP_AQ_GP3,A1,Destination[1],H1,2.0,Mg-glutamate +Source[1],384PP_AQ_GP3,A1,Destination[1],I1,0.0,Mg-glutamate 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plates_generator_destination_plate_1.json +3-PGA 6.0 plates_generator_destination_plate_1.json +NTP 0.3 plates_generator_destination_plate_1.json +NAD 0.066 plates_generator_destination_plate_1.json +Folinic acid 0.014 plates_generator_destination_plate_1.json +Spermidine 0.2 plates_generator_destination_plate_1.json +tRNA 0.04 plates_generator_destination_plate_1.json +Amino acids 0.3 plates_generator_destination_plate_1.json +CAMP 0.15 plates_generator_destination_plate_1.json +PEG 2.0 plates_generator_destination_plate_1.json diff -r 000000000000 -r 5834e4597716 test-data/plates_generator_destination_plate_1.test-1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plates_generator_destination_plate_1.test-1.json Tue Mar 28 12:35:41 2023 +0000 @@ -0,0 +1,26 @@ +{ + "Dimensions": "16x24", + "deadVolume": 0, + "Well capacity": 60000, + "Current well": "E7", + "Parameters": [ + "Spermidine", + "CAMP", + "Extract", + "CoA", + "HEPES", + "Folinic acid", + "k-glutamate", + "PEG", + "Mg-glutamate", + "Promoter", + "RBS", + "Amino acids", + "NTP", + "Water", + "NAD", + "3-PGA", + "tRNA" + ], + "Wells": "plates_generator_destination_plate_1.tsv" +} diff -r 000000000000 -r 5834e4597716 test-data/plates_generator_destination_plate_1.test-1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plates_generator_destination_plate_1.test-1.tsv Tue Mar 28 12:35:41 2023 +0000 @@ -0,0 +1,101 @@ +Well Mg-glutamate k-glutamate CoA 3-PGA NTP NAD Folinic acid Spermidine tRNA Amino acids CAMP Extract HEPES PEG Promoter RBS Water +A1 0.4 44.8 0.0 21.6 0.6 0.0 0.049 0.2 0.112 1.2 0.15 30.0 50.0 2.0 10.0 10.0 828.889 +B1 4.0 32.0 0.104 6.0 0.3 0.264 0.014 0.56 0.08 0.3 0.6 30.0 50.0 2.0 10.0 10.0 853.778 +C1 4.0 0.0 0.146 0.0 0.0 0.132 0.027 0.8 0.04 0.6 0.75 30.0 50.0 2.0 10.0 10.0 891.505 +D1 0.0 32.0 0.052 6.0 1.08 0.132 0.054 0.0 0.144 1.5 0.6 30.0 50.0 2.0 10.0 10.0 856.438 +E1 2.0 64.0 0.0 12.0 1.5 0.066 0.044 0.64 0.16 0.3 0.3 30.0 50.0 2.0 10.0 10.0 816.99 +F1 0.4 80.0 0.0 30.0 0.84 0.066 0.038 0.4 0.0 1.2 0.48 30.0 50.0 2.0 10.0 10.0 784.576 +G1 2.0 51.2 0.208 12.0 0.3 0.066 0.038 0.56 0.08 1.2 0.3 30.0 50.0 2.0 10.0 10.0 830.048 +H1 2.0 32.0 0.104 24.0 1.5 0.33 0.014 0.8 0.08 0.3 0.15 30.0 50.0 2.0 10.0 10.0 836.722 +I1 0.0 44.8 0.208 21.6 1.2 0.238 0.038 0.2 0.0 0.96 0.3 30.0 50.0 2.0 10.0 10.0 828.456 +J1 2.0 16.0 0.208 24.0 0.84 0.264 0.014 1.0 0.04 0.84 0.75 30.0 50.0 2.0 10.0 10.0 852.044 +K1 1.2 57.6 0.0 24.0 0.96 0.132 0.027 0.2 0.112 0.3 0.3 30.0 50.0 2.0 10.0 10.0 813.169 +L1 1.2 16.0 0.166 21.6 0.3 0.066 0.068 0.4 0.144 0.6 0.3 30.0 50.0 2.0 10.0 10.0 857.156 +M1 1.2 16.0 0.26 19.2 0.96 0.066 0.044 0.4 0.08 1.2 0.15 30.0 50.0 2.0 10.0 10.0 858.44 +N1 0.4 80.0 0.104 30.0 0.84 0.33 0.068 0.8 0.112 1.08 0.0 30.0 50.0 2.0 10.0 10.0 784.2660000000001 +O1 4.0 32.0 0.104 24.0 1.2 0.0 0.038 0.2 0.112 0.3 0.54 30.0 50.0 2.0 10.0 10.0 835.506 +P1 4.0 64.0 0.104 24.0 1.08 0.185 0.049 0.72 0.08 0.3 0.42 30.0 50.0 2.0 10.0 10.0 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2.0 16.0 0.208 30.0 1.5 0.066 0.044 0.56 0.04 0.3 0.15 30.0 50.0 2.0 10.0 10.0 847.1320000000001 +E9 0.4 16.0 0.187 21.6 0.6 0.066 0.014 0.4 0.2 0.0 0.42 30.0 50.0 2.0 10.0 10.0 858.113 +F9 4.0 51.2 0.104 6.0 1.2 0.238 0.0 0.2 0.04 0.0 0.42 30.0 50.0 2.0 10.0 10.0 834.598 diff -r 000000000000 -r 5834e4597716 test-data/plates_generator_source_plate_1.test-1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plates_generator_source_plate_1.test-1.json Tue Mar 28 12:35:41 2023 +0000 @@ -0,0 +1,26 @@ +{ + "Dimensions": "16x24", + "deadVolume": 15000, + "Well capacity": 60000, + "Current well": "C2", + "Parameters": [ + "Spermidine", + "CAMP", + "Extract", + "CoA", + "HEPES", + "Folinic acid", + "k-glutamate", + "PEG", + "Mg-glutamate", + "Promoter", + "RBS", + "Amino acids", + "NTP", + "Water", + "NAD", + "3-PGA", + "tRNA" + ], + "Wells": "plates_generator_source_plate_1.tsv" +} diff -r 000000000000 -r 5834e4597716 test-data/plates_generator_source_plate_1.test-1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plates_generator_source_plate_1.test-1.tsv Tue Mar 28 12:35:41 2023 +0000 @@ -0,0 +1,19 @@ +Well Mg-glutamate k-glutamate CoA 3-PGA NTP NAD Folinic acid Spermidine tRNA Amino acids CAMP Extract HEPES PEG Promoter RBS Water +A1 60000.0 +B1 60000.0 +C1 60000.0 +D1 60000.0 +E1 60000.0 +F1 60000.0 +G1 60000.0 +H1 60000.0 +I1 60000.0 +J1 60000.0 +K1 60000.0 +L1 60000.0 +M1 60000.0 +N1 60000.0 +O1 60000.0 +P1 60000.0 +A2 60000.0 +B2 60000.0 diff -r 000000000000 -r 5834e4597716 test-data/plates_generator_source_plate_1.test-2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plates_generator_source_plate_1.test-2.tsv Tue Mar 28 12:35:41 2023 +0000 @@ -0,0 +1,19 @@ +Well Mg-glutamate k-glutamate CoA 3-PGA NTP NAD Folinic acid Spermidine tRNA Amino acids CAMP Extract HEPES PEG Promoter RBS Water +A2 60000.0 +B2 60000.0 +C2 60000.0 +D2 60000.0 +E2 60000.0 +F2 60000.0 +G2 60000.0 +H2 60000.0 +I2 60000.0 +J2 60000.0 +K2 60000.0 +L2 60000.0 +M2 60000.0 +N2 60000.0 +O2 2500.0 +P2 2500.0 +Q2 60000.0 +R2 60000.0 diff -r 000000000000 -r 5834e4597716 test-data/plates_generator_volumes_summary.test-1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plates_generator_volumes_summary.test-1.tsv Tue Mar 28 12:35:41 2023 +0000 @@ -0,0 +1,18 @@ +Factor Sample+deadVolumes +Mg-glutamate 60000 +k-glutamate 60000 +CoA 60000 +3-PGA 60000 +NTP 60000 +NAD 60000 +Folinic acid 60000 +Spermidine 60000 +tRNA 60000 +Amino acids 60000 +CAMP 60000 +Extract 60000 +HEPES 60000 +PEG 60000 +Promoter 60000 +RBS 60000 +Water 120000