Mercurial > repos > tduigou > icfree_calibrator
changeset 0:d386c9d1fae5 draft
planemo upload for repository https://github.com/brsynth/icfree-ml commit 89b220357cba84350590ce79306440e78df97be5-dirty
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/calibrator.xml Fri Nov 22 11:37:49 2024 +0000 @@ -0,0 +1,110 @@ +<tool id="icfree_calibrator" name="iCFree calibrator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT"> + <description>Calculate yield based on fluorescence data and optionally apply calibration</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + cp '$initial_data_file' 'initial_data.csv' && + cp '$sampling_file' 'sampling.csv' && + cp '$ref_file' 'reference.csv' && + python -m icfree.learner.extractor + --initial_data_file 'initial_data.csv' + --sampling_file 'sampling.csv' + --output_file 'extractor.csv' + #if str($adv.num_samples) != '' + --num_samples '$adv.num_samples' + #end if + #if str($adv.num_replicates) != '' + --num_replicates '$adv.num_replicates' + #end if + && + python -m icfree.learner.calibrator + --output 'calibrated.csv' + --plot '$output_graph' + --jove_plus '$jove_plus' + --jove_minus '$jove_minus' + --r2_limit '$adv.r2_limit' + #if str($adv.num_control_points) != '' + --num_control_points '$adv.num_control_points' + #end if + #if str($adv.num_samples) != '' + --num '$adv.num_samples' + #end if + 'extractor.csv' 'reference.csv' && + mv 'calibrated.csv' '$output_calibrated' + ]]></command> + <inputs> + <param name="initial_data_file" type="data" format="csv" label="Initial file" help="Initial file"/> + <param name="sampling_file" type="data" format="csv" label="Sampling file" help="Sampling file"/> + <param name="ref_file" type="data" format="csv" label="Reference input file" help="Reference input file"/> + <param argument="jove_plus" type="integer" label="Line number for Jove+ (1-based index)" help="Line number for Jove+ (1-based index)" /> + <param argument="jove_minus" type="integer" label="Line number for Jove- (1-based index)" help="Line number for Jove- (1-based index)" /> + <section name="adv" title="Advanced Options" expanded="false"> + <param argument="num_samples" type="integer" optional="true" label="Number of samples" help="Number of samples" /> + <!-- Extractor --> + <param argument="num_replicates" type="integer" optional="true" label="Number of replicates" help="Number of replicates." /> + <!-- Calibrator --> + <param argument="r2_limit" type="float" value="0.8" label="R-squared limit for the regression" help="R-squared limit for the regression" /> + <param argument="num_control_points" type="integer" optional="true" label="Number of control points to select" help="Number of control points to select" /> + </section> + </inputs> + <outputs> + <data name="output_calibrated" format="csv" label="${tool.name} - Calibrated yields" /> + <data name="output_graph" format="png" label="${tool.name} - Graph" /> + </outputs> + <tests> + <test expect_num_outputs="2"> + <!-- python -m icfree.learner.extractor -initial_data_file calibrator.input.initial_data.csv -sampling_file calibrator.input.sampling.csv -output_file calibrator.extractor_output.1.csv --> + <!-- python -m icfree.learner.calibrator -output calibrator.output.calibrated.1.csv -jove_plus 3 -jove_minus 2 -plot calibrator.output.1.png calibrator.output.extractor.1.csv calibrator.input.ref.csv --> + <param name="initial_data_file" value="calibrator.input.initial_data.csv" /> + <param name="sampling_file" value="calibrator.input.sampling.csv" /> + <param name="ref_file" value="calibrator.input.ref.csv" /> + <param name="jove_plus" value="3" /> + <param name="jove_minus" value="2" /> + <output name="output_calibrated" ftype="csv"> + <assert_contents> + <has_n_lines n="343" /> + </assert_contents> + </output> + <output name="calibrator_graph" ftype="png" > + <assert_contents> + <has_size value="62000" delta="2000" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <!-- python -m icfree.learner.extractor -initial_data_file calibrator.input.initial_data.csv -sampling_file calibrator.input.sampling.tsv -output_file calibrator.output.extractor.2.csv -num_samples 20 -num_replicates 3 --> + <!-- python -m icfree.learner.calibrator -plot calibrator.output.2.png -output calibrator.output.2.csv -jove_plus 4 -jove_minus 3 -r2_limit 0.9 -num 20 -num_control_points 4 calibrator.output.extractor.2.csv calibrator.input.ref.csv --> + <param name="initial_data_file" value="calibrator.input.initial_data.csv" /> + <param name="sampling_file" value="calibrator.input.sampling.csv" /> + <param name="ref_file" value="calibrator.input.ref.csv" /> + <param name="num_samples" value="20" /> + <param name="num_replicates" value="3" /> + <param name="r2_limit" value="0.9" /> + <param name="num_control_points" value="4" /> + <param name="jove_plus" value="4" /> + <param name="jove_minus" value="3" /> + <output name="output_calibrated" ftype="csv"> + <assert_contents> + <has_n_lines n="21" /> + </assert_contents> + </output> + <output name="calibrator_graph" ftype="png" > + <assert_contents> + <has_size value="45000" delta="1000" /> + </assert_contents> + </output> + + </test> + + </tests> + <help><![CDATA[ +Calibrator +========== +Calculate yield based on fluorescence data and apply calibration. + +]]></help> + <expand macro="creator"/> + <expand macro="citation"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Nov 22 11:37:49 2024 +0000 @@ -0,0 +1,26 @@ +<macros> + <token name="@TOOL_VERSION@">2.5.2</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">icfree</requirement> + <yield/> + </requirements> + </xml> + <xml name="citation"> + <citations> + <citation type="bibtex"> + @unpublished{icfree + author = {Joan Hérisson, Yorgo El Moubayed}, + title = {{icfree}}, + url = {https://github.com/brsynth/icfree-ml/}, + } + </citation> + </citations> + </xml> + <xml name="creator"> + <creator> + <organization name="BioRetroSynth" url="https://github.com/brsynth"/> + </creator> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/calibrator.extractor_output.1.csv Fri Nov 22 11:37:49 2024 +0000 @@ -0,0 +1,343 @@ +Mg-glutamate,K-glutamate,Spermidine,3-PGA,NTP,HEPES,Amino acid,DNA 1,DNA 2,PEG-8000,Fluorescence Value 1,Fluorescence Average +105.04000000000002,350.0,52.52000000000001,168.78,100.96,262.5,1094.0,239.478,1485.0,524.8000000000001,36140,36140.0 +131.3,350.0,78.78,225.04,75.72,262.5,875.2,239.478,1232.55,524.8000000000001,8700,8700.0 +52.52000000000001,210.0,131.3,112.52,50.48,262.5,1094.0,239.478,1485.0,524.8000000000001,3278,3278.0 +105.04000000000002,280.0,105.04000000000002,225.04,50.48,262.5,1094.0,960.78,1485.0,524.8000000000001,20109,20109.0 +105.04000000000002,210.0,105.04000000000002,281.3,126.2,262.5,1094.0,717.0,994.95,262.40000000000003,22265,22265.0 +52.52000000000001,350.0,131.3,168.78,50.48,262.5,875.2,473.22,1232.55,262.40000000000003,22981,22981.0 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/calibrator.output.extractor.2.csv Fri Nov 22 11:37:49 2024 +0000 @@ -0,0 +1,21 @@ +Mg-glutamate,K-glutamate,Spermidine,3-PGA,NTP,HEPES,Amino acid,DNA 1,DNA 2,PEG-8000,Fluorescence Value 1,Fluorescence Value 2,Fluorescence Value 3,Fluorescence Average +105.04000000000002,350.0,52.52000000000001,168.78,100.96,262.5,1094.0,239.478,1485.0,524.8000000000001,36140,15313,9321,20258.0 +131.3,350.0,78.78,225.04,75.72,262.5,875.2,239.478,1232.55,524.8000000000001,8700,21108,3344,11050.666666666666 +52.52000000000001,210.0,131.3,112.52,50.48,262.5,1094.0,239.478,1485.0,524.8000000000001,3278,3385,2510,3057.6666666666665 +105.04000000000002,280.0,105.04000000000002,225.04,50.48,262.5,1094.0,960.78,1485.0,524.8000000000001,20109,37022,5881,21004.0 +105.04000000000002,210.0,105.04000000000002,281.3,126.2,262.5,1094.0,717.0,994.95,262.40000000000003,22265,23438,9019,18240.666666666668 +52.52000000000001,350.0,131.3,168.78,50.48,262.5,875.2,473.22,1232.55,262.40000000000003,22981,17481,4841,15101.0 +105.04000000000002,350.0,105.04000000000002,168.78,75.72,262.5,1094.0,717.0,994.95,0.0,22786,25935,3292,17337.666666666668 +52.52000000000001,280.0,105.04000000000002,225.04,100.96,262.5,875.2,473.22,1232.55,1049.6,27675,6322,32530,22175.666666666668 +26.260000000000005,210.0,78.78,281.3,100.96,262.5,656.4,717.0,1485.0,262.40000000000003,30810,27304,5806,21306.666666666668 +78.78,140.0,131.3,225.04,126.2,262.5,1094.0,960.78,994.95,262.40000000000003,16034,8048,17987,14023.0 +78.78,280.0,105.04000000000002,112.52,100.96,262.5,875.2,473.22,1232.55,787.1999999999999,22414,3780,2035,9409.666666666666 +131.3,350.0,0.0,112.52,25.24,262.5,1094.0,1434.0,1485.0,787.1999999999999,5780,23554,8456,12596.666666666666 +78.78,70.0,131.3,225.04,75.72,262.5,875.2,717.0,1232.55,524.8000000000001,9022,5965,2769,5918.666666666667 +78.78,280.0,78.78,281.3,75.72,262.5,1094.0,717.0,994.95,787.1999999999999,15814,9646,2079,9179.666666666666 +26.260000000000005,280.0,105.04000000000002,225.04,100.96,262.5,656.4,239.478,994.95,787.1999999999999,21552,7498,5982,11677.333333333334 +131.3,210.0,0.0,281.3,0.0,262.5,875.2,473.22,1485.0,524.8000000000001,2652,5456,3394,3834.0 +105.04000000000002,70.0,52.52000000000001,281.3,100.96,262.5,656.4,717.0,1485.0,524.8000000000001,11196,17492,4735,11141.0 +78.78,140.0,78.78,281.3,126.2,262.5,218.8,473.22,1485.0,262.40000000000003,18125,2873,6902,9300.0 +131.3,210.0,0.0,281.3,50.48,262.5,875.2,239.478,994.95,524.8000000000001,13258,5196,37686,18713.333333333332 +78.78,0.0,131.3,281.3,126.2,262.5,656.4,473.22,1485.0,524.8000000000001,5226,5160,12738,7708.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/destination_plate.csv Fri Nov 22 11:37:49 2024 +0000 @@ -0,0 +1,4 @@ +Well,Hela lysate,Access prot 50%,Reaction mix,RNA 1ug/uL,Water +A1,492.5,25.0,310.0,152.5,5020.0 +B1,970.0,165.0,257.5,112.5,4495.0 +C1,537.5,325.0,192.5,185.0,4760.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/instructor.access.test-2.csv Fri Nov 22 11:37:49 2024 +0000 @@ -0,0 +1,7 @@ +Source Plate Name,Source Plate Type,Source Well,Destination Plate Name,Destination Well,Transfer Volume,Sample ID +Source[1],384PP_AQ_GP3,C1,Destination[1],A1,25.0,Access prot 50% +Source[1],384PP_AQ_GP3,C1,Destination[1],B1,165.0,Access prot 50% +Source[1],384PP_AQ_GP3,C1,Destination[1],C1,325.0,Access prot 50% +Source[1],384PP_AQ_GP3,C1,Destination[1],D1,25.0,Access prot 50% +Source[1],384PP_AQ_GP3,C1,Destination[1],E1,165.0,Access prot 50% +Source[1],384PP_AQ_GP3,C1,Destination[1],F1,325.0,Access prot 50%
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/instructor.hela.test-2.csv Fri Nov 22 11:37:49 2024 +0000 @@ -0,0 +1,7 @@ +Source Plate Name,Source Plate Type,Source Well,Destination Plate Name,Destination Well,Transfer Volume,Sample ID +Source[1],384PP_AQ_CP,{A1;B1},Destination[1],A1,492.5,Hela lysate +Source[1],384PP_AQ_CP,{A1;B1},Destination[1],B1,970.0,Hela lysate +Source[1],384PP_AQ_CP,{A1;B1},Destination[1],C1,537.5,Hela lysate +Source[1],384PP_AQ_CP,{A1;B1},Destination[1],D1,492.5,Hela lysate +Source[1],384PP_AQ_CP,{A1;B1},Destination[1],E1,970.0,Hela lysate +Source[1],384PP_AQ_CP,{A1;B1},Destination[1],F1,537.5,Hela lysate
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/instructor.test-1.csv Fri Nov 22 11:37:49 2024 +0000 @@ -0,0 +1,31 @@ +Source Plate Name,Source Plate Type,Source Well,Destination Plate Name,Destination Well,Transfer Volume,Sample ID +Source[1],384PP_AQ_GP3,C1,Destination[1],A1,25.0,Access prot 50% +Source[1],384PP_AQ_GP3,C1,Destination[1],B1,165.0,Access prot 50% +Source[1],384PP_AQ_GP3,C1,Destination[1],C1,325.0,Access prot 50% +Source[1],384PP_AQ_GP3,C1,Destination[1],D1,25.0,Access prot 50% +Source[1],384PP_AQ_GP3,C1,Destination[1],E1,165.0,Access prot 50% +Source[1],384PP_AQ_GP3,C1,Destination[1],F1,325.0,Access prot 50% +Source[1],384PP_AQ_GP3,{A1;B1},Destination[1],A1,492.5,Hela lysate +Source[1],384PP_AQ_GP3,{A1;B1},Destination[1],B1,970.0,Hela lysate +Source[1],384PP_AQ_GP3,{A1;B1},Destination[1],C1,537.5,Hela lysate +Source[1],384PP_AQ_GP3,{A1;B1},Destination[1],D1,492.5,Hela lysate +Source[1],384PP_AQ_GP3,{A1;B1},Destination[1],E1,970.0,Hela lysate +Source[1],384PP_AQ_GP3,{A1;B1},Destination[1],F1,537.5,Hela lysate +Source[1],384PP_AQ_GP3,E1,Destination[1],A1,152.5,RNA 1ug/uL +Source[1],384PP_AQ_GP3,E1,Destination[1],B1,112.5,RNA 1ug/uL +Source[1],384PP_AQ_GP3,E1,Destination[1],C1,185.0,RNA 1ug/uL +Source[1],384PP_AQ_GP3,E1,Destination[1],D1,152.5,RNA 1ug/uL +Source[1],384PP_AQ_GP3,E1,Destination[1],E1,112.5,RNA 1ug/uL +Source[1],384PP_AQ_GP3,E1,Destination[1],F1,185.0,RNA 1ug/uL +Source[1],384PP_AQ_GP3,D1,Destination[1],A1,310.0,Reaction mix +Source[1],384PP_AQ_GP3,D1,Destination[1],B1,257.5,Reaction mix +Source[1],384PP_AQ_GP3,D1,Destination[1],C1,192.5,Reaction mix +Source[1],384PP_AQ_GP3,D1,Destination[1],D1,310.0,Reaction mix +Source[1],384PP_AQ_GP3,D1,Destination[1],E1,257.5,Reaction mix +Source[1],384PP_AQ_GP3,D1,Destination[1],F1,192.5,Reaction mix +Source[1],384PP_AQ_GP3,F1,Destination[1],A1,4020.0,Water +Source[1],384PP_AQ_GP3,F1,Destination[1],B1,3495.0,Water +Source[1],384PP_AQ_GP3,F1,Destination[1],C1,3760.0,Water +Source[1],384PP_AQ_GP3,F1,Destination[1],D1,4020.0,Water +Source[1],384PP_AQ_GP3,F1,Destination[1],E1,3495.0,Water +Source[1],384PP_AQ_GP3,F1,Destination[1],F1,3760.0,Water
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/instructor.test-2.csv Fri Nov 22 11:37:49 2024 +0000 @@ -0,0 +1,25 @@ +Source Plate Name,Source Plate Type,Source Well,Destination Plate Name,Destination Well,Transfer Volume,Sample ID +Source[1],384PP_AQ_GP3,C1,Destination[1],A1,25.0,Access prot 50% +Source[1],384PP_AQ_GP3,C1,Destination[1],B1,165.0,Access prot 50% +Source[1],384PP_AQ_GP3,C1,Destination[1],C1,325.0,Access prot 50% +Source[1],384PP_AQ_GP3,C1,Destination[1],D1,25.0,Access prot 50% +Source[1],384PP_AQ_GP3,C1,Destination[1],E1,165.0,Access prot 50% +Source[1],384PP_AQ_GP3,C1,Destination[1],F1,325.0,Access prot 50% +Source[1],384PP_AQ_GP3,E1,Destination[1],A1,152.5,RNA 1ug/uL +Source[1],384PP_AQ_GP3,E1,Destination[1],B1,112.5,RNA 1ug/uL +Source[1],384PP_AQ_GP3,E1,Destination[1],C1,185.0,RNA 1ug/uL +Source[1],384PP_AQ_GP3,E1,Destination[1],D1,152.5,RNA 1ug/uL +Source[1],384PP_AQ_GP3,E1,Destination[1],E1,112.5,RNA 1ug/uL +Source[1],384PP_AQ_GP3,E1,Destination[1],F1,185.0,RNA 1ug/uL +Source[1],384PP_AQ_GP3,D1,Destination[1],A1,310.0,Reaction mix +Source[1],384PP_AQ_GP3,D1,Destination[1],B1,257.5,Reaction mix +Source[1],384PP_AQ_GP3,D1,Destination[1],C1,192.5,Reaction mix +Source[1],384PP_AQ_GP3,D1,Destination[1],D1,310.0,Reaction mix +Source[1],384PP_AQ_GP3,D1,Destination[1],E1,257.5,Reaction mix +Source[1],384PP_AQ_GP3,D1,Destination[1],F1,192.5,Reaction mix +Source[1],384PP_AQ_GP3,F1,Destination[1],A1,4020.0,Water +Source[1],384PP_AQ_GP3,F1,Destination[1],B1,3495.0,Water +Source[1],384PP_AQ_GP3,F1,Destination[1],C1,3760.0,Water +Source[1],384PP_AQ_GP3,F1,Destination[1],D1,4020.0,Water +Source[1],384PP_AQ_GP3,F1,Destination[1],E1,3495.0,Water +Source[1],384PP_AQ_GP3,F1,Destination[1],F1,3760.0,Water
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plates_designer.destination_plate.test-1.csv Fri Nov 22 11:37:49 2024 +0000 @@ -0,0 +1,4 @@ +Well,Hela lysate,Access prot 50%,Reaction mix,RNA 1ug/uL,Water +A1,492.5,25.0,310.0,152.5,5020.0 +B1,970.0,165.0,257.5,112.5,4495.0 +C1,537.5,325.0,192.5,185.0,4760.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plates_designer.destination_plate.test-2.csv Fri Nov 22 11:37:49 2024 +0000 @@ -0,0 +1,7 @@ +Well,Hela lysate,Access prot 50%,Reaction mix,RNA 1ug/uL,Water +A1,492.5,25.0,310.0,152.5,4020.0 +B1,970.0,165.0,257.5,112.5,3495.0 +C1,537.5,325.0,192.5,185.0,3760.0 +D1,492.5,25.0,310.0,152.5,4020.0 +E1,970.0,165.0,257.5,112.5,3495.0 +F1,537.5,325.0,192.5,185.0,3760.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plates_designer.source_plate.test-1.csv Fri Nov 22 11:37:49 2024 +0000 @@ -0,0 +1,6 @@ +Well,Access prot 50%,Hela lysate,RNA 1ug/uL,Reaction mix,Water +A1,0.0,22000.0,0.0,0.0,0.0 +B1,20515.0,0.0,0.0,0.0,0.0 +C1,0.0,0.0,0.0,20760.0,0.0 +D1,0.0,0.0,20450.0,0.0,0.0 +E1,0.0,0.0,0.0,0.0,34275.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plates_designer.source_plate.test-2.csv Fri Nov 22 11:37:49 2024 +0000 @@ -0,0 +1,7 @@ +Well,Access prot 50%,Hela lysate,RNA 1ug/uL,Reaction mix,Water +A1,0.0,3000.0,0.0,0.0,0.0 +B1,0.0,1060.0,0.0,0.0,0.0 +C1,21030.0,0.0,0.0,0.0,0.0 +D1,0.0,0.0,0.0,1530.0,0.0 +E1,0.0,0.0,920.0,0.0,0.0 +F1,0.0,0.0,0.0,0.0,42550.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampling.test-1.csv Fri Nov 22 11:37:49 2024 +0000 @@ -0,0 +1,4 @@ +Hela lysate,Access prot 50%,Reaction mix,RNA 1ug/uL +492.5,25.0,310.0,152.5 +970.0,165.0,257.5,112.5 +537.5,325.0,192.5,185.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/source_plate.csv Fri Nov 22 11:37:49 2024 +0000 @@ -0,0 +1,6 @@ +Well,Access prot 50%,Hela lysate,RNA 1ug/uL,Reaction mix,Water +A1,0.0,22000.0,0.0,0.0,0.0 +B1,20515.0,0.0,0.0,0.0,0.0 +C1,0.0,0.0,0.0,20760.0,0.0 +D1,0.0,0.0,20450.0,0.0,0.0 +E1,0.0,0.0,0.0,0.0,34275.0