Mercurial > repos > tduigou > icfree_converter
changeset 0:5834e4597716 draft
planemo upload for repository https://github.com/brsynth/icfree-ml commit e908694368c306390bc9253f81a9249ad988970d
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--- /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 @@ + <section id="sbc-pa" name="SynBioCAD Pathway Analysis"> + <tool file="synbiocad-galaxy-wrappers/icfree/converter.xml" /> + <tool file="synbiocad-galaxy-wrappers/icfree/instructor.xml" /> + <tool file="synbiocad-galaxy-wrappers/icfree/plates_generator.xml" /> + <tool file="synbiocad-galaxy-wrappers/icfree/sampler.xml" /> + </section>
--- /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 @@ +<tool id="icfree_converter" name="iCFree converter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@"> + <description>Convert concentration values into volume values.</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command detect_errors="exit_code"><![CDATA[ + python -m icfree.converter + '$cfps_file' + '$concentrations_file' + --sample_volume '$adv.sample_volume' + --output-folder . && + mv sampling_volumes.tsv '$output_sampling' + ]]></command> + <inputs> + <param name="cfps_file" type="data" format="tabular" label="CFPS parameters and features" /> + <param name="concentrations_file" type="data" format="tabular" label="Concentrations to convert" /> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="sample_volume" type="integer" value="1000" min="1" max="100000" label="Final sample volume in each well in nL" /> + </section> + </inputs> + <outputs> + <data name="output_sampling" format="tabular" label="${tool.name}" /> + </outputs> + <tests> + <!-- test 1: check if identical outputs are produced with default parameters --> + <test> + <param name="cfps_file" value="converter_proCFPS_parameters.tsv" /> + <param name="concentrations_file" value="converter_sampling_concentrations.tsv" /> + <output name="output_sampling" file="converter_sampling_volumes.test-1.tsv" ftype="tabular" compare="diff" /> + </test> + <!-- test 2: advanced options --> + <test> + <param name="cfps_file" value="converter_proCFPS_parameters.tsv" /> + <param name="concentrations_file" value="converter_sampling_concentrations.tsv" /> + <param name="sample_volume" value="100" /> + <output name="output_sampling" file="converter_sampling_volumes.test-2.tsv" ftype="tabular" compare="diff" /> + </test> + </tests> + <help><![CDATA[ +Converter +========= + +This converter module converts concentration values into volume values, these will be used as input for the plates_generator module. + +Input +----- +* **CFPS Parameters File**: The first column is the parameter (or factor) names. The second column is the maxValue of the parameter that will be used in the sampling. The third column is the concnetration of the stock. The fourth column is the deadVolume of the parameter. This is used to calculate the volume of the parameter that will not be pipetted by the robot (because of viscosity). The fifth column is the specific ratios we want to have for this parameter. If nothing defined, then take ratios given in program options. If one single number is given, then take this number as a const value. +* **CFPS Parameters Concentrations File**: Concentration values for each cell-free parameter. + +Advanced options: +* **Sample Volume**: Final sample volume in each well in nL (default: 1000) + +Output +------ +* A TSV file with the volume values for each parameter. + ]]></help> + <expand macro="creator"/> + <expand macro="citation"/> +</tool>
--- /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 @@ +<macros> + <token name="@TOOL_VERSION@">2.1.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@LICENSE@">MIT</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">icfree</requirement> + <yield/> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <regex match="WARNING" level="warning" /> + <regex match="ERROR" level="fatal" /> + </stdio> + </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/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
--- /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 0.8 0.08 0.3 0.15 30.0 50.0 2.0 10.0 10.0 +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 +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 +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 +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 +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 +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 +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 +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 +1.2 0.0 0.208 0.0 1.08 0.238 0.049 0.56 0.2 0.96 0.75 30.0 50.0 2.0 10.0 10.0 +2.0 16.0 0.208 6.0 0.84 0.211 0.038 0.2 0.128 1.2 0.6 30.0 50.0 2.0 10.0 10.0 +4.0 64.0 0.146 16.8 0.96 0.132 0.049 0.4 0.0 0.84 0.42 30.0 50.0 2.0 10.0 10.0 +1.2 44.8 0.208 12.0 1.08 0.264 0.068 0.0 0.16 0.6 0.6 30.0 50.0 2.0 10.0 10.0 +2.0 44.8 0.26 16.8 1.2 0.185 0.044 0.72 0.0 0.6 0.3 30.0 50.0 2.0 10.0 10.0 +4.0 0.0 0.052 12.0 0.6 0.132 0.027 0.4 0.04 0.6 0.0 30.0 50.0 2.0 10.0 10.0 +4.0 32.0 0.052 16.8 1.2 0.264 0.014 0.2 0.08 0.3 0.3 30.0 50.0 2.0 10.0 10.0 +2.0 44.8 0.052 16.8 0.3 0.066 0.049 0.8 0.04 1.2 0.48 30.0 50.0 2.0 10.0 10.0 +4.0 80.0 0.0 16.8 0.3 0.264 0.054 0.56 0.16 0.6 0.15 30.0 50.0 2.0 10.0 10.0 +1.2 44.8 0.0 6.0 0.6 0.211 0.054 0.56 0.144 0.0 0.15 30.0 50.0 2.0 10.0 10.0 +2.0 0.0 0.146 21.6 1.2 0.0 0.027 0.0 0.04 0.84 0.6 30.0 50.0 2.0 10.0 10.0 +0.4 16.0 0.166 6.0 0.3 0.33 0.068 1.0 0.16 0.6 0.54 30.0 50.0 2.0 10.0 10.0 +1.2 57.6 0.208 24.0 0.3 0.211 0.038 0.4 0.2 1.08 0.75 30.0 50.0 2.0 10.0 10.0 +0.4 80.0 0.052 30.0 0.3 0.264 0.0 0.72 0.128 1.08 0.0 30.0 50.0 2.0 10.0 10.0 +2.0 32.0 0.146 12.0 1.2 0.211 0.054 0.64 0.08 0.96 0.6 30.0 50.0 2.0 10.0 10.0 +1.2 51.2 0.146 12.0 0.6 0.132 0.014 0.2 0.0 1.08 0.54 30.0 50.0 2.0 10.0 10.0 +2.0 64.0 0.052 30.0 1.2 0.066 0.068 0.8 0.128 0.3 0.15 30.0 50.0 2.0 10.0 10.0 +4.0 0.0 0.208 0.0 0.3 0.0 0.044 0.0 0.16 0.6 0.15 30.0 50.0 2.0 10.0 10.0 +1.2 64.0 0.26 0.0 0.0 0.264 0.0 0.56 0.04 1.2 0.54 30.0 50.0 2.0 10.0 10.0 +2.0 64.0 0.052 6.0 0.96 0.185 0.038 0.0 0.112 0.84 0.6 30.0 50.0 2.0 10.0 10.0 +4.0 64.0 0.187 6.0 0.3 0.185 0.027 0.4 0.112 0.3 0.15 30.0 50.0 2.0 10.0 10.0 +1.2 51.2 0.052 24.0 0.6 0.185 0.027 0.4 0.08 0.6 0.3 30.0 50.0 2.0 10.0 10.0 +4.0 16.0 0.104 24.0 0.0 0.185 0.054 0.4 0.04 1.2 0.54 30.0 50.0 2.0 10.0 10.0 +2.0 32.0 0.26 12.0 1.08 0.238 0.044 0.2 0.08 1.5 0.48 30.0 50.0 2.0 10.0 10.0 +2.0 64.0 0.187 6.0 0.6 0.33 0.038 0.8 0.144 0.3 0.15 30.0 50.0 2.0 10.0 10.0 +4.0 32.0 0.104 6.0 0.84 0.132 0.027 0.2 0.04 0.96 0.75 30.0 50.0 2.0 10.0 10.0 +4.0 0.0 0.104 6.0 0.6 0.33 0.0 1.0 0.16 1.08 0.3 30.0 50.0 2.0 10.0 10.0 +0.4 51.2 0.26 12.0 0.0 0.264 0.014 0.4 0.0 0.3 0.3 30.0 50.0 2.0 10.0 10.0 +2.0 80.0 0.187 24.0 0.6 0.264 0.027 0.8 0.08 1.2 0.6 30.0 50.0 2.0 10.0 10.0 +2.0 16.0 0.26 24.0 0.6 0.132 0.027 1.0 0.04 0.3 0.48 30.0 50.0 2.0 10.0 10.0 +2.0 57.6 0.26 6.0 1.08 0.238 0.054 0.2 0.04 0.84 0.3 30.0 50.0 2.0 10.0 10.0 +0.0 16.0 0.052 30.0 1.5 0.33 0.068 1.0 0.16 1.5 0.15 30.0 50.0 2.0 10.0 10.0 +4.0 80.0 0.146 12.0 0.84 0.066 0.054 0.2 0.08 1.08 0.54 30.0 50.0 2.0 10.0 10.0 +4.0 32.0 0.052 12.0 0.3 0.066 0.027 0.0 0.16 0.0 0.42 30.0 50.0 2.0 10.0 10.0 +2.0 16.0 0.104 30.0 0.3 0.132 0.044 1.0 0.128 0.6 0.54 30.0 50.0 2.0 10.0 10.0 +1.2 16.0 0.104 16.8 1.2 0.066 0.068 0.4 0.16 0.3 0.48 30.0 50.0 2.0 10.0 10.0 +1.2 51.2 0.187 19.2 1.5 0.264 0.014 0.0 0.2 0.84 0.15 30.0 50.0 2.0 10.0 10.0 +2.0 64.0 0.146 6.0 1.5 0.066 0.014 0.56 0.2 0.84 0.3 30.0 50.0 2.0 10.0 10.0 +0.4 16.0 0.104 12.0 0.3 0.132 0.054 0.0 0.04 0.6 0.48 30.0 50.0 2.0 10.0 10.0 +4.0 16.0 0.146 24.0 0.6 0.0 0.014 0.8 0.08 0.3 0.48 30.0 50.0 2.0 10.0 10.0 +4.0 44.8 0.052 12.0 0.96 0.211 0.0 0.0 0.08 1.5 0.3 30.0 50.0 2.0 10.0 10.0 +4.0 57.6 0.166 19.2 0.96 0.066 0.0 0.8 0.128 1.5 0.75 30.0 50.0 2.0 10.0 10.0 +0.4 16.0 0.166 16.8 0.3 0.0 0.014 1.0 0.16 1.5 0.3 30.0 50.0 2.0 10.0 10.0 +2.0 80.0 0.0 24.0 0.0 0.264 0.014 0.8 0.0 0.3 0.42 30.0 50.0 2.0 10.0 10.0 +2.0 57.6 0.052 16.8 0.6 0.066 0.014 0.72 0.128 1.5 0.15 30.0 50.0 2.0 10.0 10.0 +2.0 57.6 0.104 24.0 0.3 0.132 0.027 0.8 0.112 0.96 0.42 30.0 50.0 2.0 10.0 10.0 +0.0 0.0 0.187 19.2 0.84 0.066 0.0 0.2 0.0 0.84 0.75 30.0 50.0 2.0 10.0 10.0 +2.0 64.0 0.26 16.8 0.96 0.264 0.027 0.64 0.144 1.2 0.6 30.0 50.0 2.0 10.0 10.0 +1.2 32.0 0.104 16.8 0.6 0.132 0.027 0.72 0.08 0.6 0.15 30.0 50.0 2.0 10.0 10.0 +1.2 16.0 0.052 6.0 0.84 0.33 0.014 0.0 0.144 1.08 0.6 30.0 50.0 2.0 10.0 10.0 +1.2 64.0 0.208 6.0 0.6 0.238 0.049 0.72 0.0 0.0 0.42 30.0 50.0 2.0 10.0 10.0 +2.0 80.0 0.052 19.2 1.5 0.185 0.027 0.4 0.112 0.84 0.15 30.0 50.0 2.0 10.0 10.0 +2.0 57.6 0.052 0.0 1.08 0.238 0.014 0.64 0.08 0.6 0.3 30.0 50.0 2.0 10.0 10.0 +2.0 16.0 0.166 19.2 0.0 0.185 0.054 0.56 0.128 1.08 0.0 30.0 50.0 2.0 10.0 10.0 +0.0 32.0 0.104 12.0 0.84 0.0 0.038 0.64 0.144 0.0 0.6 30.0 50.0 2.0 10.0 10.0 +0.4 0.0 0.208 12.0 1.2 0.185 0.054 0.2 0.2 0.96 0.3 30.0 50.0 2.0 10.0 10.0 +2.0 44.8 0.26 21.6 0.0 0.33 0.014 0.8 0.2 1.5 0.42 30.0 50.0 2.0 10.0 10.0 +2.0 32.0 0.052 6.0 1.5 0.132 0.014 0.4 0.112 0.84 0.3 30.0 50.0 2.0 10.0 10.0 +2.0 32.0 0.166 19.2 1.5 0.238 0.014 0.64 0.16 0.6 0.42 30.0 50.0 2.0 10.0 10.0 +1.2 32.0 0.146 0.0 0.0 0.185 0.068 0.56 0.04 1.2 0.54 30.0 50.0 2.0 10.0 10.0 +2.0 57.6 0.052 0.0 1.2 0.211 0.027 0.72 0.04 1.2 0.75 30.0 50.0 2.0 10.0 10.0 +4.0 80.0 0.052 30.0 0.6 0.0 0.054 0.56 0.112 0.0 0.0 30.0 50.0 2.0 10.0 10.0 +0.4 16.0 0.187 0.0 1.2 0.264 0.0 0.2 0.16 1.2 0.75 30.0 50.0 2.0 10.0 10.0 +4.0 32.0 0.104 12.0 0.3 0.132 0.027 0.8 0.112 0.0 0.15 30.0 50.0 2.0 10.0 10.0 +4.0 16.0 0.208 21.6 0.0 0.264 0.049 0.2 0.0 0.0 0.15 30.0 50.0 2.0 10.0 10.0 +2.0 64.0 0.187 12.0 0.6 0.132 0.027 0.2 0.04 0.96 0.75 30.0 50.0 2.0 10.0 10.0 +2.0 32.0 0.104 30.0 0.3 0.066 0.044 0.56 0.04 0.96 0.15 30.0 50.0 2.0 10.0 10.0 +4.0 80.0 0.166 19.2 0.6 0.132 0.027 0.2 0.2 0.0 0.48 30.0 50.0 2.0 10.0 10.0 +0.4 0.0 0.208 0.0 1.5 0.211 0.068 1.0 0.08 0.3 0.0 30.0 50.0 2.0 10.0 10.0 +0.4 51.2 0.26 30.0 1.2 0.185 0.054 0.4 0.2 0.3 0.0 30.0 50.0 2.0 10.0 10.0 +0.4 51.2 0.0 12.0 0.96 0.211 0.038 0.64 0.112 0.3 0.0 30.0 50.0 2.0 10.0 10.0 +1.2 44.8 0.0 16.8 0.84 0.33 0.014 0.8 0.2 0.6 0.15 30.0 50.0 2.0 10.0 10.0 +2.0 64.0 0.052 12.0 0.84 0.0 0.014 0.2 0.04 1.2 0.42 30.0 50.0 2.0 10.0 10.0 +2.0 0.0 0.0 6.0 1.2 0.066 0.038 1.0 0.128 0.6 0.6 30.0 50.0 2.0 10.0 10.0 +1.2 44.8 0.146 21.6 1.08 0.066 0.049 0.64 0.04 1.5 0.6 30.0 50.0 2.0 10.0 10.0 +1.2 44.8 0.166 6.0 0.3 0.066 0.0 0.4 0.08 0.6 0.15 30.0 50.0 2.0 10.0 10.0 +0.4 16.0 0.146 24.0 0.6 0.0 0.068 0.4 0.16 1.5 0.42 30.0 50.0 2.0 10.0 10.0 +2.0 64.0 0.104 0.0 0.3 0.33 0.0 0.2 0.144 0.3 0.0 30.0 50.0 2.0 10.0 10.0 +1.2 32.0 0.208 6.0 0.84 0.132 0.054 0.72 0.16 0.6 0.0 30.0 50.0 2.0 10.0 10.0 +4.0 44.8 0.146 16.8 0.0 0.132 0.054 1.0 0.04 0.84 0.3 30.0 50.0 2.0 10.0 10.0 +4.0 32.0 0.052 6.0 0.3 0.185 0.038 0.4 0.08 0.84 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
--- /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 22.5 2.5 0.0 2.5 0.0 0.0 200.0 2.5 100.0 25.0 10.0 32.5 50.0 +12.5 15.0 2.5 7.5 0.0 0.0 2.5 2.5 0.0 200.0 2.5 100.0 25.0 10.0 32.5 50.0 +12.5 10.0 2.5 17.5 2.5 2.5 0.0 2.5 0.0 50.0 0.0 100.0 25.0 10.0 32.5 50.0 +0.0 12.5 2.5 15.0 2.5 2.5 2.5 0.0 0.0 160.0 2.5 100.0 25.0 10.0 32.5 50.0 +12.5 5.0 2.5 17.5 2.5 2.5 0.0 2.5 0.0 140.0 5.0 100.0 25.0 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--- /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 2.5 2.5 5.0 +0.0 0.0 2.5 2.5 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 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 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--- /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 +Source[1],384PP_AQ_GP3,A1,Destination[1],J1,2.0,Mg-glutamate +Source[1],384PP_AQ_GP3,A1,Destination[1],K1,1.2,Mg-glutamate +Source[1],384PP_AQ_GP3,A1,Destination[1],L1,1.2,Mg-glutamate 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/instructor_volumes_warnings.tsv Tue Mar 28 12:35:41 2023 +0000 @@ -0,0 +1,12 @@ +Parameter Min Max Plate +Mg-glutamate 0.4 plates_generator_destination_plate_1.json +CoA 0.052 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
--- /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" +}
--- /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 10.0 803.062 +A2 1.2 0.0 0.208 0.0 1.08 0.238 0.049 0.56 0.2 0.96 0.75 30.0 50.0 2.0 10.0 10.0 892.755 +B2 2.0 16.0 0.208 6.0 0.84 0.211 0.038 0.2 0.128 1.2 0.6 30.0 50.0 2.0 10.0 10.0 870.575 +C2 4.0 64.0 0.146 16.8 0.96 0.132 0.049 0.4 0.0 0.84 0.42 30.0 50.0 2.0 10.0 10.0 810.2529999999999 +D2 1.2 44.8 0.208 12.0 1.08 0.264 0.068 0.0 0.16 0.6 0.6 30.0 50.0 2.0 10.0 10.0 837.02 +E2 2.0 44.8 0.26 16.8 1.2 0.185 0.044 0.72 0.0 0.6 0.3 30.0 50.0 2.0 10.0 10.0 831.091 +F2 4.0 0.0 0.052 12.0 0.6 0.132 0.027 0.4 0.04 0.6 0.0 30.0 50.0 2.0 10.0 10.0 880.149 +G2 4.0 32.0 0.052 16.8 1.2 0.264 0.014 0.2 0.08 0.3 0.3 30.0 50.0 2.0 10.0 10.0 842.79 +H2 2.0 44.8 0.052 16.8 0.3 0.066 0.049 0.8 0.04 1.2 0.48 30.0 50.0 2.0 10.0 10.0 831.413 +I2 4.0 80.0 0.0 16.8 0.3 0.264 0.054 0.56 0.16 0.6 0.15 30.0 50.0 2.0 10.0 10.0 795.1120000000001 +J2 1.2 44.8 0.0 6.0 0.6 0.211 0.054 0.56 0.144 0.0 0.15 30.0 50.0 2.0 10.0 10.0 844.281 +K2 2.0 0.0 0.146 21.6 1.2 0.0 0.027 0.0 0.04 0.84 0.6 30.0 50.0 2.0 10.0 10.0 871.547 +L2 0.4 16.0 0.166 6.0 0.3 0.33 0.068 1.0 0.16 0.6 0.54 30.0 50.0 2.0 10.0 10.0 872.436 +M2 1.2 57.6 0.208 24.0 0.3 0.211 0.038 0.4 0.2 1.08 0.75 30.0 50.0 2.0 10.0 10.0 812.0129999999999 +N2 0.4 80.0 0.052 30.0 0.3 0.264 0.0 0.72 0.128 1.08 0.0 30.0 50.0 2.0 10.0 10.0 785.056 +O2 2.0 32.0 0.146 12.0 1.2 0.211 0.054 0.64 0.08 0.96 0.6 30.0 50.0 2.0 10.0 10.0 848.1089999999999 +P2 1.2 51.2 0.146 12.0 0.6 0.132 0.014 0.2 0.0 1.08 0.54 30.0 50.0 2.0 10.0 10.0 830.8879999999999 +A3 2.0 64.0 0.052 30.0 1.2 0.066 0.068 0.8 0.128 0.3 0.15 30.0 50.0 2.0 10.0 10.0 799.236 +B3 4.0 0.0 0.208 0.0 0.3 0.0 0.044 0.0 0.16 0.6 0.15 30.0 50.0 2.0 10.0 10.0 892.538 +C3 1.2 64.0 0.26 0.0 0.0 0.264 0.0 0.56 0.04 1.2 0.54 30.0 50.0 2.0 10.0 10.0 829.9359999999999 +D3 2.0 64.0 0.052 6.0 0.96 0.185 0.038 0.0 0.112 0.84 0.6 30.0 50.0 2.0 10.0 10.0 823.213 +E3 4.0 64.0 0.187 6.0 0.3 0.185 0.027 0.4 0.112 0.3 0.15 30.0 50.0 2.0 10.0 10.0 822.3389999999999 +F3 1.2 51.2 0.052 24.0 0.6 0.185 0.027 0.4 0.08 0.6 0.3 30.0 50.0 2.0 10.0 10.0 819.356 +G3 4.0 16.0 0.104 24.0 0.0 0.185 0.054 0.4 0.04 1.2 0.54 30.0 50.0 2.0 10.0 10.0 851.477 +H3 2.0 32.0 0.26 12.0 1.08 0.238 0.044 0.2 0.08 1.5 0.48 30.0 50.0 2.0 10.0 10.0 848.1179999999999 +I3 2.0 64.0 0.187 6.0 0.6 0.33 0.038 0.8 0.144 0.3 0.15 30.0 50.0 2.0 10.0 10.0 823.451 +J3 4.0 32.0 0.104 6.0 0.84 0.132 0.027 0.2 0.04 0.96 0.75 30.0 50.0 2.0 10.0 10.0 852.947 +K3 4.0 0.0 0.104 6.0 0.6 0.33 0.0 1.0 0.16 1.08 0.3 30.0 50.0 2.0 10.0 10.0 884.426 +L3 0.4 51.2 0.26 12.0 0.0 0.264 0.014 0.4 0.0 0.3 0.3 30.0 50.0 2.0 10.0 10.0 832.8620000000001 +M3 2.0 80.0 0.187 24.0 0.6 0.264 0.027 0.8 0.08 1.2 0.6 30.0 50.0 2.0 10.0 10.0 788.242 +N3 2.0 16.0 0.26 24.0 0.6 0.132 0.027 1.0 0.04 0.3 0.48 30.0 50.0 2.0 10.0 10.0 853.1610000000001 +O3 2.0 57.6 0.26 6.0 1.08 0.238 0.054 0.2 0.04 0.84 0.3 30.0 50.0 2.0 10.0 10.0 829.3879999999999 +P3 0.0 16.0 0.052 30.0 1.5 0.33 0.068 1.0 0.16 1.5 0.15 30.0 50.0 2.0 10.0 10.0 847.24 +A4 4.0 80.0 0.146 12.0 0.84 0.066 0.054 0.2 0.08 1.08 0.54 30.0 50.0 2.0 10.0 10.0 798.9939999999999 +B4 4.0 32.0 0.052 12.0 0.3 0.066 0.027 0.0 0.16 0.0 0.42 30.0 50.0 2.0 10.0 10.0 848.975 +C4 2.0 16.0 0.104 30.0 0.3 0.132 0.044 1.0 0.128 0.6 0.54 30.0 50.0 2.0 10.0 10.0 847.152 +D4 1.2 16.0 0.104 16.8 1.2 0.066 0.068 0.4 0.16 0.3 0.48 30.0 50.0 2.0 10.0 10.0 861.222 +E4 1.2 51.2 0.187 19.2 1.5 0.264 0.014 0.0 0.2 0.84 0.15 30.0 50.0 2.0 10.0 10.0 823.245 +F4 2.0 64.0 0.146 6.0 1.5 0.066 0.014 0.56 0.2 0.84 0.3 30.0 50.0 2.0 10.0 10.0 822.374 +G4 0.4 16.0 0.104 12.0 0.3 0.132 0.054 0.0 0.04 0.6 0.48 30.0 50.0 2.0 10.0 10.0 867.89 +H4 4.0 16.0 0.146 24.0 0.6 0.0 0.014 0.8 0.08 0.3 0.48 30.0 50.0 2.0 10.0 10.0 851.58 +I4 4.0 44.8 0.052 12.0 0.96 0.211 0.0 0.0 0.08 1.5 0.3 30.0 50.0 2.0 10.0 10.0 834.097 +J4 4.0 57.6 0.166 19.2 0.96 0.066 0.0 0.8 0.128 1.5 0.75 30.0 50.0 2.0 10.0 10.0 812.83 +K4 0.4 16.0 0.166 16.8 0.3 0.0 0.014 1.0 0.16 1.5 0.3 30.0 50.0 2.0 10.0 10.0 861.36 +L4 2.0 80.0 0.0 24.0 0.0 0.264 0.014 0.8 0.0 0.3 0.42 30.0 50.0 2.0 10.0 10.0 790.202 +M4 2.0 57.6 0.052 16.8 0.6 0.066 0.014 0.72 0.128 1.5 0.15 30.0 50.0 2.0 10.0 10.0 818.37 +N4 2.0 57.6 0.104 24.0 0.3 0.132 0.027 0.8 0.112 0.96 0.42 30.0 50.0 2.0 10.0 10.0 811.5450000000001 +O4 0.0 0.0 0.187 19.2 0.84 0.066 0.0 0.2 0.0 0.84 0.75 30.0 50.0 2.0 10.0 10.0 875.917 +P4 2.0 64.0 0.26 16.8 0.96 0.264 0.027 0.64 0.144 1.2 0.6 30.0 50.0 2.0 10.0 10.0 811.105 +A5 1.2 32.0 0.104 16.8 0.6 0.132 0.027 0.72 0.08 0.6 0.15 30.0 50.0 2.0 10.0 10.0 845.587 +B5 1.2 16.0 0.052 6.0 0.84 0.33 0.014 0.0 0.144 1.08 0.6 30.0 50.0 2.0 10.0 10.0 871.74 +C5 1.2 64.0 0.208 6.0 0.6 0.238 0.049 0.72 0.0 0.0 0.42 30.0 50.0 2.0 10.0 10.0 824.565 +D5 2.0 80.0 0.052 19.2 1.5 0.185 0.027 0.4 0.112 0.84 0.15 30.0 50.0 2.0 10.0 10.0 793.534 +E5 2.0 57.6 0.052 0.0 1.08 0.238 0.014 0.64 0.08 0.6 0.3 30.0 50.0 2.0 10.0 10.0 835.396 +F5 2.0 16.0 0.166 19.2 0.0 0.185 0.054 0.56 0.128 1.08 0.0 30.0 50.0 2.0 10.0 10.0 858.627 +G5 0.0 32.0 0.104 12.0 0.84 0.0 0.038 0.64 0.144 0.0 0.6 30.0 50.0 2.0 10.0 10.0 851.634 +H5 0.4 0.0 0.208 12.0 1.2 0.185 0.054 0.2 0.2 0.96 0.3 30.0 50.0 2.0 10.0 10.0 882.293 +I5 2.0 44.8 0.26 21.6 0.0 0.33 0.014 0.8 0.2 1.5 0.42 30.0 50.0 2.0 10.0 10.0 826.076 +J5 2.0 32.0 0.052 6.0 1.5 0.132 0.014 0.4 0.112 0.84 0.3 30.0 50.0 2.0 10.0 10.0 854.65 +K5 2.0 32.0 0.166 19.2 1.5 0.238 0.014 0.64 0.16 0.6 0.42 30.0 50.0 2.0 10.0 10.0 841.062 +L5 1.2 32.0 0.146 0.0 0.0 0.185 0.068 0.56 0.04 1.2 0.54 30.0 50.0 2.0 10.0 10.0 862.0609999999999 +M5 2.0 57.6 0.052 0.0 1.2 0.211 0.027 0.72 0.04 1.2 0.75 30.0 50.0 2.0 10.0 10.0 834.2 +N5 4.0 80.0 0.052 30.0 0.6 0.0 0.054 0.56 0.112 0.0 0.0 30.0 50.0 2.0 10.0 10.0 782.6220000000001 +O5 0.4 16.0 0.187 0.0 1.2 0.264 0.0 0.2 0.16 1.2 0.75 30.0 50.0 2.0 10.0 10.0 877.639 +P5 4.0 32.0 0.104 12.0 0.3 0.132 0.027 0.8 0.112 0.0 0.15 30.0 50.0 2.0 10.0 10.0 848.375 +A6 4.0 16.0 0.208 21.6 0.0 0.264 0.049 0.2 0.0 0.0 0.15 30.0 50.0 2.0 10.0 10.0 855.529 +B6 2.0 64.0 0.187 12.0 0.6 0.132 0.027 0.2 0.04 0.96 0.75 30.0 50.0 2.0 10.0 10.0 817.104 +C6 2.0 32.0 0.104 30.0 0.3 0.066 0.044 0.56 0.04 0.96 0.15 30.0 50.0 2.0 10.0 10.0 831.7760000000001 +D6 4.0 80.0 0.166 19.2 0.6 0.132 0.027 0.2 0.2 0.0 0.48 30.0 50.0 2.0 10.0 10.0 792.995 +E6 0.4 0.0 0.208 0.0 1.5 0.211 0.068 1.0 0.08 0.3 0.0 30.0 50.0 2.0 10.0 10.0 894.233 +F6 0.4 51.2 0.26 30.0 1.2 0.185 0.054 0.4 0.2 0.3 0.0 30.0 50.0 2.0 10.0 10.0 813.8009999999999 +G6 0.4 51.2 0.0 12.0 0.96 0.211 0.038 0.64 0.112 0.3 0.0 30.0 50.0 2.0 10.0 10.0 832.139 +H6 1.2 44.8 0.0 16.8 0.84 0.33 0.014 0.8 0.2 0.6 0.15 30.0 50.0 2.0 10.0 10.0 832.266 +I6 2.0 64.0 0.052 12.0 0.84 0.0 0.014 0.2 0.04 1.2 0.42 30.0 50.0 2.0 10.0 10.0 817.2339999999999 +J6 2.0 0.0 0.0 6.0 1.2 0.066 0.038 1.0 0.128 0.6 0.6 30.0 50.0 2.0 10.0 10.0 886.3679999999999 +K6 1.2 44.8 0.146 21.6 1.08 0.066 0.049 0.64 0.04 1.5 0.6 30.0 50.0 2.0 10.0 10.0 826.279 +L6 1.2 44.8 0.166 6.0 0.3 0.066 0.0 0.4 0.08 0.6 0.15 30.0 50.0 2.0 10.0 10.0 844.238 +M6 0.4 16.0 0.146 24.0 0.6 0.0 0.068 0.4 0.16 1.5 0.42 30.0 50.0 2.0 10.0 10.0 854.306 +N6 2.0 64.0 0.104 0.0 0.3 0.33 0.0 0.2 0.144 0.3 0.0 30.0 50.0 2.0 10.0 10.0 830.6220000000001 +O6 1.2 32.0 0.208 6.0 0.84 0.132 0.054 0.72 0.16 0.6 0.0 30.0 50.0 2.0 10.0 10.0 856.086 +P6 4.0 44.8 0.146 16.8 0.0 0.132 0.054 1.0 0.04 0.84 0.3 30.0 50.0 2.0 10.0 10.0 829.8879999999999 +A7 4.0 32.0 0.052 6.0 0.3 0.185 0.038 0.4 0.08 0.84 0.6 30.0 50.0 2.0 10.0 10.0 853.505 +B7 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 +C7 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 +D7 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plates_generator_destination_plate_1.test-2.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 +C3 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 +D3 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 +E3 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 +F3 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 +G3 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 +H3 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 +I3 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 +J3 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 +K3 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 +L3 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 +M3 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 +N3 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 +O3 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 +P3 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 +A4 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 +B4 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 10.0 803.062 +C4 1.2 0.0 0.208 0.0 1.08 0.238 0.049 0.56 0.2 0.96 0.75 30.0 50.0 2.0 10.0 10.0 892.755 +D4 2.0 16.0 0.208 6.0 0.84 0.211 0.038 0.2 0.128 1.2 0.6 30.0 50.0 2.0 10.0 10.0 870.575 +E4 4.0 64.0 0.146 16.8 0.96 0.132 0.049 0.4 0.0 0.84 0.42 30.0 50.0 2.0 10.0 10.0 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10.0 785.056 +A5 2.0 32.0 0.146 12.0 1.2 0.211 0.054 0.64 0.08 0.96 0.6 30.0 50.0 2.0 10.0 10.0 848.1089999999999 +B5 1.2 51.2 0.146 12.0 0.6 0.132 0.014 0.2 0.0 1.08 0.54 30.0 50.0 2.0 10.0 10.0 830.8879999999999 +C5 2.0 64.0 0.052 30.0 1.2 0.066 0.068 0.8 0.128 0.3 0.15 30.0 50.0 2.0 10.0 10.0 799.236 +D5 4.0 0.0 0.208 0.0 0.3 0.0 0.044 0.0 0.16 0.6 0.15 30.0 50.0 2.0 10.0 10.0 892.538 +E5 1.2 64.0 0.26 0.0 0.0 0.264 0.0 0.56 0.04 1.2 0.54 30.0 50.0 2.0 10.0 10.0 829.9359999999999 +F5 2.0 64.0 0.052 6.0 0.96 0.185 0.038 0.0 0.112 0.84 0.6 30.0 50.0 2.0 10.0 10.0 823.213 +G5 4.0 64.0 0.187 6.0 0.3 0.185 0.027 0.4 0.112 0.3 0.15 30.0 50.0 2.0 10.0 10.0 822.3389999999999 +H5 1.2 51.2 0.052 24.0 0.6 0.185 0.027 0.4 0.08 0.6 0.3 30.0 50.0 2.0 10.0 10.0 819.356 +I5 4.0 16.0 0.104 24.0 0.0 0.185 0.054 0.4 0.04 1.2 0.54 30.0 50.0 2.0 10.0 10.0 851.477 +J5 2.0 32.0 0.26 12.0 1.08 0.238 0.044 0.2 0.08 1.5 0.48 30.0 50.0 2.0 10.0 10.0 848.1179999999999 +K5 2.0 64.0 0.187 6.0 0.6 0.33 0.038 0.8 0.144 0.3 0.15 30.0 50.0 2.0 10.0 10.0 823.451 +L5 4.0 32.0 0.104 6.0 0.84 0.132 0.027 0.2 0.04 0.96 0.75 30.0 50.0 2.0 10.0 10.0 852.947 +M5 4.0 0.0 0.104 6.0 0.6 0.33 0.0 1.0 0.16 1.08 0.3 30.0 50.0 2.0 10.0 10.0 884.426 +N5 0.4 51.2 0.26 12.0 0.0 0.264 0.014 0.4 0.0 0.3 0.3 30.0 50.0 2.0 10.0 10.0 832.8620000000001 +O5 2.0 80.0 0.187 24.0 0.6 0.264 0.027 0.8 0.08 1.2 0.6 30.0 50.0 2.0 10.0 10.0 788.242 +P5 2.0 16.0 0.26 24.0 0.6 0.132 0.027 1.0 0.04 0.3 0.48 30.0 50.0 2.0 10.0 10.0 853.1610000000001 +A6 2.0 57.6 0.26 6.0 1.08 0.238 0.054 0.2 0.04 0.84 0.3 30.0 50.0 2.0 10.0 10.0 829.3879999999999 +B6 0.0 16.0 0.052 30.0 1.5 0.33 0.068 1.0 0.16 1.5 0.15 30.0 50.0 2.0 10.0 10.0 847.24 +C6 4.0 80.0 0.146 12.0 0.84 0.066 0.054 0.2 0.08 1.08 0.54 30.0 50.0 2.0 10.0 10.0 798.9939999999999 +D6 4.0 32.0 0.052 12.0 0.3 0.066 0.027 0.0 0.16 0.0 0.42 30.0 50.0 2.0 10.0 10.0 848.975 +E6 2.0 16.0 0.104 30.0 0.3 0.132 0.044 1.0 0.128 0.6 0.54 30.0 50.0 2.0 10.0 10.0 847.152 +F6 1.2 16.0 0.104 16.8 1.2 0.066 0.068 0.4 0.16 0.3 0.48 30.0 50.0 2.0 10.0 10.0 861.222 +G6 1.2 51.2 0.187 19.2 1.5 0.264 0.014 0.0 0.2 0.84 0.15 30.0 50.0 2.0 10.0 10.0 823.245 +H6 2.0 64.0 0.146 6.0 1.5 0.066 0.014 0.56 0.2 0.84 0.3 30.0 50.0 2.0 10.0 10.0 822.374 +I6 0.4 16.0 0.104 12.0 0.3 0.132 0.054 0.0 0.04 0.6 0.48 30.0 50.0 2.0 10.0 10.0 867.89 +J6 4.0 16.0 0.146 24.0 0.6 0.0 0.014 0.8 0.08 0.3 0.48 30.0 50.0 2.0 10.0 10.0 851.58 +K6 4.0 44.8 0.052 12.0 0.96 0.211 0.0 0.0 0.08 1.5 0.3 30.0 50.0 2.0 10.0 10.0 834.097 +L6 4.0 57.6 0.166 19.2 0.96 0.066 0.0 0.8 0.128 1.5 0.75 30.0 50.0 2.0 10.0 10.0 812.83 +M6 0.4 16.0 0.166 16.8 0.3 0.0 0.014 1.0 0.16 1.5 0.3 30.0 50.0 2.0 10.0 10.0 861.36 +N6 2.0 80.0 0.0 24.0 0.0 0.264 0.014 0.8 0.0 0.3 0.42 30.0 50.0 2.0 10.0 10.0 790.202 +O6 2.0 57.6 0.052 16.8 0.6 0.066 0.014 0.72 0.128 1.5 0.15 30.0 50.0 2.0 10.0 10.0 818.37 +P6 2.0 57.6 0.104 24.0 0.3 0.132 0.027 0.8 0.112 0.96 0.42 30.0 50.0 2.0 10.0 10.0 811.5450000000001 +A7 0.0 0.0 0.187 19.2 0.84 0.066 0.0 0.2 0.0 0.84 0.75 30.0 50.0 2.0 10.0 10.0 875.917 +B7 2.0 64.0 0.26 16.8 0.96 0.264 0.027 0.64 0.144 1.2 0.6 30.0 50.0 2.0 10.0 10.0 811.105 +C7 1.2 32.0 0.104 16.8 0.6 0.132 0.027 0.72 0.08 0.6 0.15 30.0 50.0 2.0 10.0 10.0 845.587 +D7 1.2 16.0 0.052 6.0 0.84 0.33 0.014 0.0 0.144 1.08 0.6 30.0 50.0 2.0 10.0 10.0 871.74 +E7 1.2 64.0 0.208 6.0 0.6 0.238 0.049 0.72 0.0 0.0 0.42 30.0 50.0 2.0 10.0 10.0 824.565 +F7 2.0 80.0 0.052 19.2 1.5 0.185 0.027 0.4 0.112 0.84 0.15 30.0 50.0 2.0 10.0 10.0 793.534 +G7 2.0 57.6 0.052 0.0 1.08 0.238 0.014 0.64 0.08 0.6 0.3 30.0 50.0 2.0 10.0 10.0 835.396 +H7 2.0 16.0 0.166 19.2 0.0 0.185 0.054 0.56 0.128 1.08 0.0 30.0 50.0 2.0 10.0 10.0 858.627 +I7 0.0 32.0 0.104 12.0 0.84 0.0 0.038 0.64 0.144 0.0 0.6 30.0 50.0 2.0 10.0 10.0 851.634 +J7 0.4 0.0 0.208 12.0 1.2 0.185 0.054 0.2 0.2 0.96 0.3 30.0 50.0 2.0 10.0 10.0 882.293 +K7 2.0 44.8 0.26 21.6 0.0 0.33 0.014 0.8 0.2 1.5 0.42 30.0 50.0 2.0 10.0 10.0 826.076 +L7 2.0 32.0 0.052 6.0 1.5 0.132 0.014 0.4 0.112 0.84 0.3 30.0 50.0 2.0 10.0 10.0 854.65 +M7 2.0 32.0 0.166 19.2 1.5 0.238 0.014 0.64 0.16 0.6 0.42 30.0 50.0 2.0 10.0 10.0 841.062 +N7 1.2 32.0 0.146 0.0 0.0 0.185 0.068 0.56 0.04 1.2 0.54 30.0 50.0 2.0 10.0 10.0 862.0609999999999 +O7 2.0 57.6 0.052 0.0 1.2 0.211 0.027 0.72 0.04 1.2 0.75 30.0 50.0 2.0 10.0 10.0 834.2 +P7 4.0 80.0 0.052 30.0 0.6 0.0 0.054 0.56 0.112 0.0 0.0 30.0 50.0 2.0 10.0 10.0 782.6220000000001 +A8 0.4 16.0 0.187 0.0 1.2 0.264 0.0 0.2 0.16 1.2 0.75 30.0 50.0 2.0 10.0 10.0 877.639 +B8 4.0 32.0 0.104 12.0 0.3 0.132 0.027 0.8 0.112 0.0 0.15 30.0 50.0 2.0 10.0 10.0 848.375 +C8 4.0 16.0 0.208 21.6 0.0 0.264 0.049 0.2 0.0 0.0 0.15 30.0 50.0 2.0 10.0 10.0 855.529 +D8 2.0 64.0 0.187 12.0 0.6 0.132 0.027 0.2 0.04 0.96 0.75 30.0 50.0 2.0 10.0 10.0 817.104 +E8 2.0 32.0 0.104 30.0 0.3 0.066 0.044 0.56 0.04 0.96 0.15 30.0 50.0 2.0 10.0 10.0 831.7760000000001 +F8 4.0 80.0 0.166 19.2 0.6 0.132 0.027 0.2 0.2 0.0 0.48 30.0 50.0 2.0 10.0 10.0 792.995 +G8 0.4 0.0 0.208 0.0 1.5 0.211 0.068 1.0 0.08 0.3 0.0 30.0 50.0 2.0 10.0 10.0 894.233 +H8 0.4 51.2 0.26 30.0 1.2 0.185 0.054 0.4 0.2 0.3 0.0 30.0 50.0 2.0 10.0 10.0 813.8009999999999 +I8 0.4 51.2 0.0 12.0 0.96 0.211 0.038 0.64 0.112 0.3 0.0 30.0 50.0 2.0 10.0 10.0 832.139 +J8 1.2 44.8 0.0 16.8 0.84 0.33 0.014 0.8 0.2 0.6 0.15 30.0 50.0 2.0 10.0 10.0 832.266 +K8 2.0 64.0 0.052 12.0 0.84 0.0 0.014 0.2 0.04 1.2 0.42 30.0 50.0 2.0 10.0 10.0 817.2339999999999 +L8 2.0 0.0 0.0 6.0 1.2 0.066 0.038 1.0 0.128 0.6 0.6 30.0 50.0 2.0 10.0 10.0 886.3679999999999 +M8 1.2 44.8 0.146 21.6 1.08 0.066 0.049 0.64 0.04 1.5 0.6 30.0 50.0 2.0 10.0 10.0 826.279 +N8 1.2 44.8 0.166 6.0 0.3 0.066 0.0 0.4 0.08 0.6 0.15 30.0 50.0 2.0 10.0 10.0 844.238 +O8 0.4 16.0 0.146 24.0 0.6 0.0 0.068 0.4 0.16 1.5 0.42 30.0 50.0 2.0 10.0 10.0 854.306 +P8 2.0 64.0 0.104 0.0 0.3 0.33 0.0 0.2 0.144 0.3 0.0 30.0 50.0 2.0 10.0 10.0 830.6220000000001 +A9 1.2 32.0 0.208 6.0 0.84 0.132 0.054 0.72 0.16 0.6 0.0 30.0 50.0 2.0 10.0 10.0 856.086 +B9 4.0 44.8 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--- /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" +}
--- /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
--- /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
--- /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