Mercurial > repos > tduigou > icfree_instructor
changeset 0:f93749376fe5 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 12:35:26 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/instructor.xml Tue Mar 28 12:35:26 2023 +0000 @@ -0,0 +1,102 @@ +<tool id="icfree_instructor" name="iCFree instructor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@"> + <description>Generates a list of Echo-compatible instructions to prepare samples</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command detect_errors="exit_code"><![CDATA[ + #set sps = [] + #set sws = [] + #set dps = [] + #set dws = [] + #for $x in $plates_generator: + #set $fname = str($x.element_identifier) + echo "$fname " && + ln -sfn '$x' '$fname' && + #if $fname.startswith('source') and $fname.endswith('json'): + #silent sps.append($fname) + #else if $fname.startswith('source') and $fname.endswith('tsv'): + #silent sws.append($fname) + #else if $fname.startswith('destination') and $fname.endswith('json'): + #silent dps.append($fname) + #else if $fname.startswith('destination') and $fname.endswith('tsv'): + #silent dws.append($fname) + #end if + #end for + #set s_sps = '" "'.join($sps) + #set s_sws = '" "'.join($sws) + #set s_dps = '" "'.join($dps) + #set s_dws = '" "'.join($dws) + python -m icfree.instructor + --source_plates $s_sps + --source_wells $s_sws + --dest_plates $s_dps + --dest_wells $s_dws + -spt '$source_plate' + --robot '$robot' + --output-folder '.' && + mv instructions.csv '$output_instruction' && + #if not os.path.isfile('volume_warning.tsv') + touch volume_warning.tsv && + #end if + mv volume_warning.tsv '$output_warning' + ]]></command> + <inputs> + <param name="plates_generator" type="data_collection" collection_type="list" format="json,tabular" label="Source/Destination corresponding to plate/wells" help="Output from iCFree plates generator"/> + <param name="robot" type="select" label="Robot name"> + <option value="ECHO" selected="true">ECHO</option> + </param> + <param name="source_plate" type="select" label="Source plate type"> + <option value="384PP_AQ_GP3" selected="true">384PP_AQ_GP3</option> + <option value="384_AQ_CP">384_AQ_CP</option> + </param> + </inputs> + <outputs> + <data name="output_warning" format="tsv" label="${tool.name} - Warning" /> + <data name="output_instruction" format="csv" label="${tool.name} - Instruction" /> + </outputs> + <tests> + <test> + <!-- test 1: check if identical outputs are produced with default parameters --> + <param name="plates_generator"> + <collection type="list"> + <element name="plates_generator_source_plate_1" value="plates_generator_source_plate_1.test-1.json" /> + <element name="plates_generator_source_plate_1.test-1.tsv" value="plates_generator_source_plate_1.test-1.tsv" /> + <element name="plates_generator_destination_plate_1.test-1.json" value="plates_generator_destination_plate_1.test-1.json" /> + <element name="plates_generator_destination_plate_1.test-1.tsv" value="plates_generator_destination_plate_1.test-1.tsv" /> + </collection> + </param> + <output name="output_warning" ftype="tabular"> + <assert_contents> + <has_n_lines n="12"/> + <has_line_matching expression="^Parameter\tMin\tMax\tPlate$"/> + </assert_contents> + </output> + <output name="output_instruction" file="instructor_instructions.csv" ftype="csv" compare="diff" /> + </test> + </tests> + <help><![CDATA[ +Instructor +========== + +The module generates a list of instructions to perform the experiment. + +Input +----- +Required: +* **A collection**: a collection with source/destination plates/wells, coming from iCFree plates generator tool. + +Advanced options: +----------------- +* **Robot name**: name of the robot to generate instructions for (default: "ECHO") +* **Source plate type**: type of plate used (default: "384PP_AQ_GP3") + +Output +------ +* **instructions**: contains the instructions to perform the experiment +* **volumes_warning**: contains the volumes that may cause issues with the chosen robot + ]]></help> + <expand macro="creator"/> + <expand macro="citation"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Mar 28 12:35:26 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 12:35:26 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 12:35:26 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 12:35:26 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 12:35:26 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 12:35:26 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 12:35:26 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 12:35:26 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 12:35:26 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 12:35:26 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 12:35:26 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 12:35:26 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 12:35:26 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 12:35:26 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