Mercurial > repos > tduigou > icfree_plates_generator
changeset 0:5735a13c1f5b 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 12:35:56 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/macros.xml Tue Mar 28 12:35:56 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 + @unpublished{icfree + author = {Joan Hérisson, Yorgo El Moubayed}, + title = {{icfree}}, + url = {https://github.com/brsynth/icfree-ml/}, + } + 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/plates_generator.xml Tue Mar 28 12:35:56 2023 +0000 @@ -0,0 +1,153 @@ +<tool id="icfree_plates_generator" name="iCFree plates generator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@"> + <description>Generates a list of Echo-compatible source and destination plates according a set of samples to test</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command detect_errors="exit_code"><![CDATA[ + #set factors = [] + #for $x in $adv.rep + #silent factors.append(str($x.optimize_well_volumes)) + #end for + #set sfactors = ' '.join(['"' + $x + '"' for $x in $factors]) + python -m icfree.plates_generator + '$cfps_file' + '$volume_file' + --sample_volume '$adv.sample_volume' + --source_plate_dead_volume '$adv.source_plate_dead_volume' + --dest_plate_dead_volume '$adv.dest_plate_dead_volume' + --dest-starting_well '$adv.dest_starting_well' + --src-starting_well '$adv.src_starting_well' + --nplicate '$adv.nplicate' + --keep-nil-vol '$adv.keep_nil_vol' + --source_plate_well_capacity '$adv.source_plate_well_capacity' + --dest_plate_well_capacity '$adv.dest_plate_well_capacity' + #if len(factors) > 0 + --optimize-well-volumes ${sfactors} + #end if + --plate-dimensions '$adv.plate_dimensions' + --output-folder '.' + --output-format 'tsv' && + mv volumes_summary.tsv '$volumes_summary' + ]]></command> + <inputs> + <param name="cfps_file" type="data" format="tabular" label="CFPS parameters and features" /> + <param name="volume_file" type="data" format="tabular" label="Volumes" /> + + <section name="adv" title="Advanced Options" expanded="false"> + + <param name="sample_volume" type="integer" value="1000" label="Final sample volume in each well in nL" /> + <param name="source_plate_dead_volume" type="integer" value="15000" label="Dead volume to add in the source plate in nL"/> + <param name="dest_plate_dead_volume" type="integer" value="15000" label="Dead volume to add in the destination plate in nL"/> + + <param name="dest_starting_well" type="text" value="A1" label="Starter well of destination plate to begin filling the 384 well-plate"> + <validator type="empty_field" message="Not empty"/> + <validator type="regex" message="Some letters followed by a number">^(?:[A-K]{1}([1-9]|1[0-2]))$</validator> + </param> + <param name="src_starting_well" type="text" value="A1" label="Starter well of source plate to begin filling the 384 well-plate"> + <validator type="empty_field" message="Not empty"/> + <validator type="regex" message="Some letters followed by a number">^(?:[A-K]{1}([1-9]|1[0-2]))$</validator> + </param> + + <param name="nplicate" type="integer" value="3" min="1" max="12" label="Numbers of copies of volume sets"/> + <param name="keep_nil_vol" type="boolean" truevalue="True" falsevalue="False" checked="true" display="checkboxes" label="Keep nil volumes in instructions or not"/> + + <param name="source_plate_well_capacity" type="integer" value="60000" label="Maximum volume capacity of the source plate in nL" /> + <param name="dest_plate_well_capacity" type="integer" value="60000" label="Maximum volume capacity of the dest plate in nL" /> + <param name="plate_dimensions" type="text" value="16x24" label="Dimensions of plate separated by a 'x'"> + <validator type="empty_field" message="Not empty"/> + <validator type="regex" message="An 'x' separator is expected">^(?:\d+x\d+)$</validator> + </param> + <repeat name="rep" title="Optimize well volumes" min="0"> + <param name="optimize_well_volumes" type="text" value="" label="Save volumes in source plate for all factors"> + <validator type="empty_field" message="Not empty"/> + </param> + </repeat> + + </section> + </inputs> + <outputs> + <data name="volumes_summary" format="tabular" label="${tool.name} - Volumes" /> + <collection name="output_source_dest" type="list" label="${tool.name} - Source Destination Plate"> + <discover_datasets pattern="(?P<name>source_plate_\d+\.json)$" format="json" /> + <discover_datasets pattern="(?P<name>source_plate_\d+\.tsv)$" format="tabular" /> + <discover_datasets pattern="(?P<name>destination_plate_\d+\.json)$" format="json" /> + <discover_datasets pattern="(?P<name>destination_plate_\d+\.tsv)$" format="tabular" /> + </collection> + </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="volume_file" value="converter_sampling_concentrations.tsv" /> + <output name="volumes_summary" file="plates_generator_volumes_summary.test-1.tsv" ftype="tabular" compare="diff" /> + <output_collection name="output_source_dest" type="list" count="4"> + <element name="source_plate_1.json" ftype="json"> + <assert_contents> + <has_n_lines n="26"/> + </assert_contents> + </element> + <element name="source_plate_1.tsv" file="plates_generator_source_plate_1.test-1.tsv" ftype="tabular" compare="diff" /> + <element name="destination_plate_1.json" ftype="json"> + <assert_contents> + <has_n_lines n="26"/> + </assert_contents> + </element> + <element name="destination_plate_1.tsv" file="plates_generator_destination_plate_1.test-1.tsv" ftype="tabular" compare="diff" /> + </output_collection> + </test> + <!-- test 2: advance arguments --> + <test> + <param name="cfps_file" value="converter_proCFPS_parameters.tsv" /> + <param name="volume_file" value="converter_sampling_concentrations.tsv" /> + <param name="source_plate_dead_volume" value="1500" /> + <param name="dest_plate_dead_volume" value="1000" /> + <param name="dest_starting_well" value="C3" /> + <param name="src_starting_well" value="A2" /> + <param name="nplicate" value="2" /> + <param name="keep_nil_vol" value="False" /> + <param name="plate_dimensions" value="32x32" /> + <repeat name="rep"> + <param name="optimize_well_volumes" value="RBS" /> + </repeat> + <repeat name="rep"> + <param name="optimize_well_volumes" value="Promoter" /> + </repeat> + <output_collection name="output_source_dest" type="list" count="4"> + <element name="destination_plate_1.tsv" file="plates_generator_destination_plate_1.test-2.tsv" ftype="tabular" compare="diff" /> + </output_collection> + </test> + </tests> + <help><![CDATA[ +Plates Generator +================ + +This module generates a list of source and destination plates according to the set of samples to test. + +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. +* Volume File**: File containing volumes + +Advanced Options: +----------------- +* **Sample Volume**: Final sample volume in each well in nL (default: 10000) +* **Source Plate Dead Volume**: dead volume to add in the source plate in nL (default: 15000) +* **Destination Plate Dead Volume**: dead volume to add in the dest plate in nL (default: 15000) +* **Destination Starting Well**: starter well of destination plate to begin filling the 384 well-plate. (default: A1) +* **Source Starting Well**: starter well of source plate to begin filling the 384 well-plate. (default: A1) +* **Number of replicate**: Numbers of copies of volume sets (default: 3) +* **Keep nil volumes**: Keep nil volumes in instructions or not (default: yes) +* **Source Plate Well Capacity**: Maximum volume capacity of the source plate in nL (default: 60000) +* **Destiantion Plate Well Capacity**: Maximum volume capacity of the dest plate in nL (default: 60000) +* **Optimize Well Volumes**: Save volumes in source plate for all factors. It may trigger more volume pipetting warnings. If list of factors is given (separated by blanks), save: only for these ones (default: []). +* **Plate Dimensions**: Dimensions of plate separated by a 'x', e.g. nb_rows x nb_cols (default: 16x24). + +Output +------ +* **Collection**: Collection of files describing source/destination plates/wells + ]]></help> + <expand macro="creator"/> + <expand macro="citation"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/converter_proCFPS_parameters.tsv Tue Mar 28 12:35:56 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 12:35:56 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 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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 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/converter_sampling_volumes.test-1.tsv Tue Mar 28 12:35:56 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 12:35:56 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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+Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],J1,852.044,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],K1,813.169,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],L1,857.156,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],M1,858.44,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],N1,784.2660000000001,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],O1,835.506,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],P1,803.062,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],A2,892.755,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],B2,870.575,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],C2,810.2529999999999,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],D2,837.02,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],E2,831.091,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],F2,880.149,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],G2,842.79,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],H2,831.413,Water 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+Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],E4,823.245,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],F4,822.374,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],G4,867.89,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],H4,851.58,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],I4,834.097,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],J4,812.83,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],K4,861.36,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],L4,790.202,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],M4,818.37,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],N4,811.5450000000001,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],O4,875.917,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],P4,811.105,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],A5,845.587,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],B5,871.74,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],C5,824.565,Water 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+Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],A7,853.505,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],B7,847.1320000000001,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],C7,858.113,Water +Source[1],384PP_AQ_GP3,{A2;B2},Destination[1],D7,834.598,Water
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/instructor_volumes_warnings.tsv Tue Mar 28 12:35:56 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 12:35:56 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 12:35:56 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 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plates_generator_destination_plate_1.test-2.tsv Tue Mar 28 12:35:56 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 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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 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 +C9 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 +D9 2.0 16.0 0.208 30.0 1.5 0.066 0.044 0.56 0.04 0.3 0.15 30.0 50.0 2.0 10.0 10.0 847.1320000000001 +E9 0.4 16.0 0.187 21.6 0.6 0.066 0.014 0.4 0.2 0.0 0.42 30.0 50.0 2.0 10.0 10.0 858.113 +F9 4.0 51.2 0.104 6.0 1.2 0.238 0.0 0.2 0.04 0.0 0.42 30.0 50.0 2.0 10.0 10.0 834.598
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plates_generator_source_plate_1.test-1.json Tue Mar 28 12:35:56 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 12:35:56 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 12:35:56 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 12:35:56 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