Mercurial > repos > iuc > rpbasicdesign
changeset 0:cdd6a526bdcf draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign commit bdac148247c9c3d3da3420220d006e723c718277"
| author | iuc |
|---|---|
| date | Wed, 30 Mar 2022 13:05:31 +0000 |
| parents | |
| children | e73c927dc332 |
| files | rpbasicdesign.xml test-data/biolegio_plate_lycopene.csv test-data/biolegio_plate_muconate.csv test-data/constructs_lycopene.csv test-data/constructs_muconate.csv test-data/lycopene_CrtEBI_from_selenzy.xml test-data/muconate_example.xml test-data/user_parts_plate_lycopene.csv test-data/user_parts_plate_muconate.csv |
| diffstat | 9 files changed, 6168 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpbasicdesign.xml Wed Mar 30 13:05:31 2022 +0000 @@ -0,0 +1,172 @@ +<tool id="rpbasicdesign" name="BasicDesign" version="@TOOL_VERSION@" profile="21.09"> + <description>Build DNA-BOT input files from rpSBML</description> + <macros> + <token name="@TOOL_VERSION@">1.0.1</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">rpbasicdesign</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python -m rpbasicdesign.cli + --rpsbml_file '$rpsbml_file' + #if $adv.parts_files + #set files = '" "'.join([str($file) for $file in $adv.parts_files]) + --parts_files "${files}" + #end if + --lms_id '$adv.lms_id' + --lmp_id '$adv.lmp_id' + --backbone_id '$backbone_id' + --sample_size '$sample_size' + $adv.cds_permutation + --o_dnabot_dir 'out/dnabot_in' + $adv.sbol_output + --max_enz_per_rxn $adv.max_enz_per_rxn + ]]></command> + <inputs> + <param name="rpsbml_file" type="data" format="sbml" label="rpSBML file" help="SBML file from which enzymes UniProt IDs will be collected."/> + <param argument="--backbone_id" type="text" value="BASIC_SEVA_37_CmR-p15A.1" label="Backbone part ID" help="Part ID to be used as the backbone."> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value=":" /> + <add value="." /> + <add value="-" /> + <add value="_" /> + </valid> + </sanitizer> + <validator type="empty_field" message="Backbone ID is required"/> + </param> + <param argument="--sample_size" type="integer" value="88" min="1" max="88" label="Sample size" help="Number of constructs to generate."/> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="parts_files" type="data" format="csv" optional="true" multiple="true" label="Linkers and user parts" help="List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: Standard Biolegio Parts (BBP-18500)" /> + <param argument="--lms_id" type="text" value="LMS" label="LMS part ID" help="Part ID to be used as the LMS methylated linker." > + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value=":" /> + <add value="-" /> + <add value="_" /> + <add value="." /> + </valid> + </sanitizer> + <validator type="empty_field" message="LMS ID is required"/> + </param> + <param argument="--lmp_id" type="text" value="LMP" label="LMP part ID" help="Part ID to be used as the LMP methylated linker."> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value=":" /> + <add value="-" /> + <add value="_" /> + <add value="." /> + </valid> + </sanitizer> + <validator type="empty_field" message="LMP ID is required"/> + </param> + <param argument="--cds_permutation" type="boolean" truevalue="--cds_permutation true" falsevalue="--cds_permutation false" checked="true" label="Perform CDS permutation?" help="Whether all combinations of CDS permutation should be built." /> + <param argument="--sbol_output" type="boolean" checked="false" truevalue="--o_sbol_dir out/sbol_export" falsevalue="" label="Output SBOL results?" help="Whether SBOL (Synthetic Biology Open Language) depictions of constructs should be outputted" /> + <param argument="--max_enz_per_rxn" type="integer" value="1" min="1" max="99" label="Maximum number of enyzme to consider per reaction." help="Maximum number of enyzme to consider per reaction. If more enzymes are available for a given reaction, then only the last one listed in the MIRIAM annotation section will be kept."/> + </section> + </inputs> + <outputs> + <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${tool.name} on ${rpsbml_file.name}: constructs" /> + <data name="User_parts_plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${tool.name} on ${rpsbml_file.name}: User parts plate"/> + <data name="Biolegio_plate" format="csv" from_work_dir="out/dnabot_in/biolegio_plate.csv" label="${tool.name} on ${rpsbml_file.name}: Biolegio plate"/> + <collection name="sbol_dir" type="list" label="${tool.name} on ${rpsbml_file.name}: SBOL constructs"> + <filter> adv['sbol_output'] </filter> + <discover_datasets pattern="__designation_and_ext__" format="xml" directory="out/sbol_export" /> + </collection> + </outputs> + <tests> + <test expect_num_outputs="4"> + <!-- test 1: check if identical outputs are produced (Lycopene input)--> + <param name="rpsbml_file" value="lycopene_CrtEBI_from_selenzy.xml" /> + <param name="sample_size" value="3" /> + <output name="Constructs" file="constructs_lycopene.csv" ftype="csv" compare="diff"> + <assert_contents> + <has_n_lines n="4"/> + </assert_contents> + </output> + <output name="User_parts_plate" file="user_parts_plate_lycopene.csv" ftype="csv" compare="diff"/> + <output name="Biolegio_plate" file="biolegio_plate_lycopene.csv" ftype="csv" compare="diff"/> + <param name="sbol_output" value="true" /> + <output_collection name="sbol_dir" type="list" count="3"> + <element name="BASIC_construct_A1"> + <assert_contents> + <is_valid_xml /> + <has_text text="BASIC_construct_A1" /> + <has_n_lines n="339" /> + </assert_contents> + </element> + <element name="BASIC_construct_B1"> + <assert_contents> + <is_valid_xml /> + <has_text text="BASIC_construct_B1" /> + <has_n_lines n="339" /> + </assert_contents> + </element> + <element name="BASIC_construct_C1"> + <assert_contents> + <is_valid_xml /> + <has_text text="BASIC_construct_C1" /> + <has_n_lines n="339" /> + </assert_contents> + </element> + </output_collection> + </test> + <test expect_num_outputs="3"> + <!-- test 2: check if identical outputs are produced (Muconate input)--> + <param name="rpsbml_file" value="muconate_example.xml" /> + <param name="sample_size" value="88" /> + <output name="Constructs" file="constructs_muconate.csv" ftype="csv" compare="diff"> + <assert_contents> + <has_n_lines n="89"/> + </assert_contents> + </output> + <output name="User_parts_plate" file="user_parts_plate_muconate.csv" ftype="csv" compare="diff"/> + <output name="Biolegio_plate" file="biolegio_plate_muconate.csv" ftype="csv" compare="diff"/> + </test> + </tests> + <help><![CDATA[ +rpbasicdesign +================ + +rpbasicdesign extracts enzyme IDs from rpSBML (System Biology Markup Language) files containing additionnal annotations (e.g. reaction rules ID) and produced by the RP (RetroPath) suite available in `SynBioCAD Galaxy platform <https://galaxy-synbiocad.org/>`_, to generate genetic constructs compliant with the BASIC (Biopart Assembly Standard for Idempotent Cloning) assembly approach. CSV files produced are ready to be used with DNA-Bot to generate instructions for automated build of the genetic constructs using OpenTrons liquid handling robots. + +Input +----- + +Required: + +* **rpSBML file**\ : rpSBML file from which enzymes UniProt IDs will be collected. + +Advanced options: + +* **Linkers and user parts**\ : (string) List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: ( `Standard Biolegio Parts <https://www.biolegio.com/>`_: BBP-18500). +* **LMS part ID**\ : (string) part ID to be used as the LMS methylated linker. Default: LMS. +* **LMP part ID**\ : (string) part ID to be used as the LMP methylated linker. Default: LMP. +* **Backbone part ID**\ : (string) part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1. +* **Sample size**\ : (int) Number of constructs to generate. Default: 88. +* **Perform CDS permutation?**\ : (boolean) Whether all combinations of CDS permutation should be built Default: true. +* **Maximum number of enyzme to consider per reaction**\ : (int) Maximum number of enyzme to consider per reaction. If more enzymes are available for a given reaction, then only the last one listed in the MIRIAM annotation section will be kept. (Default: 1). + +Output +------ + +* **constructs**\ : CSV construct file listing the constructs to be built. +* **User parts plate**\ : CSV file listing the DNA parts to be included into each construct. +* **Biolegio plate**\ : CSV file listing the plate coordinates of the BASIC linkers. +* **SBOL constructs**\ : (optional) one SBOL (Synthetic Biology Open Language) file is produced for each construct generated in XML format. + +Project Links +------------------ + +* `GitHub <https://github.com/brsynth/rpbasicdesign>`_ + +License +------- + +* `MIT <https://github.com/brsynth/rpbasicdesign/blob/master/LICENSE.txt>`_ + + ]]></help> + <citations> + <citation type="doi">10.1093/synbio/ysaa010</citation> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biolegio_plate_lycopene.csv Wed Mar 30 13:05:31 2022 +0000 @@ -0,0 +1,83 @@ +Part/linker,Well,Part concentration (ng/uL) +L1-S,A1, +L1-P,B1, +L2-S,A2, +L2-P,B2, +L3-S,A3, +L3-P,B3, +L4-S,A4, +L4-P,B4, +L5-S,A5, +L5-P,B5, +L6-S,A6, +L6-P,B6, +LMP-S,A7, +LMP-P,B7, +LMS-S,A8, +LMS-P,B8, +U1-S,C1, +U2-S,C2, +U3-S,C3, +U1-RBS1-P,C4, +U1-RBS2-P,C5, +U1-RBS3-P,C6, +U1-A01-P,D1, +U1-A02-P,D2, +U1-A03-P,D3, +U1-A04-P,D4, +U1-A05-P,D5, +U1-A06-P,D6, +U1-A07-P,D7, +U1-A08-P,D8, +U1-A09-P,D9, +U1-A10-P,D10, +U1-A11-P,D11 +U1-A12-P,D12, +U2-RBS1-P,C7, +U2-RBS2-P,C8, +U2-RBS3-P,C9, +U2-A01-P,E1, +U2-A02-P,E2, +U2-A03-P,E3, +U2-A04-P,E4, +U2-A05-P,E5, +U2-A06-P,E6, +U2-A07-P,E7, +U2-A08-P,E8, +U2-A09-P,E9, +U2-A10-P,E10, +U2-A11-P,E11 +U2-A12-P,E12, +U3-RBS1-P,C10, +U3-RBS2-P,C11, +U3-RBS3-P,C12, +U3-A01-P,F1, +U3-A02-P,F2, +U3-A03-P,F3, +U3-A04-P,F4, +U3-A05-P,F5, +U3-A06-P,F6, +U3-A07-P,F7, +U3-A08-P,F8, +U3-A09-P,F9, +U3-A10-P,F10, +U3-A11-P,F11 +U3-A12-P,F12, +U1-AM12-P,A10, +U1-AM24-P,B10, +U2-AM12-P,A11, +U2-AM24-P,B11, +U3-AM12-P,A12, +U3-AM24-P,B12, +LF1-S,A9, +LF1-P,B9, +LF2-S,G1, +LF2-P,H1, +LF3-S,G2, +LF3-P,H2, +LF4-S,G3, +LF4-P,H3, +LF5-S,G4, +LF5-P,H4, +LF6-S,G5, +LF6-P,H5, \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biolegio_plate_muconate.csv Wed Mar 30 13:05:31 2022 +0000 @@ -0,0 +1,83 @@ +Part/linker,Well,Part concentration (ng/uL) +L1-S,A1, +L1-P,B1, +L2-S,A2, +L2-P,B2, +L3-S,A3, +L3-P,B3, +L4-S,A4, +L4-P,B4, +L5-S,A5, +L5-P,B5, +L6-S,A6, +L6-P,B6, +LMP-S,A7, +LMP-P,B7, +LMS-S,A8, +LMS-P,B8, +U1-S,C1, +U2-S,C2, +U3-S,C3, +U1-RBS1-P,C4, +U1-RBS2-P,C5, +U1-RBS3-P,C6, +U1-A01-P,D1, +U1-A02-P,D2, +U1-A03-P,D3, +U1-A04-P,D4, +U1-A05-P,D5, +U1-A06-P,D6, +U1-A07-P,D7, +U1-A08-P,D8, +U1-A09-P,D9, +U1-A10-P,D10, +U1-A11-P,D11 +U1-A12-P,D12, +U2-RBS1-P,C7, +U2-RBS2-P,C8, +U2-RBS3-P,C9, +U2-A01-P,E1, +U2-A02-P,E2, +U2-A03-P,E3, +U2-A04-P,E4, +U2-A05-P,E5, +U2-A06-P,E6, +U2-A07-P,E7, +U2-A08-P,E8, +U2-A09-P,E9, +U2-A10-P,E10, +U2-A11-P,E11 +U2-A12-P,E12, +U3-RBS1-P,C10, +U3-RBS2-P,C11, +U3-RBS3-P,C12, +U3-A01-P,F1, +U3-A02-P,F2, +U3-A03-P,F3, +U3-A04-P,F4, +U3-A05-P,F5, +U3-A06-P,F6, +U3-A07-P,F7, +U3-A08-P,F8, +U3-A09-P,F9, +U3-A10-P,F10, +U3-A11-P,F11 +U3-A12-P,F12, +U1-AM12-P,A10, +U1-AM24-P,B10, +U2-AM12-P,A11, +U2-AM24-P,B11, +U3-AM12-P,A12, +U3-AM24-P,B12, +LF1-S,A9, +LF1-P,B9, +LF2-S,G1, +LF2-P,H1, +LF3-S,G2, +LF3-P,H2, +LF4-S,G3, +LF4-P,H3, +LF5-S,G4, +LF5-P,H4, +LF6-S,G5, +LF6-P,H5, \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/constructs_lycopene.csv Wed Mar 30 13:05:31 2022 +0000 @@ -0,0 +1,4 @@ +Well,Linker 1,Part 1,Linker 2,Part 2,Linker 3,Part 3,Linker 4,Part 4,Linker 5,Part 5,Linker 6,Part 6,Linker 7,Part 7,Linker 8,Part 8,Linker 9,Part 9,Linker 10,Part 10 +A1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS1,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,, +B1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS3,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,, +C1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS1,P21684,U3-RBS2,P21685,U2-RBS2,P21683,,,,,,,,,,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/constructs_muconate.csv Wed Mar 30 13:05:31 2022 +0000 @@ -0,0 +1,89 @@ +Well,Linker 1,Part 1,Linker 2,Part 2,Linker 3,Part 3,Linker 4,Part 4,Linker 5,Part 5,Linker 6,Part 6,Linker 7,Part 7,Linker 8,Part 8,Linker 9,Part 9,Linker 10,Part 10 +A1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U2-RBS2,O33948,U1-RBS2,O85675,,,,,,,,,,,, +B1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS3,O85675,U2-RBS2,O33948,,,,,,,,,,,, +C1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS2,O33948,U1-RBS1,O85675,,,,,,,,,,,, +D1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS3,O33948,U1-RBS3,O85675,,,,,,,,,,,, +E1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS1,O33948,U1-RBS3,O85675,,,,,,,,,,,, +F1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U1-RBS2,O85675,U2-RBS3,O33948,,,,,,,,,,,, +G1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS3,O33948,U1-RBS3,O85675,,,,,,,,,,,, +H1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS1,O33948,U1-RBS3,O85675,,,,,,,,,,,, +A2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U2-RBS2,O33948,U1-RBS3,O85675,,,,,,,,,,,, +B2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS3,O33948,U1-RBS2,O85675,,,,,,,,,,,, +C2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U2-RBS2,O33948,U1-RBS1,O85675,,,,,,,,,,,, +D2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U1-RBS1,O85675,U2-RBS1,O33948,,,,,,,,,,,, +E2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS1,O85675,U2-RBS3,O33948,,,,,,,,,,,, +F2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U2-RBS2,O33948,U1-RBS3,O85675,,,,,,,,,,,, +G2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS2,O85675,U2-RBS2,O33948,,,,,,,,,,,, +H2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS2,O33948,U1-RBS2,O85675,,,,,,,,,,,, +A3,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS3,O33948,U1-RBS2,O85675,,,,,,,,,,,, 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lycopene_CrtEBI_from_selenzy.xml Wed Mar 30 13:05:31 2022 +0000 @@ -0,0 +1,393 @@ +<?xml version="1.0" encoding="UTF-8"?> +<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" version="1" groups:required="false" fbc:required="false"> + <model metaid="a03e1bf0f20b54a66f7b4ce262ea6b0f7579c0a1e47144a649b9e2e711f6b3ed" id="RP_model_001_0001" name="001_0001" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true"> + <listOfCompartments> + <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description 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metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="MNXM8975"/> + <groups:member groups:idRef="MNXM24"/> + <groups:member groups:idRef="MNXM11"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="MNXM83"/> + <groups:member groups:idRef="MNXM132"/> + <groups:member groups:idRef="MNXM11"/> + </groups:listOfMembers> + </groups:group> + </groups:listOfGroups> + </model> +</sbml>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/muconate_example.xml Wed Mar 30 13:05:31 2022 +0000 @@ -0,0 +1,5328 @@ +<?xml version="1.0" encoding="UTF-8"?> +<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" version="1" groups:required="false" fbc:required="false"> + <model metaid="a03e1bf0f20b54a66f7b4ce262ea6b0f7579c0a1e47144a649b9e2e711f6b3ed" id="RP_model_001_0001" name="001_0001" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true"> + <listOfCompartments> + <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description 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+ </brsynth:selenzy_P05182> + <brsynth:selenzy_O09173> + <brsynth:score value="18.633"/> + <brsynth:target_ID value="10090"/> + </brsynth:selenzy_O09173> + <brsynth:selenzy_Q93099> + <brsynth:score value="18.633"/> + <brsynth:target_ID value="9606"/> + </brsynth:selenzy_Q93099> + <brsynth:selenzy_P51581> + <brsynth:score value="18.551"/> + <brsynth:target_ID value="10036"/> + </brsynth:selenzy_P51581> + <brsynth:selenzy_Q5RF05> + <brsynth:score value="18.533"/> + <brsynth:target_ID value="9601"/> + </brsynth:selenzy_Q5RF05> + <brsynth:selenzy_P21396> + <brsynth:score value="18.478"/> + <brsynth:target_ID value="10116"/> + </brsynth:selenzy_P21396> + <brsynth:selenzy_C0HJM0> + <brsynth:score value="17.738"/> + <brsynth:target_ID value="128967"/> + </brsynth:selenzy_C0HJM0> + <brsynth:selenzy_O44249> + <brsynth:score value="17.738"/> + <brsynth:target_ID value="7130"/> + </brsynth:selenzy_O44249> + <brsynth:selenzy_P11344> + <brsynth:score value="17.738"/> + <brsynth:target_ID value="10090"/> + </brsynth:selenzy_P11344> + <brsynth:selenzy_P14679> + <brsynth:score value="17.738"/> + <brsynth:target_ID value="9606"/> + </brsynth:selenzy_P14679> + <brsynth:selenzy_Q25519> + <brsynth:score value="17.738"/> + <brsynth:target_ID value="7130"/> + </brsynth:selenzy_Q25519> + <brsynth:selenzy_P05181> + <brsynth:score value="17.651"/> + <brsynth:target_ID value="9606"/> + </brsynth:selenzy_P05181> + <brsynth:selenzy_P33266> + <brsynth:score value="17.551"/> + <brsynth:target_ID value="9541"/> + </brsynth:selenzy_P33266> + <brsynth:selenzy_Q05421> + <brsynth:score value="17.551"/> + <brsynth:target_ID value="10090"/> + </brsynth:selenzy_Q05421> + <brsynth:selenzy_Q6GUQ4> + <brsynth:score value="17.551"/> + <brsynth:target_ID value="9544"/> + </brsynth:selenzy_Q6GUQ4> + <brsynth:selenzy_P35354> + <brsynth:score value="17.509"/> + <brsynth:target_ID value="9606"/> + </brsynth:selenzy_P35354> + <brsynth:selenzy_Q06278> + <brsynth:score value="17.41"/> + <brsynth:target_ID value="9606"/> + </brsynth:selenzy_Q06278> + <brsynth:selenzy_Q86B61> + <brsynth:score value="16.553"/> + <brsynth:target_ID value="7227"/> + </brsynth:selenzy_Q86B61> + <brsynth:selenzy_Q9BDE0> + <brsynth:score value="16.538"/> + <brsynth:target_ID value="9595"/> + </brsynth:selenzy_Q9BDE0> + <brsynth:selenzy_P55024> + <brsynth:score value="15.638"/> + <brsynth:target_ID value="9031"/> + </brsynth:selenzy_P55024> + <brsynth:selenzy_Q9VKJ0> + <brsynth:score value="15.633"/> + <brsynth:target_ID value="7227"/> + </brsynth:selenzy_Q9VKJ0> + <brsynth:selenzy_Q08410> + <brsynth:score value="15.538"/> + <brsynth:target_ID value="93934"/> + </brsynth:selenzy_Q08410> + <brsynth:selenzy_Q9V521> + <brsynth:score value="14.738"/> + <brsynth:target_ID value="7227"/> + </brsynth:selenzy_Q9V521> + <brsynth:selenzy_Q9W1V6> + <brsynth:score value="14.738"/> + <brsynth:target_ID value="7227"/> + </brsynth:selenzy_Q9W1V6> + <brsynth:selenzy_P55025> + <brsynth:score value="14.638"/> + <brsynth:target_ID value="8090"/> + </brsynth:selenzy_P55025> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <listOfReactants> + <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/> + <speciesReference species="MNXM4" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="MNXM1" stoichiometry="2" constant="true"/> + <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + </listOfReactions> + <groups:listOfGroups> + <groups:group metaid="_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299" groups:id="rp_pathway" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:global_score value="-1"/> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="rxn_1"/> + <groups:member groups:idRef="rxn_2"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a" groups:id="rp_intermediate_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="CMPD_0000000003"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="CMPD_0000000003"/> + <groups:member groups:idRef="MNXM4"/> + <groups:member groups:idRef="MNXM188"/> + <groups:member groups:idRef="TARGET_0000000001"/> + <groups:member groups:idRef="MNXM6"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="MNXM15"/> + <groups:member groups:idRef="MNXM1"/> + <groups:member groups:idRef="MNXM5"/> + <groups:member groups:idRef="MNXM13"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="MNXM5"/> + <groups:member groups:idRef="MNXM4"/> + <groups:member groups:idRef="MNXM188"/> + <groups:member groups:idRef="MNXM1"/> + <groups:member groups:idRef="MNXM6"/> + <groups:member groups:idRef="MNXM13"/> + <groups:member groups:idRef="MNXM15"/> + </groups:listOfMembers> + </groups:group> + </groups:listOfGroups> + </model> +</sbml>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/user_parts_plate_lycopene.csv Wed Mar 30 13:05:31 2022 +0000 @@ -0,0 +1,7 @@ +Part/linker,Well,Part concentration (ng/uL) +BASIC_SEVA_37_CmR-p15A.1,A1, +P21683,B1, +P21684,C1, +P21685,D1, +PJ23101_BASIC,E1, +PJ23119_BASIC,F1,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/user_parts_plate_muconate.csv Wed Mar 30 13:05:31 2022 +0000 @@ -0,0 +1,9 @@ +Part/linker,Well,Part concentration (ng/uL) +BASIC_SEVA_37_CmR-p15A.1,A1, +O33948,B1, +O85675,C1, +PJ23101_BASIC,D1, +PJ23104_BASIC,E1, +PJ23108_BASIC,F1, +PJ23111_BASIC,G1, +PJ23119_BASIC,H1,