Mercurial > repos > tduigou > straindesign_analyzing_model
changeset 0:b86c4ac05aab draft
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
| author | tduigou |
|---|---|
| date | Mon, 15 May 2023 14:05:41 +0000 |
| parents | |
| children | b8a2463304c3 |
| files | analyzing-model.xml config/tool_conf.xml macros.xml test-data/butanol.tsv test-data/butanol.xml test-data/iAF1260.xml.gz test-data/simulate_deletion.butanol.iAF1260.tsv |
| diffstat | 7 files changed, 703 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/analyzing-model.xml Mon May 15 14:05:41 2023 +0000 @@ -0,0 +1,97 @@ +<tool id="straindesign_analyzing_model" name="StrainDesign analyzing-model" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@"> + <description>Produce a pareto plot for a biological model</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command detect_errors="exit_code"><![CDATA[ + ## Run cmdline + python -m straindesign analyzing-model + @CMD_INPUT_MODEL@ + @CMD_INPUT_MEDIUM@ + @CMD_BIOMASS_RXN_ID@ + @CMD_TARGET_RXN_ID@ + @CMD_INPUT_PATHWAY@ + #if str('$substrate_cond.substrate_param') == 'yes' + --substrate-rxn-id '$substrate_cond.substrate_rxn_id' + #end if + --output-pareto-png '$output_png' + ]]></command> + <expand macro="env_variables"/> + <inputs> + <expand macro="input_model_sbml"/> + <expand macro="input_medium_tsv"/> + <expand macro="input_biomass_rxn_id"/> + <expand macro="input_target_rxn_id"/> + <expand macro="input_pathway_sbml"/> + <conditional name="substrate_cond"> + <param name="substrate_param" type="select" label="Provide a substrate reaction" help="Choose yourself a carbon source or it will be detected automatically"> + <option value="yes">yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <expand macro="input_substrate_rxn_id"/> + </when> + <when value="no"/> + </conditional> + </inputs> + <outputs> + <data name="output_png" format="png" label="${tool.name}" /> + </outputs> + <tests> + <test> + <!-- test 1 --> + <param name="model" ftype="sbml" value="iAF1260.xml.gz"/> + <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" /> + <param name="target_rxn_id" value="EX_tyrp_e" /> + <output name="output_png" ftype="png"> + <assert_contents> + <has_size value="30000" delta="10000"/> + </assert_contents> + </output> + </test> + <test> + <!-- test 2 --> + <param name="model" ftype="sbml" value="iAF1260.xml.gz"/> + <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" /> + <param name="target_rxn_id" value="EX_tyrp_e" /> + <param name="substrate_rxn_id" value="EX_glc__D_e" /> + <output name="output_png" ftype="png"> + <assert_contents> + <has_size value="30000" delta="10000"/> + </assert_contents> + </output> + </test> + <test> + <!-- test 3 --> + <param name="model" ftype="sbml" value="iAF1260.xml.gz"/> + <param name="pathway" ftype="sbml" value="butanol.xml" /> + <param name="medium" ftype="tabular" value="butanol.tsv" /> + <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" /> + <param name="substrate_rxn_id" value="EX_glc__D_e" /> + <param name="target_rxn_id" value="EX_1btol_e" /> + <output name="output_png" ftype="png"> + <assert_contents> + <has_size value="30000" delta="10000"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +@HELP_TITLE@ + +This tool produces a phenotypic-phase-plane plot given these datas: +* model +* reaction producing a target +* biomass reaction +These informations are optionals and will be adapted to your needs: +* an heterologous pathway +* a carbon substrate +* media composition + +@HELP_LINK@ + ]]></help> + <expand macro="creator"/> + <expand macro="citation"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config/tool_conf.xml Mon May 15 14:05:41 2023 +0000 @@ -0,0 +1,5 @@ + <section id="sbc-pa" name="SynBioCAD Pathway Analysis"> + <tool file="synbiocad-galaxy-wrappers/straindesign/analyzing-model.xml" /> + <tool file="synbiocad-galaxy-wrappers/straindesign/reduce-model.xml" /> + <tool file="synbiocad-galaxy-wrappers/straindesign/simulate-deletion.xml" /> + </section>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon May 15 14:05:41 2023 +0000 @@ -0,0 +1,97 @@ +<macros> + <!-- GLOBAL --> + <token name="@TOOL_VERSION@">3.2.2</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@LICENSE@">MIT</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">straindesign</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="doi">10.1038/s41467-022-32661-x</citation> + </citations> + </xml> + <xml name="creator"> + <creator> + <organization name="BioRetroSynth" url="https://github.com/brsynth"/> + </creator> + </xml> + <xml name="env_variables"> + <environment_variables> + <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable> + <environment_variable name="USERNAME">\$__user_email__</environment_variable> + </environment_variables> + </xml> + + <!-- CMDLINE --> +<token name="@CMD_INPUT_MODEL@"><![CDATA[ +--input-model-file '$model' +]]></token> +<token name="@CMD_INPUT_PATHWAY@"><![CDATA[ +#if $pathway +--input-pathway-file '$pathway' +#end if +]]></token> +<token name="@CMD_INPUT_MEDIUM@"><![CDATA[ +#if $medium + --input-medium-file '$medium' +#end if +]]></token> +<token name="@CMD_BIOMASS_RXN_ID@"><![CDATA[ +--biomass-rxn-id '$biomass_rxn_id' +]]></token> +<token name="@CMD_TARGET_RXN_ID@"><![CDATA[ +--target-rxn-id '$target_rxn_id' +]]></token> + + <!-- INPUT --> + <xml name="input_model_sbml"> + <param name="model" type="data" format="sbml" label="Model" help="SBML input file, model"/> + </xml> + <xml name="input_pathway_sbml"> + <param name="pathway" type="data" format="sbml" optional="True" label="Pathway" help="SBML input file, containing heterologous pathway"/> + </xml> + <xml name="input_medium_tsv"> + <param name="medium" type="data" format="tabular" optional="True" label="Medium file" help="TSV input file, no header, with three columns: reaction_id, lower_bound, upper_bound"/> + </xml> + <xml name="input_biomass_rxn_id"> + <param name="biomass_rxn_id" type="text" value="" label="Biomass reaction ID" help="Reaction ID contains no special characters"> + <validator type="empty_field" message="Biomass reaction ID is required"/> + <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator> + </param> + </xml> + <xml name="input_target_rxn_id"> + <param name="target_rxn_id" type="text" value="" label="Target reaction ID" help="Reaction ID contains no special characters"> + <validator type="empty_field" message="Target reaction ID is required"/> + <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator> + </param> + </xml> + <xml name="input_substrate_rxn_id"> + <param name="substrate_rxn_id" type="text" value="" label="Substrate reaction ID" help="Reaction ID contains no special characters"> + <validator type="empty_field" message="Target reaction ID is required"/> + <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator> + </param> + </xml> + + <!-- HELP --> +<token name="@HELP_TITLE@"><![CDATA[ +StrainDesign +============ +]]></token> +<token name="@HELP_LINK@"><![CDATA[ +Project Links +------------- + +* `straindesign <https://github.com/brsynth/straindesign>`_ +* `cameo <https://github.com/biosustain/cameo>`_ +]]></token> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/butanol.tsv Mon May 15 14:05:41 2023 +0000 @@ -0,0 +1,2 @@ +EX_glc__D_e -10.0 10.0 +EX_o2_e -5.0 5.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/butanol.xml Mon May 15 14:05:41 2023 +0000 @@ -0,0 +1,496 @@ +<?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="meta_butanol" id="butanol" fbc:strict="true"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit kind="mole" exponent="1" scale="-3" multiplier="1"/> + <unit kind="gram" exponent="-1" scale="0" multiplier="1"/> + <unit kind="second" exponent="-1" scale="0" multiplier="3600"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <fbc:listOfObjectives fbc:activeObjective="obj"> + <fbc:objective fbc:id="obj" fbc:type="maximize"> + <fbc:listOfFluxObjectives> + <fbc:fluxObjective fbc:reaction="R_EX_1btol_e" fbc:coefficient="0.5"/> + </fbc:listOfFluxObjectives> + </fbc:objective> + </fbc:listOfObjectives> + <listOfCompartments> + <compartment id="c" name="cytosol" constant="true"/> + <compartment id="p" name="periplasm" constant="true"/> + <compartment id="e" name="extracellular space" constant="true"/> + </listOfCompartments> + <listOfSpecies> + <species metaid="meta_M_co2_e" sboTerm="SBO:0000247" id="M_co2_e" name="CO2 CO2" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="CO2"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_co2_e"> + <bqbiol:is> + <rdf:Bag> + 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fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_btcoa_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_btal_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction id="R_ButanolDeh" name="Butanol dehydrogenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_btal_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_1btol_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction id="R_ButOlTrP" name="1-Butanol transporter (periplasm)" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_1btol_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_1btol_p" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction id="R_ButOlTrE" name="1-Butanol transporter (extracellular)" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_1btol_p" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_1btol_e" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + </listOfReactions> + <groups:listOfGroups> + <groups:group metaid="meta_rp_pathway" 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="meta_rp_pathway"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="R_ButCoaDeh"/> + <groups:member groups:idRef="R_ButanalDeh"/> + <groups:member groups:idRef="R_ButanolDeh"/> + <groups:member groups:idRef="R_ButOlTrP"/> + <groups:member groups:idRef="R_ButOlTrE"/> + <groups:member groups:idRef="R_EX_1btol_e"/> + </groups:listOfMembers> + </groups:group> + </groups:listOfGroups> + </model> +</sbml>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/simulate_deletion.butanol.iAF1260.tsv Mon May 15 14:05:41 2023 +0000 @@ -0,0 +1,6 @@ +reactions genes size fva_min fva_max target_flux biomass_flux yield fitness +"('ATPS4rpp',)" "(('b3735',), ('b3734',), ('b3736',), ('b3731',), ('b3732',))" 1 0.0 0.00641204819277442 0.0 0.2199110076152308 0.0 0.0 +"('TPI',)" "(('b3919',),)" 1 0.0 0.006455168431418056 0.0 0.0 0.0 0.0 +"('ALAt2pp', 'DSERt2pp', 'DALAt2pp', 'BALAt2pp', 'TPI')" "(('b4208', 'b3919'),)" 2 0.0 0.006455167733784362 0.0 0.0 0.0 0.0 +"('OPHHX', 'TPI')" "(('b3835', 'b3919'),)" 2 0.0 0.006455168423924535 0.0 0.0 0.0 0.0 +"('TPI', 'MTHFC', 'MTHFD')" "(('b0529', 'b3919'),('b3919', 'b0529'))" 2 0.0 0.006455095014414326 0.0 0.0 1.2 0.0