| Next changeset 1:1128f1e17c37 (2023-02-20) |
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Commit message:
planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f |
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added:
macros.xml simulate-deletion.xml test-data/butanol.tsv test-data/butanol.xml test-data/iAF1260.xml.gz test-data/simulate_deletion.butanol.iAF1260.tsv |
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| diff -r 000000000000 -r 33c6ffbd098f macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Oct 02 19:26:40 2022 +0000 |
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| @@ -0,0 +1,97 @@ +<macros> + <!-- GLOBAL --> + <token name="@TOOL_VERSION@">3.1.0</token> + <token name="@VERSION_SUFFIX@">1</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.-])*$</validator> + </param> + </xml> + + <!-- HELP --> +<token name="@HELP_TITLE@"><![CDATA[ +StrainDesign +============ +]]></token> +<token name="@HELP_LINK@"><![CDATA[ +Project Links +------------- + +* `straindesign <https://github.com/brsynth/straindesign>`_ +* `cameo <https://github.com/biosustain/cameo>`_ +]]></token> +</macros> |
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| diff -r 000000000000 -r 33c6ffbd098f simulate-deletion.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/simulate-deletion.xml Sun Oct 02 19:26:40 2022 +0000 |
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| @@ -0,0 +1,96 @@ +<tool id="straindesign_simulate_deletion" name="StrainDesign simulate-deletion" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@"> + <description>Search genes to delete in a biological model</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command detect_errors="exit_code"><![CDATA[ + python -m straindesign simulate-deletion + @CMD_INPUT_MODEL@ + @CMD_INPUT_PATHWAY@ + @CMD_INPUT_MEDIUM@ + @CMD_BIOMASS_RXN_ID@ + @CMD_TARGET_RXN_ID@ + --strategy '$input_strategy.strategy' + #if str($input_strategy.strategy) == 'ko': + --substrate-rxn-id '$input_strategy.substrate_rxn_id' + #if $input_strategy.annotate: + --email '$__user_email__' + #end if + #end if + #if str($max_time_cond.max_time_param) == 'yes': + --max-time '$max_time_cond.max_time' + #end if + --max-knockouts '$max_knockouts' + --output-file-tsv '$output_tsv' + ]]></command> + <expand macro="env_variables"/> + <inputs> + <expand macro="input_model_sbml"/> + <expand macro="input_pathway_sbml"/> + <expand macro="input_medium_tsv"/> + <expand macro="input_biomass_rxn_id"/> + <expand macro="input_target_rxn_id"/> + <conditional name="input_strategy"> + <param name="strategy" type="select" label="Strategy" help="Genes or Reactions to delete"> + <option value="ko" selected="True">Gene knockouts</option> + <option value="ou" >Reaction knockouts</option> + </param> + <when value="ko"> + <param name="substrate_rxn_id" type="text" value="" label="Substrate reaction ID" help="Reaction ID contains no special characters"> + <validator type="empty_field" message="Substrate reaction ID is required"/> + <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator> + </param> + <param name="annotate" type="boolean" label="Annotate the genes" checked="false" help="Please agree to use your email for query the NCBI website to annotate the genes"/> + </when> + <when value="ou"> + </when> + </conditional> + <param name="max_knockouts" type="integer" min="1" max="10" value="3" label="Number of items deleted to consider"/> + <conditional name="max_time_cond"> + <param name="max_time_param" type="select" label="Time out" help="Limit scan time"> + <option value="no" selected="True">no</option> + <option value="yes" >yes</option> + </param> + <when value="yes"> + <param name="max_time" type="integer" min="5" max="120" value="10" label="minutes"/> + </when> + <when value="no"/> + </conditional> + </inputs> + <outputs> + <data name="output_tsv" format="tabular" label="${tool.name}(${input_strategy.strategy})" /> + </outputs> + <tests> + <test> + <!-- test 1 --> + <param name="model" ftype="sbml" value="iAF1260.xml.gz" /> + <param name="pathway" ftype="sbml" value="butanol.xml" /> + <param name="medium" ftype="tabular" value="butanol.tsv" /> + <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" /> + <param name="target_rxn_id" value="EX_1btol_e" /> + <param name="substrate_rxn_id" value="EX_glc__D_e" /> + <param name="max_time_param" value="yes"/> + <param name="max_time" value="5"/> + <output name="output_tsv" ftype="tabular"> + <assert_contents> + <has_line_matching expression="^reactions\tgenes\tsize\tfva_min\tfva_max\ttarget_flux\tbiomass_flux\tyield\tfitness$"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +@HELP_TITLE@ + +This tool helps to identify gene's deletions in a biological model to optimize the reaction of a targeted compound. +The medium composition can be modified with a TSV file formatted as following: no header, with these columns "reaction id, lower_bound, upper_bound". +The strategies "ko" and "ou" find genes and reactions respectively to delete. + +Disclaimer: if you want to annotate the genes with their names, your email address will be used by the library Biopython to request the NCBI website. + +@HELP_LINK@ + ]]></help> + <expand macro="creator"/> + <expand macro="citation"/> +</tool> |
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| diff -r 000000000000 -r 33c6ffbd098f test-data/butanol.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/butanol.tsv Sun Oct 02 19:26:40 2022 +0000 |
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| @@ -0,0 +1,2 @@ +EX_glc__D_e -10.0 10.0 +EX_o2_e -5.0 5.0 |
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| diff -r 000000000000 -r 33c6ffbd098f test-data/butanol.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/butanol.xml Sun Oct 02 19:26:40 2022 +0000 |
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| b'@@ -0,0 +1,496 @@\n+<?xml version="1.0" encoding="UTF-8"?>\n+<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">\n+ <model metaid="meta_butanol" id="butanol" fbc:strict="true">\n+ <listOfUnitDefinitions>\n+ <unitDefinition id="mmol_per_gDW_per_hr">\n+ <listOfUnits>\n+ <unit kind="mole" exponent="1" scale="-3" multiplier="1"/>\n+ <unit kind="gram" exponent="-1" scale="0" multiplier="1"/>\n+ <unit kind="second" exponent="-1" scale="0" multiplier="3600"/>\n+ </listOfUnits>\n+ </unitDefinition>\n+ </listOfUnitDefinitions>\n+ <fbc:listOfObjectives fbc:activeObjective="obj">\n+ <fbc:objective fbc:id="obj" fbc:type="maximize">\n+ <fbc:listOfFluxObjectives>\n+ <fbc:fluxObjective fbc:reaction="R_EX_1btol_e" fbc:coefficient="0.5"/>\n+ </fbc:listOfFluxObjectives>\n+ </fbc:objective>\n+ </fbc:listOfObjectives>\n+ <listOfCompartments>\n+ <compartment id="c" name="cytosol" constant="true"/>\n+ <compartment id="p" name="periplasm" constant="true"/>\n+ <compartment id="e" name="extracellular space" constant="true"/>\n+ </listOfCompartments>\n+ <listOfSpecies>\n+ <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">\n+ <annotation>\n+ <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/">\n+ <rdf:Description rdf:about="#meta_M_co2_e">\n+ <bqbiol:is>\n+ <rdf:Bag>\n+ <rdf:li rdf:resource="https://identifiers.org/bigg.metabolite/co2"/>\n+ <rdf:li rdf:resource="https://identifiers.org/biocyc/META:CARBON-DIOXIDE"/>\n+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:23011"/>\n+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:3283"/>\n+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:48829"/>\n+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:16526"/>\n+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:13283"/>\n+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:13285"/>\n+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:13284"/>\n+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:13282"/>\n+ <rdf:li rdf:resource="https://identifiers.org/envipath/650babc9-9d68-4b73-9332-11972ca26f7b/compound/2ec3da94-5f50-4525-81b1-5607c5c7a3d3"/>\n+ <rdf:li rdf:resource="https://identifiers.org/envipath/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/05f60af4-0a3f-4ead-9a29-33bb0f123379"/>\n+ <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB01967"/>\n+ <rdf:li rdf:resource="https://identifiers.org/inchi_key/CURLTUGMZLYLDI-UHFFFAOYSA-N"/>\n+ <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C00011"/>\n+ <rdf:li rdf:resource="https://identifiers.org/kegg.drug/D00004"/>\n+ <rdf:li rdf:resource="https://identifiers.org/metanetx.chemical/MNXM13"/>\n+ <rdf:li rdf:resource="https://identifiers.org/reactome.compound/29376"/>\n+ <rdf:li rdf:resource="https://identifiers.org/reactome.compound/5668565"/>\n+ <rdf:li rdf:resource="https://identifiers.org/reactome.compound/189480"/>\n+ <rd'..b'cies="M_b2coa_c" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>\n+ </listOfReactants>\n+ <listOfProducts>\n+ <speciesReference species="M_btcoa_c" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>\n+ </listOfProducts>\n+ </reaction>\n+ <reaction id="R_ButanalDeh" name="Butanal dehydrogenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">\n+ <listOfReactants>\n+ <speciesReference species="M_btcoa_c" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>\n+ </listOfReactants>\n+ <listOfProducts>\n+ <speciesReference species="M_btal_c" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>\n+ </listOfProducts>\n+ </reaction>\n+ <reaction id="R_ButanolDeh" name="Butanol dehydrogenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">\n+ <listOfReactants>\n+ <speciesReference species="M_btal_c" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>\n+ </listOfReactants>\n+ <listOfProducts>\n+ <speciesReference species="M_1btol_c" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>\n+ </listOfProducts>\n+ </reaction>\n+ <reaction id="R_ButOlTrP" name="1-Butanol transporter (periplasm)" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">\n+ <listOfReactants>\n+ <speciesReference species="M_1btol_c" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>\n+ </listOfReactants>\n+ <listOfProducts>\n+ <speciesReference species="M_1btol_p" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>\n+ </listOfProducts>\n+ </reaction>\n+ <reaction id="R_ButOlTrE" name="1-Butanol transporter (extracellular)" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">\n+ <listOfReactants>\n+ <speciesReference species="M_1btol_p" stoichiometry="1" constant="true"/>\n+ </listOfReactants>\n+ <listOfProducts>\n+ <speciesReference species="M_1btol_e" stoichiometry="1" constant="true"/>\n+ </listOfProducts>\n+ </reaction>\n+ </listOfReactions>\n+ <groups:listOfGroups>\n+ <groups:group metaid="meta_rp_pathway" groups:id="rp_pathway" groups:kind="collection">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:BRSynth rdf:about="meta_rp_pathway">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ <groups:listOfMembers>\n+ <groups:member groups:idRef="R_ButCoaDeh"/>\n+ <groups:member groups:idRef="R_ButanalDeh"/>\n+ <groups:member groups:idRef="R_ButanolDeh"/>\n+ <groups:member groups:idRef="R_ButOlTrP"/>\n+ <groups:member groups:idRef="R_ButOlTrE"/>\n+ <groups:member groups:idRef="R_EX_1btol_e"/>\n+ </groups:listOfMembers>\n+ </groups:group>\n+ </groups:listOfGroups>\n+ </model>\n+</sbml>\n' |
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| diff -r 000000000000 -r 33c6ffbd098f test-data/iAF1260.xml.gz |
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| Binary file test-data/iAF1260.xml.gz has changed |
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| diff -r 000000000000 -r 33c6ffbd098f test-data/simulate_deletion.butanol.iAF1260.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/simulate_deletion.butanol.iAF1260.tsv Sun Oct 02 19:26:40 2022 +0000 |
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| @@ -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 |