Mercurial > repos > genouest > meneco
changeset 0:ec6d9e04cbc5 draft default tip
planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/meneco commit 005790d17ea244a50c9ccbd38b50a0608233c8a9
| author | genouest |
|---|---|
| date | Mon, 11 Jun 2018 08:43:56 -0400 |
| parents | |
| children | |
| files | meneco.xml test-data/ectocyc.sbml test-data/result.txt test-data/seeds.sbml test-data/targets.sbml |
| diffstat | 5 files changed, 15914 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/meneco.xml Mon Jun 11 08:43:56 2018 -0400 @@ -0,0 +1,54 @@ +<?xml version='1.0' encoding='utf-8'?> +<tool id="meneco" name="meneco" version="@VERSION@"> + <description>compute minimal completions to your draft network with reactions from a repair network</description> + <macros> + <token name="@VERSION@">1.5.2</token> + </macros> + <requirements> + <requirement type="package" version="@VERSION@">meneco</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ +meneco.py + --draftnet '${draftnet}' + #if $repairnet + --repairnet '${repairnet}' + #end if + --seeds '${seeds}' + --targets '${targets}' + ${enumerate} > '${output}' + ]]></command> + <inputs> + <param argument="--draftnet" type="data" format="xml" label="draft network" help="metabolic network in SBML format" /> + <param argument="--repairnet" type="data" optional='true' format="xml" label="repair network" help="metabolic network in SBML format" /> + <param argument="--seeds" type="data" format="xml" label="seeds" help="seeds in SBML format"/> + <param argument="--targets" type="data" format="xml" label="targets" help="targets in SBML format" /> + <param argument="--enumerate" type="boolean" truevalue="--enumerate" falsevalue="" help="enumerate all minimal completions" /> + </inputs> + <outputs> + <data format="txt" name="output" label="result.txt with ${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="draftnet" ftype="xml" value="ectocyc.sbml" /> + <param name="seeds" ftype="xml" value="seeds.sbml" /> + <param name="targets" ftype="xml" value="targets.sbml" /> + <output name="output" file="result.txt" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ + +**What it does** + +A qualitative approach to elaborating the bio-synthetic capacities of metabolic networks. Large-scale metabolic networks as well as measured data sets suffer from substantial incompleteness. This approach builds upon a formal method for analyzing large-scale metabolic networks mapping its principles into Answer Set Programming. The approach can then be used to check whether a drafted network provides the synthesis routes to comply with the required functionality. If this fails, the draft network can be completed by importing reactions from metabolic reference network stemming from other organisms until the obtained network provides the measured functionality. + +-------- + +**Project links:** + +http://bioasp.github.io/meneco/ + + ]]></help> + <citations> + <citation type="doi">10.1371/journal.pcbi.1005276</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ectocyc.sbml Mon Jun 11 08:43:56 2018 -0400 @@ -0,0 +1,15682 @@ +<?xml version="1.0" encoding="UTF-8"?> +<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1"> + <model id="EsiCyc"> + <listOfCompartments> + <compartment id="CCO__45__IN" name="CCO-IN"/> + <compartment id="CCO__45__OUT" name="CCO-OUT"/> + <compartment id="CCO__45__CYTOSOL" name="CCO-CYTOSOL"/> + </listOfCompartments> + <listOfSpecies> + <species id="Protein__45__Red__45__Disulfides" name="a protein with reduced sulfide groups: " compartment="CCO__45__CYTOSOL" initialAmount="1000" boundaryCondition="true"/> + <species id="Protein__45__Ox__45__Disulfides" name="a protein with oxidized disulfide bonds: " compartment="CCO__45__CYTOSOL" initialAmount="1000" boundaryCondition="true"/> + <species id="PHOSPHO__45__ENOL__45__PYRUVATE_CCO__45__IN" name="phosphoenolpyruvate: C3H2O6P" compartment="CCO__45__IN" initialAmount="1000" boundaryCondition="true"/> + 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+ <reaction id="RXN0__45__5267" name="RXN0-5267" reversible="false"> + <listOfReactants> + <speciesReference species="PROTON_CCO__45__IN" stoichiometry="4"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="PROTON_CCO__45__OUT" stoichiometry="4"/> + </listOfProducts> + </reaction> + <reaction id="TRANS__45__RXN__45__208" name="TRANS-RXN-208" reversible="false"> + <listOfReactants> + <speciesReference species="ASCORBATE_CCO__45__OUT" stoichiometry="1"/> + <speciesReference species="PROTON_CCO__45__OUT" stoichiometry="1"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="ASCORBATE_CCO__45__IN" stoichiometry="1"/> + <speciesReference species="PROTON_CCO__45__IN" stoichiometry="1"/> + </listOfProducts> + </reaction> + <reaction id="TRANS__45__RXN__45__210" name="TRANS-RXN-210" reversible="false"> + <listOfReactants> + <speciesReference species="PHOSPHO__45__ENOL__45__PYRUVATE_CCO__45__IN" stoichiometry="1"/> + <speciesReference species="Pi_CCO__45__OUT" stoichiometry="1"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="Pi_CCO__45__OUT" stoichiometry="1"/> + <speciesReference species="PHOSPHO__45__ENOL__45__PYRUVATE_CCO__45__OUT" stoichiometry="1"/> + </listOfProducts> + </reaction> + <reaction id="TRANS__45__RXN__45__218" name="TRANS-RXN-218" reversible="false"> + <listOfReactants> + <speciesReference species="PROTON_CCO__45__IN" stoichiometry="2"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="PROTON_CCO__45__OUT" stoichiometry="2"/> + </listOfProducts> + </reaction> + <reaction id="RXN0__45__5261" name="RXN0-5261" reversible="true"> + <listOfReactants> + <speciesReference species="PYRUVATE_CCO__45__IN" stoichiometry="1"/> + <speciesReference species="PROTON_CCO__45__IN" stoichiometry="2"/> + <speciesReference species="E__45__" stoichiometry="2"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="D__45__LACTATE_CCO__45__IN" stoichiometry="1"/> + </listOfProducts> + </reaction> + <reaction id="RXN0__45__5257" name="RXN0-5257" reversible="true"> + <listOfReactants> + <speciesReference species="DIHYDROXY__45__ACETONE__45__PHOSPHATE_CCO__45__IN" stoichiometry="1"/> + <speciesReference species="PROTON_CCO__45__IN" stoichiometry="2"/> + <speciesReference species="E__45__" stoichiometry="2"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="GLYCEROL__45__3P_CCO__45__IN" stoichiometry="1"/> + </listOfProducts> + </reaction> + <reaction id="RXN0__45__5254" name="RXN0-5254" reversible="false"> + <listOfReactants> + <speciesReference species="Menaquinones" stoichiometry="1"/> + <speciesReference species="PROTON_CCO__45__IN" stoichiometry="2"/> + <speciesReference species="E__45__" stoichiometry="2"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="Menaquinols" stoichiometry="1"/> + </listOfProducts> + </reaction> + <reaction id="RXN0__45__5244" name="RXN0-5244" reversible="false"> + <listOfReactants> + <speciesReference species="Ubiquinones" stoichiometry="1"/> + <speciesReference species="PROTON_CCO__45__IN" stoichiometry="2"/> + <speciesReference species="E__45__" stoichiometry="2"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="Ubiquinols" stoichiometry="1"/> + </listOfProducts> + </reaction> + <reaction id="RXN0__45__5259" name="RXN0-5259" reversible="false"> + <listOfReactants> + <speciesReference species="ETR__45__Quinones" stoichiometry="1"/> + <speciesReference species="PROTON_CCO__45__IN" stoichiometry="2"/> + <speciesReference species="E__45__" stoichiometry="2"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="ETR__45__Quinols" stoichiometry="1"/> + </listOfProducts> + </reaction> + <reaction id="RXN0__45__5248" name="RXN0-5248" reversible="true"> + <listOfReactants> + <speciesReference species="NAD_CCO__45__IN" stoichiometry="1"/> + <speciesReference species="PROTON_CCO__45__IN" stoichiometry="1"/> + <speciesReference species="E__45__" stoichiometry="2"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="NADH_CCO__45__IN" stoichiometry="1"/> + </listOfProducts> + </reaction> + <reaction id="RXN__45__12647" name="RXN-12647" reversible="false"> + <listOfReactants> + <speciesReference species="Oxidized__45__Plastocyanins_CCO__45__IN" stoichiometry="1"/> + <speciesReference species="E__45__" stoichiometry="1"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="Plastocyanin__45__Reduced_CCO__45__IN" stoichiometry="1"/> + </listOfProducts> + </reaction> + <reaction id="RXN__45__12648" name="RXN-12648" reversible="false"> + <listOfReactants> + <speciesReference species="PLASTOQUINONE" stoichiometry="1"/> + <speciesReference species="E__45__" stoichiometry="2"/> + <speciesReference species="PROTON_CCO__45__IN" stoichiometry="2"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="PLASTOQUINOL__45__1" stoichiometry="1"/> + </listOfProducts> + </reaction> + <reaction id="RXN0__45__5245" name="RXN0-5245" reversible="true"> + <listOfReactants> + <speciesReference species="FUM_CCO__45__IN" stoichiometry="1"/> + <speciesReference species="PROTON_CCO__45__IN" stoichiometry="2"/> + <speciesReference species="E__45__" stoichiometry="2"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="SUC_CCO__45__IN" stoichiometry="1"/> + </listOfProducts> + </reaction> + <reaction id="RXN__45__7101" name="RXN-7101" reversible="false"> + <listOfReactants> + <speciesReference species="BCCP__45__biotin__45__monomers" stoichiometry="2"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="BCCP__45__dimers" stoichiometry="1"/> + </listOfProducts> + </reaction> + <reaction id="DISULFOXRED__45__RXN" name="DISULFOXRED-RXN" reversible="true"> + <listOfReactants> + <speciesReference species="Protein__45__Red__45__Disulfides" stoichiometry="1"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="Protein__45__Ox__45__Disulfides" stoichiometry="1"/> + </listOfProducts> + </reaction> + </listOfReactions> + </model> +</sbml>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result.txt Mon Jun 11 08:43:56 2018 -0400 @@ -0,0 +1,57 @@ +Reading draft network from /tmp/tmppEicel/files/000/dataset_1.dat ... done. +Reading seeds from /tmp/tmppEicel/files/000/dataset_3.dat ... done. +Reading targets from /tmp/tmppEicel/files/000/dataset_4.dat ... done. + +Checking draftnet for unproducible targets ... done. + 51 unproducible targets: + "GLY" + "GLT" + "MET" + "CIT" + "ILE" + "HIS" + "CPD__45__13814" + "ARACHIDONIC_ACID" + "CPD__45__8119" + "LINOLEIC_ACID" + "CPD__45__14292" + "CPD__45__8117" + "GLYCOLLATE" + "CPD__45__9245" + "GLYCERATE" + "GLUTATHIONE" + "SER" + "LYS" + "CPD__45__8120" + "_4__45__AMINO__45__BUTYRATE" + "GLN" + "L__45__ASPARTATE" + "CYS" + "TYR" + "SUC" + "ARG" + "THR" + "GLC" + "ASN" + "ARACHIDIC_ACID" + "STEARIC_ACID" + "OLEATE__45__CPD" + "MANNITOL" + "VAL" + "CPD__45__7836" + "_5Z8Z11Z14Z17Z__45__EICOSAPENTAENOATE" + "PALMITATE" + "THREO__45__DS__45__ISO__45__CITRATE" + "GLYCEROL" + "D__45__ALANINE" + "PHE" + "L__45__ORNITHINE" + "PRO" + "LINOLENIC_ACID" + "CPD__45__9247" + "HOMO__45__SER" + "CPD__45__8121" + "L__45__ALPHA__45__ALANINE" + "LEU" + "DOCOSANOATE" + "TRP"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seeds.sbml Mon Jun 11 08:43:56 2018 -0400 @@ -0,0 +1,57 @@ +<?xml version="1.0" encoding="UTF-8"?> +<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1"> +<model id="EsiCyc"> + <listOfCompartments> + <compartment id="CCO__45__EXTRACELLULAR"/> + <compartment id="CCO__45__CYTOSOL"/> + <compartment id="CCO__45__OUT"/> + </listOfCompartments> + <listOfSpecies> + <species id="Acceptor" compartment="CCO__45__CYTOSOL"/> + <species id="ACP" compartment="CCO__45__CYTOSOL"/> + <species id="ADP" compartment="CCO__45__CYTOSOL"/> + <species id="AMMONIA" compartment="CCO__45__CYTOSOL"/> + <species id="AMP" compartment="CCO__45__CYTOSOL"/> + <species id="ATP" compartment="CCO__45__CYTOSOL"/> + <species id="BIOTIN" compartment="CCO__45__CYTOSOL"/> + <species id="CA__43__2" compartment="CCO__45__CYTOSOL"/> + <species id="CARBON__45__DIOXIDE" compartment="CCO__45__CYTOSOL"/> + <species id="CDP__45__12921" compartment="CCO__45__CYTOSOL"/> + <species id="CL__45__" compartment="CCO__45__CYTOSOL"/> + <species id="CO__45__A" compartment="CCO__45__CYTOSOL"/> + <species id="CPD0__45__1695" compartment="CCO__45__CYTOSOL"/> + <species id="CPD0__45__2394" compartment="CCO__45__CYTOSOL"/> + <species id="CPD__45__3" compartment="CCO__45__CYTOSOL"/> + <species id="CPD__45__315" compartment="CCO__45__CYTOSOL"/> + <species id="CU__43__" compartment="CCO__45__CYTOSOL"/> + <species id="CU__43__2" compartment="CCO__45__CYTOSOL"/> + <species id="Donor__45__H2" compartment="CCO__45__CYTOSOL"/> + <species id="EDTA" compartment="CCO__45__CYTOSOL"/> + <species id="GDP" compartment="CCO__45__CYTOSOL"/> + <species id="GTP" compartment="CCO__45__CYTOSOL"/> + <species id="HYDROGEN__45__PEROXIDE" compartment="CCO__45__CYTOSOL"/> + <species id="K__43__" compartment="CCO__45__CYTOSOL"/> + + <species id="MG__43__2" compartment="CCO__45__CYTOSOL"/> + <species id="NA__43__" compartment="CCO__45__CYTOSOL"/> + <species id="NAD__45__P__45__OR__45__NOP" compartment="CCO__45__CYTOSOL"/> + <species id="NAD" compartment="CCO__45__CYTOSOL"/> + <species id="NADH__45__P__45__OR__45__NOP" compartment="CCO__45__CYTOSOL"/> + <species id="NADH" compartment="CCO__45__CYTOSOL"/> + <species id="NADP" compartment="CCO__45__CYTOSOL"/> + <species id="NADPH" compartment="CCO__45__CYTOSOL"/> + <species id="NITRATE" compartment="CCO__45__CYTOSOL"/> + <species id="OXYGEN__45__MOLECULE" compartment="CCO__45__CYTOSOL"/> + <species id="Pi" compartment="CCO__45__CYTOSOL"/> + <species id="PPI" compartment="CCO__45__CYTOSOL"/> + <species id="PROTON" compartment="CCO__45__CYTOSOL"/> + <species id="SULFATE" compartment="CCO__45__CYTOSOL"/> + <species id="THIAMINE" compartment="CCO__45__CYTOSOL"/> + <species id="UDP" compartment="CCO__45__CYTOSOL"/> + <species id="Vitamins__45__B12" compartment="CCO__45__CYTOSOL"/> + <species id="COB__45__I__45__ALAMIN" compartment="CCO__45__CYTOSOL"/> + <species id="WATER" compartment="CCO__45__CYTOSOL"/> + <species id="ZN__43__2" compartment="CCO__45__CYTOSOL"/> + </listOfSpecies> + </model> +</sbml>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/targets.sbml Mon Jun 11 08:43:56 2018 -0400 @@ -0,0 +1,64 @@ +<?xml version="1.0" encoding="UTF-8"?> +<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1"> + <model id="EsiCyc"> + <listOfCompartments> + <compartment id="CCO__45__EXTRACELLULAR"/> + <compartment id="CCO__45__CYTOSOL"/> + <compartment id="CCO__45__OUT"/> + </listOfCompartments> + <listOfSpecies> + <species id="_4__45__AMINO__45__BUTYRATE" compartment="CCO__45__CYTOSOL"/> + <species id="_5Z8Z11Z14Z17Z__45__EICOSAPENTAENOATE" compartment="CCO__45__CYTOSOL"/> + <species id="AMMONIUM" compartment="CCO__45__CYTOSOL"/> + <species id="ARACHIDIC_ACID" compartment="CCO__45__CYTOSOL"/> + <species id="ARACHIDONIC_ACID" compartment="CCO__45__CYTOSOL"/> + <species id="ARG" compartment="CCO__45__CYTOSOL"/> + <species id="ASN" compartment="CCO__45__CYTOSOL"/> + <species id="CIT" compartment="CCO__45__CYTOSOL"/> + <species id="CPD__45__13814" compartment="CCO__45__CYTOSOL"/> + <species id="CPD__45__14292" compartment="CCO__45__CYTOSOL"/> + <species id="CPD__45__7836" compartment="CCO__45__CYTOSOL"/> + <species id="CPD__45__8117" compartment="CCO__45__CYTOSOL"/> + <species id="CPD__45__8119" compartment="CCO__45__CYTOSOL"/> + <species id="CPD__45__8120" compartment="CCO__45__CYTOSOL"/> + <species id="CPD__45__8121" compartment="CCO__45__CYTOSOL"/> + <species id="CPD__45__9245" compartment="CCO__45__CYTOSOL"/> + <species id="CPD__45__9247" compartment="CCO__45__CYTOSOL"/> + <species id="CYS" compartment="CCO__45__CYTOSOL"/> + <species id="D__45__ALANINE" compartment="CCO__45__CYTOSOL"/> + <species id="DOCOSANOATE" compartment="CCO__45__CYTOSOL"/> + <species id="GLC" compartment="CCO__45__CYTOSOL"/> + <species id="GLN" compartment="CCO__45__CYTOSOL"/> + <species id="GLT" compartment="CCO__45__CYTOSOL"/> + <species id="GLUTATHIONE" compartment="CCO__45__CYTOSOL"/> + <species id="GLY" compartment="CCO__45__CYTOSOL"/> + <species id="GLYCERATE" compartment="CCO__45__CYTOSOL"/> + <species id="GLYCEROL" compartment="CCO__45__CYTOSOL"/> + <species id="GLYCOLLATE" compartment="CCO__45__CYTOSOL"/> + <species id="HIS" compartment="CCO__45__CYTOSOL"/> + <species id="HOMO__45__SER" compartment="CCO__45__CYTOSOL"/> + <species id="ILE" compartment="CCO__45__CYTOSOL"/> + <species id="L__45__ALPHA__45__ALANINE" compartment="CCO__45__CYTOSOL"/> + <species id="L__45__ASPARTATE" compartment="CCO__45__CYTOSOL"/> + <species id="L__45__ORNITHINE" compartment="CCO__45__CYTOSOL"/> + <species id="LEU" compartment="CCO__45__CYTOSOL"/> + <species id="LINOLEIC_ACID" compartment="CCO__45__CYTOSOL"/> + <species id="LINOLENIC_ACID" compartment="CCO__45__CYTOSOL"/> + <species id="LYS" compartment="CCO__45__CYTOSOL"/> + <species id="MANNITOL" compartment="CCO__45__CYTOSOL"/> + <species id="MET" compartment="CCO__45__CYTOSOL"/> + <species id="OLEATE__45__CPD" compartment="CCO__45__CYTOSOL"/> + <species id="PALMITATE" compartment="CCO__45__CYTOSOL"/> + <species id="PHE" compartment="CCO__45__CYTOSOL"/> + <species id="PRO" compartment="CCO__45__CYTOSOL"/> + <species id="SER" compartment="CCO__45__CYTOSOL"/> + <species id="STEARIC_ACID" compartment="CCO__45__CYTOSOL"/> + <species id="SUC" compartment="CCO__45__CYTOSOL"/> + <species id="THR" compartment="CCO__45__CYTOSOL"/> + <species id="THREO__45__DS__45__ISO__45__CITRATE" compartment="CCO__45__CYTOSOL"/> + <species id="TRP" compartment="CCO__45__CYTOSOL"/> + <species id="TYR" compartment="CCO__45__CYTOSOL"/> + <species id="VAL" compartment="CCO__45__CYTOSOL"/> + </listOfSpecies> + </model> +</sbml>