Mercurial > repos > tduigou > rpfba
changeset 1:c554f15279fe draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
| author | tduigou |
|---|---|
| date | Thu, 10 Feb 2022 11:36:24 +0000 |
| parents | fb5efc456dcc |
| children | 6f0d786299ca |
| files | rpfba.xml test-data/e_coli_iML1515.sbml test-data/iCN718.xml.gz test-data/rp_001_0001_with_fba.xml |
| diffstat | 4 files changed, 101 insertions(+), 159897 deletions(-) [+] |
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--- a/rpfba.xml Tue Nov 23 16:34:29 2021 +0000 +++ b/rpfba.xml Thu Feb 10 11:36:24 2022 +0000 @@ -1,80 +1,120 @@ -<tool id="rpFBA" name="FBA" version="5.9.2"> +<tool id="rpfba" name="FBA" version="@TOOL_VERSION@" profile="19.09"> <description>Perform FBA for the RetroPath2.0 heterologous pathways</description> - <requirements> - <requirement type="package" version="5.9.2">rptools</requirement> + <macros> + <token name="@TOOL_VERSION@">5.12.1</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> </requirements> <stdio> <regex match="WARNING" level="warning" /> - <regex match="ERROR" level="fatal" /> + <regex match="ERROR" level="fatal" /> </stdio> <command detect_errors="exit_code"><![CDATA[ - python -m rptools.rpfba '$pathway' '$model' '$compartment_id' '$pathway_with_fba' - #if str($adv.merge) == "true": - --merge - #end if - --objective_rxn_id '$input_sim_type.objective_rxn_id' - --sim '$input_sim_type.sim_type' + python -m rptools.rpfba '$pathway' '$model' '$compartment_id' '$pathway_with_fba' + #if str($adv.merge) == "true": + --merge + #end if + --objective_rxn_id '$objective_rxn_id' + --sim '$input_sim_type.sim_type' #if str($adv.ignore_orphan_species) == "true": --ignore_orphan_species - #end if - --log '$adv.log_level' - #if str($input_sim_type.sim_type)=="fraction" - --biomass_rxn_id '$input_sim_type.biomass_rxn_id' - --fraction_of '$input_sim_type.fraction_of' - #end if - #if str($input_sim_type.sim_type)=="pfba" - --biomass_rxn_id '' - --fraction_of '$input_sim_type.fraction_of' - #end if - #if str($input_sim_type.sim_type)=="fba" - --biomass_rxn_id '' - --fraction_of 0.0 - #end if + #end if + --log "error" + #if str($input_sim_type.sim_type)=="fba" + --fraction_of 0.0 + #else + --fraction_of '$input_sim_type.fraction_of' + #end if + --biomass_rxn_id '$biomass_rxn_id' ]]></command> <inputs> - <param name="pathway" type="data" format="xml" label="Pathway (rpSBML)" /> - <param name="model" type="data" format="xml" label="Model (SBML)" /> - <param name="compartment_id" type="text" label="SBML compartment ID" value="MNXC3" /> + <param name="pathway" type="data" format="sbml" label="Pathway (rpSBML)" /> + <param name="model" type="data" format="sbml" label="Model (SBML)" /> + <param name="compartment_id" type="text" label="SBML compartment ID" value="c" > + <validator type="empty_field" message="A compartment ID is required"/> + </param> + <param name="objective_rxn_id" type="text" value="rxn_target" label="reaction ID to optimise" > + <validator type="empty_field" message="Reaction ID is required"/> + </param> + <param name="biomass_rxn_id" type="text" label="biomass reaction ID" value="" > + <validator type="empty_field" message="Biomass reaction ID is required"/> + </param> <conditional name="input_sim_type"> - <param name="sim_type" type="select" label="Constraint based simulation type"> + <param name="sim_type" type="select" label="Constraint based simulation type"> <option value="fraction" selected="true">Fraction of Reaction</option> <option value="fba" >FBA</option> <option value="pfba">Parsimonious FBA</option> </param> - <when value="fraction"> - <param name="fraction_of" type="float" value="0.75" label="Fraction of the optimum" /> - <param name="objective_rxn_id" type="text" value="rxn_target" label="reaction ID to optimise" /> - <param name="biomass_rxn_id" type="text" value="biomass" label="biomass reaction ID" /> - </when> - <when value="pfba"> - <param name="fraction_of" type="float" value="0.95" label="Fraction of the optimum" /> - <param name="objective_rxn_id" type="text" value="rxn_target" label="reaction ID to optimise" /> - </when> - <when value="fba"> - <param name="objective_rxn_id" type="text" value="rxn_target" label="reaction ID to optimise" /> - </when> + <when value="fraction"> + <param name="fraction_of" type="float" value="0.75" min="0" max="1.0" label="Fraction of the optimum" /> + </when> + <when value="pfba"> + <param name="fraction_of" type="float" value="0.95" min="0" max="1.0" label="Fraction of the optimum" /> + </when> + <when value="fba"> + </when> </conditional> - <section name="adv" title="Advanced Options" expanded="false"> - <param name="merge" type="boolean" label="Output the merged model?" checked="false" display="checkboxes" /> - <param name="ignore_orphan_species" type="boolean" label="Ignore metabolites that are only consumed or produced?" checked="true" /> - <param name="log_level" type="select" label="Log level"> - <option value="debug" >debug</option> - <option value="info" >info</option> - <option value="warning" >warning</option> - <option value="error" selected="true">error</option> - <option value="critical" >critical</option> - </param> - </section> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="merge" type="boolean" label="Output the merged model?" checked="false" display="checkboxes" /> + <param name="ignore_orphan_species" type="boolean" label="Ignore metabolites that are only consumed or produced?" checked="true" /> + </section> </inputs> <outputs> - <data name="pathway_with_fba" format="xml" label="${tool.name}(${input_sim_type.sim_type}) - ${pathway.name}" /> + <data name="pathway_with_fba" format="sbml" label="${tool.name}(${input_sim_type.sim_type}) - ${pathway.name}" /> </outputs> <tests> <test> - <!-- test 1: check if identical outputs are produced with default parameters --> + <!-- test 1: check if identical outputs are produced with R_BIOMASS__3 biomass name ID and BiGG model (iCN718) --> + <param name="pathway" value="rp_001_0001.xml" /> + <param name="model" value="iCN718.xml.gz" /> + <param name="biomass_rxn_id" value="R_BIOMASS__3" /> + <output name="pathway_with_fba" > + <assert_contents> + <is_valid_xml /> + <!--check fba_fraction value--> + <has_text text="5.54302" /> + <!--check fba_biomass value--> + <has_text text="1.31359" /> + <has_n_lines n="408" /> + </assert_contents> + </output> + </test> + <test> + <!-- test 2: check if identical outputs are produced with R_BIOMASS__3 biomass name ID and BiGG model (iCN718) and sim_type=fba--> <param name="pathway" value="rp_001_0001.xml" /> - <param name="model" value="e_coli_iML1515.sbml" /> - <output name="pathway_with_fba" file="rp_001_0001_with_fba.xml" ftype="xml" compare="diff" sort="true"/> + <param name="model" value="iCN718.xml.gz" /> + <param name="biomass_rxn_id" value="R_BIOMASS__3" /> + <conditional name="input_sim_type"> + <param name="sim_type" value="fba"/> + </conditional> + <output name="pathway_with_fba" > + <assert_contents> + <is_valid_xml /> + <!--check fba_fba value--> + <has_text text="16.47058" /> + <not_has_text text="fba_fraction" /> + <has_n_lines n="392" /> + </assert_contents> + </output> + </test> + <test> + <!-- test 3: check if identical outputs are produced with R_DM_biomass_c biomass name ID and BiGG model (iCN718) and sim_type=pfba--> + <param name="pathway" value="rp_001_0001.xml" /> + <param name="model" value="iCN718.xml.gz" /> + <param name="biomass_rxn_id" value="R_DM_biomass_c" /> + <conditional name="input_sim_type"> + <param name="sim_type" value="pfba"/> + </conditional> + <output name="pathway_with_fba" > + <assert_contents> + <is_valid_xml /> + <!--check fba_pfba value--> + <has_text text="2623.54248" /> + <not_has_text text="fba_fraction" /> + <has_n_lines n="392" /> + </assert_contents> + </output> </test> </tests> <help><![CDATA[ @@ -98,8 +138,8 @@ - the species is only consumed or produced with the heterologue pathway. .. image:: https://raw.githubusercontent.com/Galaxy-SynBioCAD/rpFBA/standalone/galaxy/img/rpFBA.png - :width: 60 % - :align: center + :width: 60 % + :align: center | @@ -136,7 +176,7 @@ Version ---------- -5.9.2 +5.12.1 Authors ------- @@ -152,33 +192,10 @@ Acknowledgments --------------- - * Thomas Duigou ]]></help> <citations> - <citation type="bibtex"> -@article{hucka2016sbml, - title={SBML Level 3 package: Groups, Version 1 Release 1}, - author={Hucka, Michael and Smith, Lucian P}, - journal={Journal of integrative bioinformatics}, - volume={13}, - number={3}, - pages={8--29}, - year={2016}, - publisher={De Gruyter} -} - </citation> - <citation type="bibtex"> -@article{ebrahim2013cobrapy, - title={COBRApy: COnstraints-based reconstruction and analysis for python}, - author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R}, - journal={BMC systems biology}, - volume={7}, - number={1}, - pages={74}, - year={2013}, - publisher={Springer} -} - </citation> + <citation type="doi">10.1186/1752-0509-7-74</citation> + <citation type="doi">10.1515/jib-2016-290 </citation> </citations> -</tool> \ No newline at end of file +</tool>
--- a/test-data/e_coli_iML1515.sbml Tue Nov 23 16:34:29 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,159405 +0,0 @@ -<?xml version='1.0' encoding='utf-8' standalone='no'?> -<!-- Created by ModelPolisher version 1.7 on 2018-17-24 at 23:17:12 PST with JSBML version 1.2. --> -<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" fbc:required="false" groups:required="false" level="3" sboTerm="SBO:0000624" version="1" -xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> - <model extentUnits="substance" fbc:strict="true" id="iML1515" metaid="iML1515" name="Escherichia coli str. K-12 substr. MG1655" substanceUnits="substance" timeUnits="time"> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#iML1515"> - <bqbiol:hasTaxon> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/taxonomy/511145" /> - </rdf:Bag> - </bqbiol:hasTaxon> - <bqmodel:is> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.model/iML1515" /> - </rdf:Bag> - </bqmodel:is> - <bqmodel:isDescribedBy> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/pubmed/29020004" /> - </rdf:Bag> - </bqmodel:isDescribedBy> - </rdf:Description> - </rdf:RDF> - </annotation> - <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" fbc:activeObjective="obj_biomass"> - <fbc:objective fbc:id="obj_biomass" fbc:type="maximize"> - <fbc:listOfFluxObjectives> - <fbc:fluxObjective fbc:coefficient="1" fbc:reaction="biomass" /> - 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