Mercurial > repos > iuc > rpfba
changeset 1:19be43e96154 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba commit c44f1622de870d9c869b65b4605cc8a22c33076a"
| author | iuc |
|---|---|
| date | Tue, 01 Feb 2022 13:55:41 +0000 |
| parents | 12689dfad4d1 |
| children | 79094fd479b2 |
| files | rpfba.xml |
| diffstat | 1 files changed, 13 insertions(+), 25 deletions(-) [+] |
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--- a/rpfba.xml Mon Jan 17 11:55:50 2022 +0000 +++ b/rpfba.xml Tue Feb 01 13:55:41 2022 +0000 @@ -1,7 +1,7 @@ <tool id="rpfba" name="Flux balance analysis" version="@TOOL_VERSION@" profile="19.09"> <description>for the RetroPath2.0 heterologous pathways</description> <macros> - <token name="@TOOL_VERSION@">5.11.1</token> + <token name="@TOOL_VERSION@">5.12.1</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> @@ -15,31 +15,31 @@ #if str($adv.merge) == "true": --merge #end if - --objective_rxn_id '$input_sim_type.objective_rxn_id' + --objective_rxn_id '$objective_rxn_id' --sim '$input_sim_type.sim_type' #if str($adv.ignore_orphan_species) == "true": --ignore_orphan_species #end if --log "error" - #if str($input_sim_type.sim_type)=="fraction" - --biomass_rxn_id '$biomass_rxn_id' + #if str($input_sim_type.sim_type)=="fba" + --fraction_of 0.0 + #else --fraction_of '$input_sim_type.fraction_of' #end if - #if str($input_sim_type.sim_type)=="pfba" --biomass_rxn_id '$biomass_rxn_id' - --fraction_of '$input_sim_type.fraction_of' - #end if - #if str($input_sim_type.sim_type)=="fba" - --biomass_rxn_id '$biomass_rxn_id' - --fraction_of 0.0 - #end if ]]></command> <inputs> <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="MNXC3" > + <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"> <option value="fraction" selected="true">Fraction of Reaction</option> @@ -48,25 +48,13 @@ </param> <when value="fraction"> <param name="fraction_of" type="float" value="0.75" min="0" max="1.0" label="Fraction of the optimum" /> - <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> </when> <when value="pfba"> <param name="fraction_of" type="float" value="0.95" min="0" max="1.0" label="Fraction of the optimum" /> - <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> </when> <when value="fba"> - <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> </when> </conditional> - <param name="biomass_rxn_id" type="text" value="biomass" label="biomass reaction ID" > - <validator type="empty_field" message="Biomass reaction ID is required"/> - </param> <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" /> @@ -188,7 +176,7 @@ Version ---------- -5.11.1 +5.12.1 Authors -------