# HG changeset patch
# User iuc
# Date 1643723741 0
# Node ID 19be43e96154040ab8fb89fbfa5ee51c7b6b3d07
# Parent  12689dfad4d1c31d75073f7ffc0315625441140e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba commit c44f1622de870d9c869b65b4605cc8a22c33076a"

diff -r 12689dfad4d1 -r 19be43e96154 rpfba.xml
--- 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
 -------