# HG changeset patch
# User tduigou
# Date 1644492984 0
# Node ID c554f15279fe8a375c5acd1a0b9695cb96ffba74
# Parent  fb5efc456dcc39bbaf36b22792d77e5141b9b9fa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"

diff -r fb5efc456dcc -r c554f15279fe rpfba.xml
--- 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>
diff -r fb5efc456dcc -r c554f15279fe test-data/e_coli_iML1515.sbml
--- 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" />
-        </fbc:listOfFluxObjectives>
-      </fbc:objective>
-    </fbc:listOfObjectives>
-    <fbc:listOfGeneProducts xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2">
-      <fbc:geneProduct fbc:id="G_b2551" fbc:label="b2551" metaid="G_b2551">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#G_b2551">
-              <bqbiol:is>
-                <rdf:Bag>
-                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P0A825" />
-                </rdf:Bag>
-              </bqbiol:is>
-              <bqbiol:isEncodedBy>
-                <rdf:Bag>
-                  <rdf:li rdf:resource="http://identifiers.org/asap/ABE-0008389" />
-                  <rdf:li rdf:resource="http://identifiers.org/ecogene/EG10408" />
-                  <rdf:li rdf:resource="http://identifiers.org/ncbigene/947022" />
-                  <rdf:li rdf:resource="http://identifiers.org/ncbigi/gi:16130476" />
-                </rdf:Bag>
-              </bqbiol:isEncodedBy>
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-          </rdf:RDF>
-        </annotation>
-      </fbc:geneProduct>
-      <fbc:geneProduct fbc:id="G_b0870" fbc:label="b0870" metaid="G_b0870">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#G_b0870">
-              <bqbiol:is>
-                <rdf:Bag>
-                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P75823" />
-                </rdf:Bag>
-              </bqbiol:is>
-              <bqbiol:isEncodedBy>
-                <rdf:Bag>
-                  <rdf:li rdf:resource="http://identifiers.org/asap/ABE-0002954" />
-                  <rdf:li rdf:resource="http://identifiers.org/ecogene/EG13690" />
-                  <rdf:li rdf:resource="http://identifiers.org/ncbigene/944955" />
-                  <rdf:li rdf:resource="http://identifiers.org/ncbigi/gi:16128838" />
-                </rdf:Bag>
-              </bqbiol:isEncodedBy>
-            </rdf:Description>
-          </rdf:RDF>
-        </annotation>
-      </fbc:geneProduct>
-      <fbc:geneProduct fbc:id="G_b3368" fbc:label="b3368" metaid="G_b3368">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#G_b3368">
-              <bqbiol:is>
-                <rdf:Bag>
-                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P0AEA8" />
-                </rdf:Bag>
-              </bqbiol:is>
-              <bqbiol:isEncodedBy>
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-                  <rdf:li rdf:resource="http://identifiers.org/ecogene/EG10188" />
-                  <rdf:li rdf:resource="http://identifiers.org/ncbigene/947880" />
-                  <rdf:li rdf:resource="http://identifiers.org/ncbigi/gi:16131246" />
-                </rdf:Bag>
-              </bqbiol:isEncodedBy>
-            </rdf:Description>
-          </rdf:RDF>
-        </annotation>
-      </fbc:geneProduct>
-      <fbc:geneProduct fbc:id="G_b2436" fbc:label="b2436" metaid="G_b2436">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#G_b2436">
-              <bqbiol:is>
-                <rdf:Bag>
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-                </rdf:Bag>
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-                  <rdf:li rdf:resource="http://identifiers.org/ecogene/EG12189" />
-                  <rdf:li rdf:resource="http://identifiers.org/ncbigene/946908" />
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-        </annotation>
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-        <annotation>
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-            <rdf:Description rdf:about="#G_b3500">
-              <bqbiol:is>
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-                </rdf:Bag>
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-                  <rdf:li rdf:resource="http://identifiers.org/ncbigene/948014" />
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-        <annotation>
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-                  <rdf:li rdf:resource="http://identifiers.org/ncbigene/945556" />
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-                </rdf:Bag>
-              </bqbiol:isEncodedBy>
-            </rdf:Description>
-          </rdf:RDF>
-        </annotation>
-      </fbc:geneProduct>
-      <fbc:geneProduct fbc:id="G_b2979" fbc:label="b2979" metaid="G_b2979">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#G_b2979">
-              <bqbiol:is>
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diff -r fb5efc456dcc -r c554f15279fe test-data/iCN718.xml.gz
Binary file test-data/iCN718.xml.gz has changed
diff -r fb5efc456dcc -r c554f15279fe test-data/rp_001_0001_with_fba.xml
--- a/test-data/rp_001_0001_with_fba.xml	Tue Nov 23 16:34:29 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-        <groups:listOfMembers>
-          <groups:member groups:idRef="MNXM11"/>
-          <groups:member groups:idRef="MNXM132"/>
-          <groups:member groups:idRef="MNXM83"/>
-        </groups:listOfMembers>
-      </groups:group>
-      <groups:group metaid="a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189" groups:id="rp_fba_ignored_species" groups:kind="collection">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:BRSynth rdf:about="#a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-        <groups:listOfMembers>
-          <groups:member groups:idRef="MNXM24"/>
-          <groups:member groups:idRef="MNXM8975"/>
-        </groups:listOfMembers>
-      </groups:group>
-    </groups:listOfGroups>
-  </model>
-</sbml>