Mercurial > repos > tduigou > rpfba

changeset 2:6f0d786299ca draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
author tduigou
date Fri, 18 Nov 2022 16:14:30 +0000
parents c554f15279fe
children
files rpfba.xml
diffstat 1 files changed, 25 insertions(+), 32 deletions(-) [+]
line wrap: on
line diff
--- a/rpfba.xml	Thu Feb 10 11:36:24 2022 +0000
+++ b/rpfba.xml	Fri Nov 18 16:14:30 2022 +0000
@@ -1,7 +1,8 @@
-<tool id="rpfba" name="FBA" version="@TOOL_VERSION@" profile="19.09">
-    <description>Perform FBA for the RetroPath2.0 heterologous pathways</description>
+<tool id="rpfba" name="Flux balance analysis" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
+    <description>for the RetroPath2.0 heterologous pathways</description>
     <macros>
-        <token name="@TOOL_VERSION@">5.12.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@TOOL_VERSION@">6.0.1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
@@ -34,10 +35,10 @@
         <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" >
+        <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="" >
+        <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">
@@ -66,7 +67,7 @@
     <tests>
         <test>
         <!-- 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="pathway" value="rp_001_0001_rpfba_in.xml" />
             <param name="model" value="iCN718.xml.gz" />
             <param name="biomass_rxn_id" value="R_BIOMASS__3" />
             <output name="pathway_with_fba" >
@@ -82,7 +83,7 @@
         </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="pathway" value="rp_001_0001_rpfba_in.xml" />
             <param name="model" value="iCN718.xml.gz" />
             <param name="biomass_rxn_id" value="R_BIOMASS__3" />
             <conditional name="input_sim_type">
@@ -100,7 +101,7 @@
         </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="pathway" value="rp_001_0001_rpfba_in.xml" />
             <param name="model" value="iCN718.xml.gz" />
             <param name="biomass_rxn_id" value="R_DM_biomass_c" />
             <conditional name="input_sim_type">
@@ -150,22 +151,21 @@
 
 Required:
 
+* **Pathway (rpSBML)**\ : SBML file that contains an heterologous pathway
+* **Model (SBML)**\ : GEM SBML model file
+* **Biomass reaction ID**\ : (string) biomass reaction ID that will be restricted in the "fraction" simulation type. This parameter is ignored for "fba" and "pfba"
 
-* **pathway_file**\ : (string) SBML file that contains an heterologous pathway
-* **model_filel**\ : (string) Path to the GEM SBML model
-* **compartment_id**\ : (string) Model compartment id (e.g. 'c' or 'MNXC3')
-* **outfile**\ : (string) Path to the output file
+Optional:
+
+* **SBML compartment ID**\ : (string, default='c') Model compartment id (e.g. 'c' or 'MNXC3')
+* **reaction ID to optimise**\ : (string, default=rxn_target) reaction ID to optimise. This parameters is required in all simulation type
+* **Constraint based simulation type**\ : (string, default=Fraction of Reaction) The type of constraint based modelling method. Valid options include: Fraction of Reaction, FBA, Parsimonious FBA.
+* **Fraction of the optimum**\ : (float, default=0.75) Portion of the maximal flux used to set the maximal and minimal bounds for the source reaction of the "fraction" simulation type.
 
 Advanced options:
 
-
-* **--sim**\ : (string, default=fraction) Valid options include: fraction, fba, pfba. The type of constraint based modelling method
-* **--biomass_rxn_id**\ : (string, default=biomass) biomass reaction ID that will be restricted in the "fraction" simulation type. This parameter is ignored for "fba" and "pfba"
-* **--objective_rxn_id**\ : (string, default=rxn_target) reaction ID to optimise. This parameters is required in all simulation type
-* **--fraction_of**\ : (float, default=0.75) Portion of the maximal flux used to set the maximal and minimal bounds for the source reaction of the "fraction" simulation type
-* **--merge**\ : (boolean, default=False) output the full merged model instead of heterologous pathway only
-* **--ignore_orphan_species**\ : (boolean, default=True) ignore metabolites that are only consumed or produced
-* **--log**: (string, default=error) Set the log level, choices are 'debug', 'info', 'warning', 'error', 'critical'
+* **Output the merged model?**\ : (boolean, default=False) output the full merged model instead of heterologous pathway only
+* **Ignore Orphan Species?**\ : (boolean, default=True) ignore metabolites that are only consumed or produced
 
 
 Project Links
@@ -173,27 +173,20 @@
 
 * `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rpfba>`_
 
-Version
-----------
-
-5.12.1
-
-Authors
--------
-
-* **Melchior du Lac**
-* **Joan Hérisson**
-
 License
 -------
 
-`MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
+* `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
 
 Acknowledgments
 ---------------
 
 * Thomas Duigou
     ]]></help>
+    <creator>
+        <person givenName="Joan" familyName="Hérisson" email="joan.herisson@univ-evry.fr" identifier="https://orcid.org/0000-0001-9741-0847" />
+        <person givenName="Melchior" familyName="du Lac" identifier="https://orcid.org/0000-0002-9984-4689" />
+    </creator>
     <citations>
         <citation type="doi">10.1186/1752-0509-7-74</citation>
         <citation type="doi">10.1515/jib-2016-290 </citation>