# HG changeset patch
# User tduigou
# Date 1668789315 0
# Node ID acc86f8830f7be48537b1f6093223d8e226a9fa3
# Parent  3af8a501f1b50cb3362443af0c6b409ddf53f827
planemo upload commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty

diff -r 3af8a501f1b5 -r acc86f8830f7 rpscore.xml
--- a/rpscore.xml	Thu Feb 10 12:11:57 2022 +0000
+++ b/rpscore.xml	Fri Nov 18 16:35:15 2022 +0000
@@ -1,7 +1,8 @@
-<tool id="rpscore" name="Score Pathway" version="@TOOL_VERSION@" profile="19.09">
-    <description>Computes a global score for a heterologous pathway.</description>
+<tool id="rpscore" name="Score Pathway" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
+    <description>Computes a global score for a heterologous pathway</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>
@@ -12,55 +13,47 @@
         --log "error"
     ]]></command>
     <inputs>
-        <param name="pathway" type="data" format="xml" label="Pathway (rpSBML)" />
+        <param name="pathway" type="data" format="sbml" label="Pathway (rpSBML)" />
         <section name="adv" title="Advanced Options" expanded="false">
-            <param name="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" />
+            <param argument="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" />
         </section>
     </inputs>
     <outputs>
-        <data name="scored_pathway" format="xml" label="${tool.name} - ${pathway.name}" />
+        <data name="scored_pathway" format="sbml" label="${tool.name} - ${pathway.name}" />
     </outputs>
     <tests>
         <test>
-        <!-- test 1: check if identical outputs are produced with default parameters  -->
+        <!-- check if identical outputs are produced with default parameters  -->
             <param name="pathway" value="pathway.xml" />
-            <output name="scored_pathway" file="scored_pathway.xml" ftype="xml" compare="diff" sort="true"/>
+            <output name="scored_pathway" file="scored_pathway.xml" ftype="sbml" compare="diff" sort="true"/>
         </test>
     </tests>
     <help><![CDATA[
-rpscore
-=========
-
+Score Pathway
+==============
 
 Computes a global score for a heterologous pathway. The score is calculated from a learning process based on reaction rules score, flux balance analysis and thermodynamics metrics, and the number of reactions in the pathway.
 
-
 Input
 -----
 
 Required:
 
-* **infile**\ : (string) Pathway file (rpSBML) with scores (rules, FBA, Thermo...)
-* **outfile**\ : (string) Path to write pathway file (rpSBML) with global score
+* **Pathway (rpSBML)**\ : pathway file (rpSBML) with scores (rules, FBA, Thermo...).
+* **Scored pathway**\ : pathway file (rpSBML) with global score.
 
 Advanced options:
 
-* **--no_of_rxns_thres**\ :(integer, default: 10) Number of reactions above which pathway are not scored (too long)
-
-Version
-----------
-
-5.12.1
-
-Authors
--------
-
-* **Jean-Loup Faulon**
-* **Joan Hérisson**
+* **--no_of_rxns_thres**\ :(integer, default: 10) Number of reactions above which pathway are not scored
 
 Acknowledgments
 ---------------
 
 * Thomas Duigou
+
     ]]></help>
+    <creator>
+        <person givenName="Jean-Loup" familyName="Faulon" email="jean-loup.faulon@inrae.fr" identifier="http://orcid.org/0000-0003-4274-2953" />
+        <person givenName="Joan" familyName="Hérisson" email="Joan.Herisson@univ-evry.fr" identifier="http://orcid.org/0000-0001-9741-0847" />
+    </creator>
 </tool>
\ No newline at end of file