From 98b094d55435a34538cd014caf2380cef7485676 Mon Sep 17 00:00:00 2001
From: GuillaumeG <guipagui@gmail.com>
Date: Fri, 1 Dec 2023 15:27:46 +0100
Subject: [PATCH] Update `rptools` 6.5.0 (#159)

* feat(tools): rptools, update rptools

* docs(tools): rptools, update rpfba
---
 tools/rptools/macros.xml | 2 +-
 tools/rptools/rpfba.xml  | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/tools/rptools/macros.xml b/tools/rptools/macros.xml
index 9ac9d279..36127303 100644
--- a/tools/rptools/macros.xml
+++ b/tools/rptools/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">6.4.1</token>
+    <token name="@TOOL_VERSION@">6.5.0</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
diff --git a/tools/rptools/rpfba.xml b/tools/rptools/rpfba.xml
index 93a86921..17493460 100644
--- a/tools/rptools/rpfba.xml
+++ b/tools/rptools/rpfba.xml
@@ -15,8 +15,8 @@
             #end if
                 --objective_rxn_id '$objective_rxn_id'
                 --sim '$input_sim_type.sim_type'
-            #if str($adv.ignore_orphan_species) == "true":
-                --ignore_orphan_species
+            #if str($adv.with_orphan_species) == "true":
+                --with_orphan_species
             #end if
                 --log "error"
             #if str($input_sim_type.sim_type)=="fba"
@@ -55,7 +55,7 @@
         </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="with_orphan_species" type="boolean" label="Add metabolites that are only consumed or produced?" checked="false" />
         </section>
     </inputs>
     <outputs>
@@ -165,7 +165,7 @@ Optional:
 Advanced options:
 
 * **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
+* **With Orphan Species?**\ : (boolean, default=False) add metabolites that are only consumed or produced
     ]]></help>
     <expand macro="creator"/>
     <citations>