# HG changeset patch
# User tduigou
# Date 1760003403 0
# Node ID 1edb49dfa3357a491fbe502fffb963a405f63596
# Parent  f26e7e4a42b7da97baa75c4e844d0a64994c2615
planemo upload for repository https://github.com/brsynth/retropath2_wrapper commit 4f228a8dcee36f8c5282ff3e30f67a87254a2837-dirty

diff -r f26e7e4a42b7 -r 1edb49dfa335 retropath2_wrapper.xml
--- a/retropath2_wrapper.xml	Wed Oct 08 11:10:57 2025 +0000
+++ b/retropath2_wrapper.xml	Thu Oct 09 09:50:03 2025 +0000
@@ -2,7 +2,7 @@
     profile="21.09" license="MIT">
     <description>Build a reaction network from a set of source compounds to a set of sink compounds</description>
     <macros>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <token name="@TOOL_VERSION@">3.5.0</token>
     </macros>
     <requirements>
@@ -10,27 +10,20 @@
     </requirements>
     <stdio>
         <!-- Fatal -->
-        <exit_code range="1" level="fatal" description="Cannot find source-in-sink file" />
         <regex match="It seems that the target product is already in the chassis" source="both"
-            level="fatal" description="It seems that the target product is already in the chassis" />
-        <exit_code range="2" level="fatal"
-            description="Running the RetroPath2.0 Knime program produced an OSError" />
+            level="fatal"
+            description="It seems that the target product is already in the chassis (Exit code: 1)" />
         <regex match="The following error occured" source="both" level="fatal"
-            description="The following error occured" />
-        <exit_code range="3" level="fatal" description="The InChI string is malformed" />
+            description="The following error occured (Exit code: 2)" />
         <regex match="is not a valid InChI notation" source="both" level="fatal"
-            description="is not a valid InChI notation" />
-        <exit_code range="4" level="fatal" description="Sink file is malformed" />
+            description="is not a valid InChI notation (Exit code: 3)" />
         <regex match="The sink file is malformed" source="both" level="fatal"
-            description="The sink file is malformed" />
-        <exit_code range="5" level="fatal" description="Knime installation error" />
+            description="The sink file is malformed (Exit code: 4)" />
         <!-- Warning -->
-        <exit_code range="10" level="warning" description="Source has been found in the sink" />
         <regex match="Source has been found in the sink" source="both" level="warning"
-            description="Source has been found in the sink" />
-        <exit_code range="11" level="warning" description="RetroPath2.0 has found no solution" />
+            description="Source has been found in the sink (Exit code: 10)" />
         <regex match="No solution has been found" source="both" level="warning"
-            description="No solution has been found" />
+            description="No solution has been found (Exit code: 11)" />
     </stdio>
     <command detect_errors="exit_code"><![CDATA[
         #if $sink.emptysink:
@@ -55,11 +48,7 @@
                 --quiet
             #end if
             --msc_timeout '$adv.timeout' &&
-        if compgen -G 'out/*_scope.csv' > /dev/null; then
-            cp out/*_scope.csv '$Reaction_Network';
-        else
-            cp out/results.csv '$Reaction_Network';
-        fi
+        cp out/*_scope.csv "$Reaction_Network" 2>/dev/null || cp out/results.csv "$Reaction_Network"
     ]]></command>
     <inputs>
         <param name="rulesfile" type="data" format="csv,tar" label="Rules File"