--- a/rpranker.xml	Mon Oct 24 10:14:47 2022 +0000
+++ b/rpranker.xml	Fri Nov 18 16:04:21 2022 +0000
@@ -2,7 +2,7 @@
     <description>Rank heterologous pathways according to their global score</description>
     <macros>
         <token name="@VERSION_SUFFIX@">0</token>
-        <token name="@TOOL_VERSION@">5.13.1</token>
+        <token name="@TOOL_VERSION@">6.0.1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
@@ -12,10 +12,17 @@
         <regex match="ERROR" level="fatal" />
     </stdio>
     <command detect_errors="exit_code"><![CDATA[
+        #for $file in $pathway_collection
+            ln -s $file $file.name &&
+        #end for
+
         python -m rptools.rprank
         --pathways
-        #set files = '" "'.join([str($file) for $file in $pathway_collection])
-        "${files}"
+
+        #for $file in $pathway_collection
+            $file.name
+        #end for
+
         > '$sorted_pathways'
     ]]></command>
     <inputs>

--- a/test-data/lycopene_ranked_pathways.csv	Mon Oct 24 10:14:47 2022 +0000
+++ b/test-data/lycopene_ranked_pathways.csv	Fri Nov 18 16:04:21 2022 +0000
@@ -1,10 +1,10 @@
 #Name,Score
-002_0001,0.9892438888549804
-003_0261,0.9863117098808288
-002_0011,0.9851486444473266
-002_0021,0.9851486444473266
-001_0001,0.9850856959819794
-001_0006,0.9850397169589996
-001_0011,0.9850397169589996
-003_0131,0.980250358581543
-003_0001,0.975385755300522
+rp_002_0001.xml,0.9892438888549804
+rp_003_0261.xml,0.9863117098808288
+rp_002_0011.xml,0.9851486444473266
+rp_002_0021.xml,0.9851486444473266
+rp_001_0001.xml,0.9850856959819794
+rp_001_0006.xml,0.9850397169589996
+rp_001_0011.xml,0.9850397169589996
+rp_003_0131.xml,0.980250358581543
+rp_003_0001.xml,0.975385755300522