--- a/rpranker.xml	Wed Nov 16 14:54:07 2022 +0000
+++ b/rpranker.xml	Tue Mar 28 12:10:40 2023 +0000
@@ -1,21 +1,25 @@
 <tool id="rptools_rpranker" name="Rank Pathways" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
     <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>
+        <import>macros.xml</import>
     </macros>
-    <requirements>
-        <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
-    </requirements>
+    <expand macro="requirements"/>
     <stdio>
         <regex match="WARNING" level="warning" />
         <regex match="ERROR" level="fatal" />
     </stdio>
     <command detect_errors="exit_code"><![CDATA[
+        #for $file in $pathway_collection
+            ln -s '$file' '$file.element_identifier' &&
+        #end for
+
         python -m rptools.rprank
         --pathways
-        #set files = ' '.join([ '\'%s\'' % $file for $file in $pathway_collection])
-        $files
+
+        #for $file in $pathway_collection
+            '$file.element_identifier'
+        #end for
+
         > '$sorted_pathways'
     ]]></command>
     <inputs>
@@ -27,15 +31,15 @@
     <tests>
         <test>
         <!-- test 1: check if identical outputs are produced with default parameters  -->
-            <param name="pathway_collection" value="rp_003_0261.xml,rp_003_0131.xml,rp_003_0001.xml,rp_002_0021.xml,rp_002_0011.xml,rp_002_0001.xml,rp_001_0011.xml,rp_001_0006.xml,rp_001_0001.xml"/>
-            <output name="sorted_pathways" file="lycopene_ranked_pathways.csv" ftype="csv" compare="diff" sort="true" />
+            <param name="pathway_collection" value="rp_003_0261.xml,rp_003_0131.xml,rp_003_0001.xml"/>
+            <output name="sorted_pathways" file="ranked_pathways.csv" ftype="csv" compare="diff" sort="true" />
         </test>
     </tests>
     <help><![CDATA[
 Rank Pathways
 ================
 
-Sort a list of pathways according to their global score.	  
+Sort a list of pathways according to their global score.
 
 Input
 -----
@@ -48,24 +52,9 @@
 ------
 
 * **Ranked Pathways**\ : Sorted names and scores of pathways
-
-Project Links
-------------------
-
-* `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rprank>`_
-
-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" />
-    </creator>
+    <expand macro="creator"/>
+    <citations>
+        <citation type="doi">10.1038/s41467-022-32661-x</citation>
+    </citations>
 </tool>