--- a/rpranker.xml	Fri Oct 21 14:57:59 2022 +0000
+++ b/rpranker.xml	Mon Oct 24 10:14:47 2022 +0000
@@ -14,13 +14,12 @@
     <command detect_errors="exit_code"><![CDATA[
         python -m rptools.rprank
         --pathways
-        #for $input in $pathway_collection
-            '$input'
-        #end for
+        #set files = '" "'.join([str($file) for $file in $pathway_collection])
+        "${files}"
         > '$sorted_pathways'
     ]]></command>
     <inputs>
-        <param name="pathway_collection" type="data_collection" format="sbml" collection_type="list" label="Pathways" />
+        <param name="pathway_collection" type="data" format="sbml" multiple="true" min="2" label="Pathways" />
     </inputs>
     <outputs>
         <data name="sorted_pathways" format="csv" label="Ranked Pathways" />
@@ -28,19 +27,7 @@
     <tests>
         <test>
         <!-- test 1: check if identical outputs are produced with default parameters  -->
-            <param name="pathway_collection" >
-                <collection type="list">
-                    <element name="rp_003_0261" value="rp_003_0261.xml" />
-                    <element name="rp_003_0131" value="rp_003_0131.xml" />
-                    <element name="rp_003_0001" value="rp_003_0001.xml" />
-                    <element name="rp_002_0021" value="rp_002_0021.xml" />
-                    <element name="rp_002_0011" value="rp_002_0011.xml" />
-                    <element name="rp_002_0001" value="rp_002_0001.xml" />
-                    <element name="rp_001_0011" value="rp_001_0011.xml" />
-                    <element name="rp_001_0006" value="rp_001_0006.xml" />
-                    <element name="rp_001_0001" value="rp_001_0001.xml" />
-                </collection>
-            </param>
+            <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" />
         </test>
     </tests>