--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rpranker.xml	Mon Dec 13 18:19:24 2021 +0000
@@ -0,0 +1,87 @@
+<tool id="rpranker" name="Rank Pathways" version="5.10.0">
+    <description>Rank heterologous pathways according to their global score</description>
+    <requirements>
+        <requirement type="package" version="5.10.0">rptools</requirement>
+    </requirements>
+    <stdio>
+	    <regex match="WARNING" level="warning" />
+		<regex match="ERROR" level="fatal" />
+	</stdio>
+    <command detect_errors="exit_code"><![CDATA[
+        python -m rptools.rprank
+        --pathways
+        #for $input in $pathway_collection
+            '$input'
+        #end for
+        > '$sorted_pathways'
+    ]]></command>
+    <inputs>
+        <param name="pathway_collection" type="data_collection" collection_type="list" label="Pathways" />
+    </inputs>
+    <outputs>
+        <data name="sorted_pathways" format="csv" label="Ranked Pathways" />
+    </outputs>
+    <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>
+            <output name="sorted_pathways" file="lycopene_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.	  
+
+Input
+-----
+
+Required:
+
+* **pathways**\ : (list of string) Paths to pathway (rpSBML) files
+
+Output
+------
+
+* **output**\ : (string) Sorted names and scores of pathways
+
+Project Links
+------------------
+
+* `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rprank>`_
+
+Version
+----------
+
+5.10.0
+
+License
+-------
+
+* `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
+
+Authors
+-------
+
+* **Joan Hérisson**
+
+Acknowledgments
+---------------
+
+* Thomas Duigou
+
+    ]]></help>
+</tool>
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