--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rpscore.xml	Tue Mar 28 12:07:54 2023 +0000
@@ -0,0 +1,50 @@
+<tool id="rptools_rpscore" name="Score Pathway" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
+    <description>Computes a global score for a heterologous pathway</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        python -m rptools.rpscore '$pathway' '$scored_pathway'
+        --no_of_rxns_thres '$adv.no_of_rxns_thres'
+        --log "error"
+    ]]></command>
+    <inputs>
+        <param name="pathway" type="data" format="sbml" label="Pathway (rpSBML)" />
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param argument="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="scored_pathway" format="sbml" label="${tool.name} - ${pathway.name}" />
+    </outputs>
+    <tests>
+        <test>
+        <!-- check if identical outputs are produced with default parameters  -->
+            <param name="pathway" value="pathway.xml" />
+            <output name="scored_pathway" file="scored_pathway.xml" ftype="sbml" compare="diff" sort="true"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Score Pathway
+==============
+
+Computes a global score for a heterologous pathway. The score is calculated from a learning process based on reaction rules score, flux balance analysis and thermodynamics metrics, and the number of reactions in the pathway.
+
+Input
+-----
+
+Required:
+
+* **Pathway (rpSBML)**\ : pathway file (rpSBML) with scores (rules, FBA, Thermo...).
+* **Scored pathway**\ : pathway file (rpSBML) with global score.
+
+Advanced options:
+
+* **--no_of_rxns_thres**\ :(integer, default: 10) Number of reactions above which pathway are not scored
+    ]]></help>
+    <expand macro="creator"/>
+    <citations>
+        <citation type="doi">10.1038/s41467-022-32661-x</citation>
+    </citations>
+</tool>