--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rpscore.xml	Thu Feb 10 12:17:38 2022 +0000
@@ -0,0 +1,66 @@
+<tool id="rpscore" name="Score Pathway" version="@TOOL_VERSION@" profile="19.09">
+    <description>Computes a global score for a heterologous pathway.</description>
+    <macros>
+        <token name="@TOOL_VERSION@">5.12.1</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python -m rptools.rpscore '$pathway' '$scored_pathway'
+        --no_of_rxns_thres '$adv.no_of_rxns_thres'
+        --log "error"
+    ]]></command>
+    <inputs>
+        <param name="pathway" type="data" format="xml" label="Pathway (rpSBML)" />
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param name="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="scored_pathway" format="xml" label="${tool.name} - ${pathway.name}" />
+    </outputs>
+    <tests>
+        <test>
+        <!-- test 1: check if identical outputs are produced with default parameters  -->
+            <param name="pathway" value="pathway.xml" />
+            <output name="scored_pathway" file="scored_pathway.xml" ftype="xml" compare="diff" sort="true"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+rpscore
+=========
+
+
+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:
+
+* **infile**\ : (string) Pathway file (rpSBML) with scores (rules, FBA, Thermo...)
+* **outfile**\ : (string) Path to write pathway file (rpSBML) with global score
+
+Advanced options:
+
+* **--no_of_rxns_thres**\ :(integer, default: 10) Number of reactions above which pathway are not scored (too long)
+
+Version
+----------
+
+5.12.1
+
+Authors
+-------
+
+* **Jean-Loup Faulon**
+* **Joan Hérisson**
+
+Acknowledgments
+---------------
+
+* Thomas Duigou
+    ]]></help>
+</tool>
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