<tool id="rpscore" name="Score Pathway" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <description>Computes a global score for a heterologous pathway</description>
    <macros>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@TOOL_VERSION@">6.0.1</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 '$adv.no_of_rxns_thres'
        --log "error"
    ]]></command>
    <inputs>
        <param name="pathway" type="data" format="sbml" label="Pathway (rpSBML)" />
        <section name="adv" title="Advanced Options" expanded="false">
            <param argument="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" />
        </section>
    </inputs>
    <outputs>
        <data name="scored_pathway" format="sbml" label="${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

Acknowledgments
---------------

* Thomas Duigou

    ]]></help>
    <creator>
        <person givenName="Jean-Loup" familyName="Faulon" email="jean-loup.faulon@inrae.fr" identifier="http://orcid.org/0000-0003-4274-2953" />
        <person givenName="Joan" familyName="Hérisson" email="Joan.Herisson@univ-evry.fr" identifier="http://orcid.org/0000-0001-9741-0847" />
    </creator>
</tool>