<tool id="rpranker" name="Rank Pathways" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <description>Rank heterologous pathways according to their global score</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>
    <stdio>
        <regex match="WARNING" level="warning" />
        <regex match="ERROR" level="fatal" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
        #for $file in $pathway_collection
            ln -s $file $file.name &&
        #end for

        python -m rptools.rprank
        --pathways

        #for $file in $pathway_collection
            $file.name
        #end for

        > '$sorted_pathways'
    ]]></command>
    <inputs>
        <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" />
    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical outputs are produced with default parameters  -->
            <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>
    <help><![CDATA[
Rank Pathways
================

Sort a list of pathways according to their global score.	  

Input
-----

Required:

* **Pathways**\ : List of pathway files (rpSBML)

Output
------

* **Ranked Pathways**\ : Sorted names and scores of pathways

Project Links
------------------

* `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rprank>`_

License
-------

* `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_

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

* Thomas Duigou

    ]]></help>
    <creator>
        <person givenName="Joan" familyName="Hérisson" email="joan.herisson@univ-evry.fr" identifier="https://orcid.org/0000-0001-9741-0847" />
    </creator>
</tool>