<tool id="rpranker" name="Rank Pathways" version="@TOOL_VERSION@">
    <description>Rank heterologous pathways according to their global score</description>
    <macros>
        <token name="@TOOL_VERSION@">5.12.1</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[
        python -m rptools.rprank
        --pathways
        #for $input in $pathway_collection
            '$input'
        #end for
        > '$sorted_pathways'
    ]]></command>
    <inputs>
        <param name="pathway_collection" type="data_collection" format="xml" 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
----------

5.12.1

License
-------

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

Authors
-------

* **Joan Hérisson**

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

* Thomas Duigou

    ]]></help>
</tool>