<tool id="rptools_rpranker" name="Rank Pathways" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <description>Rank heterologous pathways according to their global score</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="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.element_identifier' &&
        #end for

        python -m rptools.rprank
        --pathways

        #for $file in $pathway_collection
            '$file.element_identifier'
        #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"/>
            <output name="sorted_pathways" file="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
    ]]></help>
    <expand macro="creator"/>
    <citations>
        <citation type="doi">10.1038/s41467-022-32661-x</citation>
    </citations>
</tool>