<tool id="rptools_rpcompletion" name="Complete Reactions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <description>Completes mono-component reactions output by RetroPath2.0 with the appropriate cofactors</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <stdio>
        <exit_code range="1" level="fatal" description="Could not Xref compartment_id" />
        <exit_code range="2" level="fatal" description="ValueError returned" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
        python -m rptools.rpcompletion
        '$rp2_pathways'
        '$sink'
        '$rp2paths_compounds'
        '$rp2paths_pathways'
        completed_pathways
        --upper_flux_bound '$adv.upper_flux_bound'
        --lower_flux_bound '$adv.lower_flux_bound'
        --max_subpaths_filter '$adv.max_subpaths_filter'
        --cache-dir "\${TMPDIR:-.}"
    ]]></command>
    <inputs>
        <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />
        <param name="rp2paths_compounds" type="data" format="tabular" label="RP2paths compounds" />
        <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" />
        <param name="sink" type="data" format="csv" label="Sink from SBML" />
        <section name="adv" title="Advanced Options" expanded="false">
            <param argument="max_subpaths_filter" type="integer" value="10" min="1" max="1000" label="Max subpaths generated per pathway" help="Maximal number of subpaths to be created per master pathway." />
            <param argument="upper_flux_bound" type="integer" value="10000" min="-10000" max="10000" label="Upper flux bound" help="Upper flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." />
            <param argument="lower_flux_bound" type="integer" value="-10000" min="-10000" max="10000" label="Lower flux bound" help="Lower flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." />
        </section>
    </inputs>
    <outputs>
        <collection name="pathways" type="list" label="${tool.name}">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xml" format="xml" directory="completed_pathways" visible="false" />
        </collection>
    </outputs>
    <tests>
        <test>
        <!-- test 1: check if outputs are represented in an expected number  -->
            <param name="rp2paths_pathways" value="4-rp2paths_pathways.csv" />
            <param name="rp2paths_compounds" value="3-rp2paths_compounds.tsv" />
            <param name="rp2_pathways" value="1-rp2_metnet.csv" />
            <param name="sink" value="2-sink.csv" />
            <output_collection name="pathways" type="list" count="9"/>
        </test>
    </tests>
    <help><![CDATA[
rpCompletion
============

Completes mono-component reactions output by `RetroPath2.0 <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_ with the appropriate cofactors. Creates sub-paths when multiple reaction rules are associated with a single reaction. Input is a single pathways file produced by RP2Paths. It stands on rpCache which store pre-computed data.

Input
-----

Required:

* **RetroPath2.0 metabolic network**: RetroPath2.0 pathways file
* **Sink from SBML**: rpextractsink file containing infos on molecules in the sink
* **RP2paths compounds**: rp2paths compounds file
* **RP2paths pathways**: rp2paths pathways file

Advanced options:

* **Upper flux bound**: (integer, default=9999) Upper flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created.
* **Lower flux bound**: (integer, default=0) Lower flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created.
* **Max subpaths generated per pathway**: (integer, default=10, 0=nofilter) Maximal number of subpaths to be created per master pathway.

Output
------

* **pathways**: SBML completed pathways
    ]]></help>
    <expand macro="creator"/>
    <citations>
        <citation type="doi">10.1038/s41467-022-32661-x</citation>
    </citations>
</tool>