<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" />
        <regex match="Continuing without sink molecule" source="both" level="warning"
            description="The sink file is empty or not found" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
        TMPDIR="\${TMPDIR:-.}/rr_cache" &&
        mkdir -p "\${TMPDIR}" &&
        #if str($sink.cond) == 'empty'
            echo '"Name","InChI"' > empty_sink.csv &&
            #set sinkfile='empty_sink.csv'
        #else
            #set sinkfile=$sink.sinkfile
        #end if

        python -m rptools.rpcompletion
            '$rp2_pathways'
            $sinkfile
            '$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'
            --chemical-space '$adv.chemical_space'
            #if $adv.cofile
                --cofactors '$adv.cofile'
            #end if
            #if not $sink.error_codes
                --silent
            #end if
            --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" />
        <conditional name="sink">
            <param name="cond" type="select" label="Empty sink">
                <option value="provided" selected="True">Provided</option>
                <option value="empty">Empty</option>
            </param>
            <when value="provided">
                <param name="sinkfile" type="data" format="csv" label="Sink File"
                    help="Sink file which comprises all compounds that are considered as granted in your system." />
                <param name="error_codes" type="boolean" checked="true"
                    label="Return error codes" />
            </when>
            <when value="empty">
                <param name="error_codes" type="boolean" checked="false"
                    label="Return error codes" />
            </when>
        </conditional>
        <section name="adv" title="Advanced Options" expanded="false">
            <param argument="max_subpaths_filter" type="integer" value="10" min="0"
                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." />
            <param name="chemical_space" type="select" label="Chemical space">
                <option value="mnx4.4" selected="True">mnx4.4</option>
                <option value="mnx3.1">mnx3.1</option>
            </param>
            <param name="cofile" type="data" format="txt,tsv,tabular" optional="True"
                label="Cofactor file" />
        </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" />
            <conditional name="sink">
                <param name="cond" value="provided" />
                <param name="sinkfile" value="2-sink.csv" />
            </conditional>
            <output_collection name="pathways" type="list" count="10" />
        </test>
    </tests>
    <help><![CDATA[
rpCompletion
============

Completes mono-component reactions output by `RetroPath2.0 <https://www.doi.org/10.1016/j.ymben.2017.12.002>`_ 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.

Output
------

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