<macros>
    <token name="@TOOL_VERSION@">0.8.0</token>

    <xml name="creator">
        <creator>
            <person
                givenName="Maksym"
                familyName="Skoryk"
                url="https://github.com/maximskorik"
                identifier="0000-0003-2056-8018" />
            <person
                givenName="Helge"
                familyName="Hecht"
                url="https://github.com/hechth"
                identifier="0000-0001-6744-996X" />
            <organization
                url="https://www.recetox.muni.cz/"
                email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
                name="RECETOX MUNI" />
        </creator>
    </xml>

    <xml name="edam">
        <xrefs>
            <xref type="bio.tools">spec2vec</xref>
        </xrefs>
    </xml>

    <xml name="input_param">
        <conditional name="scores">
            <param name="use_scores" label="Use Scores Object" type="boolean" truevalue="TRUE" falsevalue="FALSE"
                   checked="false"/>
            <when value="TRUE">
                <param label="Scores object" name="scores_in" type="data" format="json"
                    help="Scores objects calculated previously using one of the matchms similarity tools." />
            </when>
            <when value="FALSE">
                <param label="Queries spectra" name="queries" type="data" format="msp,mgf"
                    help="Query mass spectra to match against references."/>
                <param label="Reference spectra" name="references" type="data" format="msp,mgf"
                    help="Reference mass spectra to match against as library."/>
            </when>
        </conditional>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1371/journal.pcbi.1008724</citation>
        </citations>
    </xml>

<token name="@init_scores@">
from matchms.importing import load_from_msp, scores_from_json
from matchms import Scores
#if $scores.use_scores
scores = scores_from_json("$scores_in")
#else
scores = Scores(references=list(load_from_msp("$references")), queries=list(load_from_msp("$queries")), is_symmetric=False)
#end if
</token>
        
<token name="@init_logger@">
from matchms import set_matchms_logger_level
set_matchms_logger_level("WARNING")
</token>

<token name="@init_model@">
import json
from spec2vec.serialization.model_importing import load_weights, Word2VecLight
    
with open("${model_metadata}", "r", encoding="utf-8") as f:
    model: dict = json.load(f)
    del (model["mapfile_path"])
    
weights = load_weights("${model_weights}", model["__weights_format"])
model = Word2VecLight(model, weights)
</token>
</macros>