<tool id="MS2snoop" name="MS2 Snoop" version="1.0.0">
    <description>
        Extraction des spectres MS1 et adduits associées + Extraction + 
        nettoyage automatisé des spectres MS2 Extraction des métadonnées
        des fichiers RAW Export en fichier idéalement en JSON
    </description>

    <requirements>
        <requirement type="package">r-base</requirement>
        <requirement type="package">r-optparse</requirement>
    </requirements>

    <command><![CDATA[
Rscript '$__tool_directory__/MS2snoop.R'
    -o $frag_result_txt
    -c $compound_txt
    -f $peaklist_frag_tsv
    -p $peaklist_preco_tsv
    --tolmz $tolmz
    --tolrt $tolrt
    --seuil_ra $seuil_ra
    --mzdecimal $mzdecimal
    --r_threshold $r_threshold
    --min_number_scan $min_number_scan
;
    ]]></command>

    <inputs>
        <param type="data" name="compound_txt" label="compounds_pos.txt" />
        <param type="data" name="peaklist_frag_tsv" label="peaklist_fragments.tsv" />
        <param type="data" name="peaklist_preco_tsv" label="peaklist_precursors.tsv" />
        <param name="tolmz" type="float" value="0.01" label="MZ Tolerence" />
        <param name="tolrt" type="integer" value="20" label="RT Telerence" />
        <param name="seuil_ra" type="float" value="0.05" label="r pearson correlation threshold between precursor and fragment absolute intensity" />
        <param name="mzdecimal" type="integer" value="0" label="nb decimal for mz" />
        <param name="r_threshold" type="float" value="0.85" label="fragment absolute intensity" />
        <param
            name="min_number_scan"
            type="integer"
            value="8"
            label="Present in at least X scan"
            help="fragments are kept if they are found in a minimum number of scans"
        />
    </inputs>
    <outputs>
        <data name="frag_result_txt" format="txt" label="compound_fragments_result.txt" />
    </outputs>
    <tests>
        <test>
            <param name="compound_txt" value="compounds_pos.txt"/>
            <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv"/>
            <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv"/>
            <output name="frag_result_txt" file="compound_fragments_result.txt" />
        </test>
    </tests>
</tool>