annotate galaxy/tools/LC-MSMS/XSeekerPreparator.xml @ 1:1c2ce385b84e draft

" master branch Updating"

<tool id="xseeker_pwepawatow"
      name="XSeeker Preparator"
      version="1.0.0"
      profile="20.04"
>
    <description>Prepare RData file from CAMERA to be visualized in XSeeker</description>
    
    <edam_operations>
        <edam_operation>operation_1812</edam_operation>
        <edam_operation>operation_0335</edam_operation>
    </edam_operations>
    
    <requirements>
        <requirement type="set_environment">R_SCRIPT_PATH</requirement>
        <!-- 
        <requirement type="package" version="4.0.0">R</requirement>
        -->
        <requirement type="package" version="4.0.0">R</requirement>
        <requirement type="package" version="1.6.6">optparse</requirement>
        <requirement type="package" version="3.10.2">xcms</requirement>
        <requirement type="package" version="1.2.1">blob</requirement>
        <requirement type="package" version="0.9.4">fst</requirement>
        <requirement type="package" version="1.4.0">stringr</requirement>
        <requirement type="package">DBModelR</requirement>
    </requirements>
    
    <stdio>

        <exit_code 
            range="1"
            level="warning"
            description="Selected samples have no data associated to them."
        />

        <exit_code 
            range="2"
            level="warning"
            description="Some samples have no data associated to them."
        />

    </stdio>

    <version_command>
        R_SCRIPT_PATH '$__tool_directory__/XSeekerPreparator.R' -v
    </version_command>

    <command>
        <![CDATA[

            R_SCRIPT_PATH '$__tool_directory__/XSeekerPreparator.R'

                -P

                --input '$input'
                --output '$output'

                #if $samples.selected
                    --samples '${",".join(samples.selected)}'
                #end if

                #if $database.archetypes
                    --archetype '${",".join($database.archetypes)}'
                #end if

                #if $database.base.kind == "tabular"
                    --compounds-csv '${database.base.tabular}'
                #else if $database.base.kind == "sql"
                    --database '${database.base.sql}'
                #end if

                #if $database.models.kind == "default"
                    --models '${base_config}'
                #else
                    --models '${database.models.url}'
                #end if

        ]]>

    </command>

    <inputs>
        <param 
            name="input"
            type="data"
            multiple="false"
            label="Rdata to prepare"
            optional="false"
            format="rdata"
        >
        </param>
        <section name="samples" title="Samples Options" expanded="false">
            <param 
                name="selected"
                type="data"
                multiple="true"
                label="Samples to visualize"
                optional="true"
                format="mzml"
            >
            </param>
        </section>

        <section name="database" title="Database Options" expanded="false">
            <param
                name="archetypes"
                type="select"
                multiple="true"
                label="Molecule family (for database's compounds enrichment)"
            >
                <option value="G" selected="true">General</option>
                <option value="H">Halogenates</option>
            </param>

            <conditional name="base">
                <param name="kind" type="select" label="File containing compound's type">
                    <option value="none" selected="true">None (deafult)</option>
                    <option value="tabular">tabular</option>
                    <option value="sql">sql</option>
                </param>
                <when value="tabular">
                    <param
                        name="tabular"
                        type="data"
                        multiple="true"
                        label="Tabular file containing compound to use in XSeeker"
                        optional="true"
                        format="tabular"
                    >
                    </param>
                </when>
                <when value="sql">
                    <param
                        name="sql"
                        type="data"
                        multiple="true"
                        label="SQL file containing compound to use in XSeeker"
                        optional="true"
                        format="sql"
                    >
                    </param>
                </when>
            </conditional>

            <conditional name="models">
                <param name="kind" type="select" label="How is the database's model defined">
                    <option value="default" selected="true">Default (regular XSeeker Database)</option>
                    <option value="url">Download model file</option>
                    <option value="git">Get versionned model file</option>
                </param>
                <when value="url">
                    <param name="url" type="text" format="url" label="File URL"/>
                </when>
                <when value="git">
                    <param name="url" type="text" format="url" label="Repo URL"/>
                </when>
            </conditional>
        </section>
    </inputs>


    <outputs>
        <data format="xseeker.sqlite" name="output" />
    </outputs>

    <configfiles>
        <configfile name="base_config">
tryCatch({
    DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER"))
}, error=function(e) {
    stop("Please, install DBModelR before you source this file.")
})

list(
    adduct=DBModelR::ModelDefinition(
        table="adduct",
        fields=list(
            name="TEXT",
            mass="FLOAT",
            charge="INTEGER",
            multi="INTEGER",
            formula_add="TEXT",
            formula_ded="TEXT",
            sign="TEXT",
            oidscore="INTEGER",
            quasi="INTEGER",
            ips="FLOAT"
        )
    ),
    cluster=DBModelR::ModelDefinition(
        table="cluster",
        fields=list(
            clusterID="INTEGER",
            formula="TEXT",
            annotation="TEXT",
            coeff="FLOAT",
            r_squared="FLOAT",
            charge="INTEGER",
            mean_rt="FLOAT",
            score="FLOAT",
            deviation="FLOAT",
            status="TEXT",
            adduct="TEXT",
            curent_group="INTEGER",
            pc_group="INTEGER",
            align_group="INTEGER",
            xcms_group="INTEGER"
        ),
        one=list("sample", "compound")
    ),
    compound=DBModelR::ModelDefinition(
        table="compound",
        fields=list(
            name="TEXT",
            common_name="TEXT",
            formula="TEXT",
            charge="INTEGER",
            date="TEXT",
            mz="FLOAT"
        )
    ),
    feature=DBModelR::ModelDefinition(
        table="feature",
        fields=list(
            featureID="INTEGER",
            mz="FLOAT",
            mz_min="FLOAT",
            mz_max="FLOAT",
            rt="FLOAT",
            rt_min="FLOAT",
            rt_max="FLOAT",
            int_o="FLOAT",
            int_b="FLOAT",
            max_o="FLOAT",
            iso="TEXT",
            abundance="FLOAT"
        ),
        one=list("cluster")
    ),
    instrument=DBModelR::ModelDefinition(
        table="instrument",
        fields=list(
            model="TEXT",
            manufacturer="TEXT",
            analyzer="TEXT",
            detector_type="TEXT",
            ion_source="TEXT"
        )
    ),
    instrument_config=DBModelR::ModelDefinition(
        table="instrument_config",
        fields=list(
            resolution="TEXT",
            agc_target="TEXT",
            maximum_IT="TEXT",
            number_of_scan_range="TEXT",
            scan_range="TEXT",
            version="TEXT"
        )
    ),
    project=DBModelR::ModelDefinition(
        table="project",
        fields=list(
            name="TEXT",
            comment="TEXT"
        ),
        one=list("sample")
    ),
    sample=DBModelR::ModelDefinition(
        table="sample",
        fields=list(
            name="TEXT",
            path="TEXT",
            polarity="TEXT",
            kind="TEXT", ## rdata or mxml or enriched_rdata
            raw="BLOB"
        ),
        one=list(
            "peak_picking_parameters",
            "pairing_parameters",
            "alignmenmt_parameters",
            "camera_parameters",
            "instrument",
            "instrument_config",
            "software",
            "smol_xcms_set"
        )
    ),
    smol_xcms_set=DBModelR::ModelDefinition(
        table="smol_xcms_set",
        fields=list(
            raw="BLOB"
        )
    ),
    software=DBModelR::ModelDefinition(
        table="software",
        fields=list(
            name="TEXT",
            version="TEXT"
        )
    ),
    peak_picking_parameters=DBModelR::ModelDefinition(
        table="peak_picking_parameters",
        fields=list(
            ppm="FLOAT",
            peakwidth="TEXT",
            snthresh="TEXT",
            prefilterStep="TEXT",
            prefilterLevel="TEXT",
            mzdiff="TEXT",
            fitgauss="TEXT",
            noise="TEXT",
            mzCenterFun="TEXT",
            integrate="INTEGER",
            firstBaselineCheck="TEXT",
            snthreshIsoROIs="TEXT",
            maxCharge="INTEGER",
            maxIso="INTEGER",
            mzIntervalExtension="TEXT"
        )
    ),
    alignmenmt_parameters=DBModelR::ModelDefinition(
        table="alignmenmt_parameters",
        fields=list(
            binSize="TEXT",
            centerSample="TEXT",
            response="TEXT",
            distFun="TEXT",
            gapInit="TEXT",
            gapExtend="TEXT",
            factorDiag="TEXT",
            factorGap="TEXT",
            localAlignment="INTEGER",
            initPenalty="TEXT",
            bw="TEXT",
            minFraction="TEXT",
            minSamples="TEXT",
            maxFeatures="TEXT"
        )
    )
)
        </configfile>
    </configfiles>
</tool>