<tool id="ramclustr_xcms" name="RAMClustR (XCMS)" version="@TOOL_VERSION@+galaxy1">
    <macros>
        <import>ramclustr_macros.xml</import>
    </macros>

    <requirements>
        <container type="docker">recetox/ramclustr:1.1.0-recetox0</container>
    </requirements>

    <inputs>
        <param name="input_xcms" label="input_xcms" type="data" format="rdata.xcms.fillpeaks" help=": containing grouped feature data for clustering by ramclustR" />
        <expand macro="parameters_required" />
        <expand macro="parameters_optional_xcms" />
        <expand macro="parameters_optional_metadata" />
    </inputs>

    <command detect_errors="aggressive"><![CDATA[
        Rscript
            -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
            -e 'x <- ramclustr_xcms(
                input_xcms = "$input_xcms",
                sr = $required.sr,
                deep_split = $required.deepSplit,
                block_size = $required.blocksize,
                mult = $required.mult,
                hmax = $required.hmax,
                collapse = $required.collapse,
                use_pheno = $required.usePheno,
                qc_inj_range = $required.qc_inj_range,
                normalize = "$required.normalize",
                min_module_size = $required.minModuleSize,
                linkage = "$required.linkage",
                mzdec = $required.mzdec,
                cor_method = "$required.cor_method",
                rt_only_low_n = $required.rt_only_low_n,
                replace_zeros = $required.replace_zeros,
                #if $optional.st
                    st = $optional.st,
                #end if
                #if $optional.maxt
                    maxt = $optional.maxt,
                #end if
                #if $optional.fftempdir
                    fftempdir = $optional.fftempdir,
                #end if
                #if $metadata.batch_order_qc
                    metadata_file = "${metadata.batch_order_qc}",
                #end if
                )'
            -e 'store_output(x, "$result", "$method_metadata", $required.merge_msp, "$spec_abundance")'
    ]]>
    </command>

    <outputs>
        <data label="${tool.name} on ${on_string}" name="result" format="RData" />
        <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" />
        <data label="Metadata for ${tool.name} on ${on_string}" name="method_metadata" format="txt"/>
        <expand macro="output_msp"/>
    </outputs>

    <tests>
        <test>
            <param name="input_xcms" value="xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
            <output name="result" file="ramclustObj_xcms_1.rdata" ftype="RData" compare="sim_size" delta="100"/>
            <output_collection name="mass_spectra" type="list">
                <element name="fill" file="fill_xcms_1.msp" ftype="msp" checksum="md5$d53ed06d6f888a88ff321f833e29bb47"/>
            </output_collection>
            <output name="method_metadata" file="metadata_xcms_1.txt" ftype="txt" checksum="md5$81db28b08860988e3966f585b0f44b0f"/>
            <output name="spec_abundance" file="spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/>
        </test>
        <test>
            <param name="input_xcms" value="xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
            <param name="batch_order_qc" value="sample_metadata_xcms_2.csv" ftype="csv" />
            <output name="result" file="ramclustObj_xcms_2.rdata" ftype="RData" compare="sim_size" delta="200"/>
            <output_collection name="mass_spectra" type="list">
                <element name="fill" file="fill_xcms_2.msp" ftype="msp" lines_diff="10"/>
            </output_collection>
            <output name="method_metadata" file="metadata_xcms_2.txt" ftype="txt" checksum="md5$286e4aa53c38c99e92202584d7407406"/>
            <output name="spec_abundance" file="spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
        </test>
    </tests>

    <help>
    Documentation
        For documentation on the tool see https://github.com/cbroeckl/RAMClustR/blob/master/vignettes/RAMClustR.Rmd

    Upstream Tools
        +-------+----------------------+----------------------+------------+
        | Name  | Output File          | Format               | Parameter  |
        +=======+======================+======================+============+
        | xcms  | xset.fillPeaks.RData | rdata.xcms.fillpeaks | xcmsObj    |
        +-------+----------------------+----------------------+------------+

        The tool takes an **xcmsSet** object as input and extracts all relevant information.

    Downstream Tools
        +---------+--------------+----------------------+
        | Name    | Output File  | Format               |
        +=========+==============+======================+
        | matchMS | Mass Spectra | collection (tgz/msp) |
        +---------+--------------+----------------------+

    @GENERAL_HELP@
    </help>

    <expand macro="citations" />
</tool>