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

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

    <inputs>
        <expand macro="parameters_csv" />
        <expand macro="parameters_required" />
        <expand macro="parameters_optional_csv" />
        <expand macro="parameters_optional_metadata" />
    </inputs>

    <command detect_errors="aggressive"><![CDATA[
        Rscript
            -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
            -e 'x <- ramclustr_csv(
                ms="$ms_csv.ms",
                idmsms="$ms_csv.idmsms",
                feature_delimiter="$ms_csv.feature_delimiter",
                sample_name_column = $ms_csv.sample_name_column,
                retention_time_column= $ms_csv.retention_time_column,
                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,
                st = $ms_csv.st,
                #if $optional.maxt
                    maxt = $optional.maxt,
                #end if
                #if $optional.fftempdir
                    fftempdir = $optional.fftempdir,
                #end if
                #if $metadata.batch_order_qc
                    metadata = "$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="ms" value="csv_test-input_1_2.csv" ftype="csv"/>
            <param name="sample_name_column" value="1"/>
            <param name="feature_delimiter" value="_"/>
            <param name="retention_time_column" value="2"/>
            <param name="st" value="5.0"/>
            <param name="sr" value="0.5"/>
            <param name="deepSplit" value="False"/>
            <param name="blocksize" value="1000"/>
            <param name="mult" value="1"/>
            <param name="hmax" value="0.3"/>
            <param name="collapse" value="True"/>
            <param name="usePheno" value="True"/>
            <param name="normalize" value="none"/>
            <param name="qc_inj_range" value="20"/>
            <param name="minModuleSize" value="2"/>
            <param name="linkage" value="average"/>
            <param name="mzdec" value="3"/>
            <param name="cor_method" value="pearson"/>
            <param name="rt_only_low_n" value="True"/>
            <param name="replace_zeros" value="True"/>
            <param name="Merge MSP Files" value="True"/>
            <param name="maxt" value="1"/>
            <output name="result" file="ramclustObj_csv_1.rdata"/>
            <output name="spec_abundance" file="spec_abundance_csv_1.csv" ftype="csv"/>
            <output name="method_metadata" file="metadata_csv_1.txt" ftype="txt"/>
            <output_collection name="mass_spectra" type="list">
                <element name="fill" file="spectra_csv_1.msp" ftype="msp"/>
            </output_collection>
        </test>
        <test>
            <param name="ms" value="csv_test-input_1_2.csv" ftype="csv"/>
            <param name="sample_name_column" value="1"/>
            <param name="feature_delimiter" value="_"/>
            <param name="retention_time_column" value="2"/>
            <param name="batch_order_qc" value="sample_metadata_csv_2.csv" ftype="csv" />
            <output name="result" file="ramclustObj_csv_2.rdata"/>
            <output name="spec_abundance" file="spec_abundance_csv_2.csv" ftype="csv"/>
            <output name="method_metadata" file="metadata_csv_2.txt" ftype="txt"/>
            <output_collection name="mass_spectra" type="list">
                <element name="fill" file="spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
            </output_collection>
        </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  |
        +=======+========================+========+============+
        | ???   | Feature Table with MS1 | csv    | ms         |
        +-------+------------------------+--------+------------+
        | ???   | Feature Table with MS2 | csv    | idmsms     |
        +-------+------------------------+--------+------------+

        The tool takes a **csv** table as input which has to fulfill the following requirements

        (1) no more than one sample (or file) name column and one feature name row;
        (2) feature names that contain the mass and retention times, separated by a constant delimiter; and
        (3) features in columns and samples in rows.

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

    @GENERAL_HELP@
    </help>

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