--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ramclustr_wrapper.R	Tue Mar 22 16:09:16 2022 +0000
@@ -0,0 +1,174 @@
+store_output <- function(
+    ramclustr_obj,
+    output_merge_msp,
+    output_spec_abundance,
+    msp_file) {
+    RAMClustR::write.msp(ramclustr_obj, one.file = output_merge_msp)
+    write.csv(ramclustr_obj$SpecAbund, file = output_spec_abundance, row.names = TRUE)
+
+    if (!is.null(msp_file)) {
+        exp.name <- ramclustr_obj$ExpDes[[1]][which(row.names(ramclustr_obj$ExpDes[[1]]) == "Experiment"), 1]
+        filename <- paste("spectra/", exp.name, ".msp", sep = "")
+        file.copy(from = filename, to = msp_file, overwrite = TRUE)
+    }
+}
+
+load_experiment_definition <- function(filename) {
+    experiment <- RAMClustR::defineExperiment(csv = filename)
+    return(experiment)
+}
+
+read_metadata <- function(filename) {
+    data <- read.csv(filename, header = TRUE, stringsAsFactors = FALSE)
+
+    if (!"qc" %in% colnames(data)) {
+        if ("sampleType" %in% colnames(data)) {
+            data$qc <- ifelse(data$sampleType == "qc", TRUE, FALSE)
+        }
+    }
+
+    if (!"order" %in% colnames(data)) {
+        if ("injectionOrder" %in% colnames(data)) {
+            names(data)[names(data) == "injectionOrder"] <- "order"
+        }
+    }
+
+    return(data)
+}
+
+ramclustr_xcms <- function(
+    input_xcms,
+    use_pheno,
+    sr,
+    st = NULL,
+    cor_method,
+    maxt,
+    linkage,
+    min_module_size,
+    hmax,
+    deep_split,
+    normalize,
+    metadata_file = NULL,
+    qc_inj_range,
+    block_size,
+    mult,
+    mzdec,
+    rt_only_low_n,
+    replace_zeros,
+    exp_design = NULL
+) {
+    obj <- load(input_xcms)
+
+    batch <- NULL
+    order <- NULL
+    qc <- NULL
+
+    if (!is.null(metadata_file)) {
+        metadata <- read_metadata(metadata_file)
+        batch <- metadata$batch
+        order <- metadata$order
+        qc <- metadata$qc
+    }
+
+    experiment <- NULL
+
+    if (!is.null(exp_design)) {
+        experiment <- load_experiment_definition(exp_design)
+    }
+
+    x <- RAMClustR::ramclustR(
+        xcmsObj = xdata,
+        st = st,
+        maxt = maxt,
+        sr = sr,
+        deepSplit = deep_split,
+        blocksize = block_size,
+        mult = mult,
+        hmax = hmax,
+        usePheno = use_pheno,
+        mspout = FALSE,
+        qc.inj.range = qc_inj_range,
+        normalize = normalize,
+        minModuleSize = min_module_size,
+        linkage = linkage,
+        mzdec = mzdec,
+        cor.method = cor_method,
+        rt.only.low.n = rt_only_low_n,
+        fftempdir = NULL,
+        replace.zeros = replace_zeros,
+        batch = batch,
+        order = order,
+        qc = qc,
+        ExpDes = experiment
+        )
+    return(x)
+}
+
+ramclustr_csv <- function(
+    ms,
+    idmsms,
+    sr,
+    st,
+    cor_method,
+    maxt,
+    linkage,
+    min_module_size,
+    hmax,
+    deep_split,
+    normalize,
+    metadata_file = NULL,
+    qc_inj_range,
+    block_size,
+    mult,
+    mzdec,
+    rt_only_low_n,
+    replace_zeros,
+    exp_design = NULL
+) {
+    if (!file.exists(idmsms))
+        idmsms <- NULL
+
+    batch <- NULL
+    order <- NULL
+    qc <- NULL
+
+    if (!is.null(metadata_file)) {
+        metadata <- read_metadata(metadata_file)
+        batch <- metadata$batch
+        order <- metadata$order
+        qc <- metadata$qc
+    }
+
+    experiment <- NULL
+
+    if (!is.null(exp_design)) {
+        experiment <- load_experiment_definition(exp_design)
+    }
+
+    x <- RAMClustR::ramclustR(
+        ms = ms,
+        idmsms = idmsms,
+        st = st,
+        maxt = maxt,
+        sr = sr,
+        deepSplit = deep_split,
+        blocksize = block_size,
+        mult = mult,
+        hmax = hmax,
+        mspout = FALSE,
+        qc.inj.range = qc_inj_range,
+        normalize = normalize,
+        minModuleSize = min_module_size,
+        linkage = linkage,
+        mzdec = mzdec,
+        cor.method = cor_method,
+        rt.only.low.n = rt_only_low_n,
+        fftempdir = NULL,
+        replace.zeros = replace_zeros,
+        batch = batch,
+        order = order,
+        qc = qc,
+        ExpDes = experiment
+        )
+        return(x)
+}