--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ramclustr_wrapper.R	Wed Jul 28 08:42:02 2021 +0000
@@ -0,0 +1,164 @@
+store_output <- function(
+    ramclustr_obj,
+    output_filename,
+    output_method_metadata,
+    output_merge_msp,
+    output_spec_abundance) {
+    save(ramclustr_obj, file = output_filename)
+    RAMClustR::write.methods(ramclustr_obj, output_method_metadata)
+    RAMClustR::write.msp(ramclustr_obj, one.file = output_merge_msp)
+    write.csv(ramclustr_obj$SpecAbund, file = output_spec_abundance, row.names = TRUE)
+}
+
+read_metadata <- function(filename) {
+    data <- read.csv(filename, header = TRUE, stringsAsFactors = FALSE)
+
+    if (!"qc" %in% colnames(data)) {
+        if ("sampleType" %in% colnames(data)) {
+            data$qc <- ifelse(data$sampleType == "qc", TRUE, FALSE)
+        }
+    }
+
+    if (!"order" %in% colnames(data)) {
+        if ("injectionOrder" %in% colnames(data)) {
+            names(data)[names(data) == "injectionOrder"] <- "order"
+        }
+    }
+
+    return(data)
+}
+
+ramclustr_xcms <- function(
+    input_xcms,
+    sr,
+    deep_split,
+    block_size,
+    mult,
+    hmax,
+    collapse,
+    use_pheno,
+    qc_inj_range,
+    normalize,
+    min_module_size,
+    linkage,
+    mzdec,
+    cor_method,
+    rt_only_low_n,
+    replace_zeros,
+    st = NULL,
+    maxt = NULL,
+    fftempdir = NULL,
+    metadata_file = NULL
+) {
+    obj <- load(input_xcms)
+
+    batch <- NULL
+    order <- NULL
+    qc <- NULL
+
+    if (!is.null(metadata_file)) {
+        metadata <- read_metadata(metadata_file)
+        batch <- metadata$batch
+        order <- metadata$order
+        qc <- metadata$qc
+    }
+
+    x <- RAMClustR::ramclustR(
+        xcmsObj = xdata,
+        st = st,
+        maxt = maxt,
+        sr = sr,
+        deepSplit = deep_split,
+        blocksize = block_size,
+        mult = mult,
+        hmax = hmax,
+        collapse = collapse,
+        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 = fftempdir,
+        replace.zeros = replace_zeros,
+        batch = batch,
+        order = order,
+        qc = qc
+        )
+    return(x)
+}
+
+ramclustr_csv <- function(
+    ms,
+    idmsms,
+    sample_name_column,
+    feature_delimiter,
+    retention_time_column,
+    sr,
+    deep_split,
+    block_size,
+    mult,
+    hmax,
+    collapse,
+    use_pheno,
+    qc_inj_range,
+    normalize,
+    min_module_size,
+    linkage,
+    mzdec,
+    cor_method,
+    rt_only_low_n,
+    replace_zeros,
+    st = NULL,
+    maxt = NULL,
+    fftempdir = NULL,
+    metadata_file = 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
+    }
+
+    x <- RAMClustR::ramclustR(
+        ms = ms,
+        idmsms = idmsms,
+        featdelim = feature_delimiter,
+        timepos = retention_time_column,
+        sampNameCol = sample_name_column,
+        st = st,
+        maxt = maxt,
+        sr = sr,
+        deepSplit = deep_split,
+        blocksize = block_size,
+        mult = mult,
+        hmax = hmax,
+        collapse = collapse,
+        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 = fftempdir,
+        replace.zeros = replace_zeros,
+        batch = batch,
+        order = order,
+        qc = qc
+        )
+        return(x)
+}