--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ramclustr_wrapper.R	Mon Dec 07 22:14:48 2020 +0000
@@ -0,0 +1,113 @@
+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)
+}
+
+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
+) {
+    obj <- load(input_xcms)
+
+    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
+        )
+    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
+) {
+    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
+        )
+        return(x)
+}