comparison XSeekerPreparator.R @ 6:207e36770d18 draft

" master branch Updating"

5:4d50e9324082

TOOL_NAME <- "XSeekerPreparator"
VERSION <- "1.1.2"

OUTPUT_SPECIFIC_TOOL <- "XSeeker_Galaxy"

ENRICHED_RDATA_VERSION <- paste("1.1.2", OUTPUT_SPECIFIC_TOOL, sep="-")
ENRICHED_RDATA_DOC <- sprintf("

    message("Features enrichment done.")
    return (NULL)
}

find_grouping_var <- function(var_meta) {
    for (grouping_var in c(".", "Bio")) {
        if (!is.null(rdata$variableMetadata[[grouping_var]])) {
            return (grouping_var)
        }
    }
    return (NULL)
}

add_sample_to_database <- function(orm, env, context, smol_xcms_set) {
    message(sprintf("Processing sample %s", env$sample_name))
    sample <- (

6:207e36770d18

TOOL_NAME <- "XSeekerPreparator"
VERSION <- "1.1.3"

OUTPUT_SPECIFIC_TOOL <- "XSeeker_Galaxy"

ENRICHED_RDATA_VERSION <- paste("1.1.2", OUTPUT_SPECIFIC_TOOL, sep="-")
ENRICHED_RDATA_DOC <- sprintf("

    message("Features enrichment done.")
    return (NULL)
}

find_grouping_var <- function(var_meta) {
    known_colnames = c(
        "name", "namecustom", "mz", "mzmin", "mzmax",
        "rt", "rtmin", "rtmax", "npeaks", "isotopes", "adduct", "pcgroup"
    )
    col_names <- colnames(var_meta)
    classes = list()
    for (name in col_names) {
        if (!(name %in% known_colnames)) {
            classes[[length(classes)+1]] = name
        }
    }
    if (length(classes) > 1) {
        stop(sprintf("Only one class expected in the variable metadata. Found %d .", length(classes)))
    }
    if (length(classes) === 0) {
        stop("Could not find any class column in your variableMetadata.")
    }
    return (classes[[1]])
}

add_sample_to_database <- function(orm, env, context, smol_xcms_set) {
    message(sprintf("Processing sample %s", env$sample_name))
    sample <- (