comparison flagRemove.R @ 9:f11c129a4227 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f

8:94a2b6571758

library(msPurity)
library(optparse)
print(sessionInfo())
option_list <- list(
    make_option(c("-o", "--out_dir"),
        type = "character", default = getwd(),

}


print(opt)

getxcmsSetObject <- function(xobject) {
    # XCMS 1.x
    if (class(xobject) == "xcmsSet") {
        return(xobject)
    }
    # XCMS 3.x
    if (class(xobject) == "XCMSnExp") {
        # Get the legacy xcmsSet object
        suppressWarnings(xset <- as(xobject, "xcmsSet"))
        xcms::sampclass(xset) <- xset@phenoData$sample_group
        return(xset)
    }
}


loadRData <- function(rdata_path, name) {
    # loads an RData file, and returns the named xset object if it is there
    load(rdata_path)
    return(get(ls()[ls() %in% name]))
}

xset <- getxcmsSetObject(loadRData(opt$xset_path, c("xset", "xdata")))

print(xset)
if (is.null(opt$samplelist)) {
    blank_class <- opt$blank_class
} else {
    samplelist <- read.table(opt$samplelist, sep = "\t", header = TRUE)
    samplelist_blank <- unique(samplelist$sample_class[samplelist$blank == "yes"])

        quit()
    }
    blank_class <- as.character(chosen_blank)
    print(blank_class)
}


if (is.null(opt$multilist)) {
    ffrm_out <- flag_remove(xset,
        pol = opt$polarity,

        file.path(opt$out_dir, "removed_peaks.tsv"),
        row.names = FALSE, sep = "\t"
    )
} else {
    # nolint start
    # TODO
    # xsets <- split(xset, multilist_df$multlist)
    #
    # mult_grps <- unique(multilist_df$multlist)
    #
    # for (mgrp in mult_grps){
    #   xset_i <- xsets[mgrp]
    #   xcms::group(xset_i,
    #
    # }
    # nolint end
}

9:f11c129a4227

library(msPurity)
library(xcms)
library(optparse)
print(sessionInfo())
option_list <- list(
    make_option(c("-o", "--out_dir"),
        type = "character", default = getwd(),

}


print(opt)

# This R function can handle both XCMS object versions (so following code
# no longer required - kept here for reference)
# getxcmsSetObject <- function(xobject) {
#   # XCMS 1.x
#   if (class(xobject) == "xcmsSet"){
#     return(xobject)
#   }
#   # XCMS 3.x
#   if (class(xobject) == "XCMSnExp") {
#     # Get the legacy xcmsSet object
#     suppressWarnings(xset <- as(xobject, "xcmsSet"))
#     if (!is.null(xset@phenoData$sample_group)){
#       xcms::sampclass(xset) <- xset@phenoData$sample_group
#     }else{
#       xcms::sampclass(xset) <- "."
#     }
#     return(xset)
#   }
# }


loadRData <- function(rdata_path, name) {
    # loads an RData file, and returns the named xset object if it is there
    load(rdata_path)
    return(get(ls()[ls() %in% name]))
}

xset <- loadRData(opt$xset_path, c("xset", "xdata"))


if (is.null(opt$samplelist)) {
    blank_class <- opt$blank_class
} else {
    samplelist <- read.table(opt$samplelist, sep = "\t", header = TRUE)
    samplelist_blank <- unique(samplelist$sample_class[samplelist$blank == "yes"])

        quit()
    }
    blank_class <- as.character(chosen_blank)
    print(blank_class)
}




if (is.null(opt$multilist)) {
    ffrm_out <- flag_remove(xset,
        pol = opt$polarity,

        file.path(opt$out_dir, "removed_peaks.tsv"),
        row.names = FALSE, sep = "\t"
    )
} else {
    # nolint start
    # TODO - potential for multilist analysis (e)
    # nolint end
}