comparison lib.r @ 31:281786a7b9a2 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f

30:4d6f4cd7c3ef

    return(variableMetadata)
}

#@author G. Le Corguille
# Draw the plotChromPeakDensity 3 per page in a pdf file
getPlotChromPeakDensity <- function(xdata) {
    pdf(file="plotChromPeakDensity.pdf", width=16, height=12)

    par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))

    group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
    names(group_colors) <- unique(xdata$sample_group)

    xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
    for (i in 1:nrow(featureDefinitions(xdata))) {
        plotChromPeakDensity(xdata, mz=c(featureDefinitions(xdata)[i,]$mzmin,featureDefinitions(xdata)[i,]$mzmax), col=group_colors, pch=16, xlim=xlim)
        legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
    }

    dev.off()
}

    exists <- file.exists(files_abs)
    files[exists] <- files_abs[exists]
    files[exists] <- sub("//","/",files[exists])

    # WHAT IS ON THE FILESYSTEM
    filesystem_filepaths <- system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T)
    filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]

    # COMPARISON
    if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
        write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())

# This function check if XML contains special caracters. It also checks integrity and completness.
#@author Misharl Monsoor [e-mail] ABiMS TEAM
checkXmlStructure <- function (directory) {
    cat("Checking XML structure...\n")

    cmd <- paste("IFS=$'\n'; for xml in $(find",directory,"-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
    capture <- system(cmd, intern=TRUE)

    if (length(capture)>0){
        #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
        write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())

#@author Misharl Monsoor [e-mail] ABiMS TEAM
deleteXmlBadCharacters<- function (directory) {
    cat("Checking Non ASCII characters in the XML...\n")

    processed <- F
    l <- system( paste("find",directory, "-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
    for (i in l){
        cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
        capture <- suppressWarnings(system(cmd, intern=TRUE))
        if (length(capture)>0){
            cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)

    if (!is.null(args$singlefile_galaxyPathNegative)) {
        singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
        singlefile_sampleNames <- args$singlefile_sampleNameNegative
    }
    if (exists("singlefile_galaxyPaths")){
        singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,","))
        singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,","))

        singlefile <- NULL
        for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
            singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
            singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]

31:281786a7b9a2

    return(variableMetadata)
}

#@author G. Le Corguille
# Draw the plotChromPeakDensity 3 per page in a pdf file
getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
    pdf(file="plotChromPeakDensity.pdf", width=16, height=12)

    par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))

    group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
    names(group_colors) <- unique(xdata$sample_group)

    xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
    for (i in 1:nrow(featureDefinitions(xdata))) {
        mzmin = featureDefinitions(xdata)[i,]$mzmin
        mzmax = featureDefinitions(xdata)[i,]$mzmax
        plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
        legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
    }

    dev.off()
}

    exists <- file.exists(files_abs)
    files[exists] <- files_abs[exists]
    files[exists] <- sub("//","/",files[exists])

    # WHAT IS ON THE FILESYSTEM
    filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
    filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]

    # COMPARISON
    if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
        write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())

# This function check if XML contains special caracters. It also checks integrity and completness.
#@author Misharl Monsoor [e-mail] ABiMS TEAM
checkXmlStructure <- function (directory) {
    cat("Checking XML structure...\n")

    cmd <- paste0("IFS=$'\n'; for xml in $(find '",directory,"' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
    capture <- system(cmd, intern=TRUE)

    if (length(capture)>0){
        #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
        write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())

#@author Misharl Monsoor [e-mail] ABiMS TEAM
deleteXmlBadCharacters<- function (directory) {
    cat("Checking Non ASCII characters in the XML...\n")

    processed <- F
    l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
    for (i in l){
        cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
        capture <- suppressWarnings(system(cmd, intern=TRUE))
        if (length(capture)>0){
            cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)

    if (!is.null(args$singlefile_galaxyPathNegative)) {
        singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
        singlefile_sampleNames <- args$singlefile_sampleNameNegative
    }
    if (exists("singlefile_galaxyPaths")){
        singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
        singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))

        singlefile <- NULL
        for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
            singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
            singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]