| Previous changeset 8:cce30b3398e0 (2016-07-06) Next changeset 10:6caa60dcc217 (2017-02-07) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 |
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modified:
README.rst abims_xcms_fillPeaks.xml lib.r macros.xml xcms.r |
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added:
test-data/faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv test-data/faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv |
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| diff -r cce30b3398e0 -r ee29f0a6e361 README.rst --- a/README.rst Wed Jul 06 17:43:29 2016 -0400 +++ b/README.rst Mon Jan 30 08:53:48 2017 -0500 |
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| @@ -2,6 +2,10 @@ Changelog/News -------------- +**Version 2.0.8 - 22/12/2016** + +- IMPROVEMENT: Add an option to export the peak list at this step without have to wait camara.annotate + **Version 2.0.7 - 06/07/2016** - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 |
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| diff -r cce30b3398e0 -r ee29f0a6e361 abims_xcms_fillPeaks.xml --- a/abims_xcms_fillPeaks.xml Wed Jul 06 17:43:29 2016 -0400 +++ b/abims_xcms_fillPeaks.xml Mon Jan 30 08:53:48 2017 -0500 |
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| b'@@ -1,6 +1,6 @@\n-<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.7">\n+<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.8">\n \n- <description>Integrate the signal in the region of that peak group not represented and create a new peak</description>\n+ <description>Integrate a sample\'s signal in regions where peak groups are not represented to create new peaks in missing areas</description>\n \n <macros>\n <import>macros.xml</import>\n@@ -10,36 +10,64 @@\n <expand macro="stdio"/>\n \n <command><![CDATA[\n- @COMMAND_XCMS_SCRIPT@ \n- xfunction fillPeaks \n- image $image \n+ @COMMAND_XCMS_SCRIPT@\n+ xfunction fillPeaks\n+ image $image\n \n xsetRdataOutput $xsetRData\n \n method $method\n \n+ #if $peaklist.peaklistBool\n+ variableMetadataOutput $variableMetadata\n+ dataMatrixOutput $dataMatrix\n+ convertRTMinute $peaklist.convertRTMinute\n+ numDigitsMZ $peaklist.numDigitsMZ\n+ numDigitsRT $peaklist.numDigitsRT\n+ intval $peaklist.intval\n+ #end if\n+\n @COMMAND_ZIPFILE_LOAD@\n \n- @COMMAND_LOG_EXIT@ \n- \n+ @COMMAND_LOG_EXIT@\n+\n ]]></command>\n \n <inputs>\n- <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (group)" />\n+ <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another xcms function (group)" />\n <param name="method" type="select" label="Filling method" help="[method] See the help section below">\n <option value="chrom" selected="true">chrom</option>\n <option value="MSW" >MSW</option>\n </param>\n- \n+ <conditional name="peaklist">\n+ <param name="peaklistBool" type="boolean" label="Get a Peak List" />\n+ <when value="true">\n+ <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>\n+ <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions\' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />\n+ <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions\' identifiers." help="Useful to avoid duplicates within identifiers" />\n+ <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">\n+ <option value="into" selected="true">into</option>\n+ <option value="maxo">maxo</option>\n+ <option value="intb">intb</option>\n+ </param>\n+ </when>\n+ <when value="false" />\n+ </conditional>\n <expand macro="zipfile_load"/>\n \n </inputs>\n \n <outputs>\n <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" />\n+ <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.fillPeaks.variableMetadata.tsv">\n+ <filter>(peaklist[\'peaklistBool\'])</filter>\n+ </data>\n+ <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.fillPeaks.dataMatrix.tsv" >\n+ <filter>(peaklist[\'peaklistBool\'])</filter>\n+ </data>\n <data name="log" format="txt" label="xset.log.txt" hidden="true" />\n </outputs>\n- \n+\n <tests>\n <!--<test>\n <param name="image" value="xset.group.retcor.group.RData"/>\n@@ -59,6 +87,12 @@\n <test>\n <param name="image" value="faahKO.xset.group.retcor.group.RData"/>\n <param name="method" value="ch'..b'hose peak groups, integrate the signal\n in the region of that peak group and create a new peak.\n@@ -117,12 +154,12 @@\n +---------------------------+------------------+-----------------------+\n | Name | Output file | Format |\n +===========================+==================+=======================+\n-|xcms.diffreport | xset.retcor.RData| rdata.xcms.fillpeaks |\n+|CAMERA.annotate | xset.retcor.RData| rdata.xcms.fillpeaks |\n +---------------------------+------------------+-----------------------+\n-|xcms.annotateDiffreport | xset.retcor.RData| rdata.xcms.fillpeaks |\n+|xcms.summary | xset.retcor.RData| rdata.xcms.fillpeaks |\n +---------------------------+------------------+-----------------------+\n \n-The output file **xset.fillpeaks** is an RData file. You can continue your analysis using it in **xcms.diffreport** or **xcms.annotateDiffreport** tool as an next step of the workflow.\n+The output file **xset.fillpeaks** is a RData file. You can continue your analysis using it in **CAMERA.annotate** or **xcms.summary** tool as a following step of your workflow.\n \n \n **General schema of the metabolomic workflow**\n@@ -159,21 +196,50 @@\n \n | "MSW" is used for peaklists without retention-time information like those from direct-infusion spectra.\n \n+\n+Get a Peak List\n+---------------\n+\n+If \'true\', the module generates two additional files corresponding to the peak list:\n+- the variable metadata file (corresponding to information about extracted ions such as mass or retention time)\n+- the data matrix (corresponding to related intensities)\n+\n+**decimal places for [mass or retention time] values in identifiers**\n+\n+ | Ions\' identifiers are constructed as MxxxTyyy where \'xxx\' is the ion median mass and \'yyy\' the ion median retention time.\n+ | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively.\n+ | Theses parameters do not affect decimal places in columns other than the identifier one.\n+\n+**Reported intensity values**\n+\n+ | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms \'intval\' parameter:\n+ | - into: integrated area of original (raw) peak\n+ | - maxo: maximum intensity of original (raw) peak\n+ | - intb: baseline corrected integrated peak area (only available if peak detection was done by \xe2\x80\x98findPeaks.centWave\xe2\x80\x99)\n+\n ------------\n Output files\n ------------\n \n xset.fillPeaks.RData : rdata.xcms.fillpeaks format\n \n- | Rdata file that will be used in the **xcms.diffreport** or **xcms.annotateDiffreport** step of the workflow.\n- \n+ | Rdata file that will be used in the **CAMERA.annotate** or **xcms.summary** step of the workflow.\n+\n+xset.variableMetadata.tsv : tabular format\n+\n+ | Table containing information about ions; can be used as one input of **Quality_Metrics** or **Generic_filter* modules.\n+\n+xset.dataMatrix.tsv : tabular format\n+\n+ | Table containing ions\' intensities; can be used as one input of **Quality_Metrics** or **Generic_filter* modules.\n+\n ------\n \n-.. class:: infomark \n+.. class:: infomark\n \n-The output file is an group.RData file. You can continue your analysis using it in **xcms.diffreport** or **xcms.annotateDiffreport** tool.\n+The output file is a xset.fillPeaks.RData file. You can continue your analysis using it in **CAMERA.annotate** or **xcms.summary** tool.\n \n- \n+\n ---------------------------------------------------\n \n ---------------\n@@ -189,7 +255,8 @@\n ----------\n \n | method -> **chrom**\n- \n+ | Get a Peak List -> **false**\n+\n \n Output files\n ------------\n@@ -202,6 +269,10 @@\n Changelog/News\n --------------\n \n+**Version 2.0.8 - 22/12/2016**\n+\n+- IMPROVEMENT: Add an option to export the peak list at this step without having to wait for CAMERA.annotate\n+\n **Version 2.0.7 - 06/07/2016**\n \n - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0\n' |
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| diff -r cce30b3398e0 -r ee29f0a6e361 lib.r --- a/lib.r Wed Jul 06 17:43:29 2016 -0400 +++ b/lib.r Mon Jan 30 08:53:48 2017 -0500 |
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| b'@@ -1,14 +1,59 @@\n-# lib.r version="2.0.1"\n #Authors ABiMS TEAM\n-#Lib.r for Galaxy Workflow4Metabo\n+#Lib.r for Galaxy Workflow4Metabolomics xcms tools\n+#\n+#version 2.4: lecorguille\n+# add getPeaklistW4M\n+#version 2.3: yguitton\n+# correction for empty PDF when only 1 class\n #version 2.2\n-#Based on lib.r 2.1\n-#Modifications made by Guitton Yann \n-#correct bug in Base Peak Chromatogram (BPC) option, not only TIC when scanrange used in xcmsSet\n-#Note if scanrange is used a warning is prompted in R console but do not stop PDF generation\n+# correct bug in Base Peak Chromatogram (BPC) option, not only TIC when scanrange used in xcmsSet\n+# Note if scanrange is used a warning is prompted in R console but do not stop PDF generation\n+#version 2.1: yguitton\n+# Modifications made by Guitton Yann\n \n \n+#@author G. Le Corguille\n+#This function convert if it is required the Retention Time in minutes\n+RTSecondToMinute <- function(variableMetadata, convertRTMinute) {\n+ if (convertRTMinute){\n+ #converting the retention times (seconds) into minutes\n+ print("converting the retention times into minutes in the variableMetadata")\n+ variableMetadata[,"rt"]=variableMetadata[,"rt"]/60\n+ variableMetadata[,"rtmin"]=variableMetadata[,"rtmin"]/60\n+ variableMetadata[,"rtmax"]=variableMetadata[,"rtmax"]/60\n+ }\n+ return (variableMetadata)\n+}\n \n+#@author G. Le Corguille\n+#This function format ions identifiers\n+formatIonIdentifiers <- function(dataData, numDigitsRT=0, numDigitsMZ=0) {\n+ return(make.unique(paste0("M",round(dataData[,"mz"],numDigitsMZ),"T",round(dataData[,"rt"],numDigitsRT))))\n+}\n+\n+#@author G. Le Corguille\n+# value: intensity values to be used into, maxo or intb\n+getPeaklistW4M <- function(xset, intval="into",convertRTMinute=F,numDigitsMZ=4,numDigitsRT=0,variableMetadataOutput,dataMatrixOutput) {\n+ groups <- xset@groups\n+ values <- groupval(xset, "medret", value=intval)\n+ \n+ # renamming of the column rtmed to rt to fit with camera peaklist function output\n+ colnames(groups)[colnames(groups)=="rtmed"] <- "rt"\n+ colnames(groups)[colnames(groups)=="mzmed"] <- "mz"\n+ \n+ ids <- formatIonIdentifiers(groups, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)\n+ groups = RTSecondToMinute(groups, convertRTMinute)\n+\n+ rownames(groups) = ids\n+ rownames(values) = ids\n+\n+ #@TODO: add "name" as the first column name\n+ #colnames(groups)[1] = "name"\n+ #colnames(values)[1] = "name"\n+\n+ write.table(groups, file=variableMetadataOutput,sep="\\t",quote=F,row.names = T,col.names = NA)\n+ write.table(values, file=dataMatrixOutput,sep="\\t",quote=F,row.names = T,col.names = NA)\n+}\n \n #@author Y. Guitton\n getBPC <- function(file,rtcor=NULL, ...) {\n@@ -44,13 +89,13 @@\n for (j in 1:N) {\n \n TIC[[j]] <- getBPC(files[j])\n- #good for raw \n+ #good for raw\n # seems strange for corrected\n #errors if scanrange used in xcmsSetgeneration\n if (!is.null(xcmsSet) && rt == "corrected")\n rtcor <- xcmsSet@rt$corrected[[j]] else\n rtcor <- NULL\n- \n+\n TIC[[j]] <- getBPC(files[j],rtcor=rtcor)\n # TIC[[j]][,1]<-rtcor\n }\n@@ -68,11 +113,11 @@\n \n \n ##plot start\n- \n+\n if (length(class)>2){\n for (k in 1:(length(class)-1)){\n for (l in (k+1):length(class)){\n- #print(paste(class[k],"vs",class[l],sep=" ")) \n+ #print(paste(class[k],"vs",class[l],sep=" "))\n plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \\n","BPCs_",class[k]," vs ",class[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC")\n colvect<-NULL\n for (j in 1:length(classnames[[k]])) {\n@@ -115,6 +160,24 @@\n \n }#end length ==2\n \n+ #case where only one class\n+ if (length(class)==1){\n+ k=1\n+\t\tylim = range(sapply(TIC, function(x) range(x[,2])))\n+ colvect<-NULL\n+ plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \\n","BPCs_",class[k], sep=""), xlab = "Retention Tim'..b'cmsSet@phenoData[,1]==class[i])\n }\n- \n+\n N <- length(files)\n TIC <- vector("list",N)\n \n@@ -178,7 +241,7 @@\n if (length(class)>2){\n for (k in 1:(length(class)-1)){\n for (l in (k+1):length(class)){\n- #print(paste(class[k],"vs",class[l],sep=" ")) \n+ #print(paste(class[k],"vs",class[l],sep=" "))\n plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \\n","TICs_",class[k]," vs ",class[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC")\n colvect<-NULL\n for (j in 1:length(classnames[[k]])) {\n@@ -219,6 +282,25 @@\n legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)\n \n }#end length ==2\n+\n+ #case where only one class\n+ if (length(class)==1){\n+\t k=1\n+\t ylim = range(sapply(TIC, function(x) range(x[,2])))\n+\n+\t plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \\n","TICs_",class[k], sep=""), xlab = "Retention Time (min)", ylab = "TIC")\n+ colvect<-NULL\n+\t\tfor (j in 1:length(classnames[[k]])) {\n+ tic <- TIC[[classnames[[k]][j]]]\n+\t\t\t# points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")\n+\t\t\tpoints(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")\n+ colvect<-append(colvect,cols[classnames[[k]][j]])\n+\t }\n+\n+\t\tlegend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch)\n+\n+\t}#end length ==1\n+\n dev.off() #pdf(pdfname,w=16,h=10)\n \n invisible(TIC)\n@@ -237,7 +319,7 @@\n sampleMetadata=xset@phenoData\n sampleNamesOrigin=rownames(sampleMetadata)\n sampleNamesMakeNames=make.names(sampleNamesOrigin)\n- \n+\n if (any(duplicated(sampleNamesMakeNames))) {\n write("\\n\\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())\n for (sampleName in sampleNamesOrigin) {\n@@ -285,7 +367,7 @@\n \n #Set the polarity attribute\n sampleMetadata$polarity[sampleMetadata$sampleMetadata==samplename]=polarity\n- \n+\n #Delete xcmsRaw object because it creates a bug for the fillpeaks step\n rm(xcmsRaw)\n }\n@@ -321,7 +403,7 @@\n filesystem_filepaths=filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]\n \n # COMPARISON\n- if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) { \n+ if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {\n write("\\n\\nERROR: List of the files which will not be imported by xcmsSet",stderr())\n write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())\n stop("\\n\\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")\n@@ -347,7 +429,7 @@\n write(capture, stderr())\n stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")\n }\n- \n+\n }\n \n \n@@ -359,7 +441,7 @@\n cat("Checking Non ASCII characters in the XML...\\n")\n \n processed=F\n- l=system( paste("find",directory, "-not -name \'\\\\.*\' -not -path \'*conda-env*\' -type f -iname \'*.*ml*\'"),intern=TRUE) \n+ l=system( paste("find",directory, "-not -name \'\\\\.*\' -not -path \'*conda-env*\' -type f -iname \'*.*ml*\'"),intern=TRUE)\n for (i in l){\n cmd=paste("LC_ALL=C grep \'[^ -~]\' \\"",i,"\\"",sep="")\n capture=suppressWarnings(system(cmd,intern=TRUE))\n@@ -368,7 +450,7 @@\n print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )\n c=system(cmd,intern=TRUE)\n capture=""\n- processed=T \n+ processed=T\n }\n }\n if (processed) cat("\\n\\n")\n@@ -376,7 +458,7 @@\n }\n \n \n-## \n+##\n ## This function will compute MD5 checksum to check the data integrity\n ##\n #@author Gildas Le Corguille lecorguille@sb-roscoff.fr\n@@ -397,4 +479,3 @@\n \n return(as.matrix(md5sum(files)))\n }\n-\n' |
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| diff -r cce30b3398e0 -r ee29f0a6e361 macros.xml --- a/macros.xml Wed Jul 06 17:43:29 2016 -0400 +++ b/macros.xml Mon Jan 30 08:53:48 2017 -0500 |
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| @@ -2,7 +2,6 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="3.1.2">R</requirement> <requirement type="package" version="0.4_1">r-snow</requirement> <requirement type="package" version="1.46.0">bioconductor-xcms</requirement> <requirement type="package" version="1.1_4">r-batch</requirement> @@ -40,7 +39,7 @@ <conditional name="zipfile_load_conditional"> <param name="zipfile_load_select" type="select" label="Resubmit your zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." > <option value="no" >no need</option> - <option value="yes" selected="peakgroups">yes</option> + <option value="yes">yes</option> </param> <when value="no"> </when> |
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| diff -r cce30b3398e0 -r ee29f0a6e361 test-data/faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv Mon Jan 30 08:53:48 2017 -0500 |
| b |
| b'@@ -0,0 +1,8158 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|
| b |
| diff -r cce30b3398e0 -r ee29f0a6e361 test-data/faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv Mon Jan 30 08:53:48 2017 -0500 |
| b |
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|
| b |
| diff -r cce30b3398e0 -r ee29f0a6e361 xcms.r --- a/xcms.r Wed Jul 06 17:43:29 2016 -0400 +++ b/xcms.r Mon Jan 30 08:53:48 2017 -0500 |
| [ |
| @@ -19,7 +19,7 @@ cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="") } source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } -cat("\n\n"); +cat("\n\n"); @@ -64,18 +64,35 @@ xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL } +#saving the specific parameters rplotspdf = "Rplots.pdf" if (!is.null(listArguments[["rplotspdf"]])){ rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL } - sampleMetadataOutput = "sampleMetadata.tsv" if (!is.null(listArguments[["sampleMetadataOutput"]])){ sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL } - - - +variableMetadataOutput = "variableMetadata.tsv" +if (!is.null(listArguments[["variableMetadataOutput"]])){ + variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL +} +dataMatrixOutput = "dataMatrix.tsv" +if (!is.null(listArguments[["dataMatrixOutput"]])){ + dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL +} +if (!is.null(listArguments[["convertRTMinute"]])){ + convertRTMinute = listArguments[["convertRTMinute"]]; listArguments[["convertRTMinute"]]=NULL +} +if (!is.null(listArguments[["numDigitsMZ"]])){ + numDigitsMZ = listArguments[["numDigitsMZ"]]; listArguments[["numDigitsMZ"]]=NULL +} +if (!is.null(listArguments[["numDigitsRT"]])){ + numDigitsRT = listArguments[["numDigitsRT"]]; listArguments[["numDigitsRT"]]=NULL +} +if (!is.null(listArguments[["intval"]])){ + intval = listArguments[["intval"]]; listArguments[["intval"]]=NULL +} if (thefunction %in% c("xcmsSet","retcor")) { ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL @@ -116,15 +133,15 @@ suppressWarnings(unzip(zipfile, unzip="unzip")) #get the directory name - filesInZip=unzip(zipfile, list=T); + filesInZip=unzip(zipfile, list=T); directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))); directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] directory = "." if (length(directories) == 1) directory = directories - + cat("files_root_directory\t",directory,"\n") - # + # md5sumList=list("origin"=getMd5sum(directory)) # Check and fix if there are non ASCII characters. If so, they will be removed from the *mzXML mzML files. @@ -187,6 +204,8 @@ #execution of the function "thefunction" with the parameters given in "listArguments" + +cat("\t\tCOMPUTE\n") xset = do.call(thefunction, listArguments) @@ -200,7 +219,7 @@ xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths) if(exists("zipfile") && (zipfile!="")) { - + #Modify the samples names (erase the path) for(i in 1:length(sampnames(xset))){ @@ -217,17 +236,24 @@ # -- TIC -- if (thefunction == "xcmsSet") { + cat("\t\tGET TIC GRAPH\n") sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput) getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw") getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf) } else if (thefunction == "retcor") { + cat("\t\tGET TIC GRAPH\n") getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected") getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf) } +if (thefunction == "fillPeaks") { + cat("\t\tGET THE PEAK LIST\n") + getPeaklistW4M(xset,intval,convertRTMinute,numDigitsMZ,numDigitsRT,variableMetadataOutput,dataMatrixOutput) +} + + cat("\n\n") - # ----- EXPORT ----- cat("\tXSET OBJECT INFO\n") @@ -243,4 +269,3 @@ cat("\tDONE\n") - |