# HG changeset patch
# User workflow4metabolomics
# Date 1564171218 14400
# Node ID db9bc2c27a0ac0e5f64780cd8f5b394645db0469
# Parent 2184c0435edf3ecb8e46594ac335a3dc712eca9f
planemo upload commit d51a0d0a26833671b79711ee18d782e84f301e76
diff -r 2184c0435edf -r db9bc2c27a0a CAMERA.r
--- a/CAMERA.r Fri Apr 12 10:45:52 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,157 +0,0 @@
-#!/usr/bin/env Rscript
-# CAMERA.r version="2.2.1"
-
-
-
-# ----- PACKAGE -----
-cat("\tSESSION INFO\n")
-
-pkgs=c("CAMERA","multtest","batch")
-for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
-
-sessioninfo = sessionInfo()
-cat(sessioninfo$R.version$version.string,"\n")
-cat("Main packages:\n")
-for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
-cat("Other loaded packages:\n")
-for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
-
-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");
-
-
-
-# ----- ARGUMENTS -----
-cat("\tARGUMENTS INFO\n")
-
-listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
-write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')
-
-cat("\n\n");
-
-
-# ----- PROCESSING INFILE -----
-cat("\tINFILE PROCESSING INFO\n")
-
-#image is an .RData file necessary to use xset variable given by previous tools
-if (!is.null(listArguments[["image"]])){
- load(listArguments[["image"]]); listArguments[["image"]]=NULL
-}
-
-if (listArguments[["xfunction"]] %in% c("combinexsAnnos")) {
- load(listArguments[["image_pos"]])
- xaP=xa
- listOFlistArgumentsP=listOFlistArguments
- if (exists("xsAnnotate_object")) xaP=xsAnnotate_object
-
- diffrepP=NULL
- if (exists("diffrep")) diffrepP=diffrep
-
- load(listArguments[["image_neg"]])
- xaN=xa
- listOFlistArgumentsN=listOFlistArguments
- if (exists("xsAnnotate_object")) xaN=xsAnnotate_object
-
- diffrepN=NULL
- if (exists("diffrep")) diffrepN=diffrep
-}
-
-
-cat("\n\n")
-
-
-# ----- ARGUMENTS PROCESSING -----
-cat("\tARGUMENTS PROCESSING INFO\n")
-
-# Save arguments to generate a report
-if (!exists("listOFlistArguments")) listOFlistArguments=list()
-listOFlistArguments[[paste(format(Sys.time(), "%y%m%d-%H:%M:%S_"),listArguments[["xfunction"]],sep="")]] = listArguments
-
-
-#saving the commun parameters
-thefunction = listArguments[["xfunction"]]
-listArguments[["xfunction"]]=NULL #delete from the list of arguments
-
-xsetRdataOutput = paste(thefunction,"RData",sep=".")
-if (!is.null(listArguments[["xsetRdataOutput"]])){
- xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL
-}
-
-rplotspdf = "Rplots.pdf"
-if (!is.null(listArguments[["rplotspdf"]])){
- rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
-}
-
-variableMetadataOutput = "variableMetadata.tsv"
-if (!is.null(listArguments[["variableMetadataOutput"]])){
- variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL
-}
-
-#Import the different functions
-source_local("lib.r")
-
-# We unzip automatically the chromatograms from the zip files.
-if (thefunction %in% c("annotatediff")) {
- if (!exists("zipfile")) zipfile=NULL
- if (!exists("singlefile")) singlefile=NULL
- rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments)
- zipfile = rawFilePath$zipfile
- singlefile = rawFilePath$singlefile
- listArguments = rawFilePath$listArguments
- directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
-}
-
-# Because so far CAMERA isn't compatible with the new XCMSnExp object
-if (exists("xdata")){
- xset <- getxcmsSetObject(xdata)
-}
-
-# addition of xset object to the list of arguments in the first position
-if (exists("xset")){
- listArguments=append(list(xset), listArguments)
-}
-
-cat("\n\n")
-
-
-
-
-# ----- PROCESSING INFO -----
-cat("\tMAIN PROCESSING INFO\n")
-
-#change the default display settings
-pdf(file=rplotspdf, width=16, height=12)
-
-if (thefunction %in% c("annotatediff")) {
- results_list=annotatediff(xset=xset,listArguments=listArguments,variableMetadataOutput=variableMetadataOutput)
- xa=results_list[["xa"]]
- diffrep=results_list[["diffrep"]]
- variableMetadata=results_list[["variableMetadata"]]
-
- cat("\n\n")
- cat("\tXSET OBJECT INFO\n")
- print(xa)
-}
-
-if (thefunction %in% c("combinexsAnnos")) {
- cAnnot=combinexsAnnos_function(
- xaP=xaP,xaN=xaN,
- listOFlistArgumentsP=listOFlistArgumentsP,listOFlistArgumentsN=listOFlistArgumentsN,
- diffrepP=diffrepP,diffrepN=diffrepN,
- pos=listArguments[["pos"]],tol=listArguments[["tol"]],ruleset=listArguments[["ruleset"]],keep_meta=listArguments[["keep_meta"]],
- convertRTMinute=listArguments[["convertRTMinute"]], numDigitsMZ=listArguments[["numDigitsMZ"]], numDigitsRT=listArguments[["numDigitsRT"]],
- variableMetadataOutput=variableMetadataOutput
- )
-}
-
-dev.off()
-
-
-#saving R data in .Rdata file to save the variables used in the present tool
-objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFlistArguments","zipfile","singlefile")
-save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput)
-
-cat("\n\n")
-
-cat("\tDONE\n")
diff -r 2184c0435edf -r db9bc2c27a0a CAMERA_annotateDiffreport.r
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CAMERA_annotateDiffreport.r Fri Jul 26 16:00:18 2019 -0400
@@ -0,0 +1,78 @@
+#!/usr/bin/env Rscript
+
+# ----- PACKAGE -----
+cat("\tSESSION INFO\n")
+
+#Import the different functions
+source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
+source_local("lib.r")
+
+pkgs=c("CAMERA","multtest","batch")
+loadAndDisplayPackages(pkgs)
+cat("\n\n");
+
+# ----- ARGUMENTS -----
+cat("\tARGUMENTS INFO\n")
+
+args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
+write.table(as.matrix(args), col.names=F, quote=F, sep='\t')
+
+cat("\n\n");
+
+
+# ----- PROCESSING INFILE -----
+cat("\tINFILE PROCESSING INFO\n")
+
+#image is an .RData file necessary to use xset variable given by previous tools
+load(args$image); args$image=NULL
+
+cat("\n\n")
+
+
+# ----- ARGUMENTS PROCESSING -----
+cat("\tARGUMENTS PROCESSING INFO\n")
+
+# Save arguments to generate a report
+if (!exists("listOFargs")) listOFargs=list()
+listOFargs[[format(Sys.time(), "%y%m%d-%H:%M:%S_annotatediff")]] = args
+
+# We unzip automatically the chromatograms from the zip files.
+if (!exists("zipfile")) zipfile=NULL
+if (!exists("singlefile")) singlefile=NULL
+rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, args)
+zipfile = rawFilePath$zipfile
+singlefile = rawFilePath$singlefile
+args = rawFilePath$args
+directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
+
+# Because so far CAMERA isn't compatible with the new XCMSnExp object
+if (exists("xdata")){
+ xset <- getxcmsSetObject(xdata)
+}
+
+cat("\n\n")
+
+
+# ----- PROCESSING INFO -----
+cat("\tMAIN PROCESSING INFO\n")
+
+results_list=annotatediff(xset=xset,args=args,variableMetadataOutput="variableMetadata.tsv")
+xa=results_list$xa
+diffrep=results_list$diffrep
+variableMetadata=results_list$variableMetadata
+
+cat("\n\n")
+
+# ----- EXPORT -----
+
+cat("\tXSET OBJECT INFO\n")
+print(xa)
+cat("\n\n")
+
+#saving R data in .Rdata file to save the variables used in the present tool
+objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFargs","zipfile","singlefile")
+save(list=objects2save[objects2save %in% ls()], file="annotatediff.RData")
+
+cat("\n\n")
+
+cat("\tDONE\n")
diff -r 2184c0435edf -r db9bc2c27a0a README.rst
--- a/README.rst Fri Apr 12 10:45:52 2019 -0400
+++ b/README.rst Fri Jul 26 16:00:18 2019 -0400
@@ -5,8 +5,11 @@
**Version 2.2.5 - 09/04/2019**
- NEW: zip export are back for pictures (eic and boxplot) and diffreport tables
+
- UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_)
+- UPGRADE: refactoring of internal code
+
**Version 2.2.4 - 09/10/2018**
- NES: CAMERA.annotate no longer export a DataMatrix. fillChromPeaks does the job
diff -r 2184c0435edf -r db9bc2c27a0a abims_CAMERA_annotateDiffreport.xml
--- a/abims_CAMERA_annotateDiffreport.xml Fri Apr 12 10:45:52 2019 -0400
+++ b/abims_CAMERA_annotateDiffreport.xml Fri Jul 26 16:00:18 2019 -0400
@@ -10,15 +10,11 @@
-
-
+
+
quick_block['quick'] == 'FALSE'
-
+
quick_block['quick'] == 'TRUE'
@@ -447,8 +439,11 @@
**Version 2.2.5 - 09/04/2019**
- NEW: zip export are back for pictures (eic and boxplot) and diffreport tables
+
- UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_)
+- UPGRADE: refactoring of internal code
+
**Version 2.2.4 - 09/10/2018**
- NEW: CAMERA.annotate no longer export a DataMatrix. fillChromPeaks does the job
diff -r 2184c0435edf -r db9bc2c27a0a lib.r
--- a/lib.r Fri Apr 12 10:45:52 2019 -0400
+++ b/lib.r Fri Jul 26 16:00:18 2019 -0400
@@ -1,5 +1,31 @@
# lib.r
+#@author G. Le Corguille
+# solve an issue with batch if arguments are logical TRUE/FALSE
+parseCommandArgs <- function(...) {
+ args <- batch::parseCommandArgs(...)
+ for (key in names(args)) {
+ if (args[key] %in% c("TRUE","FALSE"))
+ args[key] = as.logical(args[key])
+ }
+ return(args)
+}
+
+#@author G. Le Corguille
+# This function will
+# - load the packages
+# - display the sessionInfo
+loadAndDisplayPackages <- function(pkgs) {
+ for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
+
+ sessioninfo = sessionInfo()
+ cat(sessioninfo$R.version$version.string,"\n")
+ cat("Main packages:\n")
+ for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
+ cat("Other loaded packages:\n")
+ for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
+}
+
# This function retrieve a xset like object
#@author Gildas Le Corguille lecorguille@sb-roscoff.fr
getxcmsSetObject <- function(xobject) {
@@ -69,7 +95,7 @@
}
#The function annotateDiffreport without the corr function which bugs
-annotatediff <- function(xset=xset, listArguments=listArguments, variableMetadataOutput="variableMetadata.tsv") {
+annotatediff <- function(xset=xset, args=args, variableMetadataOutput="variableMetadata.tsv") {
# Resolve the bug with x11, with the function png
options(bitmapType='cairo')
@@ -77,52 +103,52 @@
res=try(is.null(xset@filled))
# ------ annot -------
- listArguments[["calcCiS"]]=as.logical(listArguments[["calcCiS"]])
- listArguments[["calcIso"]]=as.logical(listArguments[["calcIso"]])
- listArguments[["calcCaS"]]=as.logical(listArguments[["calcCaS"]])
+ args$calcCiS=as.logical(args$calcCiS)
+ args$calcIso=as.logical(args$calcIso)
+ args$calcCaS=as.logical(args$calcCaS)
# common parameters
- listArguments4annotate = list(object=xset,
- nSlaves=listArguments[["nSlaves"]],sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],
- maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]],
- ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]],
- polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]])
+ args4annotate = list(object=xset,
+ nSlaves=args$nSlaves,sigma=args$sigma,perfwhm=args$perfwhm,
+ maxcharge=args$maxcharge,maxiso=args$maxiso,minfrac=args$minfrac,
+ ppm=args$ppm,mzabs=args$mzabs,quick=args$quick,
+ polarity=args$polarity,max_peaks=args$max_peaks,intval=args$intval)
# quick == FALSE
- if(listArguments[["quick"]]==FALSE) {
- listArguments4annotate = append(listArguments4annotate,
- list(graphMethod=listArguments[["graphMethod"]],cor_eic_th=listArguments[["cor_eic_th"]],pval=listArguments[["pval"]],
- calcCiS=listArguments[["calcCiS"]],calcIso=listArguments[["calcIso"]],calcCaS=listArguments[["calcCaS"]]))
+ if(args$quick==FALSE) {
+ args4annotate = append(args4annotate,
+ list(graphMethod=args$graphMethod,cor_eic_th=args$cor_eic_th,pval=args$pval,
+ calcCiS=args$calcCiS,calcIso=args$calcIso,calcCaS=args$calcCaS))
# no ruleset
- if (!is.null(listArguments[["multiplier"]])) {
- listArguments4annotate = append(listArguments4annotate,
- list(multiplier=listArguments[["multiplier"]]))
+ if (!is.null(args$multiplier)) {
+ args4annotate = append(args4annotate,
+ list(multiplier=args$multiplier))
}
# ruleset
else {
- rulset=read.table(listArguments[["rules"]], h=T, sep=";")
- if (ncol(rulset) < 4) rulset=read.table(listArguments[["rules"]], h=T, sep="\t")
- if (ncol(rulset) < 4) rulset=read.table(listArguments[["rules"]], h=T, sep=",")
+ rulset=read.table(args$rules, h=T, sep=";")
+ if (ncol(rulset) < 4) rulset=read.table(args$rules, h=T, sep="\t")
+ if (ncol(rulset) < 4) rulset=read.table(args$rules, h=T, sep=",")
if (ncol(rulset) < 4) {
error_message="Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation"
print(error_message)
stop(error_message)
}
- listArguments4annotate = append(listArguments4annotate,
+ args4annotate = append(args4annotate,
list(rules=rulset))
}
}
# launch annotate
- xa = do.call("annotate", listArguments4annotate)
- peakList=getPeaklist(xa,intval=listArguments[["intval"]])
+ xa = do.call("annotate", args4annotate)
+ peakList=getPeaklist(xa,intval=args$intval)
peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
# --- Multi condition : diffreport ---
diffrepOri=NULL
- if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))>=2) {
+ if (!is.null(args$runDiffreport) & nlevels(sampclass(xset))>=2) {
#Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
res=try(is.null(xset@filled))
classes=levels(sampclass(xset))
@@ -133,7 +159,10 @@
if(i+n <= length(classes)){
filebase=paste(classes[i],class2=classes[i+n],sep="-vs-")
- diffrep=diffreport(object=xset,class1=classes[i],class2=classes[i+n],filebase=filebase,eicmax=listArguments[["eicmax"]],eicwidth=listArguments[["eicwidth"]],sortpval=TRUE,value=listArguments[["value"]],h=listArguments[["h"]],w=listArguments[["w"]],mzdec=listArguments[["mzdec"]],missing=0)
+ diffrep=diffreport(
+ object=xset,class1=classes[i],class2=classes[i+n],
+ filebase=filebase,eicmax=args$eicmax,eicwidth=args$eicwidth,
+ sortpval=TRUE,value=args$value,h=args$h,w=args$w,mzdec=args$mzdec,missing=0)
diffrepOri = diffrep
@@ -145,37 +174,37 @@
diffrep = merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F)
diffrep = cbind(diffrep[,!(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))],diffrep[,(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))])
- diffrep = RTSecondToMinute(diffrep, listArguments[["convertRTMinute"]])
- diffrep = formatIonIdentifiers(diffrep, numDigitsRT=listArguments[["numDigitsRT"]], numDigitsMZ=listArguments[["numDigitsMZ"]])
+ diffrep = RTSecondToMinute(diffrep, args$convertRTMinute)
+ diffrep = formatIonIdentifiers(diffrep, numDigitsRT=args$numDigitsRT, numDigitsMZ=args$numDigitsMZ)
- if(listArguments[["sortpval"]]){
+ if(args$sortpval){
diffrep=diffrep[order(diffrep$pvalue), ]
}
dir.create("tabular", showWarnings = FALSE)
write.table(diffrep, sep="\t", quote=FALSE, row.names=FALSE, file=paste("tabular/",filebase,"_tsv.tabular",sep=""))
- if (listArguments[["eicmax"]] != 0) {
- if (listArguments[["png2"]] == "pdf")
+ if (args$eicmax != 0) {
+ if (args$png2 == "pdf")
diffreport_png2pdf(filebase)
}
}
}
}
- if (listArguments[["png2"]] == "zip")
+ if (args$png2 == "zip")
diffreport_png2zip()
- if (listArguments[["tabular2"]] == "zip")
+ if (args$tabular2 == "zip")
diffreport_tabular2zip()
}
# --- variableMetadata ---
variableMetadata=peakList[,!(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]
- variableMetadata = RTSecondToMinute(variableMetadata, listArguments[["convertRTMinute"]])
- variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=listArguments[["numDigitsRT"]], numDigitsMZ=listArguments[["numDigitsMZ"]])
+ variableMetadata = RTSecondToMinute(variableMetadata, args$convertRTMinute)
+ variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=args$numDigitsRT, numDigitsMZ=args$numDigitsMZ)
# if we have 2 conditions, we keep stat of diffrep
- if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))==2) {
+ if (!is.null(args$runDiffreport) & nlevels(sampclass(xset))==2) {
variableMetadata = merge(variableMetadata, diffrep[,c("name","fold","tstat","pvalue")],by.x="name", by.y="name", sort=F)
- if(exists("listArguments[[\"sortpval\"]]")){
+ if(exists("args[[\"sortpval\"]]")){
variableMetadata=variableMetadata[order(variableMetadata$pvalue), ]
}
}
@@ -188,7 +217,9 @@
}
-combinexsAnnos_function <- function(xaP, xaN, listOFlistArgumentsP,listOFlistArgumentsN, diffrepP=NULL,diffrepN=NULL,pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, convertRTMinute=F, numDigitsMZ=0, numDigitsRT=0, variableMetadataOutput="variableMetadata.tsv"){
+combinexsAnnos_function <- function(xaP, xaN, diffrepP=NULL,diffrepN=NULL,
+ pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, convertRTMinute=F, numDigitsMZ=0,
+ numDigitsRT=0, variableMetadataOutput="variableMetadata.tsv"){
#Load the two Rdata to extract the xset objects from positive and negative mode
cat("\tObject xset from positive mode\n")
@@ -215,11 +246,9 @@
if(pos){
xa=xaP
- listOFlistArgumentsP=listOFlistArguments
mode="neg. Mode"
} else {
xa=xaN
- listOFlistArgumentsN=listOFlistArguments
mode="pos. Mode"
}
@@ -256,22 +285,22 @@
}
# This function get the raw file path from the arguments
-getRawfilePathFromArguments <- function(singlefile, zipfile, listArguments) {
- if (!is.null(listArguments[["zipfile"]])) zipfile = listArguments[["zipfile"]]
- if (!is.null(listArguments[["zipfilePositive"]])) zipfile = listArguments[["zipfilePositive"]]
- if (!is.null(listArguments[["zipfileNegative"]])) zipfile = listArguments[["zipfileNegative"]]
+getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
+ if (!is.null(args$zipfile)) zipfile = args$zipfile
+ if (!is.null(args$zipfilePositive)) zipfile = args$zipfilePositive
+ if (!is.null(args$zipfileNegative)) zipfile = args$zipfileNegative
- if (!is.null(listArguments[["singlefile_galaxyPath"]])) {
- singlefile_galaxyPaths = listArguments[["singlefile_galaxyPath"]];
- singlefile_sampleNames = listArguments[["singlefile_sampleName"]]
+ if (!is.null(args$singlefile_galaxyPath)) {
+ singlefile_galaxyPaths = args$singlefile_galaxyPath;
+ singlefile_sampleNames = args$singlefile_sampleName
}
- if (!is.null(listArguments[["singlefile_galaxyPathPositive"]])) {
- singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathPositive"]];
- singlefile_sampleNames = listArguments[["singlefile_sampleNamePositive"]]
+ if (!is.null(args$singlefile_galaxyPathPositive)) {
+ singlefile_galaxyPaths = args$singlefile_galaxyPathPositive;
+ singlefile_sampleNames = args$singlefile_sampleNamePositive
}
- if (!is.null(listArguments[["singlefile_galaxyPathNegative"]])) {
- singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathNegative"]];
- singlefile_sampleNames = listArguments[["singlefile_sampleNameNegative"]]
+ if (!is.null(args$singlefile_galaxyPathNegative)) {
+ singlefile_galaxyPaths = args$singlefile_galaxyPathNegative;
+ singlefile_sampleNames = args$singlefile_sampleNameNegative
}
if (exists("singlefile_galaxyPaths")){
singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,","))
@@ -284,10 +313,13 @@
singlefile[[singlefile_sampleName]] = singlefile_galaxyPath
}
}
- for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
- listArguments[[argument]]=NULL
+ for (argument in c("zipfile", "zipfilePositive", "zipfileNegative",
+ "singlefile_galaxyPath", "singlefile_sampleName",
+ "singlefile_galaxyPathPositive", "singlefile_sampleNamePositive",
+ "singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
+ args[[argument]]=NULL
}
- return(list(zipfile=zipfile, singlefile=singlefile, listArguments=listArguments))
+ return(list(zipfile=zipfile, singlefile=singlefile, args=args))
}
diff -r 2184c0435edf -r db9bc2c27a0a macros.xml
--- a/macros.xml Fri Apr 12 10:45:52 2019 -0400
+++ b/macros.xml Fri Jul 26 16:00:18 2019 -0400
@@ -15,9 +15,7 @@
-
- LC_ALL=C Rscript $__tool_directory__/CAMERA.r
-
+ LC_ALL=C Rscript $__tool_directory__/
diff -r 2184c0435edf -r db9bc2c27a0a repository_dependencies.xml
--- a/repository_dependencies.xml Fri Apr 12 10:45:52 2019 -0400
+++ b/repository_dependencies.xml Fri Jul 26 16:00:18 2019 -0400
@@ -1,5 +1,5 @@
-
+
\ No newline at end of file