# HG changeset patch
# User lecorguille
# Date 1486303022 18000
# Node ID 20a75ba4345b9b8dec3207308bfec8fc9242f922
# Parent  c04568596f4031f05f2f6c1b12a1546dc17ad428
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907

diff -r c04568596f40 -r 20a75ba4345b README.rst
--- a/README.rst	Mon Jan 30 08:51:40 2017 -0500
+++ b/README.rst	Sun Feb 05 08:57:02 2017 -0500
@@ -2,6 +2,10 @@
 Changelog/News
 --------------
 
+**Version 2.1.0 - 03/02/2017**
+
+- IMPROVEMENT: xcms.retcor can deal with merged individual data
+
 **Version 2.0.8 - 22/12/2016**
 
 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
@@ -31,12 +35,3 @@
 
 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
 
-
-Test Status
------------
-
-Planemo test using conda: passed
-
-Planemo test using source env.sh: passed
-
-Planemo shed_test : passed
diff -r c04568596f40 -r 20a75ba4345b abims_xcms_retcor.xml
--- a/abims_xcms_retcor.xml	Mon Jan 30 08:51:40 2017 -0500
+++ b/abims_xcms_retcor.xml	Sun Feb 05 08:57:02 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.8">
+<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.1.0">
 
     <description>Retention Time Correction using retcor function from xcms R package </description>
 
@@ -33,7 +33,7 @@
             #end if
         #end if
 
-        @COMMAND_ZIPFILE_LOAD@
+        @COMMAND_FILE_LOAD@
 
         @COMMAND_LOG_EXIT@
     ]]></command>
@@ -82,7 +82,7 @@
             </when>
         </conditional>
 
-        <expand macro="zipfile_load"/>
+        <expand macro="file_load"/>
 
     </inputs>
 
@@ -133,8 +133,33 @@
             <param name="methods|options|span" value="0.2"/>
             <param name="methods|options|family" value="gaussian"/>
             <param name="methods|options|plottype" value="deviation"/>
-            <param name="zipfile_load_conditional|zipfile_load_select" value="yes" />
-            <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip"  ftype="zip" />
+            <param name="file_load_conditional|file_load_select" value="yes" />
+            <param name="file_load_conditional|inputs|input" value="zip_file" />
+            <param name="file_load_conditional|inputs|zip_file" value="faahKO_reduce.zip"  ftype="zip" />
+            <output name="log">
+                <assert_contents>
+                    <has_text text="object with 4 samples" />
+                    <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
+                    <has_text text="Mass range: 200.1-600 m/z" />
+                    <has_text text="Peaks: 9251 (about 2313 per sample)" />
+                    <has_text text="Peak Groups: 0" />
+                    <has_text text="Sample classes: KO, WT" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="image" value="faahKO-single-class.xset.group.RData"/>
+            <param name="methods|method" value="peakgroups"/>
+            <param name="methods|smooth" value="loess"/>
+            <param name="methods|extra" value="1"/>
+            <param name="methods|missing" value="1"/>
+            <param name="methods|options|option" value="show"/>
+            <param name="methods|options|span" value="0.2"/>
+            <param name="methods|options|family" value="gaussian"/>
+            <param name="methods|options|plottype" value="deviation"/>
+            <param name="file_load_conditional|file_load_select" value="yes" />
+            <param name="file_load_conditional|inputs|input" value="single_file" />
+            <param name="file_load_conditional|inputs|single_file" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF"  ftype="netcdf" />
             <output name="log">
                 <assert_contents>
                     <has_text text="object with 4 samples" />
@@ -298,6 +323,10 @@
 Changelog/News
 --------------
 
+**Version 2.1.0 - 03/02/2017**
+
+- IMPROVEMENT: xcms.retcor can deal with merged individual data
+
 **Version 2.0.8 - 22/12/2016**
 
 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
diff -r c04568596f40 -r 20a75ba4345b lib.r
--- a/lib.r	Mon Jan 30 08:51:40 2017 -0500
+++ b/lib.r	Sun Feb 05 08:57:02 2017 -0500
@@ -36,11 +36,11 @@
 getPeaklistW4M <- function(xset, intval="into",convertRTMinute=F,numDigitsMZ=4,numDigitsRT=0,variableMetadataOutput,dataMatrixOutput) {
     groups <- xset@groups
     values <- groupval(xset, "medret", value=intval)
-    
+
     # renamming of the column rtmed to rt to fit with camera peaklist function output
     colnames(groups)[colnames(groups)=="rtmed"] <- "rt"
     colnames(groups)[colnames(groups)=="mzmed"] <- "mz"
-    
+
     ids <- formatIonIdentifiers(groups, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
     groups = RTSecondToMinute(groups, convertRTMinute)
 
@@ -57,138 +57,139 @@
 
 #@author Y. Guitton
 getBPC <- function(file,rtcor=NULL, ...) {
-  object <- xcmsRaw(file)
-  sel <- profRange(object, ...)
-  cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE]))
-  #plotChrom(xcmsRaw(file), base=T)
+    object <- xcmsRaw(file)
+    sel <- profRange(object, ...)
+    cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE]))
+    #plotChrom(xcmsRaw(file), base=T)
 }
 
 #@author Y. Guitton
 getBPCs <- function (xcmsSet=NULL, pdfname="BPCs.pdf",rt=c("raw","corrected"), scanrange=NULL) {
-  cat("Creating BIC pdf...\n")
+    cat("Creating BIC pdf...\n")
 
-  if (is.null(xcmsSet)) {
-    cat("Enter an xcmsSet \n")
-    stop()
-  } else {
-    files <- filepaths(xcmsSet)
-  }
+    if (is.null(xcmsSet)) {
+        cat("Enter an xcmsSet \n")
+        stop()
+    } else {
+        files <- filepaths(xcmsSet)
+    }
 
-  class<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class
+    phenoDataClass<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class
 
-  classnames<-vector("list",length(class))
-  for (i in 1:length(class)){
-    classnames[[i]]<-which( xcmsSet@phenoData[,1]==class[i])
-  }
+    classnames<-vector("list",length(phenoDataClass))
+    for (i in 1:length(phenoDataClass)){
+        classnames[[i]]<-which( xcmsSet@phenoData[,1]==phenoDataClass[i])
+    }
 
-  N <- dim(phenoData(xcmsSet))[1]
+    N <- dim(phenoData(xcmsSet))[1]
 
-  TIC <- vector("list",N)
+    TIC <- vector("list",N)
 
 
-  for (j in 1:N) {
+    for (j in 1:N) {
 
-    TIC[[j]] <- getBPC(files[j])
-    #good for raw
-    # seems strange for corrected
-    #errors if scanrange used in xcmsSetgeneration
-    if (!is.null(xcmsSet) && rt == "corrected")
-    rtcor <- xcmsSet@rt$corrected[[j]] else
-    rtcor <- NULL
+        TIC[[j]] <- getBPC(files[j])
+        #good for raw
+        # seems strange for corrected
+        #errors if scanrange used in xcmsSetgeneration
+        if (!is.null(xcmsSet) && rt == "corrected")
+            rtcor <- xcmsSet@rt$corrected[[j]]
+        else
+            rtcor <- NULL
 
-    TIC[[j]] <- getBPC(files[j],rtcor=rtcor)
-    # TIC[[j]][,1]<-rtcor
-  }
+        TIC[[j]] <- getBPC(files[j],rtcor=rtcor)
+        # TIC[[j]][,1]<-rtcor
+    }
 
 
 
-  pdf(pdfname,w=16,h=10)
-  cols <- rainbow(N)
-  lty = 1:N
-  pch = 1:N
-  #search for max x and max y in BPCs
-  xlim = range(sapply(TIC, function(x) range(x[,1])))
-  ylim = range(sapply(TIC, function(x) range(x[,2])))
-  ylim = c(-ylim[2], ylim[2])
+    pdf(pdfname,w=16,h=10)
+    cols <- rainbow(N)
+    lty = 1:N
+    pch = 1:N
+    #search for max x and max y in BPCs
+    xlim = range(sapply(TIC, function(x) range(x[,1])))
+    ylim = range(sapply(TIC, function(x) range(x[,2])))
+    ylim = c(-ylim[2], ylim[2])
 
 
-  ##plot start
+    ##plot start
 
-  if (length(class)>2){
-    for (k in 1:(length(class)-1)){
-      for (l in (k+1):length(class)){
-        #print(paste(class[k],"vs",class[l],sep=" "))
-        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")
+    if (length(phenoDataClass)>2){
+        for (k in 1:(length(phenoDataClass)-1)){
+            for (l in (k+1):length(phenoDataClass)){
+                #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" "))
+                plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
+                colvect<-NULL
+                for (j in 1:length(classnames[[k]])) {
+                    tic <- TIC[[classnames[[k]][j]]]
+                    # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
+                    points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
+                    colvect<-append(colvect,cols[classnames[[k]][j]])
+                }
+                for (j in 1:length(classnames[[l]])) {
+                    # i=class2names[j]
+                    tic <- TIC[[classnames[[l]][j]]]
+                    points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
+                    colvect<-append(colvect,cols[classnames[[l]][j]])
+                }
+                legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
+            }
+        }
+    }#end if length >2
+
+    if (length(phenoDataClass)==2){
+        k=1
+        l=2
         colvect<-NULL
+        plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
+
         for (j in 1:length(classnames[[k]])) {
-          tic <- TIC[[classnames[[k]][j]]]
-          # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
-          points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
-          colvect<-append(colvect,cols[classnames[[k]][j]])
+
+            tic <- TIC[[classnames[[k]][j]]]
+            # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
+            points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
+            colvect<-append(colvect,cols[classnames[[k]][j]])
         }
         for (j in 1:length(classnames[[l]])) {
-          # i=class2names[j]
-          tic <- TIC[[classnames[[l]][j]]]
-          points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
-          colvect<-append(colvect,cols[classnames[[l]][j]])
+            # i=class2names[j]
+            tic <- TIC[[classnames[[l]][j]]]
+            points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
+            colvect<-append(colvect,cols[classnames[[l]][j]])
         }
         legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
-      }
-    }
-  }#end if length >2
+
+    }#end length ==2
 
-  if (length(class)==2){
-    k=1
-    l=2
-    colvect<-NULL
-    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")
-
-    for (j in 1:length(classnames[[k]])) {
+    #case where only one class
+    if (length(phenoDataClass)==1){
+        k=1
+        ylim = range(sapply(TIC, function(x) range(x[,2])))
+        colvect<-NULL
+        plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
 
-      tic <- TIC[[classnames[[k]][j]]]
-      # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
-      points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
-      colvect<-append(colvect,cols[classnames[[k]][j]])
-    }
-    for (j in 1:length(classnames[[l]])) {
-      # i=class2names[j]
-      tic <- TIC[[classnames[[l]][j]]]
-      points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
-      colvect<-append(colvect,cols[classnames[[l]][j]])
-    }
-    legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
-
-  }#end length ==2
+        for (j in 1:length(classnames[[k]])) {
+            tic <- TIC[[classnames[[k]][j]]]
+            # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
+            points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
+            colvect<-append(colvect,cols[classnames[[k]][j]])
+        }
 
-  #case where only one class
-  if (length(class)==1){
-    k=1
-		ylim = range(sapply(TIC, function(x) range(x[,2])))
-    colvect<-NULL
-    plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",class[k], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
+        legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch)
+
+    }#end length ==1
 
-    for (j in 1:length(classnames[[k]])) {
-      tic <- TIC[[classnames[[k]][j]]]
-      # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
-      points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
-      colvect<-append(colvect,cols[classnames[[k]][j]])
-    }
+    dev.off() #pdf(pdfname,w=16,h=10)
 
-    legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch)
-
-  }#end length ==1
-
-  dev.off() #pdf(pdfname,w=16,h=10)
-
-  invisible(TIC)
+    invisible(TIC)
 }
 
 
 
 #@author Y. Guitton
 getTIC <- function(file,rtcor=NULL) {
-  object <- xcmsRaw(file)
-  cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object,mzrange=range(object@env$mz))$intensity)
+    object <- xcmsRaw(file)
+    cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object,mzrange=range(object@env$mz))$intensity)
 }
 
 ##
@@ -196,114 +197,112 @@
 ##
 #@author Y. Guitton
 getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf",rt=c("raw","corrected")) {
-  cat("Creating TIC pdf...\n")
+    cat("Creating TIC pdf...\n")
 
-  if (is.null(xcmsSet)) {
-    filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
-    filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
-    if (is.null(files))
-      files <- getwd()
-    info <- file.info(files)
-    listed <- list.files(files[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
-    files <- c(files[!info$isdir], listed)
-  } else {
-    files <- filepaths(xcmsSet)
-  }
-
-  class<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class
+    if (is.null(xcmsSet)) {
+        filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
+        filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
+        if (is.null(files))
+            files <- getwd()
+        info <- file.info(files)
+        listed <- list.files(files[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
+        files <- c(files[!info$isdir], listed)
+    } else {
+        files <- filepaths(xcmsSet)
+    }
 
-  classnames<-vector("list",length(class))
-  for (i in 1:length(class)){
-    classnames[[i]]<-which( xcmsSet@phenoData[,1]==class[i])
-  }
+    phenoDataClass<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class
+    classnames<-vector("list",length(phenoDataClass))
+    for (i in 1:length(phenoDataClass)){
+        classnames[[i]]<-which( xcmsSet@phenoData[,1]==phenoDataClass[i])
+    }
 
-  N <- length(files)
-  TIC <- vector("list",N)
+    N <- length(files)
+    TIC <- vector("list",N)
 
-  for (i in 1:N) {
-    if (!is.null(xcmsSet) && rt == "corrected")
-      rtcor <- xcmsSet@rt$corrected[[i]] else
-    rtcor <- NULL
-    TIC[[i]] <- getTIC(files[i],rtcor=rtcor)
-  }
+    for (i in 1:N) {
+        if (!is.null(xcmsSet) && rt == "corrected")
+            rtcor <- xcmsSet@rt$corrected[[i]] else
+        rtcor <- NULL
+        TIC[[i]] <- getTIC(files[i],rtcor=rtcor)
+    }
 
-  pdf(pdfname,w=16,h=10)
-  cols <- rainbow(N)
-  lty = 1:N
-  pch = 1:N
-  #search for max x and max y in TICs
-  xlim = range(sapply(TIC, function(x) range(x[,1])))
-  ylim = range(sapply(TIC, function(x) range(x[,2])))
-  ylim = c(-ylim[2], ylim[2])
+    pdf(pdfname,w=16,h=10)
+    cols <- rainbow(N)
+    lty = 1:N
+    pch = 1:N
+    #search for max x and max y in TICs
+    xlim = range(sapply(TIC, function(x) range(x[,1])))
+    ylim = range(sapply(TIC, function(x) range(x[,2])))
+    ylim = c(-ylim[2], ylim[2])
 
 
-  ##plot start
-  if (length(class)>2){
-    for (k in 1:(length(class)-1)){
-      for (l in (k+1):length(class)){
-        #print(paste(class[k],"vs",class[l],sep=" "))
-        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")
+    ##plot start
+    if (length(phenoDataClass)>2){
+        for (k in 1:(length(phenoDataClass)-1)){
+            for (l in (k+1):length(phenoDataClass)){
+                #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" "))
+                plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC")
+                colvect<-NULL
+                for (j in 1:length(classnames[[k]])) {
+                    tic <- TIC[[classnames[[k]][j]]]
+                    # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
+                    points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
+                    colvect<-append(colvect,cols[classnames[[k]][j]])
+                }
+                for (j in 1:length(classnames[[l]])) {
+                    # i=class2names[j]
+                    tic <- TIC[[classnames[[l]][j]]]
+                    points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
+                    colvect<-append(colvect,cols[classnames[[l]][j]])
+                }
+                legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
+            }
+        }
+    }#end if length >2
+    if (length(phenoDataClass)==2){
+        k=1
+        l=2
+
+        plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC")
         colvect<-NULL
         for (j in 1:length(classnames[[k]])) {
-
-          tic <- TIC[[classnames[[k]][j]]]
-          # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
-          points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
-          colvect<-append(colvect,cols[classnames[[k]][j]])
+            tic <- TIC[[classnames[[k]][j]]]
+            # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
+            points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
+            colvect<-append(colvect,cols[classnames[[k]][j]])
         }
         for (j in 1:length(classnames[[l]])) {
-          # i=class2names[j]
-          tic <- TIC[[classnames[[l]][j]]]
-          points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
-          colvect<-append(colvect,cols[classnames[[l]][j]])
+            # i=class2names[j]
+            tic <- TIC[[classnames[[l]][j]]]
+            points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
+            colvect<-append(colvect,cols[classnames[[l]][j]])
         }
         legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
-      }
-    }
-  }#end if length >2
-  if (length(class)==2){
-    k=1
-    l=2
+
+    }#end length ==2
 
-    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")
-    colvect<-NULL
-    for (j in 1:length(classnames[[k]])) {
-      tic <- TIC[[classnames[[k]][j]]]
-      # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
-      points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
-      colvect<-append(colvect,cols[classnames[[k]][j]])
-    }
-    for (j in 1:length(classnames[[l]])) {
-      # i=class2names[j]
-      tic <- TIC[[classnames[[l]][j]]]
-      points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
-      colvect<-append(colvect,cols[classnames[[l]][j]])
-    }
-    legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
+    #case where only one class
+    if (length(phenoDataClass)==1){
+        k=1
+        ylim = range(sapply(TIC, function(x) range(x[,2])))
 
-  }#end length ==2
-
-  #case where only one class
-  if (length(class)==1){
-	  k=1
-	  ylim = range(sapply(TIC, function(x) range(x[,2])))
+        plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k], sep=""), xlab = "Retention Time (min)", ylab = "TIC")
+        colvect<-NULL
+        for (j in 1:length(classnames[[k]])) {
+            tic <- TIC[[classnames[[k]][j]]]
+            # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
+            points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
+            colvect<-append(colvect,cols[classnames[[k]][j]])
+        }
 
-	  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")
-    colvect<-NULL
-		for (j in 1:length(classnames[[k]])) {
-      tic <- TIC[[classnames[[k]][j]]]
-			# points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
-			points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
-      colvect<-append(colvect,cols[classnames[[k]][j]])
-	  }
+        legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch)
+
+    }#end length ==1
 
-		legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch)
-
-	}#end length ==1
+    dev.off() #pdf(pdfname,w=16,h=10)
 
-  dev.off() #pdf(pdfname,w=16,h=10)
-
-  invisible(TIC)
+    invisible(TIC)
 }
 
 
@@ -313,70 +312,70 @@
 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
 getSampleMetadata <- function(xcmsSet=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
-  cat("Creating the sampleMetadata file...\n")
-
-  #Create the sampleMetada dataframe
-  sampleMetadata=xset@phenoData
-  sampleNamesOrigin=rownames(sampleMetadata)
-  sampleNamesMakeNames=make.names(sampleNamesOrigin)
+    cat("Creating the sampleMetadata file...\n")
 
-  if (any(duplicated(sampleNamesMakeNames))) {
-    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())
-    for (sampleName in sampleNamesOrigin) {
-      write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
-    }
-    stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
-  }
-
-  if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
-    cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n")
-    for (sampleName in sampleNamesOrigin) {
-      cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
-    }
-  }
-
-  sampleMetadata$sampleMetadata=sampleNamesMakeNames
-  sampleMetadata=cbind(sampleMetadata["sampleMetadata"],sampleMetadata["class"]) #Reorder columns
-  rownames(sampleMetadata)=NULL
+    #Create the sampleMetada dataframe
+    sampleMetadata=xset@phenoData
+    sampleNamesOrigin=rownames(sampleMetadata)
+    sampleNamesMakeNames=make.names(sampleNamesOrigin)
 
-  #Create a list of files name in the current directory
-  list_files=xset@filepaths
-  #For each sample file, the following actions are done
-  for (file in list_files){
-    #Check if the file is in the CDF format
-    if (!mzR:::netCDFIsFile(file)){
-
-      # If the column isn't exist, with add one filled with NA
-      if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity=NA
+    if (any(duplicated(sampleNamesMakeNames))) {
+        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())
+        for (sampleName in sampleNamesOrigin) {
+            write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
+        }
+        stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
+    }
 
-      #Create a simple xcmsRaw object for each sample
-      xcmsRaw=xcmsRaw(file)
-      #Extract the polarity (a list of polarities)
-      polarity=xcmsRaw@polarity
-      #Verify if all the scans have the same polarity
-      uniq_list=unique(polarity)
-      if (length(uniq_list)>1){
-        polarity="mixed"
-      } else {
-        polarity=as.character(uniq_list)
-      }
-      #Transforms the character to obtain only the sample name
-      filename=basename(file)
-      library(tools)
-      samplename=file_path_sans_ext(filename)
-
-      #Set the polarity attribute
-      sampleMetadata$polarity[sampleMetadata$sampleMetadata==samplename]=polarity
-
-      #Delete xcmsRaw object because it creates a bug for the fillpeaks step
-      rm(xcmsRaw)
+    if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
+        cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n")
+        for (sampleName in sampleNamesOrigin) {
+            cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
+        }
     }
 
-  }
+    sampleMetadata$sampleMetadata=sampleNamesMakeNames
+    sampleMetadata=cbind(sampleMetadata["sampleMetadata"],sampleMetadata["class"]) #Reorder columns
+    rownames(sampleMetadata)=NULL
+
+    #Create a list of files name in the current directory
+    list_files=xset@filepaths
+    #For each sample file, the following actions are done
+    for (file in list_files){
+        #Check if the file is in the CDF format
+        if (!mzR:::netCDFIsFile(file)){
+
+            # If the column isn't exist, with add one filled with NA
+            if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity=NA
 
-  write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
+            #Create a simple xcmsRaw object for each sample
+            xcmsRaw=xcmsRaw(file)
+            #Extract the polarity (a list of polarities)
+            polarity=xcmsRaw@polarity
+            #Verify if all the scans have the same polarity
+            uniq_list=unique(polarity)
+            if (length(uniq_list)>1){
+                polarity="mixed"
+            } else {
+                polarity=as.character(uniq_list)
+            }
+            #Transforms the character to obtain only the sample name
+            filename=basename(file)
+            library(tools)
+            samplename=file_path_sans_ext(filename)
 
-  return(list("sampleNamesOrigin"=sampleNamesOrigin,"sampleNamesMakeNames"=sampleNamesMakeNames))
+            #Set the polarity attribute
+            sampleMetadata$polarity[sampleMetadata$sampleMetadata==samplename]=polarity
+
+            #Delete xcmsRaw object because it creates a bug for the fillpeaks step
+            rm(xcmsRaw)
+        }
+
+    }
+
+    write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
+
+    return(list("sampleNamesOrigin"=sampleNamesOrigin,"sampleNamesMakeNames"=sampleNamesMakeNames))
 
 }
 
@@ -386,29 +385,28 @@
 ##
 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
 checkFilesCompatibilityWithXcms <- function(directory) {
-  cat("Checking files filenames compatibilities with xmcs...\n")
-  # WHAT XCMS WILL FIND
-  filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
-  filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
-  info <- file.info(directory)
-  listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
-  files <- c(directory[!info$isdir], listed)
-  files_abs <- file.path(getwd(), files)
-  exists <- file.exists(files_abs)
-  files[exists] <- files_abs[exists]
-  files[exists] <- sub("//","/",files[exists])
+    cat("Checking files filenames compatibilities with xmcs...\n")
+    # WHAT XCMS WILL FIND
+    filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
+    filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
+    info <- file.info(directory)
+    listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
+    files <- c(directory[!info$isdir], listed)
+    files_abs <- file.path(getwd(), files)
+    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)]
+    # 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())
-    write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
-    stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
-
-  }
+    # 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())
+        write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
+        stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
+    }
 }
 
 
@@ -418,17 +416,17 @@
 ##
 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
 checkXmlStructure <- function (directory) {
-  cat("Checking XML structure...\n")
+    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 $xml;fi; done;")
-  capture=system(cmd,intern=TRUE)
+    cmd=paste("IFS=$'\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())
-    write(capture, stderr())
-    stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
-  }
+    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())
+        write(capture, stderr())
+        stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
+    }
 
 }
 
@@ -438,23 +436,23 @@
 ##
 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
 deleteXmlBadCharacters<- function (directory) {
-  cat("Checking Non ASCII characters in the XML...\n")
+    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)
-      print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
-      c=system(cmd,intern=TRUE)
-      capture=""
-      processed=T
+    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)
+            print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
+            c=system(cmd,intern=TRUE)
+            capture=""
+            processed=T
+        }
     }
-  }
-  if (processed) cat("\n\n")
-  return(processed)
+    if (processed) cat("\n\n")
+    return(processed)
 }
 
 
@@ -463,19 +461,19 @@
 ##
 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
 getMd5sum <- function (directory) {
-  cat("Compute md5 checksum...\n")
-  # WHAT XCMS WILL FIND
-  filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
-  filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
-  info <- file.info(directory)
-  listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
-  files <- c(directory[!info$isdir], listed)
-  exists <- file.exists(files)
-  files <- files[exists]
+    cat("Compute md5 checksum...\n")
+    # WHAT XCMS WILL FIND
+    filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
+    filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
+    info <- file.info(directory)
+    listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
+    files <- c(directory[!info$isdir], listed)
+    exists <- file.exists(files)
+    files <- files[exists]
 
-  library(tools)
+    library(tools)
 
-  #cat("\n\n")
+    #cat("\n\n")
 
-  return(as.matrix(md5sum(files)))
+    return(as.matrix(md5sum(files)))
 }
diff -r c04568596f40 -r 20a75ba4345b macros.xml
--- a/macros.xml	Mon Jan 30 08:51:40 2017 -0500
+++ b/macros.xml	Sun Feb 05 08:57:02 2017 -0500
@@ -7,6 +7,11 @@
             <requirement type="package" version="1.1_4">r-batch</requirement>
         </requirements>
     </xml>
+    <xml name="requirements_light">
+        <requirements>
+            <requirement type="package" version="1.46.0">bioconductor-xcms</requirement>
+        </requirements>
+    </xml>
     <xml name="stdio">
         <stdio>
             <exit_code range="1" level="fatal" />
@@ -27,24 +32,40 @@
 
     <!-- zipfile load for planemo test -->
 
-    <token name="@COMMAND_ZIPFILE_LOAD@">
-        #if $zipfile_load_conditional.zipfile_load_select == "yes":
-            #if $zipfile_load_conditional.zip_file:
-                zipfile $zipfile_load_conditional.zip_file
+    <token name="@COMMAND_FILE_LOAD@">
+        #if $file_load_conditional.file_load_select == "yes":
+            #if $file_load_conditional.inputs.input == "zip_file":
+                zipfile $file_load_conditional.inputs.zip_file
+            #else
+                #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_conditional.inputs.single_file ] )
+                #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_conditional.inputs.single_file ] )
+
+                singlefile_galaxyPath $singlefile_galaxyPath singlefile_sampleName $singlefile_sampleName
             #end if
         #end if
     </token>
 
-    <xml name="zipfile_load">
-        <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." >
+    <xml name="file_load">
+        <conditional name="file_load_conditional">
+            <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." >
                 <option value="no" >no need</option>
-                <option value="yes">yes</option>
+                <option value="yes" >yes</option>
             </param>
             <when value="no">
             </when>
             <when value="yes">
-                <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
+                <conditional name="inputs">
+                    <param name="input" type="select" label="Choose your inputs method" >
+                        <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>
+                        <option value="single_file">A mzXML or netCDF file from your history</option>
+                    </param>
+                    <when value="zip_file">
+                        <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
+                    </when>
+                    <when value="single_file">
+                        <param name="single_file" type="data" format="mzxml,netcdf" label="Single file"  multiple="true"/>
+                    </when>
+                </conditional>
             </when>
         </conditional>
     </xml>
@@ -54,7 +75,7 @@
     <token name="@HELP_AUTHORS@">
 .. class:: infomark
 
-**Authors**  Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu 
+**Authors**  Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu
 
 .. class:: infomark
 
diff -r c04568596f40 -r 20a75ba4345b planemo_test.sh
--- a/planemo_test.sh	Mon Jan 30 08:51:40 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-# Example of planemo command to launch test
-
-# -- Use of installed package environments
-# after having installing package on a local galaxy instance
-source /w/galaxy/dev/shed_tools_tool_dependency_dir/R/3.1.2/iuc/package_r_3_1_2/1ca39eb16186/env.sh
-source /w/galaxy/dev/shed_tools_tool_dependency_dir/bioconductor-xcms/1.44.0/lecorguille/package_bioconductor_xcms_1_44_0/0c38f7d43e08/env.sh
-planemo test --install_galaxy
-
-#All 1 test(s) executed passed.
-#abims_xcms_retcor[0]: passed
-
-
-# -- Use of conda dependencies
-planemo conda_init --conda_prefix /tmp/mc
-planemo conda_install --conda_prefix /tmp/mc . 
-planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution
-
-#All 1 test(s) executed passed.
-#abims_xcms_retcor[0]: passed
-
-
-# -- Use of shed_test
-planemo shed_test --install_galaxy --galaxy_branch "dev" -t testtoolshed
-#All 1 test(s) executed passed.
-#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/2.0.6[0]: passed
diff -r c04568596f40 -r 20a75ba4345b test-data/faahKO-single-class.xset.group.RData
Binary file test-data/faahKO-single-class.xset.group.RData has changed
diff -r c04568596f40 -r 20a75ba4345b test-data/ko15.CDF
Binary file test-data/ko15.CDF has changed
diff -r c04568596f40 -r 20a75ba4345b test-data/ko16.CDF
Binary file test-data/ko16.CDF has changed
diff -r c04568596f40 -r 20a75ba4345b test-data/wt15.CDF
Binary file test-data/wt15.CDF has changed
diff -r c04568596f40 -r 20a75ba4345b test-data/wt16.CDF
Binary file test-data/wt16.CDF has changed
diff -r c04568596f40 -r 20a75ba4345b xcms.r
--- a/xcms.r	Mon Jan 30 08:51:40 2017 -0500
+++ b/xcms.r	Sun Feb 05 08:57:02 2017 -0500
@@ -15,8 +15,8 @@
 #pkgs=c("xcms","batch")
 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch")
 for(pkg in pkgs) {
-  suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
-  cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
+    suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
+    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");
@@ -38,7 +38,7 @@
 
 #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
+    load(listArguments[["image"]]); listArguments[["image"]]=NULL
 }
 
 #Import the different functions
@@ -61,13 +61,13 @@
 
 xsetRdataOutput = paste(thefunction,"RData",sep=".")
 if (!is.null(listArguments[["xsetRdataOutput"]])){
-  xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL
+    xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL
 }
 
 #saving the specific parameters
 rplotspdf = "Rplots.pdf"
 if (!is.null(listArguments[["rplotspdf"]])){
-  rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
+    rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
 }
 sampleMetadataOutput = "sampleMetadata.tsv"
 if (!is.null(listArguments[["sampleMetadataOutput"]])){
@@ -75,28 +75,28 @@
 }
 variableMetadataOutput = "variableMetadata.tsv"
 if (!is.null(listArguments[["variableMetadataOutput"]])){
-  variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL
+    variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL
 }
 dataMatrixOutput = "dataMatrix.tsv"
 if (!is.null(listArguments[["dataMatrixOutput"]])){
-  dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL
+    dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL
 }
 if (!is.null(listArguments[["convertRTMinute"]])){
-  convertRTMinute = listArguments[["convertRTMinute"]]; listArguments[["convertRTMinute"]]=NULL
+    convertRTMinute = listArguments[["convertRTMinute"]]; listArguments[["convertRTMinute"]]=NULL
 }
 if (!is.null(listArguments[["numDigitsMZ"]])){
-  numDigitsMZ = listArguments[["numDigitsMZ"]]; listArguments[["numDigitsMZ"]]=NULL
+    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
+    intval = listArguments[["intval"]]; listArguments[["intval"]]=NULL
 }
 
 if (thefunction %in% c("xcmsSet","retcor")) {
-  ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL
-  bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL
+    ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL
+    bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL
 }
 
 #necessary to unzip .zip file uploaded to Galaxy
@@ -104,67 +104,75 @@
 
 
 if (!is.null(listArguments[["zipfile"]])){
-  zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
+    zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
 }
 
-if (!is.null(listArguments[["library"]])){
-  directory=listArguments[["library"]]; listArguments[["library"]]=NULL
-  if(!file.exists(directory)){
-    error_message=paste("Cannot access the directory:",directory,". Please verify if the directory exists or not.")
-    print(error_message)
-    stop(error_message)
-  }
+if (!is.null(listArguments[["singlefile_galaxyPath"]])){
+    singlefile_galaxyPaths = unlist(strsplit(listArguments[["singlefile_galaxyPath"]],",")); listArguments[["singlefile_galaxyPath"]]=NULL
+    singlefile_sampleNames = unlist(strsplit(listArguments[["singlefile_sampleName"]],",")); listArguments[["singlefile_sampleName"]]=NULL
+
+    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]
+        singlefile[[singlefile_sampleName]] = singlefile_galaxyPath
+    }
 }
 
 # We unzip automatically the chromatograms from the zip files.
 if (thefunction %in% c("xcmsSet","retcor","fillPeaks"))  {
-  if(exists("zipfile") && (zipfile!="")) {
-    if(!file.exists(zipfile)){
-      error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
-      print(error_message)
-      stop(error_message)
-    }
+    if(exists("singlefile") && (length("singlefile")>0)) {
+        for (singlefile_sampleName in names(singlefile)) {
+            singlefile_galaxyPath = singlefile[[singlefile_sampleName]]
+            if(!file.exists(singlefile_galaxyPath)){
+                error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
+                print(error_message); stop(error_message)
+            }
 
-    #list all file in the zip file
-    #zip_files=unzip(zipfile,list=T)[,"Name"]
+            file.symlink(singlefile_galaxyPath,singlefile_sampleName)
+        }
+        directory = "."
 
-
-    #unzip
-    suppressWarnings(unzip(zipfile, unzip="unzip"))
+        md5sumList=list("origin"=getMd5sum(directory))
 
-    #get the directory name
-    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
+    }
+    if(exists("zipfile") && (zipfile!="")) {
+        if(!file.exists(zipfile)){
+            error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
+            print(error_message)
+            stop(error_message)
+        }
 
-    cat("files_root_directory\t",directory,"\n")
+        #list all file in the zip file
+        #zip_files=unzip(zipfile,list=T)[,"Name"]
 
-    #
-    md5sumList=list("origin"=getMd5sum(directory))
+        #unzip
+        suppressWarnings(unzip(zipfile, unzip="unzip"))
 
-    # Check and fix if there are non ASCII characters. If so, they will be removed from the *mzXML mzML files.
-    # Remove because can create issue with some clean files
-    #@TODO: fix me
-    #if (deleteXmlBadCharacters(directory)) {
-    #  md5sumList=list("removalBadCharacters"=getMd5sum(directory))
-    #}
+        #get the directory name
+        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))
+    }
 }
 
 #addition of the directory to the list of arguments in the first position
 if (thefunction == "xcmsSet") {
-  checkXmlStructure(directory)
-  checkFilesCompatibilityWithXcms(directory)
-  listArguments=append(directory, listArguments)
+    checkXmlStructure(directory)
+    checkFilesCompatibilityWithXcms(directory)
+    listArguments=append(directory, listArguments)
 }
 
 
 #addition of xset object to the list of arguments in the first position
 if (exists("xset")){
-  listArguments=append(list(xset), listArguments)
+    listArguments=append(list(xset), listArguments)
 }
 
 cat("\n\n")
@@ -172,8 +180,6 @@
 
 
 
-
-
 # ----- MAIN PROCESSING INFO -----
 cat("\tMAIN PROCESSING INFO\n")
 
@@ -181,12 +187,12 @@
 #Verification of a group step before doing the fillpeaks job.
 
 if (thefunction == "fillPeaks") {
-  res=try(is.null(groupnames(xset)))
-  if (class(res) == "try-error"){
-    error<-geterrmessage()
-    write(error, stderr())
-    stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step")
-  }
+    res=try(is.null(groupnames(xset)))
+    if (class(res) == "try-error"){
+        error<-geterrmessage()
+        write(error, stderr())
+        stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step")
+    }
 
 }
 
@@ -194,7 +200,7 @@
 #dev.new(file="Rplots.pdf", width=16, height=12)
 pdf(file=rplotspdf, width=16, height=12)
 if (thefunction == "group") {
-  par(mfrow=c(2,2))
+    par(mfrow=c(2,2))
 }
 #else if (thefunction == "retcor") {
 #try to change the legend display
@@ -215,40 +221,40 @@
 
 if (thefunction  == "xcmsSet") {
 
-  #transform the files absolute pathways into relative pathways
-  xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths)
+    #transform the files absolute pathways into relative pathways
+    xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths)
 
-  if(exists("zipfile") && (zipfile!="")) {
+    if(exists("zipfile") && (zipfile!="")) {
 
-    #Modify the samples names (erase the path)
-    for(i in 1:length(sampnames(xset))){
+        #Modify the samples names (erase the path)
+        for(i in 1:length(sampnames(xset))){
 
-      sample_name=unlist(strsplit(sampnames(xset)[i], "/"))
-      sample_name=sample_name[length(sample_name)]
-      sample_name= unlist(strsplit(sample_name,"[.]"))[1]
-      sampnames(xset)[i]=sample_name
+            sample_name=unlist(strsplit(sampnames(xset)[i], "/"))
+            sample_name=sample_name[length(sample_name)]
+            sample_name= unlist(strsplit(sample_name,"[.]"))[1]
+            sampnames(xset)[i]=sample_name
+
+        }
 
     }
 
-  }
-
 }
 
 # -- 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)
+    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)
+    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("\t\tGET THE PEAK LIST\n")
+    getPeaklistW4M(xset,intval,convertRTMinute,numDigitsMZ,numDigitsRT,variableMetadataOutput,dataMatrixOutput)
 }
 
 
@@ -262,7 +268,7 @@
 
 
 #saving R data in .Rdata file to save the variables used in the present tool
-objects2save = c("xset","zipfile","listOFlistArguments","md5sumList","sampleNamesList")
+objects2save = c("xset","zipfile","singlefile","listOFlistArguments","md5sumList","sampleNamesList")
 save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput)
 
 cat("\n\n")