diff lib.r @ 31:281786a7b9a2 draft

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

--- a/lib.r	Thu Mar 01 04:16:45 2018 -0500
+++ b/lib.r	Mon Mar 05 04:17:36 2018 -0500
@@ -52,7 +52,7 @@
 
 #@author G. Le Corguille
 # Draw the plotChromPeakDensity 3 per page in a pdf file
-getPlotChromPeakDensity <- function(xdata) {
+getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
     pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
 
     par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
@@ -62,7 +62,9 @@
 
     xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
     for (i in 1:nrow(featureDefinitions(xdata))) {
-        plotChromPeakDensity(xdata, mz=c(featureDefinitions(xdata)[i,]$mzmin,featureDefinitions(xdata)[i,]$mzmax), col=group_colors, pch=16, xlim=xlim)
+        mzmin = featureDefinitions(xdata)[i,]$mzmin
+        mzmax = featureDefinitions(xdata)[i,]$mzmax
+        plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
         legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
     }
 
@@ -431,7 +433,7 @@
     files[exists] <- sub("//","/",files[exists])
 
     # WHAT IS ON THE FILESYSTEM
-    filesystem_filepaths <- system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T)
+    filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
     filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
 
     # COMPARISON
@@ -461,7 +463,7 @@
 checkXmlStructure <- function (directory) {
     cat("Checking XML structure...\n")
 
-    cmd <- paste("IFS=$'\n'; for xml in $(find",directory,"-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
+    cmd <- paste0("IFS=$'\n'; for xml in $(find '",directory,"' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
     capture <- system(cmd, intern=TRUE)
 
     if (length(capture)>0){
@@ -480,7 +482,7 @@
     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)
+    l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
     for (i in l){
         cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
         capture <- suppressWarnings(system(cmd, intern=TRUE))
@@ -538,8 +540,8 @@
         singlefile_sampleNames <- args$singlefile_sampleNameNegative
     }
     if (exists("singlefile_galaxyPaths")){
-        singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,","))
-        singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,","))
+        singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
+        singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))
 
         singlefile <- NULL
         for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {