Fix RScript input

workflow/apps/r/interactions.R

@@ -26,28 +26,28 @@ args <- commandArgs(TRUE)
 inputFile <- args[1]
 
 # Set output dir
-if (length(args) > 2) {
+if (length(args) >= 2) {
   outDir <- args[2]
 } else {
   outDir <- "/ZScores/" # for legacy workflow
 }
 
 # Set StudyInfo file path
-if (length(args) > 3) {
+if (length(args) >= 3) {
   studyInfo <- args[3]
 } else {
   studyInfo <- "../Code/StudyInfo.csv" # for legacy workflow
 }
 
 # Set SGDgeneList file path
-if (length(args) > 4) {
+if (length(args) >= 4) {
   SGDgeneList <- args[4]
 } else {
   SGDgeneList <- "../Code/SGD_features.tab" # for legacy workflow
 }
 
 # Set standard deviation
-if (length(args) > 5) {
+if (length(args) >= 5) {
   delBGFactor <- args[5]
 } else {
   # User prompt for std multiplier Value
@@ -78,11 +78,9 @@ expNumber <- as.numeric(sub("^.*?(\\d+)$", "\\1", getwd()))
 Labels[expNumber,3] <- delBGFactor
 write.csv(Labels,file=studyInfo,row.names = FALSE)
 
-###############################################################################
-################### BEGIN USER DATA SELECTION SECTION #########################
-###############################################################################
+# BEGIN USER DATA SELECTION SECTION
 
-#read in the data
+# Read in the data
 X <- read.delim(inputFile,skip=2,as.is=T,row.names=1,strip.white=TRUE)
 X <- X[!(X[[1]]%in%c("","Scan")),]
 #X <- X[!(X[[1]]%in%c(61:76)),]  #Remove dAmp plates which are Scans 61 thru 76