diff tool-data/.Rhistory @ 2:e1bb35f6ca28 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/.Rhistory	Thu Jan 14 18:13:18 2016 -0500
@@ -0,0 +1,512 @@
+}
+channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
+return(paste0(sample, "-", channel))
+}
+coreSampleNames = list()
+for(i in seq(2, length(multiplexData), 4))
+{
+firstGroupNum = 0.75 * i
+print(getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames))
+sampleNames[i-1] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\1\\4", sampleNames[i-1], perl=T)
+sampleNames[i] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\2\\4", sampleNames[i], perl=T)
+sampleNames[i+1] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\3\\4", sampleNames[i+1], perl=T)
+print(sampleNames[i-1])
+print(sampleNames[i])
+print(sampleNames[i+1])
+#ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
+#ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
+#ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
+}
+getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames)
+{
+sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T)
+if(is.null(coreSampleNames[[sample]]))
+{
+coreSampleNames[[sample]] = 1
+}
+else
+{
+sample = paste0(sample, incrementChar("A", coreSampleNames[[sample]]))
+coreSampleNames[[sample]] = coreSampleNames[[sample]] + 1
+}
+channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
+coreSampleNames <<- coreSampleNames
+return(paste0(sample, "-", channel))
+}
+coreSampleNames = list()
+for(i in seq(2, length(multiplexData), 4))
+{
+firstGroupNum = 0.75 * i
+print(getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames))
+sampleNames[i-1] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\1\\4", sampleNames[i-1], perl=T)
+sampleNames[i] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\2\\4", sampleNames[i], perl=T)
+sampleNames[i+1] = sub("(\\S+?)_(\\S+?)_(\\S+?)(\\.iTRAQ.\\d+)", "\\3\\4", sampleNames[i+1], perl=T)
+#print(sampleNames[i-1])
+#print(sampleNames[i])
+#print(sampleNames[i+1])
+#ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
+#ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
+#ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
+}
+sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))]
+incrementChar = function(c, step=1) { return(rawToChar(as.raw(as.integer(charToRaw(c))+step))); }
+getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames)
+{
+sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T)
+if(is.null(coreSampleNames[[sample]]))
+{
+coreSampleNames[[sample]] = 1
+}
+else
+{
+sample = paste0(sample, incrementChar("A", coreSampleNames[[sample]]))
+coreSampleNames[[sample]] = coreSampleNames[[sample]] + 1
+}
+channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
+coreSampleNames <<- coreSampleNames
+return(paste0(sample, "-", channel))
+}
+coreSampleNames = list()
+for(i in seq(2, length(multiplexData), 4))
+{
+firstGroupNum = 0.75 * i
+sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)
+sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames)
+sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames)
+print(sampleNames[i-1])
+print(sampleNames[i])
+print(sampleNames[i+1])
+#ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
+#ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
+#ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
+}
+sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))]
+incrementChar = function(c, step=1) { return(rawToChar(as.raw(as.integer(charToRaw(c))+step))); }
+getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames)
+{
+sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T)
+if(is.null(coreSampleNames[[sample]]))
+{
+coreSampleNames[[sample]] = 1
+}
+else
+{
+sample = paste0(sample, "-", incrementChar("A", coreSampleNames[[sample]]))
+coreSampleNames[[sample]] = coreSampleNames[[sample]] + 1
+}
+channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
+coreSampleNames <<- coreSampleNames
+return(paste0(sample, "-", channel))
+}
+coreSampleNames = list()
+for(i in seq(2, length(multiplexData), 4))
+{
+firstGroupNum = 0.75 * i
+sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)
+sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames)
+sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames)
+print(sampleNames[i-1])
+print(sampleNames[i])
+print(sampleNames[i+1])
+#ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
+#ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
+#ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
+}
+sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))]
+incrementChar = function(c, step=1) { return(rawToChar(as.raw(as.integer(charToRaw(c))+step))); }
+getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames)
+{
+sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T)
+if(is.null(coreSampleNames[[sample]]))
+{
+coreSampleNames[[sample]] = 1
+}
+else
+{
+oldCount = coreSampleNames[[sample]]
+sample = paste0(sample, "-", incrementChar("A", oldCount))
+coreSampleNames[[sample]] = oldCount + 1
+}
+channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
+coreSampleNames <<- coreSampleNames
+return(paste0(sample, "-", channel))
+}
+coreSampleNames = list()
+for(i in seq(2, length(multiplexData), 4))
+{
+firstGroupNum = 0.75 * i
+sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)
+sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames)
+sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames)
+print(sampleNames[i-1])
+print(sampleNames[i])
+print(sampleNames[i+1])
+#ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
+#ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
+#ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
+}
+sort(coreSampleNames)
+sort(coreSampleNames[1])
+coreSampleNames[1]
+coreSampleNames[2]
+coreSampleNames[1,]
+coreSampleNames[,1]
+simplify2array(coreSampleNames)
+order(coreSampleNames)
+order(coreSampleNames[1])
+sort(simplify2array(coreSampleNames))
+order(coreSampleNames)
+as.matrix(cores)
+as.matrix(coreSampleNames)
+order(as.matrix(coreSampleNames))
+names(as.matrix(coreSampleNames))
+names(coreSampleNames)
+sort(names(coreSampleNames))
+sort(sampleNames)
+sampleNames = sampleNames[c(rep(c(T,T,T,F), numSamples/3))]
+sort(sampleNames)
+ratios = matrix(nrow=dim(multiplexData)[1], ncol=numSamples, dimnames=list(multiplexData[,1], sampleNames))
+View(ratios)
+for(i in seq(2, length(multiplexData), 4))
+{
+firstGroupNum = 0.75 * i
+ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
+ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
+ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
+}
+View(ratios)
+filepath = "H:/data/CPTAC/TCGA-Broad-Breast/global-Broad.cct"
+outputFilepath = sub(".cct", "-demultiplexed-ratios.cct", filepath, fixed=T)
+source('~/.active-rstudio-document')
+write.csv(format(ratios, digits=4), file=outputFilepath, quote=F)
+demultiplexNetGestaltITRAQ_CCT = function(filepath)
+{
+outputFilepath = sub(".cct", "-demultiplexed-ratios.cct", filepath, fixed=T)
+multiplexData = read.table(filepath, sep="\t", header=T)
+numSamples = 0.75*(dim(multiplexData)[2]-1)
+sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))]
+coreSampleNames = list()
+for(i in seq(2, length(multiplexData), 4))
+{
+firstGroupNum = 0.75 * i
+sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)
+sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames)
+sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames)
+}
+sampleNames = sampleNames[c(rep(c(T,T,T,F), numSamples/3))]
+ratios = matrix(nrow=dim(multiplexData)[1], ncol=numSamples, dimnames=list(multiplexData[,1], sampleNames))
+for(i in seq(2, length(multiplexData), 4))
+{
+firstGroupNum = 0.75 * i
+ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
+ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
+ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
+}
+write.csv(format(ratios, digits=4), file=outputFilepath, quote=F)
+}
+source('~/.active-rstudio-document')
+source('~/.active-rstudio-document')
+write.table(format(ratios, digits=4), file=outputFilepath, quote=F, row.names=T, sep="\t")
+write.table(format(ratios, digits=4), file=outputFilepath, quote=F, row.names=T, col.names=T, sep="\t")
+write.table(format(cbind(rownames(ratios), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t")
+write.table(format(cbind(c("GeneSymbol", rownames(ratios)), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t")
+c("GeneSymbol", rownames(ratios))
+head(c("GeneSymbol", rownames(ratios)))
+cbind(c("GeneSymbol", rownames(ratios)), ratios), digits=4)
+cbind(c("GeneSymbol", rownames(ratios))
+)
+cbind(c("GeneSymbol", rownames(ratios)), ratios)
+write.table(format(cbind(c(GeneSymbol=rownames(ratios)), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t")
+write.table(format(cbind(c(GeneSymbol=rownames(ratios)), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t")
+write.table(format(cbind(GeneSymbol=rownames(ratios), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t")
+source('~/.active-rstudio-document')
+write.table(format(cbind(GeneSymbol=rownames(ratios), ratios), digits=4), file=outputFilepath, quote=F, row.names=F, sep="\t", options(digits=2))
+write.table(cbind(GeneSymbol=rownames(ratios), ratios), file=outputFilepath, quote=F, row.names=F, sep="\t", options(digits=4))
+options(digits=4)
+write.table(cbind(GeneSymbol=rownames(ratios), ratios), file=outputFilepath, quote=F, row.names=F, sep="\t")
+source('~/.active-rstudio-document')
+demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/phospho-Broad.cct")
+demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/phospho-Broad.cct")
+rm("*")
+rm("")
+rm
+rm()
+?rm
+getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames)
+{
+innerSampleNames = coreSampleNames
+sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T)
+if(is.null(innerSampleNames[[sample]]))
+{
+innerSampleNames[[sample]] = 1
+}
+else
+{
+oldCount = innerSampleNames[[sample]]
+sample = paste0(sample, "-", incrementChar("A", oldCount))
+innerSampleNames[[sample]] = oldCount + 1
+}
+channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
+eval.parent(substitute(coreSampleNames = innerSampleNames))
+return(paste0(sample, "-", channel))
+}
+demultiplexNetGestaltITRAQ_CCT = function(filepath)
+{
+outputFilepath = sub(".cct", "-demultiplexed-ratios.cct", filepath, fixed=T)
+multiplexData = read.table(filepath, sep="\t", header=T)
+numSamples = 0.75*(dim(multiplexData)[2]-1)
+sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))]
+coreSampleNames = list()
+for(i in seq(2, length(multiplexData), 4))
+{
+firstGroupNum = 0.75 * i
+sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)
+sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames)
+sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames)
+}
+sampleNames = sampleNames[c(rep(c(T,T,T,F), numSamples/3))]
+ratios = matrix(nrow=dim(multiplexData)[1], ncol=numSamples, dimnames=list(multiplexData[,1], sampleNames))
+for(i in seq(2, length(multiplexData), 4))
+{
+firstGroupNum = 0.75 * i
+ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
+ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
+ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
+}
+options(digits=4)
+write.table(cbind(GeneSymbol=rownames(ratios), ratios), file=outputFilepath, quote=F, row.names=F, sep="\t")
+}
+demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/phospho-Broad.cct")
+?substittue
+?substitute
+getMultiplexSampleName = function(mergedSampleName, tokenIndex, coreSampleNames)
+{
+innerSampleNames = coreSampleNames
+sample = sub("(\\S+?)_(\\S+?)_(\\S+?)\\.iTRAQ\\.\\d+", paste0("\\", tokenIndex), mergedSampleName, perl=T)
+if(is.null(innerSampleNames[[sample]]))
+{
+innerSampleNames[[sample]] = 1
+}
+else
+{
+oldCount = innerSampleNames[[sample]]
+sample = paste0(sample, "-", incrementChar("A", oldCount))
+innerSampleNames[[sample]] = oldCount + 1
+}
+channel = sub("\\S+?\\.(iTRAQ\\.\\d+)", "\\1", mergedSampleName, perl=T)
+eval.parent(substitute(coreSampleNames<-innerSampleNames))
+return(paste0(sample, "-", channel))
+}
+demultiplexNetGestaltITRAQ_CCT = function(filepath)
+{
+outputFilepath = sub(".cct", "-demultiplexed-ratios.cct", filepath, fixed=T)
+multiplexData = read.table(filepath, sep="\t", header=T)
+numSamples = 0.75*(dim(multiplexData)[2]-1)
+sampleNames = colnames(multiplexData)[-1]#[c(F, rep(c(T,T,T,F), numSamples/3))]
+coreSampleNames = list()
+for(i in seq(2, length(multiplexData), 4))
+{
+firstGroupNum = 0.75 * i
+sampleNames[i-1] = getMultiplexSampleName(sampleNames[i-1], 1, coreSampleNames)
+sampleNames[i] = getMultiplexSampleName(sampleNames[i], 2, coreSampleNames)
+sampleNames[i+1] = getMultiplexSampleName(sampleNames[i+1], 3, coreSampleNames)
+}
+sampleNames = sampleNames[c(rep(c(T,T,T,F), numSamples/3))]
+ratios = matrix(nrow=dim(multiplexData)[1], ncol=numSamples, dimnames=list(multiplexData[,1], sampleNames))
+for(i in seq(2, length(multiplexData), 4))
+{
+firstGroupNum = 0.75 * i
+ratios[,firstGroupNum] = ZeroSafeDivide(multiplexData[,i], multiplexData[,i+3])
+ratios[,firstGroupNum+1] = ZeroSafeDivide(multiplexData[,i+1], multiplexData[,i+3])
+ratios[,firstGroupNum+2] = ZeroSafeDivide(multiplexData[,i+2], multiplexData[,i+3])
+}
+options(digits=4)
+write.table(cbind(GeneSymbol=rownames(ratios), ratios), file=outputFilepath, quote=F, row.names=F, sep="\t")
+}
+demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/phospho-Broad.cct")
+demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-Broad-Breast/global-Broad.cct")
+demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-PNNL-Ovarian/phospho-PNNL.cct")
+demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-PNNL-Ovarian/global-PNNL.cct")
+demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-PNNL-Ovarian/phospho-PNNL.cct")
+demultiplexNetGestaltITRAQ_CCT("H:/data/CPTAC/TCGA-PNNL-Ovarian/global-PNNL.cct")
+ratios_ordered = ratios[,order(names(ratios))]
+ratios_ordered = ratios[order(names(ratios)),]
+names(ratios)
+colnames(ratios)
+ratios_ordered = ratios[order(colnames(ratios)),]
+ratios_ordered = ratios[,order(colnames(ratios))]
+View(ratios_ordered)
+source('~/.active-rstudio-document')
+source('~/.active-rstudio-document')
+source('~/.active-rstudio-document')
+source('~/.active-rstudio-document')
+biocLite("RGalaxy")
+source("https://bioconductor.org/biocLite.R")
+biocLite("RGalaxy")
+source('~/.active-rstudio-document')
+source('~/.active-rstudio-document')
+source('~/.active-rstudio-document')
+galaxyHome="/galaxy-central"
+galaxy("addTwoNumbers",
+galaxyConfig=
+GalaxyConfig(galaxyHome, "mytool", "Test Section",
+"testSectionId")
+)
+galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
+galaxy("addTwoNumbers",
+galaxyConfig=
+GalaxyConfig(galaxyHome, "mytool", "Test Section",
+"testSectionId")
+)
+galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
+galaxy("addTwoNumbers",
+galaxyConfig=
+GalaxyConfig(galaxyHome, "mytool", "Test Section",
+"testSectionId")
+)
+?GalaxyConfig
+galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
+galaxy("addTwoNumbers",
+galaxyConfig=
+GalaxyConfig(galaxyHome, "mytool", "Test Section",
+"testSectionId")
+)
+galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
+galaxy("addTwoNumbers",
+galaxyConfig=
+GalaxyConfig(galaxyHome, "mytool", "Test Section",
+"testSectionId")
+)
+source('~/.active-rstudio-document')
+galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
+galaxy("addTwoNumbers",
+galaxyConfig=
+GalaxyConfig(galaxyHome, "mytool", "Test Section",
+"testSectionId")
+)
+galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
+galaxy("addTwoNumbers",
+galaxyConfig=
+GalaxyConfig(galaxyHome, "mytool", "Test Section",
+"testSectionId")
+)
+galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
+galaxy("PrepareAnnotationGENCODE_g",
+galaxyConfig=
+GalaxyConfig(galaxyHome, "mytool", "Test Section",
+"testSectionId")
+)
+PrepareAnnotationGENCODE_g <- function() {}
+galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
+galaxy("PrepareAnnotationGENCODE_g",
+galaxyConfig=
+GalaxyConfig(galaxyHome, "mytool", "Test Section",
+"testSectionId")
+)
+PrepareAnnotationGENCODE_g <- function(gtfFile = GalaxyInputFile(required = TRUE),
+CDSfasta = GalaxyInputFile(required = TRUE),
+pepfasta = GalaxyInputFile(required = TRUE),
+annotation_path = GalaxyCharacterParam(required = TRUE),
+dbsnp = GalaxySelectParam(c(`First Choice` = "NULL", `Second Choice` =
+"snp135")), splice_matrix = GalaxyLogicalParam(checked = TRUE),
+COSMIC = GalaxyLogicalParam(checked = TRUE), ...)
+{
+}
+PrepareAnnotationGENCODE_g <- function(gtfFile = GalaxyInputFile(required = TRUE),
+CDSfasta = GalaxyInputFile(required = TRUE),
+pepfasta = GalaxyInputFile(required = TRUE),
+annotation_path = GalaxyCharacterParam(required = TRUE),
+dbsnp = GalaxySelectParam(c(`First Choice` = "NULL", `Second Choice` =
+"snp135")), splice_matrix = GalaxyLogicalParam(checked = TRUE),
+COSMIC = GalaxyLogicalParam(checked = TRUE), ...)
+{
+}
+galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
+galaxy("PrepareAnnotationGENCODE_g",
+galaxyConfig=
+GalaxyConfig(galaxyHome, "mytool", "Test Section",
+"testSectionId")
+)
+source('~/.active-rstudio-document')
+PrepareAnnotationGENCODE_g <- function(gtfFile = GalaxyInputFile(required = TRUE),
+CDSfasta = GalaxyInputFile(required = TRUE),
+pepfasta = GalaxyInputFile(required = TRUE),
+annotation_path = GalaxyCharacterParam(required = TRUE),
+dbsnp = GalaxySelectParam(c(`First Choice` = "NULL", `Second Choice` =
+"snp135")), splice_matrix = GalaxyLogicalParam(checked = TRUE),
+COSMIC = GalaxyLogicalParam(checked = TRUE), ...)
+{
+}
+galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
+galaxy("PrepareAnnotationGENCODE_g",
+galaxyConfig=
+GalaxyConfig(galaxyHome, "mytool", "Test Section",
+"testSectionId")
+)
+source('~/.active-rstudio-document')
+source('~/.active-rstudio-document')
+source('~/.active-rstudio-document')
+source('~/.active-rstudio-document')
+source('~/.active-rstudio-document')
+source('~/.active-rstudio-document')
+source('~/.active-rstudio-document')
+source('~/.active-rstudio-document')
+?wtf
+print "why doesn't this work"
+print( )"why doesn't this work")
+print("why doesn't this work")
+source('~/.active-rstudio-document')
+galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
+galaxy("addTwoNumbers",
+galaxyConfig=
+GalaxyConfig(galaxyHome, "mytool", "Test Section",
+"testSectionId")
+)
+source('~/.active-rstudio-document')
+source('~/.active-rstudio-document')
+PrepareAnnotationGENCODE <- function(gtfFile = GalaxyInputFile(required = TRUE),
+CDSfasta = GalaxyInputFile(required = TRUE),
+pepfasta = GalaxyInputFile(required = TRUE),
+annotation_path = GalaxyCharacterParam(required = TRUE),
+COSMIC = GalaxyLogicalParam(checked = TRUE),
+output = GalaxyOutput("sum", "txt"))
+{
+print("why doesn't this work")
+}
+source('~/.active-rstudio-document')
+source('~/.active-rstudio-document')
+source('~/.active-rstudio-document')
+library(RGalaxy)
+source('~/.active-rstudio-document')
+galaxyHome="C:\\Users\\chambem2\\.vagrant\\precise64\\bingomics-galaxy\\vagrant\\export\\src\\galaxy"
+galaxy("PrepareAnnotationGENCODE",
+galaxyConfig=
+GalaxyConfig(galaxyHome, "mytool", "Test Section",
+"testSectionId")
+)
+source('~/.active-rstudio-document')
+str(addTwoNumbers)
+addTwoNumbers
+packageName()
+packageName(addTwoNumbers)
+packageName("addTwoNumbers")
+source('~/.active-rstudio-document')
+source('~/.active-rstudio-document', echo=TRUE)
+source('~/.active-rstudio-document', echo=TRUE)
+str(addTwoNumbers)
+str(addTwoNumbers2)
+env(addTwoNumbers)
+environmentName
+environmentName()
+env.profile()
+namespace:base
+library(namespace)
+source('~/.active-rstudio-document', echo=TRUE)
+source("https://bioconductor.org/biocLite.R")
+biocLite("customProDB")
+library("customProDB", lib.loc="C:/Users/chambem2/Google Drive/Marvin Documents/R/win-library/3.1")
+setwd("C:/Users/chambem2/.vagrant/precise64/bingomics-galaxy/vagrant/export/src/tools-galaxyp-chambm/tools/bumbershoot/psm_to_sam/tool-data")
+bamFile <- system.file("extdata/bams", "test1_sort.bam", package="customProDB")
+easyRun(bamFile=bamFile, annotation_path=".")
+easyRun(bamFile=bamFile, annotation_path=".")
+easyRun(bamFile=bamFile, annotation_path=".", outfile_path=".", outfile_name="test.fasta")