Mercurial > repos > galaxyp > psm_to_sam

}
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")
author	galaxyp
date	Thu, 14 Jan 2016 18:13:18 -0500
parents
children