Mercurial > repos > davidecangelosi > pipe_t

changeset 5:29a8df9f543d draft

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planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit a52ad1b746d5e5042b2114f5a9228d157b0e4787
author davidecangelosi
date Mon, 06 May 2019 06:33:33 -0400
parents e248cd7769e8
children d1cabb2bc795
files pipe-t.R
diffstat 1 files changed, 2 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/pipe-t.R	Mon May 06 06:31:30 2019 -0400
+++ b/pipe-t.R	Mon May 06 06:33:33 2019 -0400
@@ -393,7 +393,8 @@
       raw<- readCtDataDav(files = as.vector(files$sampleName), header=FALSE,  format="plain", path = path, sample.info=phenoData,n.features = as.numeric(nfeatures))
     },
     "SDS"={
-      columns<- list(feature=3, Ct=6, flag=11)
+      #columns<- list(feature=3, Ct=6, flag=11)
+      columns <-SDS = list(flag = "Omit",feature = "Detector", type = "Task", position = "Wells", Ct = "Ct")
       metadata <- data.frame(labelDescription = c("sampleName", "Treatment"),  row.names = c("sampleName", "Treatment"))
       phenoData <- new("AnnotatedDataFrame", data = files, varMetadata = metadata)
       rownames(phenoData)=as.vector(files$sampleName)