annotate sm_Tax4Fun.R @ 12:879bd8a024dc draft default tip

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1 # The function -------------------------------------
2 #---------------------------------------------------
3 GalaxyFrogsTax <- function(input.file,
4                       reference,
5                       output.file = "Tax4FunProfile.txt"
6                       ) {
7 library(Tax4Fun)
8 folderReferenceData<- reference  
9 
10 Tax4FunOutput<-Tax4Fun(importSilvaNgsData(input.file), folderReferenceData) # optionnal: fctProfiling = TRUE, refProfile = "UProc", shortReadMode = TRUE, normCopyNo = TRUE)
11 #folderReferenceData (required): a character vector with one character string indicating the folder location of the unzipped reference data. The reference data can be  obtained  from  the  Tax4Fun  website  http://tax4fun.gobics.de/  ("SILVA  Reference data").
12 #reference = "/galaxydata/galaxy-preprod/my_tools/sm_Tax4Fun/SILVA123/"
13 
14 Tax4FunProfile <- Tax4FunOutput$Tax4FunProfile
15 Tax4FunProfile <- data.frame(t(Tax4FunOutput$Tax4FunProfile))
16 #View(Tax4FunProfile)
17 
18 write.table(Tax4FunProfile, "Tax4FunProfile.txt", sep="\t")
19 
20 } #fin de la fonction