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10
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1 # The function -------------------------------------
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2 #---------------------------------------------------
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3 GalaxyFrogsTax <- function(input.file,
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4 reference,
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5 output.file = "Tax4FunProfile.txt"
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6 ) {
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7 library(Tax4Fun)
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8 folderReferenceData<- reference
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9
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10 Tax4FunOutput<-Tax4Fun(importSilvaNgsData(input.file), folderReferenceData) # optionnal: fctProfiling = TRUE, refProfile = "UProc", shortReadMode = TRUE, normCopyNo = TRUE)
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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").
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12 #reference = "/galaxydata/galaxy-preprod/my_tools/sm_Tax4Fun/SILVA123/"
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13
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14 Tax4FunProfile <- Tax4FunOutput$Tax4FunProfile
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15 Tax4FunProfile <- data.frame(t(Tax4FunOutput$Tax4FunProfile))
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16 #View(Tax4FunProfile)
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17
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18 write.table(Tax4FunProfile, "Tax4FunProfile.txt", sep="\t")
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19
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20 } #fin de la fonction
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