| Previous changeset 9:bd5ba02b1f71 (2017-12-21) Next changeset 11:702db6efce51 (2017-12-21) |
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Commit message:
Uploaded |
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added:
sm_Tax4Fun.R |
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| diff -r bd5ba02b1f71 -r 444f1e7fe177 sm_Tax4Fun.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sm_Tax4Fun.R Thu Dec 21 09:09:09 2017 -0500 |
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| @@ -0,0 +1,20 @@ +# The function ------------------------------------- +#--------------------------------------------------- +GalaxyFrogsTax <- function(input.file, + reference, + output.file = "Tax4FunProfile.txt" + ) { +library(Tax4Fun) +folderReferenceData<- reference + +Tax4FunOutput<-Tax4Fun(importSilvaNgsData(input.file), folderReferenceData) # optionnal: fctProfiling = TRUE, refProfile = "UProc", shortReadMode = TRUE, normCopyNo = TRUE) +#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"). +#reference = "/galaxydata/galaxy-preprod/my_tools/sm_Tax4Fun/SILVA123/" + +Tax4FunProfile <- Tax4FunOutput$Tax4FunProfile +Tax4FunProfile <- data.frame(t(Tax4FunOutput$Tax4FunProfile)) +#View(Tax4FunProfile) + +write.table(Tax4FunProfile, "Tax4FunProfile.txt", sep="\t") + +} #fin de la fonction |