# HG changeset patch
# User sarahinraauzeville
# Date 1513865349 18000
# Node ID 444f1e7fe1777e7063f32f61fd05b004514d76cd
# Parent  bd5ba02b1f717434f2e72bf8c05d0b9fae1729a0
Uploaded

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
@@ -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