Mercurial > repos > ecology > vigiechiro_idcorrect_2ndlayer
diff Id_Tidy.R @ 1:f3fc8d243b1a draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
| author | ecology |
|---|---|
| date | Fri, 26 Apr 2019 12:20:52 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Id_Tidy.R Fri Apr 26 12:20:52 2019 -0400 @@ -0,0 +1,17 @@ +suppressMessages(library(data.table)) + +args <- commandArgs(trailingOnly = TRUE) +#print(args) +filename=args[2] + +DataPar=fread(args[1]) #ids +DataPar$participation=substr(filename,nchar(filename)-40,nchar(filename)-17) +#DataPar$participation=substr(args[1],nchar(args[1])-40,nchar(args[1])-17) +test1=duplicated(cbind(DataPar$'nom du fichier',DataPar$tadarida_taxon)) +test2=(DataPar$tadarida_taxon=="empty") +DataPar=subset(DataPar,(!test1)|(test2)) +DataPar$tadarida_probabilite[DataPar$tadarida_probabilite==""]="0" +DataPar$tadarida_probabilite=as.numeric(DataPar$tadarida_probabilite) + +#write.table(DataPar,paste0(substr(args[1],nchar(args[1])-40,nchar(args[1])-17),"-DataCorrC2.csv"),row.names=F,sep="\t") +write.table(DataPar,"Id_tidy.tabular",row.names=F,sep="\t")