Mercurial > repos > sblanck > mpagenomics
diff filter.R @ 4:3fcbb8030fcc draft
"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
| author | sblanck |
|---|---|
| date | Mon, 12 Apr 2021 14:47:09 +0000 |
| parents | 4d539083cf7f |
| children |
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--- a/filter.R Tue Jun 16 04:34:09 2020 -0400 +++ b/filter.R Mon Apr 12 14:47:09 2021 +0000 @@ -15,6 +15,7 @@ make_option("--nbcall",type="character",default=NULL, dest="nbcall"), make_option("--length",type="character",default=NULL, dest="length"), make_option("--probes",type="character",default=NULL, dest="probes"), + make_option("--settings_signal",type="character",default=NULL, dest="settings_signal"), make_option("--outputlog",type="character",default=NULL, dest="outputlog"), make_option("--log",type="character",default=NULL, dest="log") ); @@ -35,6 +36,7 @@ nbcall=opt$nbcall length=as.numeric(opt$length) probes=as.numeric(opt$probes) +signal=opt$settings_signal log=opt$log outputlog=opt$outputlog @@ -47,14 +49,20 @@ nbcall_tmp <- strsplit(nbcall,",") nbcall_vecstring <-unlist(nbcall_tmp) -nbcall_vecstring - library(MPAgenomics) -workdir=file.path(tmp_dir, "mpagenomics") +workdir=file.path(tmp_dir) +if (!dir.exists(workdir)) + dir.create(workdir, showWarnings = TRUE, recursive = TRUE) setwd(workdir) segcall = read.table(input, header = TRUE) -filtercall=filterSeg(segcall,length,probes,nbcall_vecstring) +if (signal=="fracB") { + segcall=cbind(segcall,calls=rep("normal",nrow(segcall))) + filtercall=filterSeg(segcall,length,probes,nbcall_vecstring) + filtercall=filtercall[,1:(ncol(filtercall)-1)] +} else { + filtercall=filterSeg(segcall,length,probes,nbcall_vecstring) +} #sink(output) #print(format(filtercall),row.names=FALSE) #sink()