Mercurial > repos > proteore > proteore_ms_observation_pepatlas

comparison Get_ms-ms_observations.R @ 10:ef723082fc54 draft default tip

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"planemo upload commit b061341e1157cccd90e33b945bc17705880b3e57"
author proteore
date Mon, 04 May 2020 03:29:36 -0400
parents 14c890ff105a
children
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9:14c890ff105a 10:ef723082fc54
75 tissue=paste(strsplit(file_name,"_")[[1]][1:2],collapse="_") 75 tissue=paste(strsplit(file_name,"_")[[1]][1:2],collapse="_")
76 return (c(date,tissue,file_name,path)) 76 return (c(date,tissue,file_name,path))
77 } 77 }
78 78
79 clean_ids <- function(ids){ 79 clean_ids <- function(ids){
80 80 ids = gsub(" ",NA,ids)
81 ids = gsub(" ","",ids) 81 ids = gsub("^$|^ $", NA, ids)
82 ids = ids[which(ids!="")] 82 ids = gsub("NA",NA,ids)
83 ids = ids[which(ids!="NA")]
84 ids = ids[!is.na(ids)]
85
86 return(ids) 83 return(ids)
87 } 84 }
88 85
89 main = function() { 86 main = function() {
90 args <- commandArgs(TRUE) 87 args <- commandArgs(TRUE)
106 # Parse arguments 103 # Parse arguments
107 parseArgs <- function(x) strsplit(sub("^--", "", x), "=") 104 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
108 argsDF <- as.data.frame(do.call("rbind", parseArgs(args))) 105 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
109 args <- as.list(as.character(argsDF$V2)) 106 args <- as.list(as.character(argsDF$V2))
110 names(args) <- argsDF$V1 107 names(args) <- argsDF$V1
111
112 #save(args,file="/Users/David/work/ProteoRE/tools/Get_ms-ms_observations/args.Rda")
113 load("/Users/David/work/ProteoRE/tools/Get_ms-ms_observations/args.Rda")
114 108
115 # Extract input 109 # Extract input
116 input_type = args$input_type 110 input_type = args$input_type
117 if (input_type == "list") { 111 if (input_type == "list") {
118 input = unlist(strsplit(strsplit(args$input, "[ \t\n]+")[[1]],";")) 112 input = unlist(strsplit(strsplit(args$input, "[ \t\n]+")[[1]],";"))