comparison build_peca.R @ 2:36b7a5891000 draft

planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
author caleb-easterly
date Thu, 22 Feb 2018 11:28:22 -0500
parents
children
comparison
equal deleted inserted replaced
1:34c1ae5e99ac 2:36b7a5891000
1 #!/usr/bin/env Rscript
2
3 library(PECA)
4
5 # Set up R error handling to go to stderr
6 options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
7
8 # Avoid crashing Galaxy with an UTF8 error on German LC settings
9 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
10
11 main <- function() {
12 args <- commandArgs(trailingOnly = TRUE)
13
14 # read first argument, which is quant file (proteins in rows, samples in columns)
15 quant_file <- read.delim(args[1],
16 na.strings = c("0", "NA"),
17 sep = '\t')
18
19 # read 2nd and 3rd argument, which are path to files with group 1 and 2 column indices
20 group1_ind_file <- read.csv(args[2], header = FALSE)[1, ]
21 group2_ind_file <- read.csv(args[3], header = FALSE)[1, ]
22
23 # read 4th argument, which is output file name
24 out_file <- args[4]
25
26 # get vectors of column names
27 df_names <- colnames(quant_file)
28 group1_names <- df_names[group1_ind_file]
29 group2_names <- df_names[group2_ind_file]
30
31 # run PECA_df
32 # id column is first column (hard-coded)
33 results <- PECA_df(quant_file, group1_names, group2_names, id = df_names[1])
34
35 # put add protein names column
36 results$prot <- row.names(results)
37 results <- results[, c("prot", "slr", "t", "score", "n", "p", "p.fdr")]
38
39 # write to output
40 write.table(results, file=out_file,
41 quote=FALSE,
42 sep ='\t',
43 row.names = FALSE)
44 }
45
46 main()