diff build_peca.R @ 13:4dcfde657dc3 draft default tip

planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca

--- a/build_peca.R	Thu Mar 08 18:33:47 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-#!/usr/bin/env Rscript
-
-library(PECA)
-
-# Set up R error handling to go to stderr
-options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
-
-# Avoid crashing Galaxy with an UTF8 error on German LC settings
-loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
-
-main <- function() {
-    args <- commandArgs(trailingOnly = TRUE)
-        
-    # read first argument, which is quant file (proteins in rows, samples in columns)
-    quant_file <- read.delim(args[1],
-                           na.strings = c("0", "NA"),
-                           sep = '\t')
-
-    # read 2nd and 3rd argument, which are path to files with group 1 and 2 column indices 
-    group1_ind_file <- read.csv(args[2], header = FALSE)[1, ]
-    group2_ind_file <- read.csv(args[3], header = FALSE)[1, ]
-
-    # read 4th argument, which is output file name
-    out_file <- args[4]
-
-    # get vectors of column names
-    df_names <- colnames(quant_file)
-    group1_names <- df_names[group1_ind_file]
-    group2_names <- df_names[group2_ind_file]
- 
-    # run PECA_df
-    # id column is first column (hard-coded)
-    results <- PECA_df(quant_file, group1_names, group2_names, id = df_names[1])
-
-    # put add protein names column
-    results$prot <- row.names(results)
-    results <- results[, c("prot", "slr", "t", "score", "n", "p", "p.fdr")]
- 
-    # write to output
-    write.table(results, file=out_file,
-               quote=FALSE,
-               sep ='\t', 
-               row.names = FALSE)
-}
-
-main()