Mercurial > repos > caleb-easterly > peca
diff peca.R @ 5:5a39fa8a235a draft
planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
author | caleb-easterly |
---|---|
date | Thu, 22 Feb 2018 11:45:43 -0500 |
parents | 784c107c5861 |
children | e16cd77cf9f7 |
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--- a/peca.R Thu Feb 22 11:35:33 2018 -0500 +++ b/peca.R Thu Feb 22 11:45:43 2018 -0500 @@ -20,8 +20,11 @@ group1_ind_file <- as.vector(as.matrix(read.csv(args[2], header = FALSE)[1, ])) group2_ind_file <- as.vector(as.matrix(read.csv(args[3], header = FALSE)[1, ])) + # test type + ttype <- args[4] + # read 4th argument, which is output file name - out_file <- args[4] + out_file <- args[5] # get vectors of column names df_names <- colnames(quant_file) @@ -30,7 +33,11 @@ # run PECA_df # id column is first column (hard-coded) - results <- PECA_df(quant_file, group1_names, group2_names, id = df_names[1]) + results <- PECA_df(quant_file, + group1_names, + group2_names, + type=ttype, + id = df_names[1]) # put add protein names column results$prot <- row.names(results)