diff peca.R @ 5:5a39fa8a235a draft

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

--- 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)