changeset 2:36b7a5891000 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build_peca.R	Thu Feb 22 11:28:22 2018 -0500
@@ -0,0 +1,46 @@
+#!/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()

--- a/peca.xml	Wed Feb 21 16:57:49 2018 -0500
+++ b/peca.xml	Thu Feb 22 11:28:22 2018 -0500
@@ -4,11 +4,10 @@
         <requirement type="package" version="0.7">r-dbi</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        ## write group 1 to file
+        ## write groups to file
         echo '$group1' > group1.txt &&
         echo '$group2' > group2.txt && 
-        cat group1.txt &&
-        Rscript --vanilla '$__tool_directory__/peca.R' '$input' '$group1' '$group2' '$output'
+        Rscript --vanilla '$__tool_directory__/peca.R' '$input' group1.txt group2.txt '$output'
     ]]></command>
     <inputs>
         <param name="input" type="data" format="tabular"/>