# HG changeset patch
# User mvdbeek
# Date 1456504963 18000
# Node ID 5fb82111ec62c22d39e74f602d900e1369dd365f
# Parent  1b03f62329005f2ff65fefe31add83a45ae8674d
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty

diff -r 1b03f6232900 -r 5fb82111ec62 goseq.r
--- a/goseq.r	Fri Feb 26 08:49:59 2016 -0500
+++ b/goseq.r	Fri Feb 26 11:42:43 2016 -0500
@@ -1,6 +1,6 @@
 sink(stdout(), type = "message")
-library(goseq)
-library(optparse)
+suppressWarnings(suppressMessages(library(goseq)))
+suppressWarnings(suppressMessages(library(optparse)))
 
 option_list <- list(
     make_option(c("-d", "--dge_file"), type="character", help="Path to file with differential gene expression result"),
@@ -34,15 +34,13 @@
 sample_vs_wallenius_plot = args$sample_vs_wallenius_plot
 repcnt = args$repcnt
 
-
 # format DE genes into vector suitable for use with goseq
 dge_table = read.delim(dge_file, header = TRUE, sep="\t", check.names = FALSE)
 genes = as.integer(dge_table[,p_adj_column]<p_adj_cutoff)
 names(genes) = dge_table[,1] # Assuming first row contains gene names
 
 # Get gene lengths
-
-if (length_file) {
+if (length_file !=FALSE) {
   length_table = read.delim(length_file, header=TRUE, sep="\t", check.names=FALSE, row.names=TRUE)
   gene_lengths = length_table[names(genes),]$length
   } else {
@@ -53,7 +51,7 @@
 
 pdf(length_bias_plot)
 pwf=nullp(genes, genome, gene_id, gene_lengths)
-dev.off()
+message = dev.off()
 # wallenius approximation of p-values
 GO.wall=goseq(pwf, genome, gene_id)
 
@@ -68,7 +66,7 @@
      xlab="log10(Wallenius p-values)",ylab="log10(Sampling p-values)",
      xlim=c(-3,0))
      abline(0,1,col=3,lty=2)
-  dev.off()
+  message = dev.off()
   write.table(GO.samp, sampling_tab, sep="\t", row.names = FALSE, quote = FALSE)
 }
 
diff -r 1b03f6232900 -r 5fb82111ec62 goseq.xml
--- a/goseq.xml	Fri Feb 26 08:49:59 2016 -0500
+++ b/goseq.xml	Fri Feb 26 11:42:43 2016 -0500
@@ -48,11 +48,11 @@
         <data format="pdf" label="Plot P-value from sampling against wallenius distribution" name="sample_vs_wallenius_plot">
             <filter>repcnt != 0</filter>
         </data>
-        <data format="tabular" label="Ranked category list - wallenius" name="wallenius_tab" />
+        <data format="tabular" label="Ranked category list - no length bias correction" name="nobias_tab" />
         <data format="tabular" label="Ranked category list - sampling" name="sampling_tab">
             <filter>repcnt != 0</filter>
         </data>
-        <data format="tabular" label="Ranked category list - no length bias correction" name="nobias_tab" />
+        <data format="tabular" label="Ranked category list - wallenius approx. of p-values" name="wallenius_tab" />
     </outputs>
     <tests>
         <test>