# HG changeset patch
# User proteore
# Date 1521816437 14400
# Node ID 715002a394ec5c7e6a7f1986ba4ab39031105eb6
# Parent  ed226f0e5625c2fad0c46489302e10555406b7be
planemo upload commit b36435833bf54f90f62cc240f2cda1c889161b23-dirty

diff -r ed226f0e5625 -r 715002a394ec goprofiles.R
--- a/goprofiles.R	Wed Mar 14 12:51:53 2018 -0400
+++ b/goprofiles.R	Fri Mar 23 10:47:17 2018 -0400
@@ -2,20 +2,22 @@
 library(org.Hs.eg.db)
 library(goProfiles)
 
-# Read file and return file content as data.frame?
+# Read file and return file content as data.frame
 readfile = function(filename, header) {
   if (header == "true") {
-    # Read only the first line of the files as data (without headers):
-    headers <- read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE)
-    #Read the data of the files (skipping the first row):
-    file <- read.table(filename, skip = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE)
+    # Read only first line of the file as header:
+    headers <- read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
+    #Read the data of the files (skipping the first row)
+    file <- read.table(filename, skip = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
     # Remove empty rows
-    file <- file[!apply(is.na(file) | file == "", 1, all),]
-    #And assign the headers of step two to the data:
+    file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
+    #And assign the header to the data
     names(file) <- headers
   }
   else {
-    file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE)
+    file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
+    # Remove empty rows
+    file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
   }
   return(file)
 }
@@ -175,7 +177,7 @@
 
   input_type = args$input_type
   if (input_type == "text") {
-    input = strsplit(args$input, " ")[[1]]
+    input = strsplit(args$input, "[ \t\n]+")[[1]]
   }
   else if (input_type == "file") {
     filename = args$input
diff -r ed226f0e5625 -r 715002a394ec goprofiles.xml
--- a/goprofiles.xml	Wed Mar 14 12:51:53 2018 -0400
+++ b/goprofiles.xml	Fri Mar 23 10:47:17 2018 -0400
@@ -44,7 +44,7 @@
         <conditional name="input" >
             <param name="ids" type="select" label="Enter your ID list (only Entrez Gene ID or UniProt accession number allowed" help="Copy/paste or ID list from a file (e.g. table)" >
                 <option value="text">Copy/paste your identifiers</option>
-                <option value="file">Input file containing your identifiers</option>
+                <option value="file" selected="true">Input file containing your identifiers</option>
             </param>
             <when value="text" >
                 <param name="text" type="text" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >