# HG changeset patch
# User proteore
# Date 1521043472 14400
# Node ID 867d47ff782c6221e2565c7bf9293581e835f6bb
# Parent  bbb17bca9ec194bdf1f69c5ac4117ed8a62c2f34
planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty

diff -r bbb17bca9ec1 -r 867d47ff782c README.rst
--- a/README.rst	Thu Mar 08 10:47:00 2018 -0500
+++ b/README.rst	Wed Mar 14 12:04:32 2018 -0400
@@ -21,8 +21,8 @@
 
 **Databases**
 
-Annotations have been retrieved from the neXtProt database (Gaudet et  al., 2017) via a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985)
+Annotations have been retrieved from the neXtProt database released on 01/08/2017 (Gaudet et  al., 2017) via a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985)
 
 **Outputs**
 
-The output is a tabular file. The initial columns are kept and columns are be added according to which annotation you have selected. 
\ No newline at end of file
+The output is a tabular file. The initial columns are kept and columns are be added according to which annotation you have selected.  
diff -r bbb17bca9ec1 -r 867d47ff782c prot_features.xml
--- a/prot_features.xml	Thu Mar 08 10:47:00 2018 -0500
+++ b/prot_features.xml	Wed Mar 14 12:04:32 2018 -0400
@@ -123,7 +123,7 @@
 
 **Databases**
 
-Annotations have been retrieved from the neXtProt database (Gaudet et  al., 2017) via a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985)
+Annotations have been retrieved from the neXtProt database released on 01/08/2017 (Gaudet et  al., 2017) via a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985)
 
 **Outputs**
 
diff -r bbb17bca9ec1 -r 867d47ff782c protein_features.R
--- a/protein_features.R	Thu Mar 08 10:47:00 2018 -0500
+++ b/protein_features.R	Wed Mar 14 12:04:32 2018 -0400
@@ -70,8 +70,12 @@
       input = c(input, strsplit(row, ";")[[1]][1])
     }
   }
+
+  # Read reference file
   nextprot_file = args$nextprot
-  nextprot = human_id_map = read.table(nextprot_file, header = TRUE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings = "")
+  nextprot = read.table(nextprot_file, header = TRUE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings = "", quote = "")
+  
+  # Parse arguments
   typeid = args$type
   P1_args = strsplit(args$argsP1, ",")[[1]]
   P2_args = strsplit(args$argsP2, ",")[[1]]
@@ -130,4 +134,4 @@
   } 
 
 }
-protein_features()
\ No newline at end of file
+protein_features()