# HG changeset patch
# User bornea
# Date 1465396592 14400
# Node ID 8031a47f67c6cf813d411c723314beb00360cce5
# Parent  09b89febcf987dd3ef2701e06a715bbdce89b12a
Uploaded

diff -r 09b89febcf98 -r 8031a47f67c6 SAINT_preprocessing.xml
--- a/SAINT_preprocessing.xml	Thu May 19 12:12:00 2016 -0400
+++ b/SAINT_preprocessing.xml	Wed Jun 08 10:36:32 2016 -0400
@@ -32,7 +32,7 @@
       <option value="MaxQuant">MaxQuant</option>
       <option value="Scaffold">Scaffold</option> 
     </param>
-    <param format="dat" name="input" type="data" label="Scaffold or MaxQuant proteinGroup Output"/>
+    <param format="dat" name="input" type="data" label="Scaffold or MaxQuant peptides Output"/>
     <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
     <param type="data" name="fasta_db" format="fasta"  label="Provide Uniprot Fasta database" optional="true"/>
     <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
@@ -50,6 +50,18 @@
     <data format="txt" name="Bait_file" label="Bait File" />
   </outputs>
   <stdio>
+    <regex match="Error: bad bait"
+           source="stdout"
+           level="fatal"
+           description="Error: bad bait"/>
+    <regex match="IOError: [Errno 2] No such file or directory: './tukeys_output.txt'"
+           source="stderr"
+           level="fatal"
+           description="Error: Scaffold/MaxQuant mismatch. Check job settings."/>
+    <regex match="bait_temp_file = open(sys.argv[10], 'r')"
+           source="stderr"
+           level="fatal"
+           description="Error: Bait create settings mismatch. Check job settings."/>
     <regex match="Error|error"
 	   source="stdout"
            level="fatal"
@@ -58,10 +70,6 @@
      source="stderr"
            level="fatal"
            description="Unknown error"/>
-    <regex match="Error: bad bait"
-           source="stdout"
-           level="fatal"
-           description="Error: bad bait"/>
   </stdio> 
 
   <tests>