# HG changeset patch
# User bornea
# Date 1472348533 14400
# Node ID 81db20bfc3496c0cc6fcbc327cd3f53405b75f19
# Parent  0b4450bdc6a950b11cff7e14da85d236f84f87ee
Uploaded

diff -r 0b4450bdc6a9 -r 81db20bfc349 SAINT_preprocessing.xml
--- a/SAINT_preprocessing.xml	Sat Aug 27 21:38:03 2016 -0400
+++ b/SAINT_preprocessing.xml	Sat Aug 27 21:42:13 2016 -0400
@@ -2,7 +2,7 @@
   <description></description>
   <command interpreter="python">
     #if (str($type_select.type) == 'Scaffold'):
-      SAINT_preprocessing.py $type_select.input $type_select.preybool $type_select.fasta_db $type_select.Inter_file $type_select.Prey_file 
+      SAINT_preprocessing.py $type_select.input $type_select.preybool $type_select.fasta_db $Inter_file $Prey_file 
       "
         #for $ba in $bait
          ${ba.bait1}
@@ -10,9 +10,9 @@
          ${ba.T_C}
         #end for
         "
-      $type_select.Bait_file \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in
+      $Bait_file \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in
     #elif (str($type_select.type) == 'MaxQuant'):
-      SAINT_preprocessing_mq_pep.py $type_select.input $type_select.preybool $type_select.fasta_db $type_select.Inter_file $type_select.Prey_file 
+      SAINT_preprocessing_mq_pep.py $type_select.input $type_select.preybool $type_select.fasta_db $Inter_file $Prey_file 
         "
         #for $ba in $bait
           ${ba.bait1}
@@ -20,9 +20,9 @@
           ${ba.T_C}
         #end for
         "
-      $type_select.Bait_file \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in
+      $Bait_file \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in
     #elif (str($type_select.type) == 'Peptideshaker'):
-      Protein_report_processing.py "$type_select.input" $type_select.Bait_file $type_select.use_metric $type_select.fasta_db $type_select.preybool 
+      Protein_report_processing.py "$type_select.input" $Bait_file $type_select.use_metric $type_select.fasta_db $type_select.preybool 
         "
         #for $ba in $bait
           ${ba.bait1}
@@ -30,7 +30,7 @@
           ${ba.T_C}
         #end for
         "
-      \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in $type_select.Inter_file $type_select.Prey_file
+      \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in $Inter_file $Prey_file
     #end if
   </command>
   <requirements>