Mercurial > repos > bornea > saint_preprocessing

diff SAINT_preprocessing.xml @ 62:81db20bfc349 draft

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Uploaded
author bornea
date Sat, 27 Aug 2016 21:42:13 -0400
parents 0b4450bdc6a9
children 1972ccdbeb16
line wrap: on
line diff
--- 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>