# HG changeset patch
# User bornea
# Date 1472348283 14400
# Node ID 0b4450bdc6a950b11cff7e14da85d236f84f87ee
# Parent  3c0ed536029ef35fcfe634ada92024b93f99dcb3
Uploaded

diff -r 3c0ed536029e -r 0b4450bdc6a9 SAINT_preprocessing.xml
--- a/SAINT_preprocessing.xml	Sat Aug 27 21:29:26 2016 -0400
+++ b/SAINT_preprocessing.xml	Sat Aug 27 21:38:03 2016 -0400
@@ -2,7 +2,7 @@
   <description></description>
   <command interpreter="python">
     #if (str($type_select.type) == 'Scaffold'):
-      SAINT_preprocessing.py $input $preybool $fasta_db $Inter_file $Prey_file 
+      SAINT_preprocessing.py $type_select.input $type_select.preybool $type_select.fasta_db $type_select.Inter_file $type_select.Prey_file 
       "
         #for $ba in $bait
          ${ba.bait1}
@@ -10,9 +10,9 @@
          ${ba.T_C}
         #end for
         "
-      $Bait_file \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in
+      $type_select.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 $input $preybool $fasta_db $Inter_file $Prey_file 
+      SAINT_preprocessing_mq_pep.py $type_select.input $type_select.preybool $type_select.fasta_db $type_select.Inter_file $type_select.Prey_file 
         "
         #for $ba in $bait
           ${ba.bait1}
@@ -20,9 +20,9 @@
           ${ba.T_C}
         #end for
         "
-      $Bait_file \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in
+      $type_select.Bait_file \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in
     #elif (str($type_select.type) == 'Peptideshaker'):
-      Protein_report_processing.py "$input" $Bait_file $use_metric $fasta_db $preybool 
+      Protein_report_processing.py "$type_select.input" $type_select.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/ $bait_bool $bait_file_in $Inter_file $Prey_file
+      \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in $type_select.Inter_file $type_select.Prey_file
     #end if
   </command>
   <requirements>
@@ -49,11 +49,6 @@
         <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?"/>
         <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
-        <repeat name="bait" title="Bait Create">
-          <param name="bait1" type="text" size="100" label="Bait"/>
-          <param name="assign" type="text" size="100" label="Group Assignment"/>
-          <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/> 
-        </repeat>
       </when>
       <when value="Scaffold">
         <param format="dat" name="input" type="data" label="Scaffold Output"/>
@@ -61,11 +56,6 @@
         <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?"/>
         <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
-        <repeat name="bait" title="Bait Create">
-          <param name="bait1" type="text" size="100" label="Bait"/>
-          <param name="assign" type="text" size="100" label="Group Assignment"/>
-          <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/> 
-        </repeat>
       </when>
       <when value="Peptideshaker">
         <param format="dat" name="input" type="data" label="Peptideshaker Output" multiple="true"/>
@@ -80,13 +70,13 @@
         <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?"/>
         <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
-        <repeat name="bait" title="Bait Create">
-          <param name="bait1" type="text" size="100" label="Bait"/>
-          <param name="assign" type="text" size="100" label="Group Assignment"/>
-          <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/> 
-        </repeat>
       </when>
     </conditional>
+    <repeat name="bait" title="Bait Create">
+      <param name="bait1" type="text" size="100" label="Bait"/>
+      <param name="assign" type="text" size="100" label="Group Assignment"/>
+      <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/> 
+    </repeat>
   </inputs>
   <outputs>
     <data format="txt" name="Inter_file" label="Inter File"/>