# HG changeset patch
# User bornea
# Date 1472350321 14400
# Node ID 1972ccdbeb16f4e526bfde8bec144318019ee117
# Parent  81db20bfc3496c0cc6fcbc327cd3f53405b75f19
Uploaded

diff -r 81db20bfc349 -r 1972ccdbeb16 SAINT_preprocessing.xml
--- a/SAINT_preprocessing.xml	Sat Aug 27 21:42:13 2016 -0400
+++ b/SAINT_preprocessing.xml	Sat Aug 27 22:12:01 2016 -0400
@@ -31,6 +31,16 @@
         #end for
         "
       \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in $Inter_file $Prey_file
+    #elif (str($type_select.type) == 'mzIdentML'):
+      Protein_report_processing.py "$type_select.input" $type_select.bait_file_in $type_select.preybool $type_select.fasta_db \$INSTALL_RUN_PATH/ 
+        "
+        #for $ba in $bait
+          ${ba.bait1}
+          ${ba.assign}
+          ${ba.T_C}
+        #end for
+        "
+      $type_select.bait_bool $Prey_file $Bait_file $Inter_file 
     #end if
   </command>
   <requirements>
@@ -42,6 +52,7 @@
         <option value="MaxQuant">MaxQuant</option>
         <option value="Scaffold">Scaffold</option>
         <option value="Peptideshaker">Peptideshaker</option> 
+        <option value="mzIdentML">mzIdentML</option> 
       </param>
       <when value="MaxQuant">
         <param format="dat" name="input" type="data" label="MaxQuant peptides Output"/>
@@ -71,6 +82,13 @@
         <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"/>
       </when>
+      <when value="mzIdentML">
+        <param format="dat" name="input" type="data" label="mzIdentML Files" multiple="true"/>
+        <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?"/>
+        <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
+      </when>
     </conditional>
     <repeat name="bait" title="Bait Create">
       <param name="bait1" type="text" size="100" label="Bait"/>