diff peptide_indexer.xml @ 4:1183846e70a1 draft

Uploaded

--- a/peptide_indexer.xml	Fri May 10 17:31:59 2013 -0400
+++ b/peptide_indexer.xml	Wed Jun 19 13:15:44 2013 -0400
@@ -16,9 +16,7 @@
 fasta=$database
 out=$output
 decoy_string=$decoy_string
-#if $decoy_string_position == "prefix"
-prefix=true
-#end if
+prefix=$prefix
 $extact_search
 $write_protein_sequence
 $keep_unreferenced_proteins
@@ -29,9 +27,9 @@
     <param name="input1" label="Identification Input" type="data" format="idxml" />
     <param name="database" label="Database" type="data" format="fasta" />
     <param name="decoy_string" type="text" value="_rev" label="Decoy string"/>
-    <param name="decoy_string_position" type="select" label="Decoy Position">
-      <option value="suffix" selected="true">Suffix</option>
-      <option value="prefix">Prefix</option>
+    <param name="prefix" type="select" label="Decoy Position">
+      <option value="false" selected="true">Suffix</option>
+      <option value="true">Prefix</option>
     </param>    
     <param name="extact_search" label="Exact Search" type="boolean" truevalue="" falsevalue="full_tolerant_search=true" checked="true" />
     <param name="write_protein_sequence" type="boolean" truevalue="write_protein_sequence=true" falsevalue="" checked="false" label="Store Protein Sequences" />