# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1422024350 -3600
# Node ID e38e97bc902de66a3e87a9c2b356a70d86da57f3
# Parent  1a6fa343b981164ba42bbf8c1b562130b0e47582
added comment

diff -r 1a6fa343b981 -r e38e97bc902d masscomb_dbsearch_converter.xml
--- a/masscomb_dbsearch_converter.xml	Fri Feb 07 15:55:38 2014 +0100
+++ b/masscomb_dbsearch_converter.xml	Fri Jan 23 15:45:50 2015 +0100
@@ -45,7 +45,7 @@
 	      		<param name="inputFile" type="data" format="omx" label="MS/MS search results"/>
 	      	</when>
 	      	<when value="proteomediscoverer_pepxml">
-	      		<param name="inputFile" type="data" format="pepxml" label="MS/MS search results (pepxml)"/>
+	      		<param name="inputFile" type="data" format="any" label="MS/MS search results (pepxml)"/>
 	      	</when>
 	      </conditional>
 	    </when>
@@ -70,7 +70,11 @@
 	  </conditional>
 	  <param name="outputMsMsFragmentationData" type="boolean" checked="false" 
 	  label="Output MS/MS fragmentation data" 
-	  help="NB: this will add to the output also the fragment ions related to each peptide identification"/>
+	  help="NB: this will add to the output also the fragment ions related to each peptide identification. 
+	  NB2: Fragment ion annotation data is 
+		inferred based on new calculations triggered by this conversion tool. 
+		This is done because fragment ion annotation information is not present 
+		in X!Tandem file (X!Tandem SLEDGEHAMMER (2013.09.01) and previous)"/>
      	
 	</inputs>
 	<outputs>