# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1422625990 -3600
# Node ID 6107b74eeb1128bc8cabdc5aed585c33817a8b39
# Parent  34c4e7e0f23b1fc6fc60bf523a1f4843f05a5077
improved documentation

diff -r 34c4e7e0f23b -r 6107b74eeb11 napq.xml
--- a/napq.xml	Fri Jan 30 14:37:28 2015 +0100
+++ b/napq.xml	Fri Jan 30 14:53:10 2015 +0100
@@ -20,8 +20,11 @@
 	
 	<inputs>
 
-   		<repeat name="identificationFileList" title="Peptide identification files" help="Set of MS/MS peptide identification files that have some form of quantification data coupled to it (e.g. MSE identifications&amp;intensity).">
-   			<param name="identificationsFile" type="data" format="apml,mzidentml,prims.fileset.zip" label="Identifications file (APML or MZIDENTML or MZIDENTML fileSet)" />
+   		<repeat name="identificationFileList" title="(Filtered) Peptide identification files" help="Set of MS/MS peptide identification files that have some form of 
+   		quantification data coupled to it (e.g. MSE identifications&amp;intensity). This list of peptide identifications is 
+   		preferably pre-processed by a tool (e.g. MsFilt) that filters out as much as possible false-positive peptide identifications.">
+   			<param name="identificationsFile" type="data" format="apml,prims.fileset.zip" label="Identifications file ([APML] or [MZIDENTML fileSet])" 
+   			     help="When using MsFilt, select MsFilt's APML output file here."/>
    		</repeat>
 
 		<param name="namingConventionCodesForSamples" type="text" size="100" value=""