--- a/quantifere.xml	Fri Aug 01 17:22:37 2014 +0200
+++ b/quantifere.xml	Mon Jan 26 06:24:15 2015 +0100
@@ -56,6 +56,8 @@
      				way different peptide identifications from the same sample but measured 
      				in different fractions can be merged together. Otherwise each (fraction) file
      				is seen as a separate sample."/> <!-- could do regular expressions as well but this would be hard for biologists, e.g. _F\d\b -->
+     				<!-- on help above: the given codes are removed from source name...separate features are clustered, not peptides, peptides
+     				     are quantified based on summing features (raw), or summing patterns : TODO document the quantification columns present in the output CSV -->
      		</when>
      		<when value="No">
      		</when>
@@ -89,15 +91,17 @@
 		sample intensity values correlation. Set here the minimum correlation expected between grouped members. This is used to guide the clustering algorithm."/>
 
 		<!--  simple extra heuristics to remove some "noise" protein hits  -->
-		<param name="minProtCoverage" type="float" size="10" value="5.0" label="Minimum protein coverage (%)" help="This will remove proteins that have a too small 
-		portion of their sequence covered by peptide matches."/>
+		<param name="minProtCoverage" type="float" size="10" value="0.0" label="Minimum protein coverage (%)" help="Set this to e.g. 5.0 if you have protein coverage 
+		information in your data. This will remove proteins that have a too small portion of their sequence covered by peptide matches."/>
+		<!-- TODO : ADD warning to report if this is left 0 and no coverage is found ...or maybe validate the other way around-->
 		
 		<param name="minAboveAverageHits" type="integer" size="10" value="1" label="Minimum number of different peptide matches with a score above average" 
 		help="This will remove proteins that do not have enough reasonable peptides hits."/>
 
 		<param name="minNrIdsForInferencePeptide" type="integer" size="10" value="1" label="Minimum number of peptide identifications for inference peptides" 
 		help="Minimum number of peptide identifications a peptide needs to be used as inference peptide for secondary proteins."/>
-
+		<!--  currently, when one feature clusters with foreign peptide, then it is not inference peptide anymore...quite strict, could be less strict
+		      by letting user indicate for example: 90% of features should be inference features...then it is an inference pep. See QuantifereTool.inferSecondaryProteins() -->
 
      	<param name="functionalAnnotationCSV" type="data" format="csv,txt,tsv" optional="true" 
      	label="(Functional)annotation mapping file (csv or tsv format)" 
@@ -207,6 +211,20 @@
 .. _Cytoscape chartplugin: http://apps.cytoscape.org/apps/chartplugin
 
 
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+Pieter N. J. Lukasse and Antoine H. P. America (2014).
+Protein Inference Using Peptide Quantification Patterns.
+http://dx.doi.org/10.1021/pr401072g
+
 
   </help>
+  <citations>
+        <citation type="doi">10.1021/pr401072g</citation> <!-- example 
+        see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
+        -->
+   </citations>
 </tool>