--- a/term_mapper.xml	Mon Mar 23 22:11:39 2015 +0100
+++ b/term_mapper.xml	Sat Mar 28 14:28:45 2015 +0100
@@ -29,16 +29,21 @@
 		#if $genObservations.genObservationsFile == True
 			-outputObservationsFileName $outputObservationsFileName
         	-quantifColumn "$genObservations.quantifColumn" 
+        	-multipleMappingSolution $genObservations.multipleMappingSolution
+        	-filterZeros $genObservations.filterZeros
  		#end if
 		
 		-mappedTermsColName $mappedTermsColName
 		-numberOfHeaderLines $numberOfHeaderLines
+		
+		-htmlReportFile $htmlReportFile
+	    -htmlReportFilesPath $htmlReportFile.files_path
         	    
 	</command>
 	
 	<inputs>
 	 	
-  		<param name="inputFileName" type="data" format="tabular,csv" label="Target file (TSV/CSV)" />
+  		<param name="inputFileName" type="data" format="tabular,csv,txt" label="Target file (TSV/CSV)" />
   		
   		<param name="inputIdColumnName" type="text" size="50" value="" label="ID column name" 
   			help="Name of the column containing the identification codes (in the given input file)"/>
@@ -65,7 +70,7 @@
 	    </param>
 		
 		
-  		<param name="mappingFileIdColName" type="text" size="50" value="" label="ID column name (in lookup table)" help="Name of the ID column for the lookup"/>
+  		<param name="mappingFileIdColName" type="text" size="50" value="" label="ID column name or number (in lookup table)" help="Name (or number) of the ID column for the lookup"/>
   		
   		<conditional name="mappingIdCol">
      		<param name="mappingIdHasPrefix" type="boolean" truevalue="Yes" falsevalue="No" checked="false" 
@@ -87,7 +92,7 @@
   		             found it will try the second one, and so forth. "/>
   		
   		
-  		<param name="mappedTermsColName" type="text" size="50" value="Mapped terms" label="Name to give to the new column:" 
+  		<param name="mappedTermsColName" type="text" size="50" value="Mapped terms" label="Name to give to the new column" 
   		       help="Name to give to the new column that will be added to the target file. This new column is the one
   		             that will contain the respectively mapped terms."/>
   		
@@ -98,14 +103,22 @@
      			<param name="quantifColumn" type="text" size="50" value="" 
      				label="(Optional) Values column name" 
      				help="Name of the column containing the quantification values (in the given input file)"/>
+     			<param name="multipleMappingSolution" type="select"  
+     			       label="(when using values column above) What to do when multiple items map to the same term"
+     			       help="When e.g. two Uniprot codes map to the same KEGG code, which quantification value to use">
+     				<option value="not" selected="true">Do nothing, leave as is</option>
+     				<option value="max" >Use max value</option>
+	    			<option value="min">Use min value</option>
+	    			<option value="avg">Use avg value</option>
+	    		</param>
+	    		<param name="filterZeros" type="boolean" checked="false" 
+		     	       label="Filter zeros"
+		     	       help="Filter out the items that have quantification value = 0"/> 
      		</when>
      		<when value="No">
 			</when>
 		</conditional>
-     	
-     	
-
-     	
+   	
      	
 	</inputs>
 	<outputs>
@@ -114,11 +127,10 @@
 		#else:
        		<data name="outputFileName" format="csv" label="${tool.name} on ${on_string}: annotated file " ></data>
    		#end if
-	  
-	  <data name="outputObservationsFileName" format="tabular" label="${tool.name} on ${on_string}: term observations file (TSV)">
-	  	<!-- If the expression is false, the file is not created -->
-	  	<filter>( genObservations.genObservationsFile == True )</filter>
-	  </data>
+	  #if $genObservations.genObservationsFile == True :
+	  	<data name="outputObservationsFileName" format="tabular" label="${tool.name} on ${on_string}: term observations file (TSV)"></data>
+	  #end if
+	  <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - HTML report"/>
 	</outputs>
 	<tests>
 	  <!--  find out how to use -->
@@ -187,7 +199,8 @@
 
 *Ready to use proteomics links:*
 
-http://rest.genome.jp/link/uniprot/pti  (Phaeodactylum Tri.)
+http://rest.genome.jp/link/uniprot/pti  (Phaeodactylum Tricornutum)
+http://rest.genome.jp/link/pti/uniprot
 
 http://rest.genome.jp/link/uniprot/hsa  (Homo Sapiens)
 
@@ -198,6 +211,8 @@
 
 http://www.uniprot.org/taxonomy/
 
+http://www.uniprot.org/uniprot/?sort=&amp;desc=&amp;query=proteome:UP000000759&amp;fil=&amp;format=tab&amp;force=yes&amp;columns=id,go-id  (Phaeodactylum Tricornutum)
+
 
 -----