# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1427549325 -3600
# Node ID 89264646e45892c99531784ff72e613b02c14264
# Parent  97e10319d86fefdcf97806203304ea6f523c749f
improvements release

diff -r 97e10319d86f -r 89264646e458 OntologyAndObservationsVis.jar
Binary file OntologyAndObservationsVis.jar has changed
diff -r 97e10319d86f -r 89264646e458 README.rst
--- a/README.rst	Mon Mar 23 22:11:39 2015 +0100
+++ b/README.rst	Sat Mar 28 14:28:45 2015 +0100
@@ -20,6 +20,9 @@
 ============== ======================================================================
 Date            Changes
 -------------- ----------------------------------------------------------------------
+March 2015     * improvements release, refactored TermMapperTool (made this more
+                 generic / multi-purpose lookup / cross-reference tool); added
+                 support for quantification method in OntologyVis circles plot;
 August 2014    * improvements release
 May 2014       * first release via Tool Shed
 ============== ======================================================================
diff -r 97e10319d86f -r 89264646e458 TermMapperTool.jar
Binary file TermMapperTool.jar has changed
diff -r 97e10319d86f -r 89264646e458 ontologyvis.xml
--- a/ontologyvis.xml	Mon Mar 23 22:11:39 2015 +0100
+++ b/ontologyvis.xml	Sat Mar 28 14:28:45 2015 +0100
@@ -1,4 +1,4 @@
-<tool name="OntologyVis" id="ontologyVis" version="0.0.1">
+<tool name="OntologyVis" id="ontologyVis" version="0.0.2">
 	<description>visualize 'ontology mapped' quantitative results</description>
 	<!-- 
 	   For remote debugging start you listener on port 8000 and use the following as command interpreter:
@@ -12,7 +12,10 @@
 		-maxDepth $maxDepth
 		-allowedOntologySubsets $allowedOntologySubsets
 		
-		-sizingType $sizingType 
+		-sizingMethod $sizing.sizingMethod 
+		#if $sizing.sizingMethod == "quantification_based"
+			-circleSizeScale $sizing.circleSizeScale 
+ 		#end if
 				
  		-showObservationItems $showObservationItems
  		-oneTermOnlyAnnotation $oneTermOnlyAnnotation
@@ -39,12 +42,27 @@
 	                             ontology entries that are generic (not belonging to any subset) and ontology entries that are 
 	                             marked as being part of one of the allowed subsets are added to the result list of entries."/>
      	
-     	<param name="sizingType" type="select" 
-	   		label="Sizing" 
-	   		help="How to size the ontology terms in the final output. See details in documentation below.">
-	    	<option value="simple" selected="true">Simple sizing</option>
-	    	<option value="quantification_based">(TODO)Quantification based sizing</option>
-		</param>
+     	<conditional name="sizing">
+	     	<param name="sizingMethod" type="select" 
+		   		label="Sizing" 
+		   		help="How to size the ontology terms in the final output. See details in documentation below.">
+		    	<option value="simple" selected="true">Simple sizing</option>
+		    	<option value="quantification_based">Quantification based sizing</option>
+			</param>
+			<when value="quantification_based">
+				<param name="circleSizeScale" type="select" 
+		   		label="Circle sizes scale" 
+		   		help="How to adjust the circle sizes according to the quantification value.">
+			    	<option value="2" selected="true">log2</option>
+			    	<option value="10" selected="true">log10</option>
+			    	<option value="-1" >None</option>	    	
+				</param>
+			</when>
+			<when value="simple">
+			</when>
+		</conditional>
+		
+		
      	<param name="showObservationItems" type="boolean" checked="true" 
      	  label="Display individual observation items" 
      	  help="Whether to render the individual observation items in the visualization. Disable this if you expect many (thousands) of 
diff -r 97e10319d86f -r 89264646e458 term_mapper.xml
--- 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)
+
 
 -----