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comparison ontologyvis.xml @ 9:89264646e458

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improvements release
author pieter.lukasse@wur.nl
date Sat, 28 Mar 2015 14:28:45 +0100
parents eb0b7889dd08
children 65850557aae9
comparison
equal deleted inserted replaced
8:97e10319d86f 9:89264646e458
1 <tool name="OntologyVis" id="ontologyVis" version="0.0.1"> 1 <tool name="OntologyVis" id="ontologyVis" version="0.0.2">
2 <description>visualize 'ontology mapped' quantitative results</description> 2 <description>visualize 'ontology mapped' quantitative results</description>
3 <!-- 3 <!--
4 For remote debugging start you listener on port 8000 and use the following as command interpreter: 4 For remote debugging start you listener on port 8000 and use the following as command interpreter:
5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
6 --> 6 -->
10 -ontologyObservationsFile $ontologyObservationsFile 10 -ontologyObservationsFile $ontologyObservationsFile
11 11
12 -maxDepth $maxDepth 12 -maxDepth $maxDepth
13 -allowedOntologySubsets $allowedOntologySubsets 13 -allowedOntologySubsets $allowedOntologySubsets
14 14
15 -sizingType $sizingType 15 -sizingMethod $sizing.sizingMethod
16 #if $sizing.sizingMethod == "quantification_based"
17 -circleSizeScale $sizing.circleSizeScale
18 #end if
16 19
17 -showObservationItems $showObservationItems 20 -showObservationItems $showObservationItems
18 -oneTermOnlyAnnotation $oneTermOnlyAnnotation 21 -oneTermOnlyAnnotation $oneTermOnlyAnnotation
19 -allowMultipleSuperClasses $allowMultipleSuperClasses 22 -allowMultipleSuperClasses $allowMultipleSuperClasses
20 23
37 <param name="allowedOntologySubsets" type="text" size="100" value="" label="(Optional) Ontology subsets" 40 <param name="allowedOntologySubsets" type="text" size="100" value="" label="(Optional) Ontology subsets"
38 help="Specify the comma-separated list of ontology subsets to use. If set, only the 41 help="Specify the comma-separated list of ontology subsets to use. If set, only the
39 ontology entries that are generic (not belonging to any subset) and ontology entries that are 42 ontology entries that are generic (not belonging to any subset) and ontology entries that are
40 marked as being part of one of the allowed subsets are added to the result list of entries."/> 43 marked as being part of one of the allowed subsets are added to the result list of entries."/>
41 44
42 <param name="sizingType" type="select" 45 <conditional name="sizing">
43 label="Sizing" 46 <param name="sizingMethod" type="select"
44 help="How to size the ontology terms in the final output. See details in documentation below."> 47 label="Sizing"
45 <option value="simple" selected="true">Simple sizing</option> 48 help="How to size the ontology terms in the final output. See details in documentation below.">
46 <option value="quantification_based">(TODO)Quantification based sizing</option> 49 <option value="simple" selected="true">Simple sizing</option>
47 </param> 50 <option value="quantification_based">Quantification based sizing</option>
51 </param>
52 <when value="quantification_based">
53 <param name="circleSizeScale" type="select"
54 label="Circle sizes scale"
55 help="How to adjust the circle sizes according to the quantification value.">
56 <option value="2" selected="true">log2</option>
57 <option value="10" selected="true">log10</option>
58 <option value="-1" >None</option>
59 </param>
60 </when>
61 <when value="simple">
62 </when>
63 </conditional>
64
65
48 <param name="showObservationItems" type="boolean" checked="true" 66 <param name="showObservationItems" type="boolean" checked="true"
49 label="Display individual observation items" 67 label="Display individual observation items"
50 help="Whether to render the individual observation items in the visualization. Disable this if you expect many (thousands) of 68 help="Whether to render the individual observation items in the visualization. Disable this if you expect many (thousands) of
51 individual observation items per ontology entry."/> 69 individual observation items per ontology entry."/>
52 70