Mercurial > repos > pieterlukasse > primo_multiomics

comparison ontologyvis.xml @ 5:eb0b7889dd08

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
added more parameters/options and made Ontology observations file optional;
author pieter.lukasse@wur.nl
date Fri, 01 Aug 2014 17:20:02 +0200
parents b868e946247a
children 89264646e458
comparison
equal deleted inserted replaced
4:b868e946247a 5:eb0b7889dd08
9 -ontologyFile $ontologyFile 9 -ontologyFile $ontologyFile
10 -ontologyObservationsFile $ontologyObservationsFile 10 -ontologyObservationsFile $ontologyObservationsFile
11 11
12 -maxDepth $maxDepth 12 -maxDepth $maxDepth
13 -allowedOntologySubsets $allowedOntologySubsets 13 -allowedOntologySubsets $allowedOntologySubsets
14 14
15 -htmlReportFile $htmlReportFile 15 -sizingType $sizingType
16 -htmlReportFilesPath $htmlReportFile.files_path 16
17 17 -showObservationItems $showObservationItems
18 -oneTermOnlyAnnotation $oneTermOnlyAnnotation
19 -allowMultipleSuperClasses $allowMultipleSuperClasses
20
21 -htmlReportFile $htmlReportFile
22 -htmlReportFilesPath $htmlReportFile.files_path
23
24
18 </command> 25 </command>
19 26
20 <inputs> 27 <inputs>
21 28
22 <param name="ontologyFile" type="data" format="obo" label="Ontology file (.obo)" /> 29 <param name="ontologyFile" type="data" format="obo" label="Ontology file (.obo)" />
23 <param name="ontologyObservationsFile" type="data" format="tabular" label="Ontology observations file (TSV)" /> 30 <param name="ontologyObservationsFile" type="data" format="tabular" optional="true"
31 label="(Optional) Ontology observations file (TSV)" />
24 32
25 <param name="maxDepth" type="integer" value="10" label="Maximum depth" 33 <param name="maxDepth" type="integer" value="10" label="Maximum depth"
26 help="Maximum depth for the level of detail to show in the visualization"/> 34 help="Maximum depth for the level of detail to show in the visualization"/>
27 35
28 36
29 <param name="allowedOntologySubsets" type="text" size="100" value="" label="(Optional) Ontology subsets" 37 <param name="allowedOntologySubsets" type="text" size="100" value="" label="(Optional) Ontology subsets"
30 help="Specify the comma-separated list of ontology subsets to use. If set, only the 38 help="Specify the comma-separated list of ontology subsets to use. If set, only the
31 ontology entries that are generic (not belonging to any subset) and ontology entries that are 39 ontology entries that are generic (not belonging to any subset) and ontology entries that are
32 marked as being part of one of the allowed subsets are added to the result list of entries."/> 40 marked as being part of one of the allowed subsets are added to the result list of entries."/>
41
42 <param name="sizingType" type="select"
43 label="Sizing"
44 help="How to size the ontology terms in the final output. See details in documentation below.">
45 <option value="simple" selected="true">Simple sizing</option>
46 <option value="quantification_based">(TODO)Quantification based sizing</option>
47 </param>
48 <param name="showObservationItems" type="boolean" checked="true"
49 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
51 individual observation items per ontology entry."/>
52
53 <param name="oneTermOnlyAnnotation" type="boolean" checked="true"
54 label="Use only one annotation per observation items"
55 help="Check this to force each observation item to keep only one of its ontology annotations,
56 as a form of redundancy reduction. If checked, the algorithm will
57 keep the ontology annotation that has most other (sibling) observation items."/>
58
59 <param name="allowMultipleSuperClasses" type="boolean" checked="false"
60 label="Allow ontology terms to be nested under more than one super class"
61 help="Some ontology classes have multiple super classes. Check this to allow
62 nesting the classes under each of its super classes. Not checking this option
63 will cause the ontology classes that have more than one super class to
64 be nested under the super class that has (initially) most observation items
65 under it (directly or in its sub classes)."/>
33 66
34 </inputs> 67 </inputs>
35 <outputs> 68 <outputs>
36 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string}: ontology observations report (HTML)"></data> 69 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string}: ontology observations report (HTML)"></data>
37 </outputs> 70 </outputs>
42 </tests> 75 </tests>
43 <help> 76 <help>
44 77
45 .. class:: infomark 78 .. class:: infomark
46 79
47 This tool is responsible for ....
48
49 80
50 -----
51 81
52 **Output** 82 **Output**
53 83
54 This method will .... 84 This method will generate different visualizations to allow exploring 'ontology annotated' results.
85 It generates ontology circles and ontology pie chart visualizations.
86
87 Circles:
88 The inner circles (white circles) are the most specific (or at depth=maximum depth) level of detail containing
89 the individual observation items.
90
91 Sizing:
92 * Simple sizing: Each observation item is given the same size. The more observation items found for a certain ontology circle, the bigger it will be.
93 * Quantification based sizing: Each observation item is sized according to the given quantification column.
94
95 Colors:
96 * Red borders show the items that have more than one parent in the given ontology scheme. The current visualization avoids redundancy by placing each
97 circle inside the parent circle where it has more siblings with observations (not yet an iterative process, so nr of siblings is calculated only at start).
98
99
55 100
56 </help> 101 </help>
57 </tool> 102 </tool>