Mercurial > repos > pieterlukasse > primo_multiomics
annotate ontologyvis.xml @ 14:7dfda218dca1 default tip
small fix
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Sat, 28 Mar 2015 21:33:55 +0100 |
| parents | a4c4656ad9e0 |
| children |
| rev | line source |
|---|---|
| 9 | 1 <tool name="OntologyVis" id="ontologyVis" version="0.0.2"> |
| 4 | 2 <description>visualize 'ontology mapped' quantitative results</description> |
| 3 <!-- | |
| 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 | |
| 6 --> | |
| 7 <command interpreter="java -jar "> | |
| 8 OntologyAndObservationsVis.jar | |
| 9 -ontologyFile $ontologyFile | |
| 10 -ontologyObservationsFile $ontologyObservationsFile | |
| 11 | |
| 12 -maxDepth $maxDepth | |
| 13 -allowedOntologySubsets $allowedOntologySubsets | |
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14 |
| 9 | 15 -sizingMethod $sizing.sizingMethod |
| 16 #if $sizing.sizingMethod == "quantification_based" | |
| 17 -circleSizeScale $sizing.circleSizeScale | |
| 18 #end if | |
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19 |
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20 -showObservationItems $showObservationItems |
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21 -oneTermOnlyAnnotation $oneTermOnlyAnnotation |
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22 -allowMultipleSuperClasses $allowMultipleSuperClasses |
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23 |
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24 -htmlReportFile $htmlReportFile |
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25 -htmlReportFilesPath $htmlReportFile.files_path |
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26 |
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parents:
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27 |
| 4 | 28 </command> |
| 29 | |
| 30 <inputs> | |
| 31 | |
| 32 <param name="ontologyFile" type="data" format="obo" label="Ontology file (.obo)" /> | |
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33 <param name="ontologyObservationsFile" type="data" format="tabular" optional="true" |
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eb0b7889dd08
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parents:
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34 label="(Optional) Ontology observations file (TSV)" /> |
| 4 | 35 |
| 36 <param name="maxDepth" type="integer" value="10" label="Maximum depth" | |
| 37 help="Maximum depth for the level of detail to show in the visualization"/> | |
| 38 | |
| 39 | |
| 40 <param name="allowedOntologySubsets" type="text" size="100" value="" label="(Optional) Ontology subsets" | |
| 41 help="Specify the comma-separated list of ontology subsets to use. If set, only the | |
| 42 ontology entries that are generic (not belonging to any subset) and ontology entries that are | |
| 43 marked as being part of one of the allowed subsets are added to the result list of entries."/> | |
| 44 | |
| 9 | 45 <conditional name="sizing"> |
| 46 <param name="sizingMethod" type="select" | |
| 47 label="Sizing" | |
| 10 | 48 help="How to size the ontology terms. See details in documentation below."> |
| 9 | 49 <option value="simple" selected="true">Simple sizing</option> |
| 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> | |
| 10 | 58 <option value="99" >None</option> |
| 9 | 59 </param> |
| 60 </when> | |
| 61 <when value="simple"> | |
| 62 </when> | |
| 63 </conditional> | |
| 64 | |
| 65 | |
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parents:
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66 <param name="showObservationItems" type="boolean" checked="true" |
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67 label="Display individual observation items" |
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68 help="Whether to render the individual observation items in the visualization. Disable this if you expect many (thousands) of |
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69 individual observation items per ontology entry."/> |
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eb0b7889dd08
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pieter.lukasse@wur.nl
parents:
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70 |
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eb0b7889dd08
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parents:
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changeset
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71 <param name="oneTermOnlyAnnotation" type="boolean" checked="true" |
| 13 | 72 label="Try to use only one term per observation items" |
| 73 help="If checked, the algorithm will try to reduce the number of terms to which an | |
| 74 observation item is associated. The observation item can still appear in more than one | |
| 75 term circle, but the algorithm will try to reduce this by preferring the bigger circles."/> | |
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eb0b7889dd08
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pieter.lukasse@wur.nl
parents:
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diff
changeset
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76 |
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eb0b7889dd08
added more parameters/options and made Ontology observations file optional;
pieter.lukasse@wur.nl
parents:
4
diff
changeset
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77 <param name="allowMultipleSuperClasses" type="boolean" checked="false" |
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eb0b7889dd08
added more parameters/options and made Ontology observations file optional;
pieter.lukasse@wur.nl
parents:
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diff
changeset
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78 label="Allow ontology terms to be nested under more than one super class" |
| 13 | 79 help="Some ontology classes can have multiple super classes. Check this to allow |
| 80 nesting the classes under each of its super classes. Even when NOT checking this option, | |
| 81 the ontology classes can still appear in more than one | |
| 82 term circle/superclass, but the algorithm will try to reduce this by preferring the bigger circles."/> | |
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eb0b7889dd08
added more parameters/options and made Ontology observations file optional;
pieter.lukasse@wur.nl
parents:
4
diff
changeset
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83 |
| 4 | 84 </inputs> |
| 85 <outputs> | |
| 86 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string}: ontology observations report (HTML)"></data> | |
| 87 </outputs> | |
| 88 <tests> | |
| 89 <!-- find out how to use --> | |
| 90 <test> | |
| 91 </test> | |
| 92 </tests> | |
| 93 <help> | |
| 94 | |
| 95 .. class:: infomark | |
| 96 | |
| 97 | |
| 98 | |
| 99 **Output** | |
| 100 | |
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parents:
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101 This method will generate different visualizations to allow exploring 'ontology annotated' results. |
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eb0b7889dd08
added more parameters/options and made Ontology observations file optional;
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parents:
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102 It generates ontology circles and ontology pie chart visualizations. |
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eb0b7889dd08
added more parameters/options and made Ontology observations file optional;
pieter.lukasse@wur.nl
parents:
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changeset
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103 |
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eb0b7889dd08
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pieter.lukasse@wur.nl
parents:
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104 Circles: |
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eb0b7889dd08
added more parameters/options and made Ontology observations file optional;
pieter.lukasse@wur.nl
parents:
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changeset
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105 The inner circles (white circles) are the most specific (or at depth=maximum depth) level of detail containing |
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eb0b7889dd08
added more parameters/options and made Ontology observations file optional;
pieter.lukasse@wur.nl
parents:
4
diff
changeset
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106 the individual observation items. |
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eb0b7889dd08
added more parameters/options and made Ontology observations file optional;
pieter.lukasse@wur.nl
parents:
4
diff
changeset
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107 |
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eb0b7889dd08
added more parameters/options and made Ontology observations file optional;
pieter.lukasse@wur.nl
parents:
4
diff
changeset
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108 Sizing: |
|
eb0b7889dd08
added more parameters/options and made Ontology observations file optional;
pieter.lukasse@wur.nl
parents:
4
diff
changeset
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109 * 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. |
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eb0b7889dd08
added more parameters/options and made Ontology observations file optional;
pieter.lukasse@wur.nl
parents:
4
diff
changeset
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110 * Quantification based sizing: Each observation item is sized according to the given quantification column. |
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eb0b7889dd08
added more parameters/options and made Ontology observations file optional;
pieter.lukasse@wur.nl
parents:
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diff
changeset
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111 |
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eb0b7889dd08
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parents:
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112 Colors: |
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eb0b7889dd08
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113 * Red borders show the items that have more than one parent in the given ontology scheme. The current visualization avoids redundancy by placing each |
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eb0b7889dd08
added more parameters/options and made Ontology observations file optional;
pieter.lukasse@wur.nl
parents:
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diff
changeset
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114 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). |
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eb0b7889dd08
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parents:
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115 |
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parents:
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116 |
| 4 | 117 |
| 118 </help> | |
| 119 </tool> |