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1 <tool name="OntologyVis" id="ontologyVis" version="0.0.1">
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2 <description>visualize 'ontology mapped' quantitative results</description>
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3 <!--
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4 For remote debugging start you listener on port 8000 and use the following as command interpreter:
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5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
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6 -->
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7 <command interpreter="java -jar ">
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8 OntologyAndObservationsVis.jar
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9 -ontologyFile $ontologyFile
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10 -ontologyObservationsFile $ontologyObservationsFile
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11
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12 -maxDepth $maxDepth
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13 -allowedOntologySubsets $allowedOntologySubsets
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14
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15 -htmlReportFile $htmlReportFile
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16 -htmlReportFilesPath $htmlReportFile.files_path
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17
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18 </command>
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19
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20 <inputs>
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21
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22 <param name="ontologyFile" type="data" format="obo" label="Ontology file (.obo)" />
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23 <param name="ontologyObservationsFile" type="data" format="tabular" label="Ontology observations file (TSV)" />
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24
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25 <param name="maxDepth" type="integer" value="10" label="Maximum depth"
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26 help="Maximum depth for the level of detail to show in the visualization"/>
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27
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28
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29 <param name="allowedOntologySubsets" type="text" size="100" value="" label="(Optional) Ontology subsets"
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30 help="Specify the comma-separated list of ontology subsets to use. If set, only the
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31 ontology entries that are generic (not belonging to any subset) and ontology entries that are
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32 marked as being part of one of the allowed subsets are added to the result list of entries."/>
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33
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34 </inputs>
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35 <outputs>
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36 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string}: ontology observations report (HTML)"></data>
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37 </outputs>
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38 <tests>
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39 <!-- find out how to use -->
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40 <test>
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41 </test>
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42 </tests>
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43 <help>
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44
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45 .. class:: infomark
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46
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47 This tool is responsible for ....
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48
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49
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50 -----
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51
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52 **Output**
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53
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54 This method will ....
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55
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56 </help>
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57 </tool>
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