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8
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1 <tool id="ontologizer" name="ontologizer" version="0.0.14">
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2 <description>from http://compbio.charite.de/contao/</description>
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3 <requirements>
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13
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4 <requirement type="set_environment">ONTOLOGIZER_JAR_PATH</requirement>
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9
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5 <requirement type="package" version="0.0.1">ontologizer-jar</requirement>
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8
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6 </requirements>
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7 <command>java -Xmx2G -jar $ONTOLOGIZER_JAR --go $go --association $gaf --population $pop --studyset $study --dot 0.05 > $output</command>
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8 <inputs>
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10
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9 <param name="go" type="text" label="Gene ontology" />
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10 <param name="gaf" type="text" label="Gene association file" />
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11 <param name="pop" type="text" label="population gene set" />
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12 <param name="study" type="text" label="study gene set" />
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8
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13 </inputs>
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14 <outputs>
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15 <!-- need to figure out how to handle multiple outputs -->
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9
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16 <data type="text" name="output" />
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8
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17 </outputs>
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18 <tests>
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19 <!-- see http://wiki.galaxyproject.org/Admin/Tools/Writing%20Tests -->
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20 <test>
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21 <param name="go" file="ontologizer/test.obo" />
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22 <param name="gaf" file="ontologizer/test.gaf" />
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23 <param name="pop" file="ontologizer/test.gs" />
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24 <param name="study" file="ontologizer/test.gs" />
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25 <output name="output" file="test.output"/>
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26 </test>
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27 </tests>
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28
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29
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30 <help>
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31 see http://compbio.charite.de/contao/index.php/ontologizer2.html
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32 </help>
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33
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34 </tool>
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35
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36
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