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16
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1 <tool id="vgx_converter" name="SIF-to-JGF" version="0.0.5">
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15
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2 <description>Converts a SIF file to a JSON Graph Format (JGF) file for visualization in VisualGraphX</description>
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1
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3 <command interpreter="python">vgx_converter.py $input1 $delimiter $input2 $output</command>
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4 <inputs>
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5 <param format="txt" name="input1" type="data" label="Network"/>
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6 <param format="tabular" name="input2" type="data" optional="true" label="Attributes"/>
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7 <param name="delimiter" type="select" label="Delimiter">
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8 <option value="tab" selected="true">tab-delimited</option>
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9 <option value="space">space-delimited</option>
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10 </param>
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11 </inputs>
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12 <outputs>
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17
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13 <data format="json" name="output"/>
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1
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14 </outputs>
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15
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16 <help>
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15
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17 This tool converts the simple interaction format (.sif) to the JavaScript Graph Format JGF (.jgf)
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1
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18 that can be visualized using VisualGraphX. Furthermore, a attributes list can be provided to enhance
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19 the information of the nodes in the graph.
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20 </help>
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21
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22 <tests>
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23 <test>
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16
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24 <param name="input1" value="CoVennTree_network.sif"/>
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1
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25 <param name="delimiter" value="space"/>
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26 <param name="input2" value="CoVennTree.venn"/>
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27 <param name="output" value="CoVennTree.jgf"/>
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1
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28 </test>
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29 <test>
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16
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30 <param name="input1" value="Apoptosis.sif"/>
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1
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31 <param name="delimiter" value="tab"/>
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16
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32 <param name="output" value="Apoptosis.jgf"/>
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1
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33 </test>
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34 </tests>
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35
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36 </tool>
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37
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