1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
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3 <runnerClassName>compbio.runner.predictors.Jpred</runnerClassName>
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6 <name>Prediction without PSI-BLAST hits</name>
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8 Toggle allowing Jpred to make predictions even when there are no
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11 <optionNames>-pred-nohits</optionNames>
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12 <furtherDetails>prog_docs/jpred.txt</furtherDetails>
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16 <name>JABAWS configuration</name>
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18 Configure Jpred to work within JABAWS
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20 <optionNames>-jabaws</optionNames>
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21 <furtherDetails>prog_docs/jpred.txt</furtherDetails>
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24 <prmSeparator> </prmSeparator>
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26 <parameters isRequired="false">
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27 <name>UNIREF database</name>
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29 Path to UNIREF database for PSI-BLAST querying
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31 <optionNames>-dbpath</optionNames>
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32 <furtherDetails>prog_docs/jpred.txt</furtherDetails>
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33 <defaultValue>/data/UNIREFdb</defaultValue>
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36 <parameters isRequired="true">
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37 <name>UNIREF database name</name>
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39 Number of (combined guide tree/HMM) iterations
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41 <optionNames>-dbname</optionNames>
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42 <furtherDetails>prog_docs/jpred.txt</furtherDetails>
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43 <defaultValue>ported_db</defaultValue>
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44 <possibleValues>uniref90</possibleValues>
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45 <possibleValues>ported_db</possibleValues>
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46 <possibleValues>cluster</possibleValues>
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49 <parameters isRequired="false">
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50 <name>Number of CPUs</name>
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52 Number of CPU used by Jpred. Maximum value is 8
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54 <optionNames>-ncpu</optionNames>
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55 <furtherDetails>prog_docs/jpred.txt</furtherDetails>
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56 <defaultValue>1</defaultValue>
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58 <type>Integer</type>
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