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annotate test-data/strict_qc.json @ 15:41102a84e387 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
author iuc
date Sat, 08 Oct 2022 20:03:17 +0000
parents d82fc956ab4d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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456e4dadb905 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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1 {
4
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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2 "schemaVersion": "1.2.0",
1
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3 "privateMutations": {
456e4dadb905 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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4 "enabled": true,
456e4dadb905 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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5 "typical": 5,
456e4dadb905 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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6 "cutoff": 10
456e4dadb905 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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7 },
456e4dadb905 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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8 "missingData": {
456e4dadb905 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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9 "enabled": true,
456e4dadb905 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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10 "missingDataThreshold": 10,
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11 "scoreBias": 300
456e4dadb905 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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12 },
456e4dadb905 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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13 "snpClusters": {
456e4dadb905 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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14 "enabled": true,
456e4dadb905 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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15 "windowSize": 100,
456e4dadb905 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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16 "clusterCutOff": 1,
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17 "scoreWeight": 20
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18 },
456e4dadb905 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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19 "mixedSites": {
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20 "enabled": true,
456e4dadb905 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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21 "mixedSitesThreshold": 5
4
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22 },
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23 "frameShifts": {
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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24 "enabled": true,
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25 "ignoredFrameShifts": [
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26 { "geneName": "ORF3a", "codonRange": {"begin": 256, "end": 276} },
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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27 { "geneName": "ORF3a", "codonRange": {"begin": 258, "end": 276} },
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28 { "geneName": "ORF7a", "codonRange": {"begin": 61, "end": 122} },
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29 { "geneName": "ORF7a", "codonRange": {"begin": 62, "end": 122} },
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30 { "geneName": "ORF7a", "codonRange": {"begin": 76, "end": 122} },
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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31 { "geneName": "ORF7a", "codonRange": {"begin": 101, "end": 122} },
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32 { "geneName": "ORF7b", "codonRange": {"begin": 41, "end": 44} },
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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33 { "geneName": "ORF8", "codonRange": {"begin": 107, "end": 122} },
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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34 { "geneName": "ORF8", "codonRange": {"begin": 119, "end": 122} },
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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35 { "geneName": "ORF8", "codonRange": {"begin": 120, "end": 122} },
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36 { "geneName": "ORF8", "codonRange": {"begin": 121, "end": 123} }
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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37 ]
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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38 },
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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39 "stopCodons": {
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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40 "enabled": true,
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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41 "ignoredStopCodons": [
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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42 {"geneName": "ORF7a", "codon": 61},
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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43 {"geneName": "ORF7a", "codon": 93},
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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44 {"geneName": "ORF7b", "codon": 32},
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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45 {"geneName": "ORF7b", "codon": 38},
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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46 {"geneName": "ORF8", "codon": 17},
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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47 {"geneName": "ORF8", "codon": 18},
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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48 {"geneName": "ORF8", "codon": 25},
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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49 {"geneName": "ORF8", "codon": 26},
d82fc956ab4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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50 {"geneName": "ORF8", "codon": 58},
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51 {"geneName": "ORF8", "codon": 66},
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52 {"geneName": "ORF8", "codon": 67},
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53 {"geneName": "ORF8", "codon": 105}
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54 ]
1
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55 }
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56 }