Mercurial > repos > iuc > nextclade

annotate test-data/strict_qc.json @ 17:07ab9bd68a02 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
author iuc
date Thu, 04 Aug 2022 06:58:48 +0000
parents f6db3ce6ed1c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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1 {
7
f6db3ce6ed1c "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",
0
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3 "privateMutations": {
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4 "enabled": true,
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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5 "typical": 5,
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6 "cutoff": 10
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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7 },
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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8 "missingData": {
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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9 "enabled": true,
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10 "missingDataThreshold": 10,
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11 "scoreBias": 300
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12 },
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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13 "snpClusters": {
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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14 "enabled": true,
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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15 "windowSize": 100,
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16 "clusterCutOff": 1,
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17 "scoreWeight": 20
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18 },
615f484bdb4a "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,
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21 "mixedSitesThreshold": 5
7
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22 },
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23 "frameShifts": {
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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} },
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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} },
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31 { "geneName": "ORF7a", "codonRange": {"begin": 101, "end": 122} },
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32 { "geneName": "ORF7b", "codonRange": {"begin": 41, "end": 44} },
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33 { "geneName": "ORF8", "codonRange": {"begin": 107, "end": 122} },
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34 { "geneName": "ORF8", "codonRange": {"begin": 119, "end": 122} },
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35 { "geneName": "ORF8", "codonRange": {"begin": 120, "end": 122} },
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36 { "geneName": "ORF8", "codonRange": {"begin": 121, "end": 123} }
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37 ]
f6db3ce6ed1c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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38 },
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39 "stopCodons": {
f6db3ce6ed1c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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40 "enabled": true,
f6db3ce6ed1c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
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41 "ignoredStopCodons": [
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42 {"geneName": "ORF7a", "codon": 61},
f6db3ce6ed1c "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},
f6db3ce6ed1c "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},
f6db3ce6ed1c "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},
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46 {"geneName": "ORF8", "codon": 17},
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47 {"geneName": "ORF8", "codon": 18},
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48 {"geneName": "ORF8", "codon": 25},
f6db3ce6ed1c "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},
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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 ]
0
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55 }
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56 }