Mercurial > repos > iuc > sarscov2summary

annotate test-data/meme.json @ 0:4ad8b610ea41 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
author iuc
date Mon, 04 May 2020 05:42:35 -0400
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4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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1278 ]
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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1279 },
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1280 "headers": [
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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1281 ["alpha;", "Synonymous substitution rate at a site"],
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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1282 ["&beta;<sup>-</sup>", "Non-synonymous substitution rate at a site for the negative/neutral evolution component"],
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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1283 ["p<sup>-</sup>", "Mixture distribution weight allocated to &beta;<sup>-</sup>; loosely -- the proportion of the tree evolving neutrally or under negative selection"],
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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1284 ["&beta;<sup>+</sup>", "Non-synonymous substitution rate at a site for the positive/neutral evolution component"],
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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diff changeset
1285 ["p<sup>+</sup>", "Mixture distribution weight allocated to &beta;<sup>+</sup>; loosely -- the proportion of the tree evolving neutrally or under positive selection"],
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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diff changeset
1286 ["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p<sup>+</sup> &gt; 0 <emph>and<emph> &beta;<sup>+</sup> &gt; &alpha;"],
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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diff changeset
1287 ["p-value", "Asymptotic p-value for episodic diversification, i.e., p<sup>+</sup> &gt; 0 <emph>and<emph> &beta;<sup>+</sup> &gt; &alpha;"],
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
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diff changeset
1288 ["# branches under selection", "The (very approximate and rough) estimate of how many branches may have been under selection at this site, i.e., had an empirical Bayes factor of 100 or more for the &beta;<sup>+</sup> rate"],
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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diff changeset
1289 ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"],
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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1290 ["MEME LogL", "Site Log-likelihood under the MEME model"],
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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1291 ["FEL LogL", "Site Log-likelihood under the FEL model"]
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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1292 ]
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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1293 },
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1294 "analysis":{
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1295 "authors":"Sergei L. Kosakovsky Pond, Steven Weaver",
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1296 "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.",
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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1297 "contact":"spond@temple.edu",
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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1298 "info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (&alpha;) and a two-category mixture of non-synonymous\n (&beta;-, with proportion p-, and &beta;+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if &beta;+ > &alpha; at a site.\n The estimates aggregate information over a proportion of branches at a site,\n so the signal is derived from\n episodic diversification, which is a combination of strength of selection [effect size] and\n the proportion of the tree affected. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ",
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1299 "requirements":"in-frame codon alignment and a phylogenetic tree",
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1300 "version":"2.1.2"
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1301 },
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1302 "branch attributes":{
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1303 "0":{
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1304 "MN988713":{
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1305 "Global MG94xREV":0,
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1306 "Nucleotide GTR":0,
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1307 "original name":"MN988713"
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1308 },
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1309 "MT263436":{
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1310 "Global MG94xREV":0,
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1311 "Nucleotide GTR":0,
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1312 "original name":"MT263436"
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1313 },
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1314 "MT263450":{
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1315 "Global MG94xREV":0.0002667317765692254,
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1316 "Nucleotide GTR":0.0002618728984518801,
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1317 "original name":"MT263450"
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1318 },
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1319 "MT263469":{
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1320 "Global MG94xREV":0.0002668305373938125,
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1321 "Nucleotide GTR":0.0002619448694224783,
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1322 "original name":"MT263469"
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diff changeset
1408 },
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diff changeset
1409 "EBF site 665 (partition 1)":{
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1410 "attribute type":"branch label",
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1411 "display order":667
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diff changeset
1412 },
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diff changeset
1413 "EBF site 67 (partition 1)":{
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1414 "attribute type":"branch label",
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diff changeset
1415 "display order":69
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diff changeset
1416 },
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diff changeset
1417 "EBF site 74 (partition 1)":{
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1418 "attribute type":"branch label",
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1419 "display order":76
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diff changeset
1420 },
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1421 "EBF site 824 (partition 1)":{
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1422 "attribute type":"branch label",
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1424 },
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diff changeset
1425 "Global MG94xREV":{
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1426 "attribute type":"branch length",
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1427 "display order":1
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diff changeset
1428 },
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diff changeset
1429 "Nucleotide GTR":{
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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1430 "attribute type":"branch length",
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diff changeset
1432 },
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1433 "original name":{
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1434 "attribute type":"node label",
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1436 }
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
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1439 "data partitions":{
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1440 "0":{
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4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
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diff changeset
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diff changeset
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diff changeset
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iuc
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1512 ],
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iuc
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1513 "Log Likelihood":-5046.748329267292,
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iuc
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1514 "Rate Distributions":{
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1515 "non-synonymous/synonymous rate ratio for *background*": [
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iuc
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1516 [0.1425553249428705, 1]
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1517 ],
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1518 "non-synonymous/synonymous rate ratio for *test*": [
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1520 ]
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1521 },
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1522 "display order":1,
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1523 "estimated parameters":28
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1524 },
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diff changeset
1525 "Nucleotide GTR":{
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1526 "AIC-c":10521.28687405917,
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1527 "Equilibrium frequencies": [
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iuc
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1532 ],
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iuc
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1533 "Log Likelihood":-5233.625428883045,
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1534 "Rate Distributions":{
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iuc
parents:
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1535 "Substitution rate from nucleotide A to nucleotide C":0,
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iuc
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1536 "Substitution rate from nucleotide A to nucleotide G":1,
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iuc
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1537 "Substitution rate from nucleotide A to nucleotide T":0.1847804107859,
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iuc
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1538 "Substitution rate from nucleotide C to nucleotide G":0,
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iuc
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1539 "Substitution rate from nucleotide C to nucleotide T":0.5743828140832303,
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iuc
parents:
diff changeset
1540 "Substitution rate from nucleotide G to nucleotide T":0.2950953831288027
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iuc
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1541 },
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iuc
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1542 "display order":0,
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iuc
parents:
diff changeset
1543 "estimated parameters":27
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1544 }
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1545 },
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1546 "input":{
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1547 "file name":"/galaxy-repl/main/jobdir/028/157/28157295/working/./meme_input.fa",
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1548 "number of sequences":11,
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1549 "number of sites":1273,
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1550 "partition count":1,
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1551 "trees":{
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1552 "0":"(MN988713,MT292573,MT263469,MT350282,MultiSeq0_24,(MT292570,MT293207,MT345866,MT263436,MultiSeq1_15)Node6,MT263450)"
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1553 }
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1554 },
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1555 "tested":{
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1556 "0":{
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1557 "MN988713":"background",
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1558 "MT263436":"background",
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1559 "MT263450":"background",
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1560 "MT263469":"background",
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1561 "MT292570":"background",
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1562 "MT292573":"background",
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1563 "MT293207":"background",
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1564 "MT345866":"background",
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1565 "MT350282":"background",
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1566 "MultiSeq0_24":"background",
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1567 "MultiSeq1_15":"background",
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1568 "Node6":"test"
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1569 }
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1570 },
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1571 "timers":{
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1572 "MEME analysis":{
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1573 "order":2,
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1574 "timer":3
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1575 },
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1576 "Model fitting":{
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1577 "order":1,
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1578 "timer":5
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1579 },
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1580 "Total time":{
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1581 "order":0,
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1582 "timer":9
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1583 }
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1584 }
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1585 }