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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472" |
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modified:
macros.xml test-data/strict_qc.json |
| b |
| diff -r b3ff7225da03 -r d82fc956ab4d macros.xml --- a/macros.xml Sat Sep 25 18:18:28 2021 +0000 +++ b/macros.xml Fri Oct 01 07:47:02 2021 +0000 |
| b |
| @@ -1,6 +1,6 @@ <macros> <!-- same version number is used for nextclade and nextalign releases, even though they are distinct tools --> - <token name="@TOOL_VERSION@">1.3.0</token> + <token name="@TOOL_VERSION@">1.4.0</token> <xml name="citations"> <citations> <citation type="bibtex">@online{nextclade, @@ -57,4 +57,4 @@ You can use the tool to analyze sequences before you upload them to a database, or if you want to assign Nextstrain clades to a set of sequences. ]]></token> -</macros> \ No newline at end of file +</macros> |
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| diff -r b3ff7225da03 -r d82fc956ab4d test-data/strict_qc.json --- a/test-data/strict_qc.json Sat Sep 25 18:18:28 2021 +0000 +++ b/test-data/strict_qc.json Fri Oct 01 07:47:02 2021 +0000 |
| [ |
| @@ -1,4 +1,5 @@ { + "schemaVersion": "1.2.0", "privateMutations": { "enabled": true, "typical": 5, @@ -18,5 +19,38 @@ "mixedSites": { "enabled": true, "mixedSitesThreshold": 5 + }, + "frameShifts": { + "enabled": true, + "ignoredFrameShifts": [ + { "geneName": "ORF3a", "codonRange": {"begin": 256, "end": 276} }, + { "geneName": "ORF3a", "codonRange": {"begin": 258, "end": 276} }, + { "geneName": "ORF7a", "codonRange": {"begin": 61, "end": 122} }, + { "geneName": "ORF7a", "codonRange": {"begin": 62, "end": 122} }, + { "geneName": "ORF7a", "codonRange": {"begin": 76, "end": 122} }, + { "geneName": "ORF7a", "codonRange": {"begin": 101, "end": 122} }, + { "geneName": "ORF7b", "codonRange": {"begin": 41, "end": 44} }, + { "geneName": "ORF8", "codonRange": {"begin": 107, "end": 122} }, + { "geneName": "ORF8", "codonRange": {"begin": 119, "end": 122} }, + { "geneName": "ORF8", "codonRange": {"begin": 120, "end": 122} }, + { "geneName": "ORF8", "codonRange": {"begin": 121, "end": 123} } + ] + }, + "stopCodons": { + "enabled": true, + "ignoredStopCodons": [ + {"geneName": "ORF7a", "codon": 61}, + {"geneName": "ORF7a", "codon": 93}, + {"geneName": "ORF7b", "codon": 32}, + {"geneName": "ORF7b", "codon": 38}, + {"geneName": "ORF8", "codon": 17}, + {"geneName": "ORF8", "codon": 18}, + {"geneName": "ORF8", "codon": 25}, + {"geneName": "ORF8", "codon": 26}, + {"geneName": "ORF8", "codon": 58}, + {"geneName": "ORF8", "codon": 66}, + {"geneName": "ORF8", "codon": 67}, + {"geneName": "ORF8", "codon": 105} + ] } } |