# HG changeset patch
# User iuc
# Date 1633074422 0
# Node ID d82fc956ab4dd2dc6c870cdb4156b60eac1def7f
# Parent  b3ff7225da033ce7a0f01c209920190b1d5bd07b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"

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
@@ -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>
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}
+    ]
   }
 }