# HG changeset patch
# User iuc
# Date 1633074444 0
# Node ID f6db3ce6ed1c6e33a133210b05b5ce414c79802c
# Parent  1e0234b878098100dc1bfe92c0ac98c33128b75a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"

diff -r 1e0234b87809 -r f6db3ce6ed1c macros.xml
--- a/macros.xml	Sat Sep 25 18:18:54 2021 +0000
+++ b/macros.xml	Fri Oct 01 07:47:24 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 1e0234b87809 -r f6db3ce6ed1c nextclade.xml
--- a/nextclade.xml	Sat Sep 25 18:18:54 2021 +0000
+++ b/nextclade.xml	Fri Oct 01 07:47:24 2021 +0000
@@ -101,7 +101,7 @@
         <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)">            
             <filter>outputs and "report_tsv" in outputs</filter>
             <actions>
-                <action name="column_names" type="metadata" default="seqName,clade,qc.overallScore,qc.overallStatus,totalSubstitutions,totalDeletions,totalInsertions,totalAminoacidSubstitutions,totalAminoacidDeletions,totalMissing,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertions,aaSubstitutions,aaDeletions,missing,nonACGTNs,pcrPrimerChanges,alignmentScore,alignmentStart,alignmentEnd,qc.missingData.missingDataThreshold,qc.missingData.score,qc.missingData.status,qc.missingData.totalMissing,qc.mixedSites.mixedSitesThreshold,qc.mixedSites.score,qc.mixedSites.status,qc.mixedSites.totalMixedSites,qc.privateMutations.cutoff,qc.privateMutations.excess,qc.privateMutations.score,qc.privateMutations.status,qc.privateMutations.total,qc.snpClusters.clusteredSNPs,qc.snpClusters.score,qc.snpClusters.status,qc.snpClusters.totalSNPs,qc.frameShifts.frameShifts,qc.frameShifts.totalFrameShifts,qc.frameShifts.score,qc.frameShifts.status,qc.stopCodons.stopCodons,qc.stopCodons.totalStopCodons,qc.stopCodons.score,qc.stopCodons.status,errors" />                
+                <action name="column_names" type="metadata" default="seqName,clade,qc.overallScore,qc.overallStatus,totalSubstitutions,totalDeletions,totalInsertions,totalFrameShifts,totalAminoacidSubstitutions,totalAminoacidDeletions,totalMissing,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertions,frameShifts,aaSubstitutions,aaDeletions,missing,nonACGTNs,pcrPrimerChanges,alignmentScore,alignmentStart,alignmentEnd,qc.missingData.missingDataThreshold,qc.missingData.score,qc.missingData.status,qc.missingData.totalMissing,qc.mixedSites.mixedSitesThreshold,qc.mixedSites.score,qc.mixedSites.status,qc.mixedSites.totalMixedSites,qc.privateMutations.cutoff,qc.privateMutations.excess,qc.privateMutations.score,qc.privateMutations.status,qc.privateMutations.total,qc.snpClusters.clusteredSNPs,qc.snpClusters.score,qc.snpClusters.status,qc.snpClusters.totalSNPs,qc.frameShifts.frameShifts,qc.frameShifts.totalFrameShifts,qc.frameShifts.frameShiftsIgnored,qc.frameShifts.totalFrameShiftsIgnored,qc.frameShifts.score,qc.frameShifts.status,qc.stopCodons.stopCodons,qc.stopCodons.totalStopCodons,qc.stopCodons.score,qc.stopCodons.status,errors" />
             </actions>
         </data>
         <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)">
@@ -121,7 +121,7 @@
             <param name="organism" value="sars-cov-2" />
             <output name="report_tsv">
                 <assert_contents>
-                    <has_n_columns n="48" />
+                    <has_n_columns n="52" />
                     <has_text text="20A" />
                 </assert_contents>
             </output>
@@ -132,7 +132,7 @@
             <param name="organism" value="sars-cov-2" />
             <output name="report_tsv">
                 <assert_contents>
-                    <has_n_columns n="48" />
+                    <has_n_columns n="52" />
                     <has_text text="20A" />
                 </assert_contents>
             </output>
@@ -143,7 +143,7 @@
             </output>
             <output name="output_tree">
                 <assert_contents>
-                    <has_text text='"build_url": "https://github.com/nextstrain/nextclade"' />
+                    <has_text text='"title": "QC Status"' />
                 </assert_contents>
             </output>
         </test>
@@ -157,7 +157,7 @@
             </conditional>
             <output name="report_tsv">
                 <assert_contents>
-                    <has_n_columns n="48" />
+                    <has_n_columns n="52" />
                     <has_text text="mediocre" />
                 </assert_contents>
             </output>
diff -r 1e0234b87809 -r f6db3ce6ed1c test-data/strict_qc.json
--- a/test-data/strict_qc.json	Sat Sep 25 18:18:54 2021 +0000
+++ b/test-data/strict_qc.json	Fri Oct 01 07:47:24 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}
+    ]
   }
 }