# HG changeset patch
# User iuc
# Date 1710422768 0
# Node ID 4f634922846222d563fa93ac812c0235dee2c498
# Parent  128ba8da994f4aa127d7fe96ca69e8b08684c7e3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit bc6ba57599c6516bd728e7311ba0a53188622edf

diff -r 128ba8da994f -r 4f6349228462 macros.xml
--- a/macros.xml	Sat Oct 08 20:03:50 2022 +0000
+++ b/macros.xml	Thu Mar 14 13:26:08 2024 +0000
@@ -53,6 +53,11 @@
             </when>
         </conditional>
     </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">nextclade</xref>
+        </xrefs>
+    </xml>
     <!--
         help
     -->
diff -r 128ba8da994f -r 4f6349228462 nextclade.xml
--- a/nextclade.xml	Sat Oct 08 20:03:50 2022 +0000
+++ b/nextclade.xml	Thu Mar 14 13:26:08 2024 +0000
@@ -9,6 +9,7 @@
              this tool and exclude any requiring a future nextclade version 3. -->
         <token name="@COMPATIBILITY_SPEC@"><![CDATA[(^1\..+$|^2\.[0-4](\..+)*$)]]></token>
     </macros>
+    <expand macro="xrefs"/>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">nextclade</requirement>
         <requirement type="package" version="9.0">coreutils</requirement>
@@ -164,7 +165,7 @@
             <param name="organism" value="sars-cov-2"/>
             <output name="report_tsv">
                 <assert_contents>
-                    <has_n_columns n="67"/>
+                    <has_n_columns n="71"/>
                     <has_text text="20A"/>
                 </assert_contents>
             </output>
@@ -178,7 +179,7 @@
             <param name="organism" value="sars-cov-2"/>
             <output name="report_tsv">
                 <assert_contents>
-                    <has_n_columns n="67"/>
+                    <has_n_columns n="71"/>
                     <has_text text="20A"/>
                 </assert_contents>
                 <metadata name="column_names" value="seqName,clade,Nextclade_pango,qc.overallScore,qc.overallStatus,totalSubstitutions,totalDeletions,totalInsertions,totalFrameShifts,totalAminoacidSubstitutions,totalAminoacidDeletions,totalAminoacidInsertions,totalMissing,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertions,privateNucMutations.reversionSubstitutions,privateNucMutations.labeledSubstitutions,privateNucMutations.unlabeledSubstitutions,privateNucMutations.totalReversionSubstitutions,privateNucMutations.totalLabeledSubstitutions,privateNucMutations.totalUnlabeledSubstitutions,privateNucMutations.totalPrivateSubstitutions,frameShifts,aaSubstitutions,aaDeletions,aaInsertions,missing,nonACGTNs,pcrPrimerChanges,alignmentScore,alignmentStart,alignmentEnd,coverage,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,isReverseComplement,failedGenes,warnings,errors"/>
@@ -207,7 +208,7 @@
             </conditional>
             <output name="report_tsv">
                 <assert_contents>
-                    <has_n_columns n="67"/>
+                    <has_n_columns n="71"/>
                     <has_text text="mediocre"/>
                 </assert_contents>
             </output>
@@ -225,7 +226,7 @@
             </conditional>
             <output name="report_tsv">
                 <assert_contents>
-                    <has_n_columns n="67"/>
+                    <has_n_columns n="71"/>
                     <has_text text="mediocre"/>
                 </assert_contents>
             </output>