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Add bio.tools ref to nextclade #5859

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merged 2 commits into from
Mar 14, 2024
Merged

Add bio.tools ref to nextclade #5859

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9d5bc43
Add bio.tools ref to nextclade
RZ9082 Mar 13, 2024
fa81c8a
Adjust has_n_columns
RZ9082 Mar 14, 2024
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5 changes: 5 additions & 0 deletions tools/nextclade/macros.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,11 @@
</when>
</conditional>
</xml>
<xml name="xrefs">
<xrefs>
<xref type="bio.tools">nextclade</xref>
</xrefs>
</xml>
<!--
help
-->
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1 change: 1 addition & 0 deletions tools/nextclade/nextalign.xml
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Expand Up @@ -4,6 +4,7 @@
<import>macros.xml</import>
<token name="@VERSION_SUFFIX@">0</token>
</macros>
<expand macro="xrefs"/>
<requirements>
<requirement type="package" version="@TOOL_VERSION@">nextalign</requirement>
</requirements>
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9 changes: 5 additions & 4 deletions tools/nextclade/nextclade.xml
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Expand Up @@ -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>
Expand Down Expand Up @@ -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>
Expand All @@ -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"/>
Expand Down Expand Up @@ -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>
Expand All @@ -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>
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