| Previous changeset 19:128ba8da994f (2022-10-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit bc6ba57599c6516bd728e7311ba0a53188622edf |
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modified:
macros.xml nextclade.xml |
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| 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 |
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| @@ -53,6 +53,11 @@ </when> </conditional> </xml> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">nextclade</xref> + </xrefs> + </xml> <!-- help --> |
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| 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 |
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| @@ -9,6 +9,7 @@ this tool and exclude any requiring a future nextclade version 3. --> <token name="@COMPATIBILITY_SPEC@"><*$)]]></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> |