Mercurial > repos > iuc > nextclade
diff nextclade.xml @ 7:f6db3ce6ed1c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
author | iuc |
---|---|
date | Fri, 01 Oct 2021 07:47:24 +0000 |
parents | 1e0234b87809 |
children | 56b1a13d9680 |
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--- 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>