diff nextclade.xml @ 7:f6db3ce6ed1c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"

--- 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>