# HG changeset patch
# User iuc
# Date 1665259276 0
# Node ID 5f0d8f9f311a718dff6138cedc4061b6db6e90ab
# Parent  8251e0ff00f8d33803006e8ae02b91d88f2dfa29
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8

diff -r 8251e0ff00f8 -r 5f0d8f9f311a macros.xml
--- a/macros.xml	Thu Aug 04 06:57:31 2022 +0000
+++ b/macros.xml	Sat Oct 08 20:01:16 2022 +0000
@@ -1,6 +1,6 @@
 <macros>
     <!-- same version number is used for nextclade and nextalign releases, even though they are distinct tools -->
-    <token name="@TOOL_VERSION@">2.4.0</token>
+    <token name="@TOOL_VERSION@">2.7.0</token>
     <xml name="citations">
         <citations>
             <citation type="bibtex">@online{nextclade,
@@ -10,10 +10,9 @@
                 urldate = {2021-03-26}
                 }
             </citation>
-            <yield />
+            <yield/>
         </citations>
     </xml>
-
     <!--
         command
     -->
@@ -24,7 +23,6 @@
         ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
     #end if
 ]]></token>
-
     <token name="@QUERY_FASTA@"><![CDATA[
     #if $input_fasta.is_of_type('fasta.gz')
         #set $query = 'query.fa.gz'
@@ -36,7 +34,6 @@
     <!--
         inputs
     -->
-
     <xml name="reference">
         <conditional name="reference_source">
             <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
@@ -56,7 +53,6 @@
             </when>
         </conditional>
     </xml>
-
     <!--
         help
     -->
@@ -64,5 +60,11 @@
 Nextclade is a tool that identifies differences between your sequences and a reference sequence, uses these differences to assign your sequences to clades, and reports potential sequence quality issues in your data.
 You can use the tool to analyze sequences before you upload them to a database, or if you want to assign Nextstrain clades to a set of sequences.
 ]]></token>
-
+    <xml name="column_metadata" tokens="dataset_name" token_extra_columns="">
+        <!-- the columns in use are dependent on the dataset (i.e. database) - and extra columns seem to always be added in the same place -->
+        <!-- note that the tool is assuming that the dataset columns remain static: this might be an incorrect assumption in the future -->
+        <when value="@DATASET_NAME@">
+            <action name="column_names" type="metadata" default="seqName,clade,@EXTRA_COLUMNS@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"/>
+        </when>
+    </xml>
 </macros>