changeset 15:41102a84e387 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8

--- a/macros.xml	Thu Aug 04 06:59:23 2022 +0000
+++ b/macros.xml	Sat Oct 08 20:03:17 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,@[e-mail],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>