# HG changeset patch
# User iuc
# Date 1621545018 0
# Node ID 495c19a625389c7c811d5c20b3d40e8ec65b4635
# Parent  919cc9dc23f07c15b0bcd09e0f514d727483432a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"

diff -r 919cc9dc23f0 -r 495c19a62538 nextclade.xml
--- a/nextclade.xml	Mon Apr 26 19:08:26 2021 +0000
+++ b/nextclade.xml	Thu May 20 21:10:18 2021 +0000
@@ -2,8 +2,8 @@
     <description></description>
     <macros>
         <import>macros.xml</import>
-        <token name="@TOOL_VERSION@">0.14.2</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@TOOL_VERSION@">0.14.3</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">nextclade_js</requirement>
@@ -12,7 +12,11 @@
         nextclade
         --input-fasta '${input_fasta}'
         #if $outputs and "report_tsv" in $outputs
-            --output-tsv '${report_tsv}'
+            #if $include_header
+                --output-tsv '$report_tsv'
+            #else
+                --output-tsv report.tsv
+            #end if
         #end if 
         #if $outputs and "report_json" in $outputs
             --output-json '${report_json}'
@@ -37,6 +41,9 @@
                 --input-pcr-primers '${adv.input_pcr_primers}'
             #end if
         #end if
+        #if $outputs and "report_tsv" in $outputs and not $include_header
+            && tail -n+2 report.tsv >'$report_tsv'
+        #end if 
     ]]></command>
     <inputs>
         <param argument="--input-fasta" name="input_fasta" type="data" format="fasta" label="SARS-CoV-2 consensus sequences (FASTA)" />
@@ -45,6 +52,8 @@
             <option value="report_tsv" selected="true">Tabular format report</option>
             <option value="output_tree">Auspice v2 tree file (JSON format)</option>
         </param>
+        <param name="include_header" type="boolean" label="Include header line in output file" 
+            truevalue="true" falsevalue="false" />        
         <conditional name="adv">
             <param name="advanced_options" type="select" label="Use advanced options" >
                 <option value="yes">Yes</option>
@@ -62,8 +71,14 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)">
+        <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)">            
             <filter>outputs and "report_tsv" in outputs</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="seqName,clade,qc.overallScore,qc.overallStatus,totalGaps,totalInsertions,totalMissing,totalMutations,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertionsmissing,nonACGTNs,pcrPrimerChanges,aaSubstitutions,totalAminoacidSubstitutions,aaDeletions,totalAminoacidDeletions,alignmentEnd,alignmentScore,alignmentStart,qc.missingData.miss
+                ingDataThreshold,qc.missingData.score,qc.missingData.status,qc.missingData.totalMissing,qc.mixedSites.mixedSitesThreshold,qc.mixedSites.score,qc.mixedSites.status,qc.mixedSit
+                es.totalMixedSites,qc.privateMutations.cutoff,qc.privateMutations.excess,qc.privateMutations.score,qc.privateMutations.status,qc.privateMutations.total,qc.snpClusters.clus
+                teredSNPs,qc.snpClusters.score,qc.snpClusters.status,qc.snpClusters.totalSNPs,errors" />
+            </actions>
         </data>
         <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)">
             <filter>outputs and "report_json" in outputs</filter>
@@ -78,6 +93,7 @@
             <param name="outputs" value="report_tsv" />
             <output name="report_tsv">
                 <assert_contents>
+                    <has_n_columns n="41" />
                     <has_text text="20A" />
                 </assert_contents>
             </output>
@@ -87,6 +103,7 @@
             <param name="outputs" value="report_tsv,report_json,output_tree" />
             <output name="report_tsv">
                 <assert_contents>
+                    <has_n_columns n="41" />
                     <has_text text="20A" />
                 </assert_contents>
             </output>
@@ -110,6 +127,7 @@
             </conditional>
             <output name="report_tsv">
                 <assert_contents>
+                    <has_n_columns n="41" />
                     <has_text text="mediocre" />
                 </assert_contents>
             </output>