# HG changeset patch
# User iuc
# Date 1621545120 0
# Node ID 6cd62b6d2b5cd67e252dc510acdc070d3631ddb5
# Parent  0f20ed06ed6c01b7424cb35e41e4ede25522c0f6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"

diff -r 0f20ed06ed6c -r 6cd62b6d2b5c nextclade.xml
--- a/nextclade.xml	Tue Apr 27 11:10:56 2021 +0000
+++ b/nextclade.xml	Thu May 20 21:12:00 2021 +0000
@@ -2,7 +2,7 @@
     <description></description>
     <macros>
         <import>macros.xml</import>
-        <token name="@TOOL_VERSION@">0.14.2</token>
+        <token name="@TOOL_VERSION@">0.14.3</token>
         <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
@@ -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}'
@@ -37,8 +41,8 @@
                 --input-pcr-primers '${adv.input_pcr_primers}'
             #end if
         #end if
-        #if $outputs and "report_tsv" in $outputs
-        && tail -n-1 report.tsv >'$report_tsv'
+        #if $outputs and "report_tsv" in $outputs and not $include_header
+            && tail -n+2 report.tsv >'$report_tsv'
         #end if 
     ]]></command>
     <inputs>
@@ -48,6 +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>