# HG changeset patch
# User iuc
# Date 1661964029 0
# Node ID feb40665d7cd712027c864ed9b8a6580f932c759
# Parent  07ab9bd68a029b9495c9674551b2050ad2d772b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e72bef3964ce9d0c52ef2713d177684dfbee4cfb

diff -r 07ab9bd68a02 -r feb40665d7cd nextclade.xml
--- a/nextclade.xml	Thu Aug 04 06:58:48 2022 +0000
+++ b/nextclade.xml	Wed Aug 31 16:40:29 2022 +0000
@@ -68,7 +68,7 @@
         #end if 
     ]]></command>
     <inputs>
-        <param argument="--input-fasta" name="input_fasta" type="data" format="fasta,fasta.gz" label="FASTA file with input sequences" />
+        <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="FASTA file with input sequences" />
         <param name="organism" type="select" label="Organism">
             <option value="sars-cov-2" selected="true">SARS-CoV-2</option>
             <option value="sars-cov-2-no-recomb">SARS-CoV-2 without recombinants</option>
@@ -114,13 +114,13 @@
                 <option value="no" selected="true">No</option>
             </param>
             <when value="yes">
-                <param argument="--input-qc-config" name="input_qc_config" type="data" label="Quality Control (QC) Config file" format="json" optional="true" help="QC config json file containing custom QC configuration" />
-                <param argument="--input-root-seq" name="input_root_seq" type="data" label="Custom root sequence" format="txt" optional="true" help="Text file containing custom root sequence" />
-                <param argument="--input-tree" name="input_tree" type="data" label="Custom reference tree" format="json" optional="true" help="Auspice JSON v2 file containing custom reference tree" />
-                <param argument="--input-gene-map" name="input_gene_map" type="data" label="Custom gene map" format="json" optional="true" help="JSON file containing custom gene map. Gene map (sometimes also called 'gene annotations') is used to resolve aminoacid changes in genes" />
-                <param argument="--input-pcr-primers" name="input_pcr_primers" type="data" label="Custom PCR primer sites" format="json" optional="true" help="CSV file containing a list of custom PCR primer sites. These are used to report mutations in these sites" />
-                <param argument="--input-virus-properties" name="input_virus_properties" type="data" label="Configuration and data specific to a pathogen" format="json" optional="true" help="For more info on the virus properties JSON file, see the Nextclade documentation." />
-                <param argument="--include-reference" name="include_reference" truevalue="--include-reference" falsevalue="" type="boolean" label="Include reference sequence in FASTA alignment output" help="The FASTA alignment is an optional output of nextclade. Select this option to include the reference sequence in that alignment file" />                
+                <param argument="--input-qc-config" type="data" label="Quality Control (QC) Config file" format="json" optional="true" help="QC config json file containing custom QC configuration" />
+                <param argument="--input-root-seq" type="data" label="Custom root sequence" format="txt" optional="true" help="Text file containing custom root sequence" />
+                <param argument="--input-tree" type="data" label="Custom reference tree" format="json" optional="true" help="Auspice JSON v2 file containing custom reference tree" />
+                <param argument="--input-gene-map" type="data" label="Custom gene map" format="json" optional="true" help="JSON file containing custom gene map. Gene map (sometimes also called 'gene annotations') is used to resolve aminoacid changes in genes" />
+                <param argument="--input-pcr-primers" type="data" label="Custom PCR primer sites" format="json" optional="true" help="CSV file containing a list of custom PCR primer sites. These are used to report mutations in these sites" />
+                <param argument="--input-virus-properties" type="data" label="Configuration and data specific to a pathogen" format="json" optional="true" help="For more info on the virus properties JSON file, see the Nextclade documentation." />
+                <param argument="--include-reference" truevalue="--include-reference" falsevalue="" type="boolean" label="Include reference sequence in FASTA alignment output" help="The FASTA alignment is an optional output of nextclade. Select this option to include the reference sequence in that alignment file" />                
             </when>
             <when value="no">
             </when>
@@ -228,7 +228,7 @@
             <param name="organism" value="MPXV" />
             <output name="report_tsv">
                 <assert_contents>
-                    <has_n_columns n="66" />
+                    <has_n_columns n="67" />
                     <has_text text="hMPXV-1" />
                 </assert_contents>
             </output>