--- a/nextclade.xml	Mon Jan 17 08:46:25 2022 +0000
+++ b/nextclade.xml	Thu Jan 27 14:02:59 2022 +0000
@@ -11,35 +11,29 @@
     <version_command>nextclade --version-detailed</version_command>
     <command detect_errors="exit_code"><![CDATA[
         nextclade dataset get -n '${organism}' -o db &&
-        #set $input_qc_config = "db/qc.json"
-        #set $input_root_seq = "db/reference.fasta"
-        #set $input_tree = "db/tree.json"
-        #set $input_gene_map = "db/genemap.gff"
-        #set $input_pcr_primers = "db/primers.csv"
-        #if str($adv.advanced_options) == "yes"
+        nextclade run
+        --input-fasta '${input_fasta}'
+        --input-dataset db/
+        #if $adv.advanced_options == 'yes'
             #if $adv.input_qc_config
-                #set $input_qc_config = $adv.input_qc_config
+                --input-qc-config '$adv.input_qc_config'
             #end if
             #if $adv.input_root_seq
-                #set $input_root_seq = $adv.input_root_seq
+                --input-root-seq '$adv.input_root_seq'
             #end if
             #if $adv.input_tree
-                #set $input_tree = $adv.input_tree
+                --input-tree '$adv.input_tree'
             #end if
             #if $adv.input_gene_map
-                #set $input_gene_map = $adv.input_gene_map
+                --input-gene-map '$adv.input_gene_map'
             #end if 
             #if $adv.input_pcr_primers
-                #set $input_pcr_primers = $adv.input_pcr_primers
+                --input-pcr-primers '$adv.input_pcr_primers'
             #end if
-        #end if 
-        nextclade
-        --input-fasta '${input_fasta}'
-        --input-qc-config '${input_qc_config}'
-        --input-root-seq '${input_root_seq}'
-        --input-tree '${input_tree}'
-        --input-gene-map '${input_gene_map}'
-        --input-pcr-primers '${input_pcr_primers}'
+            #if $adv.input_virus_properties
+                --input-virus-properties '$adv.input_virus_properties'
+            #end if
+        #end if
         #if $outputs and "report_tsv" in $outputs
             #if $include_header
                 --output-tsv '$report_tsv'
@@ -91,7 +85,8 @@
                 <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="--include-reference" name="include_reference" 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-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" />                
             </when>
             <when value="no">
             </when>
@@ -101,7 +96,7 @@
         <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,totalSubstitutions,totalDeletions,totalInsertions,totalFrameShifts,totalAminoacidSubstitutions,totalAminoacidDeletions,totalMissing,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertions,frameShifts,aaSubstitutions,aaDeletions,missing,nonACGTNs,pcrPrimerChanges,alignmentScore,alignmentStart,alignmentEnd,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,errors" />
+                <action name="column_names" type="metadata" default="seqName,clade,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,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,errors" />
             </actions>
         </data>
         <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)">
@@ -121,7 +116,7 @@
             <param name="organism" value="sars-cov-2" />
             <output name="report_tsv">
                 <assert_contents>
-                    <has_n_columns n="53" />
+                    <has_n_columns n="62" />
                     <has_text text="20A" />
                 </assert_contents>
             </output>
@@ -132,7 +127,7 @@
             <param name="organism" value="sars-cov-2" />
             <output name="report_tsv">
                 <assert_contents>
-                    <has_n_columns n="53" />
+                    <has_n_columns n="62" />
                     <has_text text="20A" />
                 </assert_contents>
             </output>
@@ -157,11 +152,27 @@
             </conditional>
             <output name="report_tsv">
                 <assert_contents>
-                    <has_n_columns n="53" />
+                    <has_n_columns n="62" />
                     <has_text text="mediocre" />
                 </assert_contents>
             </output>
         </test>
+        <test expect_num_outputs="2">
+            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
+            <param name="outputs" value="report_tsv,output_fasta" />
+            <param name="organism" value="sars-cov-2" />
+            <conditional name="adv">
+                <param name="advanced_options" value="yes" />
+                <param name="include_reference" value="true" />
+            </conditional>
+            <output name="report_tsv">
+                <assert_contents>
+                    <has_n_columns n="62" />
+                    <has_text text="mediocre" />
+                </assert_contents>
+            </output>
+            <output name="output_fasta" value="output_alignment.fasta" ftype="fasta" />
+        </test>
     </tests>
     <help><![CDATA[
 
@@ -171,6 +182,8 @@
 
 Nextclade_ assigns clades, calls mutations and performs sequence quality checks on SARS-CoV-2 genomes.
 
+For a description of nextclade's configuration files, see the `nextclade documentation <https://docs.nextstrain.org/projects/nextclade/en/latest/index.html>`_.
+
 **Input**
 
 Input is a FASTA file containing one or more SARS-CoV-2 consensus genomes.