--- a/nextclade.xml	Mon Jun 07 12:39:36 2021 +0000
+++ b/nextclade.xml	Mon Aug 23 12:26:05 2021 +0000
@@ -2,15 +2,45 @@
     <description></description>
     <macros>
         <import>macros.xml</import>
-        <token name="@TOOL_VERSION@">0.14.4</token>
+        <token name="@TOOL_VERSION@">1.2.3</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
-        <requirement type="package" version="@TOOL_VERSION@">nextclade_js</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">nextclade</requirement>
+        <requirement type="package">coreutils</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+        export DB_PATH="\$(dirname "\$(dirname "\$(which nextclade)")")/share/nextclade" &&
+        ln -s "\$DB_PATH" 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"
+            #if $adv.input_qc_config
+                #set $input_qc_config = $adv.input_qc_config
+            #end if
+            #if $adv.input_root_seq
+                #set $input_root_seq = $adv.input_root_seq
+            #end if
+            #if $adv.input_tree
+                #set $input_tree = $adv.input_tree
+            #end if
+            #if $adv.input_gene_map
+                #set $input_gene_map = $adv.input_gene_map
+            #end if 
+            #if $adv.input_pcr_primers
+                #set $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 $outputs and "report_tsv" in $outputs
             #if $include_header
                 --output-tsv '$report_tsv'
@@ -24,21 +54,10 @@
         #if $outputs and "output_tree" in $outputs
             --output-tree '${output_tree}'
         #end if
-        #if str($adv.advanced_options) == "yes"
-            #if $adv.input_qc_config
-                --input-qc-config '${adv.input_qc_config}'
-            #end if
-            #if $adv.input_root_seq
-                --input-root-seq '${adv.input_root_seq}'
-            #end if
-            #if $adv.input_tree
-                --input-tree '${adv.input_tree}'
-            #end if
-            #if $adv.input_gene_map
-                --input-gene-map '${adv.input_gene_map}'
-            #end if 
-            #if $adv.input_pcr_primers
-                --input-pcr-primers '${adv.input_pcr_primers}'
+        #if $outputs and "output_fasta" in $outputs
+            --output-fasta "${output_fasta}"
+            #if str($adv.advanced_options) == "yes"
+                $adv.include_reference
             #end if
         #end if
         #if $outputs and "report_tsv" in $outputs and not $include_header
@@ -51,6 +70,7 @@
             <option value="report_json">JSON format report</option>
             <option value="report_tsv" selected="true">Tabular format report</option>
             <option value="output_tree">Auspice v2 tree file (JSON format)</option>
+            <option value="output_fasta">Aligned sequences (FASTA format)</option>
         </param>
         <param name="include_header" type="boolean" label="Include header line in output file" 
             truevalue="true" falsevalue="false" />        
@@ -65,6 +85,7 @@
                 <param argument="--input-tree" name="input_tree" type="data" label="Custom reference tree" format="json" optional="true" help="Auspice JSON v2 file containing custom reference tree" />
                 <param argument="--input-gene-map" name="input_gene_map" type="data" label="Custom gene map" format="json" optional="true" help="JSON file containing custom gene map. Gene map (sometimes also called 'gene annotations') is used to resolve aminoacid changes in genes" />
                 <param argument="--input-pcr-primers" name="input_pcr_primers" type="data" label="Custom PCR primer sites" format="json" optional="true" help="CSV file containing a list of custom PCR primer sites. These are used to report mutations in these sites" />
+                <param argument="--include-reference" name="include_reference" type="boolean" label="Include reference sequence in FASTA alignment output" help="The FASTA alignment is an optional output of nextclade. Select this option to include the reference sequence in that alignment file" />                
             </when>
             <when value="no">
             </when>
@@ -74,10 +95,7 @@
         <data name="report_tsv" format="tabular" label="${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,totalGaps,totalInsertions,totalMissing,totalMutations,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertions,missing,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" />
+                <action name="column_names" type="metadata" default="seqName,clade,qc.overallScore,qc.overallStatus,totalSubstitutions,totalDeletions,totalInsertions,totalAminoacidSubstitutions,totalAminoacidDeletions,totalMissing,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertions,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.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 ${on_string} (JSON report)">
@@ -86,6 +104,9 @@
         <data name="output_tree" format="json" label="${tool.name} on ${on_string} (Auspice v2 tree)">
             <filter>outputs and "output_tree" in outputs</filter>
         </data>
+        <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA alignment)">
+            <filter>outputs and "output_fasta" in outputs</filter>
+        </data>
     </outputs>
     <tests>
         <test expect_num_outputs="1">
@@ -93,7 +114,7 @@
             <param name="outputs" value="report_tsv" />
             <output name="report_tsv">
                 <assert_contents>
-                    <has_n_columns n="41" />
+                    <has_n_columns n="48" />
                     <has_text text="20A" />
                 </assert_contents>
             </output>
@@ -103,7 +124,7 @@
             <param name="outputs" value="report_tsv,report_json,output_tree" />
             <output name="report_tsv">
                 <assert_contents>
-                    <has_n_columns n="41" />
+                    <has_n_columns n="48" />
                     <has_text text="20A" />
                 </assert_contents>
             </output>
@@ -127,7 +148,7 @@
             </conditional>
             <output name="report_tsv">
                 <assert_contents>
-                    <has_n_columns n="41" />
+                    <has_n_columns n="48" />
                     <has_text text="mediocre" />
                 </assert_contents>
             </output>