--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nextclade.xml	Mon Apr 26 19:10:28 2021 +0000
@@ -0,0 +1,144 @@
+<tool id="nextclade" name="Nextclade" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@TOOL_VERSION@">0.14.2</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">nextclade_js</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        nextclade
+        --input-fasta '${input_fasta}'
+        #if $outputs and "report_tsv" in $outputs
+            --output-tsv '${report_tsv}'
+        #end if 
+        #if $outputs and "report_json" in $outputs
+            --output-json '${report_json}'
+        #end if 
+        #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}'
+            #end if
+        #end if
+    ]]></command>
+    <inputs>
+        <param argument="--input-fasta" name="input_fasta" type="data" format="fasta" label="SARS-CoV-2 consensus sequences (FASTA)" />
+        <param name="outputs" type="select" label="Output options" help="Output reports and optionally tree" multiple="true">
+            <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>
+        </param>
+        <conditional name="adv">
+            <param name="advanced_options" type="select" label="Use advanced options" >
+                <option value="yes">Yes</option>
+                <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" />
+            </when>
+            <when value="no">
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)">
+            <filter>outputs and "report_tsv" in outputs</filter>
+        </data>
+        <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)">
+            <filter>outputs and "report_json" in outputs</filter>
+        </data>
+        <data name="output_tree" format="json" label="${tool.name} on ${on_string} (Auspice v2 tree)">
+            <filter>outputs and "output_tree" in outputs</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
+            <param name="outputs" value="report_tsv" />
+            <output name="report_tsv">
+                <assert_contents>
+                    <has_text text="20A" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="3">
+            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
+            <param name="outputs" value="report_tsv,report_json,output_tree" />
+            <output name="report_tsv">
+                <assert_contents>
+                    <has_text text="20A" />
+                </assert_contents>
+            </output>
+            <output name="report_json">
+                <assert_contents>
+                    <has_text text='"pos": 240,' />
+                </assert_contents>
+            </output>
+            <output name="output_tree">
+                <assert_contents>
+                    <has_text text='"build_url": "https://github.com/nextstrain/nextclade"' />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
+            <param name="outputs" value="report_tsv" />
+            <conditional name="adv">
+                <param name="advanced_options" value="yes" />
+                <param name="input_qc_config" value="strict_qc.json" ftype="json" />
+            </conditional>
+            <output name="report_tsv">
+                <assert_contents>
+                    <has_text text="mediocre" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+Nextclade_ assigns clades, calls mutations and performs sequence quality checks on SARS-CoV-2 genomes.
+
+**Input**
+
+Input is a FASTA file containing one or more SARS-CoV-2 consensus genomes.
+
+**Output**
+
+Outputs can include:
+
+* A tabular format file with a report, one line per input sequence
+
+* A JSON format file with the same information as is present in the tabular report
+
+* An Auspice v2 tree file in JSON format
+
+.. _Nextclade: https://github.com/nextstrain/nextclade
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>