--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/nextclade_dm.xml	Sat Jul 30 08:09:42 2022 +0000
@@ -0,0 +1,121 @@
+<tool id="data_manager_nextclade" name="nextclade data manager" version="0.0.1+galaxy0" tool_type="manage_data" profile="20.01">
+
+    <requirements>
+        <requirement type="package" version="3.8">python</requirement>
+        <requirement type="package" version="2.3.0">nextclade</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    #set $data_table = $__app__.tool_data_tables.get('nextclade')
+    #if $data_table is not None and len($data_table.get_fields()) != 0
+        #set $known_revisions = '--known_revisions=' + ','.join([row[0] for row in $data_table.get_fields()])
+    #else
+        #set $known_revisions = ''
+    #end if
+    #if str($additional_datasets).strip() != ''
+        #if str($datasets) != ''
+            #set $dataset_list = $datasets + ',' + str($additional_datasets).strip()
+        #else
+            #set $dataset_list = str($additional_datasets)
+        #end if
+    #else
+        #set $dataset_list = str($datasets)
+    #end if
+    python '$__tool_directory__/nextclade_dm.py'
+        $known_revisions
+        #if $release.which == "latest"
+            --latest
+        #else if $release.which == "date_range"
+            #if str($release.start_date).strip() != ""
+                --start_date '$release.start_date'
+            #end if
+            #if str($release.end_date).strip() != ""
+                --end_date '$release.end_date'
+            #end if
+        #end if
+        --datasets '$dataset_list'        
+        'nextclade'
+        '${output_file}'
+    ]]></command>
+    <inputs>
+        <param name="datasets" type="select" label="Select nextclade datasets" multiple="true">
+            <option value="sars-cov-2" selected="true">SARS-CoV-2</option>
+            <option value="MPXV">Monkeypox (All Clades)</option>
+            <option value="hMPXV">Human Monkeypox (hMPXV)</option>
+            <option value="hMPXV_B1">Human Monkeypox Clade B.1</option>
+            <option value="flu_h1n1pdm_ha">Influenza A H1N1pdm HA</option>
+            <option value="flu_h3n2_ha">Influenza A H3N2 HA</option>
+            <option value="flu_vic_ha">Influenza B Victoria HA</option>
+            <option value="flu_yam_ha">Influenza B Yamagata HA</option>
+            <option value="sars-cov-2-no-recomb">SARS-CoV-2 without recombinants</option>
+        </param>
+        <param name="additional_datasets" type="text" label="Additional nextclade dataset names" help="If you want to download datasets that are not in the list above, enter their names here, separated by commas">
+            <validator type="regex" message="Dataset names consist of letters, numbers, underscore and hyphens, with multiple names separated by ,">^[-A-Za-z0-9_]?[-A-Za-z0-9_,]*$</validator>
+        </param>
+        <conditional name="release">
+            <param name="which" type="select" label="Select nextclade dataset(s) release">
+                <option value="latest" selected="true">Latest</option>
+                <option value="date_range">Date range</option>
+            </param>
+            <when value="latest">
+            </when>
+            <when value="date_range">
+                <param name="start_date" type="text" label="Start date (YYYY-MM-DD)" help="Don't download models older than this date" optional="true">
+                    <validator type="regex" message="Dates are in YYYY-MM-DD format">\d{4}-\d{2}-\d{2}$</validator>
+                </param>
+                <param name="end_date" type="text" label="End date (YYYY-MM-DD)" help="Don't download models newer than this date" optional="true">
+                    <validator type="regex" message="Dates are in YYYY-MM-DD format">\d{4}-\d{2}-\d{2}$</validator>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="data_manager_json"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <conditional name="release">
+                <param name="which" value="date_range" />
+                <param name="start_date" value="2022-03-01" />
+                <param name="end_date" value="2022-04-01" />
+            </conditional>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text='"database_name": "sars-cov-2"' />
+                    <has_text text='sars-cov-2_2022-03-31T12-00-00Z' />
+                    <has_text text='sars-cov-2_2022-03-24T12-00-00Z' />
+                    <has_text text='sars-cov-2_2022-03-14T12-00-00Z"' />
+                    <has_text text='"min_nextclade_version": "1.10.0"' />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="datasets" value="MPXV,hMPXV" />
+            <conditional name="release">
+                <param name="which" value="latest" />
+            </conditional>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text='"database_name": "MPXV"' />
+                    <has_text text='"database_name": "hMPXV"' />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This data managers fetches databases for the nextclade_ viral genome typing tool and
+        updates the nextclade database.
+
+        The default is to fetch the latest version of the data tables, but ranges of dates
+        can also be specified to fetch releases that are within those dates. The data manager
+        has a built-in list of databases that can be fetched and users can specify ones by name
+        if they want something that is not on the list.
+
+        The data manager will read the existing data tables and not re-download or replace databases
+        that are already present in those data tables.
+
+        .. _nextclade: https://clades.nextstrain.org/
+    ]]></help>
+    <citations>
+        <citation type="doi">10.21105/joss.03773</citation>
+    </citations>
+</tool>