--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Apr 08 07:52:26 2021 +0000
@@ -0,0 +1,64 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.1.6</token>
+    <xml name="requirements">
+        <requirements>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">@online{nextclade,
+                title={nextclade},
+                year = 2021,
+                url = {https://github.com/nextstrain/nextclade},
+                urldate = {2021-03-26}
+                }
+            </citation>
+            <yield />
+        </citations>
+    </xml>
+
+    <!--
+        command
+    -->
+    <token name="@REF_FASTA@"><![CDATA[
+    #if $reference_source.reference_source_selector == 'history':
+        ln -f -s '$reference_source.ref_file' reference.fa &&
+    #else:
+        ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
+    #end if
+]]></token>
+
+    <!--
+        inputs
+    -->
+
+    <xml name="reference">
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
+                <option value="cached">Use a built-in genome</option>
+                <option value="history">Use a genome from history</option>
+            </param>
+            <when value="cached">
+                <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
+                    <options from_data_table="all_fasta">
+                        <filter type="sort_by" column="2"/>
+                    </options>
+                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+                </param>
+            </when>
+            <when value="history">
+                <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference"/>
+            </when>
+        </conditional>
+    </xml>
+
+    <!--
+        help
+    -->
+    <token name="@NEXTCLADE@"><![CDATA[
+Nextclade is a tool that identifies differences between your sequences and a reference sequence, uses these differences to assign your sequences to clades, and reports potential sequence quality issues in your data.
+You can use the tool to analyze sequences before you upload them to a database, or if you want to assign Nextstrain clades to a set of sequences.
+]]></token>
+
+</macros>
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