--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Jan 24 21:35:56 2020 +0000
@@ -0,0 +1,72 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">snippy</requirement>
+            <requirement type="package" version="1.32">tar</requirement>
+            <yield />
+        </requirements>
+    </xml>
+
+    <xml name="version_command">
+        <version_command><![CDATA[snippy --version]]></version_command>
+    </xml>
+
+    <token name="@REFERENCE_SOURCE_FILE@">
+        <![CDATA[
+        #if $reference_source.reference_source_selector == 'history'
+            #if $reference_source.ref_file.is_of_type("fasta")
+                ln -sf '$reference_source.ref_file' 'ref.fna' &&
+            #elif $reference_source.ref_file.is_of_type("genbank")
+                ln -sf '$reference_source.ref_file' 'ref.gbk' &&
+            #end if
+        #elif $reference_source.reference_source_selector == 'cached'
+            ln -sf '$reference_source.ref_file.fields.path' 'ref.fna' &&
+        #end if]]>
+    </token>
+
+    <token name="@REFERENCE_COMMAND@">
+        <![CDATA[
+        #if $reference_source.reference_source_selector == 'history'
+            #if $reference_source.ref_file.is_of_type("fasta")
+                --ref 'ref.fna'
+            #elif $reference_source.ref_file.is_of_type("genbank")
+                --ref 'ref.gbk'
+            #end if
+        #elif $reference_source.reference_source_selector == 'cached'
+            --ref 'ref.fna'
+        #end if
+        ]]>
+    </token>
+
+    <xml name="reference_selector">
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below. If you would like to perform self-mapping select `history` here, then choose your input file as reference.">
+                <option value="cached">Use a built-in genome index</option>
+                <option value="history">Use a genome from history and build index</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">
+                        <validator type="no_options" message="No reference genomes are available" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="ref_file" type="data" format="fasta,genbank" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference" />
+            </when>
+        </conditional>
+    </xml>
+
+    <token name="@VERSION@">4.4.5</token>
+
+    <xml name="citations">
+      <citations>
+          <citation type="bibtex">@UNPUBLISHED{Seemann2013,
+              author = "Seemann T",
+              title = "snippy: fast bacterial variant calling from NGS reads",
+              year = "2015",
+              note = "https://github.com/tseemann/snippy",
+              url = "https://github.com/tseemann/snippy"}</citation>
+      </citations>
+    </xml>
+</macros>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snippy_clean_full_aln.xml	Fri Jan 24 21:35:56 2020 +0000
@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="snippy_clean_full_aln" name="snippy-clean_full_aln" version="@VERSION@+galaxy0">
+    <description>
+        Replace any non-standard sequence characters with 'N' in snippy 'core.full.aln' file.
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        snippy-clean_full_aln
+            ${'full_aln'}
+            > ${'clean_full_aln'}
+    ]]></command>
+
+    <inputs>
+        <param name="full_aln" type="data" multiple="true" format="fasta" label="Snippy core.full.aln file" help="" />
+    </inputs>
+
+    <outputs>
+        <data format="fasta" name="clean_full_aln" label="${tool.name} on ${on_string} cleaned core alignment fasta" />
+    </outputs>
+
+    <tests>
+    </tests>
+
+    <help><![CDATA[
+    ]]></help>
+    <expand macro="citations" />
+</tool>