--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snippy-core.xml	Thu Jun 09 20:15:42 2016 -0400
@@ -0,0 +1,67 @@
+<tool id="snippy-core" name="snippy-core" version="0.2.0">
+
+  <requirements>
+      <requirement type="package" version="3.0">snippy</requirement>
+  </requirements>
+  <stdio>
+      <exit_code range="1:" />
+  </stdio>
+
+    <command interpreter="perl">
+      <![CDATA[
+
+        snippy_core_wrapper.pl
+        $is_reference
+        --mincov $mincov
+        --indirs '${" ".join(map(str, $indirs))}'
+
+    ]]></command>
+
+    <inputs>
+      <param name="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" />
+      <param name="is_reference" type="boolean" checked="true" truevalue="--noref" falsevalue="" label="Exclude reference" help="Don't include the reference file in the alignment." />
+      <param name="mincov" type="integer" value="10" min="1" label="Minimum coverage" help="Minimum depth of coverage to consider core (default '10')" />
+    </inputs>
+
+    <outputs>
+      <data format="fasta" name="alignment_fasta" label="${tool.name} on ${on_string} core alignment fasta" from_work_dir="core.aln" />
+      <data format="tabular" name="alignment_table" label="${tool.name} on ${on_string} core alignment table" from_work_dir="core.tab" />
+      <data format="txt" name="alignment_summary" label="${tool.name} on ${on_string} core alignment summary" from_work_dir="core.txt" />
+    </outputs>
+
+    <help><![CDATA[
+Synopsis:
+  Combine multiple Snippy folders into a core SNP alignment
+
+Usage:
+  ../../snippy/bin/snippy-core [options] [--noref] snippyDir1/ snippyDir2/ snippyDir3/ ...
+
+Options:
+
+  --help!         This help.
+
+  --quiet!        No output to stderr (default '0').
+
+  --verbose!      Verbose output (default '0').
+
+  --inprefix=s    Preferred input prefix of Snippy files (default 'snps').
+
+  --prefix=s      Output file prefix (default 'core').
+
+  --noref!        Exclude reference (default '0').
+
+  --mincov=i      Minimum depth of coverage to consider core (default '10').
+
+  --aformat=s     Output alignment format: nexus fasta phylip maf clustalw ... (default 'fasta').
+
+    ]]></help>
+
+  <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@UNPUBLISHED{Seemann2013,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"}</citation>
+  </citations>
+
+</tool>