diff snippy.xml @ 13:259aa64b2c99 draft

Updated to new version of snippy with static binaries

--- a/snippy.xml	Wed Jun 08 21:55:50 2016 -0400
+++ b/snippy.xml	Wed Jun 08 22:05:09 2016 -0400
@@ -1,9 +1,10 @@
 <tool id="snippy" name="snippy" version="0.2.0">
-  <macros>
-      <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements" />
-  <expand macro="stdio" />
+  <requirements>
+      <requirement type="package" version="3.0">snippy</requirement>
+  </requirements>
+  <stdio>
+      <exit_code range="1:" />
+  </stdio>
 
     <command><![CDATA[
       #if str( $reftype.ref_type_selector ) == "fasta"
@@ -193,7 +194,14 @@
   --bwaopt [X]      Extra BWA MEM options, eg. -x pacbio (default '')
 
     ]]></help>
-    <expand macro="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@UNPUBLISHED{Seemann2013,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"}</citation>
+      <yield />
+  </citations>
 
 
 </tool>