diff snippy.xml @ 11:68a43b0593a3 draft

Updated to new version of snippy with static binaries

--- a/snippy.xml	Wed Jun 08 09:56:14 2016 -0400
+++ b/snippy.xml	Wed Jun 08 21:55:09 2016 -0400
@@ -1,10 +1,9 @@
 <tool id="snippy" name="snippy" version="0.2.0">
-    <requirements>
-      <requirement type="package" version="3.0">snippy</requirement>
-    </requirements>
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
+  <macros>
+      <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <expand macro="stdio" />
 
     <command><![CDATA[
       #if str( $reftype.ref_type_selector ) == "fasta"
@@ -55,7 +54,7 @@
 
       &&
 
-      bgzip -c out > out.bgz
+      gzip -cr out > out.gz
 
 
     ]]></command>
@@ -194,14 +193,7 @@
   --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@UNPUBLISHED{Seemann2013,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>
-    </citations>
 
 </tool>