diff snippy-core.xml @ 13:259aa64b2c99 draft

Updated to new version of snippy with static binaries

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snippy-core.xml	Wed Jun 08 22:05:09 2016 -0400
@@ -0,0 +1,31 @@
+<tool id="snippy-core" name="snippy-core" version="0.1.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command><![CDATA[
+        TODO: Fill in command template.
+    ]]></command>
+    <inputs>
+    </inputs>
+    <outputs>
+    </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>
+    <expand macro="citations" />
+</tool>
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