Mercurial > repos > simon-gladman > snippy

changeset 13:259aa64b2c99 draft

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Updated to new version of snippy with static binaries
author simon-gladman
date Wed, 08 Jun 2016 22:05:09 -0400
parents 970c6b527062
children 01690d2343b3
files snippy-core.old snippy-core.xml snippy.xml
diffstat 3 files changed, 45 insertions(+), 37 deletions(-) [+]
line wrap: on
line diff
--- a/snippy-core.old	Wed Jun 08 21:55:50 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-<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>
\ No newline at end of file
--- /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>
\ No newline at end of file
--- 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>