Mercurial > repos > simon-gladman > snippy

comparison snippy.xml @ 13:259aa64b2c99 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
12:970c6b527062 13:259aa64b2c99
1 <tool id="snippy" name="snippy" version="0.2.0"> 1 <tool id="snippy" name="snippy" version="0.2.0">
2 <macros> 2 <requirements>
3 <import>macros.xml</import> 3 <requirement type="package" version="3.0">snippy</requirement>
4 </macros> 4 </requirements>
5 <expand macro="requirements" /> 5 <stdio>
6 <expand macro="stdio" /> 6 <exit_code range="1:" />
7 </stdio>
7 8
8 <command><![CDATA[ 9 <command><![CDATA[
9 #if str( $reftype.ref_type_selector ) == "fasta" 10 #if str( $reftype.ref_type_selector ) == "fasta"
10 cp $reftype.ref foo.fna && 11 cp $reftype.ref foo.fna &&
11 #end if 12 #end if
191 --rgid [X] Use this @RG ID: in the BAM header (default '') 192 --rgid [X] Use this @RG ID: in the BAM header (default '')
192 193
193 --bwaopt [X] Extra BWA MEM options, eg. -x pacbio (default '') 194 --bwaopt [X] Extra BWA MEM options, eg. -x pacbio (default '')
194 195
195 ]]></help> 196 ]]></help>
196 <expand macro="citations" /> 197 <citations>
198 <citation type="bibtex">@UNPUBLISHED{Seemann2013,
199 author = "Seemann T",
200 title = "snippy: fast bacterial variant calling from NGS reads",
201 year = "2015",
202 note = "https://github.com/tseemann/snippy"}</citation>
203 <yield />
204 </citations>
197 205
198 206
199 </tool> 207 </tool>