Mercurial > repos > simon-gladman > snippy

<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>
author	simon-gladman
date	Wed, 08 Jun 2016 23:46:47 -0400
parents	259aa64b2c99
children	bcb74072d3a6