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annotate snippy-core.xml @ 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
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children bcb74072d3a6
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1 <tool id="snippy-core" name="snippy-core" version="0.1.0">
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2 <macros>
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3 <import>macros.xml</import>
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4 </macros>
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5 <expand macro="requirements" />
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6 <expand macro="stdio" />
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7 <command><![CDATA[
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8 TODO: Fill in command template.
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9 ]]></command>
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10 <inputs>
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11 </inputs>
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12 <outputs>
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13 </outputs>
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14 <help><![CDATA[
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15 Synopsis:
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16 Combine multiple Snippy folders into a core SNP alignment
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17 Usage:
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18 ../../snippy/bin/snippy-core [options] [--noref] snippyDir1/ snippyDir2/ snippyDir3/ ...
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19 Options:
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20 --help! This help.
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21 --quiet! No output to stderr (default '0').
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22 --verbose! Verbose output (default '0').
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23 --inprefix=s Preferred input prefix of Snippy files (default 'snps').
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24 --prefix=s Output file prefix (default 'core').
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25 --noref! Exclude reference (default '0').
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26 --mincov=i Minimum depth of coverage to consider core (default '10').
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27 --aformat=s Output alignment format: nexus fasta phylip maf clustalw ... (default 'fasta').
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28
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29 ]]></help>
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30 <expand macro="citations" />
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31 </tool>