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1 <tool id="join_nucmer" name="join_nucmer" version="">
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1
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2 <description>Join multiple mummer output files in a phenetic matrix</description>
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3 <command>
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4 <![CDATA[
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5 perl $__tool_directory__/join_nucmer.pl $output_file ${" ".join(map(str, $input_file))}
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6 ]]>
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7 </command>
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8
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9 <inputs>
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10 <param name="input_file" format="tsv" type="data" multiple="true" label="show-snps tabular output" help="join mutiple nucmer output files" />
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11 </inputs>
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12
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13 <outputs>
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14 <data format="tsv" name="output_file" label="${tool.name} on ${on_string} consolidated variants file" />
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15 </outputs>
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16 <stdio>
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17 <exit_code range="1:" level="fatal" />
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18 </stdio>
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19 <help>
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20 **What it does?**
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21
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22 This tool is used to merge variant calls, in nucmer format, into a single tabular file. The output file will have as may columns as
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23 the number of genomes provided in input. And as many rows as the number of variants observed in the genomes. For every genome assembly and
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24 variant a simple binary code 1= present, 0=absent will be used to indicate whether that genome carries a specific variant.
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25 This table should be provided to the FunAnn tool to obtain the functional annotation of the variants.
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26
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27 </help>
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28
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29 <tests>
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30 <test>
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31 </test>
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32 </tests>
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33
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34 </tool>
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