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1 <tool id="multiFasCorGAT" name="multiFC" version="1">
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2 <description> Process multi-fasta files to derive a phenetic matrix of genetic variants.</description>
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3 <requirements>
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4 <requirement type="package" >perl</requirement>
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5 <requirement type="package" >wget</requirement>
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6 <requirement type="package" >mummer</requirement>
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7 </requirements>
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8 <command> <![CDATA[
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9 ln -s $__tool_directory__/align.pl . 2>>$log &&
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10 perl align.pl --multi $infile --out $ofile 2>>$log
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11 ]]>
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12 </command>
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13 <inputs>
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14 <param format="fasta" name="infile" type="data" label="multifasta" help="Multifasta file of SARS-CoV-2 genomes"/>
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15 </inputs>
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16
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17 <outputs>
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18 <data format="txt" name="log" label="${tool.name} on ${on_string}: log file "/>
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19 <data format="tsv" name="ofile" label="${tool.name} on ${on_string}: tsv "/>
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20 </outputs>
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21
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22 <stdio>
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23 </stdio>
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24
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25 <tests>
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26 <test>
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27 </test>
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28 </tests>
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29
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30 <help>
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31 **What it does?**
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32
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33 This tool is used to align SARS-CoV-2 genes, in multifasta format. Genomes will be aligned to the reference SARS-CoV-2 genome using nucmer.
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34 The output will consist in a single tabular file with as may columns as the number of genomes provided in input. And as many rows as the
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35 number of variants observed in the genomes. For every genome assembly and variant a simple binary code 1= present, 0=absent will be used to
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36 indicate whether that genome carries a specific variant. This table should be provided to the FunAnn tool to obtain the functional annotation
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37 of the variants.
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38
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39 </help>
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40 <citations>
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41 </citations>
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42 </tool>
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43
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