view multifasta/multi_fasta_process.xml @ 0:3f6d4e4340e8 draft

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<tool id="multiFasCorGAT" name="multiFC" version="1">
  <description> Process multi-fasta files to derive a phenetic matrix of genetic variants.</description>
  <requirements>
    <requirement type="package" >perl</requirement>
    <requirement type="package" >wget</requirement>
    <requirement type="package" >mummer</requirement>
  </requirements>
  <command> <![CDATA[
        ln -s $__tool_directory__/align.pl . 2>>$log &&
	perl align.pl --multi $infile --out $ofile 2>>$log
    ]]>
  </command>
<inputs>
	<param format="fasta" name="infile" type="data" label="multifasta" help="Multifasta file of SARS-CoV-2 genomes"/>
</inputs>

<outputs>
	<data format="txt" name="log" label="${tool.name} on ${on_string}: log file "/>
	<data format="tsv" name="ofile" label="${tool.name} on ${on_string}: tsv "/>
</outputs>

<stdio>
</stdio>

<tests>
	<test>
	</test>
</tests>

<help>
	        **What it does?**

        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.
	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 
	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 
	indicate whether that genome carries a specific variant. This table should be provided to the FunAnn tool to obtain the functional annotation 
	of the variants.

</help>
  <citations>
  </citations>
</tool>