view FunAnn/funct_annot.xml @ 1:40b81942976a draft default tip

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<tool id="FunAnn" name="FunAnn" version="1">
  <description> </description>
  <requirements>
    <requirement type="package" >perl</requirement>
    <requirement type="package" >wget</requirement>
    <requirement type="package" >gzip</requirement>
  </requirements>
  <command> <![CDATA[
        cp $__tool_directory__/annotate.pl . 2>>$log &&
	perl annotate.pl $infile $outfile 2>>$log
          ]]>
  </command>
  <inputs>
	<param name="infile" format="txt" type="data" label="merged show-snps tabular ouput" help="annotates SARS-CoV-2 variants" />
  </inputs>
  <outputs>
	<data format="tsv" name="outfile" label="${tool.name} on ${on_string}: Functional annotation of SARS-CoV-2 genomes in tabular format " />
	<data format="txt" name="log" label="${tool.name} on ${on_string}: log file "/>
  </outputs>
  <help>
	**What it does?**
	
This program reads a tabular formatted file, in pseudo vcf format, as obtained from the **join_nucmer** utility and performs functional annotation of SARS-CoV-2 variants. Please notice that the program performs minimum error checks, and that it is designed to work exclusively with the reference annotation of the SARS-CoV-2 genome as available from Genbank.

The output file is again, a tabular file delineated by tabs, and providing different types of annotations for the variants included in the input file. A more detailed description of the output format can be found at : https://github.com/matteo14c/SARS-CoV-2_annot . 
   </help>
  <citations>
  </citations>
</tool>