view nucmer_snp/nucmer_snps.xml @ 2:4f557e248e9d draft default tip

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<tool id="nucmer_snp" name="nucmer_snp" version="">
  <description>Align single fasta files to SARS-CoV-2 genome and call genetic variants</description>
  <requirements>
    <requirement type="package" version="4.0.0beta2-5" >mummer4</requirement>
    <requirement type="package" >mesa-libgl-devel-cos7-aarch64</requirement>
  </requirements>
  <command>
 <![CDATA[
 nucmer --prefix=ref_qry $reference $genome2 &&

 show-snps -Clr ./ref_qry.delta > $output_file

  ]]>
  </command>

  <inputs>
    <param name="reference" format="fasta" type="data" label="Reference genome fasta file" help="reference SARS-CoV-2 genome " />
    <param name="genome2" format="fasta" type="data" label="Genome fasta" help="input genome for nucmer " />
  </inputs>
  <outputs>
    <data format="tsv" name="output_file" label="${tool.name} on ${on_string}:Variant file in nucmer format" />
  </outputs>
  <stdio>
    <exit_code range="1:" level="fatal" />
  </stdio>
  <help>
	**What it does**

	This simple wrapper is used to align a SARS-CoV-2 genome assembly to the reference genome as available from Genbank (NC_045512).
	This wrapper run nucmer with default parameters to align genomes. Variants are extracted from the nucmer delta file by the
	show-snps utility.
	Output files obtained from this software should be concatenated with the join_nucmer utility before functional annotation.
  
  </help>

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

</tool>