Mercurial > repos > elixir-it > corgat_nucmer_snp
changeset 0:b92610d193a7 draft
Uploaded
| author | elixir-it |
|---|---|
| date | Thu, 23 Jul 2020 12:59:07 +0000 |
| parents | |
| children | 33def392143b |
| files | nucmer_snp/nucmer_snps.xml |
| diffstat | 1 files changed, 42 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nucmer_snp/nucmer_snps.xml Thu Jul 23 12:59:07 2020 +0000 @@ -0,0 +1,42 @@ +<tool id="nucmer_snp" name="nucmer_snp" version=""> + <description></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). + A copy of the genome, is also found on this Galaxy server under Shared Data -> Data Libraries -> SARS-CoV-2-REF. + 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>