Mercurial > repos > elixir-it > corgat_nucmer_snp
comparison nucmer_snp/nucmer_snps.xml @ 0:b92610d193a7 draft
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author | elixir-it |
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date | Thu, 23 Jul 2020 12:59:07 +0000 |
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children | 33def392143b |
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-1:000000000000 | 0:b92610d193a7 |
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1 <tool id="nucmer_snp" name="nucmer_snp" version=""> | |
2 <description></description> | |
3 <requirements> | |
4 <requirement type="package" version="4.0.0beta2-5" >mummer4</requirement> | |
5 <requirement type="package" >mesa-libgl-devel-cos7-aarch64</requirement> | |
6 </requirements> | |
7 <command> | |
8 <![CDATA[ | |
9 nucmer --prefix=ref_qry $reference $genome2 && | |
10 | |
11 show-snps -Clr ./ref_qry.delta > $output_file | |
12 | |
13 ]]> | |
14 </command> | |
15 | |
16 <inputs> | |
17 <param name="reference" format="fasta" type="data" label="Reference genome fasta file" help="reference SARS-CoV-2 genome " /> | |
18 <param name="genome2" format="fasta" type="data" label="Genome fasta" help="input genome for nucmer " /> | |
19 </inputs> | |
20 <outputs> | |
21 <data format="tsv" name="output_file" label="${tool.name} on ${on_string}:Variant file in nucmer format" /> | |
22 </outputs> | |
23 <stdio> | |
24 <exit_code range="1:" level="fatal" /> | |
25 </stdio> | |
26 <help> | |
27 **What it does** | |
28 | |
29 This simple wrapper is used to align a SARS-CoV-2 genome assembly to the reference genome as available from Genbank (NC_045512). | |
30 A copy of the genome, is also found on this Galaxy server under Shared Data -> Data Libraries -> SARS-CoV-2-REF. | |
31 This wrapper run nucmer with default parameters to align genomes. Variants are extracted from the nucmer delta file by the | |
32 show-snps utility. | |
33 Output files obtained from this software should be concatenated with the join_nucmer utility before functional annotation. | |
34 | |
35 </help> | |
36 | |
37 <tests> | |
38 <test> | |
39 </test> | |
40 </tests> | |
41 | |
42 </tool> |