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