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1 <tool id="FunAnn" name="FunAnn" version="1">
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2 <description> </description>
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3 <requirements>
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4 <requirement type="package" >perl</requirement>
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5 <requirement type="package" >wget</requirement>
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6 <requirement type="package" >gzip</requirement>
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7 </requirements>
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8 <command> <![CDATA[
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9 ## ln -s $__tool_directory__/GCA_009858895.3_ASM985889v3_genomic.fna 2>>$log &&
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10 cp $__tool_directory__/annotate.pl . 2>>$log &&
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11 perl annotate.pl $infile $outfile 2>>$log
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12 ]]>
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13 </command>
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14 <inputs>
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15 <param name="infile" format="txt" type="data" label="merged show-snps tabular ouput" help="annotates SARS-CoV-2 variants" />
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16 </inputs>
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17 <outputs>
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18 <data format="tsv" name="outfile" label="${tool.name} on ${on_string}: Functional annotation of SARS-CoV-2 genomes in tabular format " />
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19 <data format="txt" name="log" label="${tool.name} on ${on_string}: log file "/>
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20 </outputs>
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21 <help>
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22 **What it does?**
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23
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24 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. A copy of the genome in fasta format can be found also in this Galaxy, under Shared Data -> Data Libraries -> SARS-CoV-2-REF.
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25
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26
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27 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 .
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28 </help>
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29 <citations>
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30 </citations>
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31 </tool>
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