Mercurial > repos > elixir-it > corgat_funann
comparison FunAnn/funct_annot.xml @ 0:1886293c2243 draft
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| author | elixir-it |
|---|---|
| date | Thu, 23 Jul 2020 12:49:09 +0000 |
| parents | |
| children | 9b8afa0b6da4 |
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| -1:000000000000 | 0:1886293c2243 |
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| 1 <tool id="FunAnn" name="FunAnn" version="1"> | |
| 2 <description> </description> | |
| 3 <requirements> | |
| 4 <requirement type="package" >perl</requirement> | |
| 5 <requirement type="package" >wget</requirement> | |
| 6 <requirement type="package" >gzip</requirement> | |
| 7 </requirements> | |
| 8 <command> <![CDATA[ | |
| 9 ## ln -s $__tool_directory__/GCA_009858895.3_ASM985889v3_genomic.fna 2>>$log && | |
| 10 cp $__tool_directory__/annotate.pl . 2>>$log && | |
| 11 perl annotate.pl $infile $outfile 2>>$log | |
| 12 ]]> | |
| 13 </command> | |
| 14 <inputs> | |
| 15 <param name="infile" format="txt" type="data" label="merged show-snps tabular ouput" help="annotates SARS-CoV-2 variants" /> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data format="tsv" name="outfile" label="${tool.name} on ${on_string}: Functional annotation of SARS-CoV-2 genomes in tabular format " /> | |
| 19 <data format="txt" name="log" label="${tool.name} on ${on_string}: log file "/> | |
| 20 </outputs> | |
| 21 <help> | |
| 22 **What it does?** | |
| 23 | |
| 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. | |
| 25 | |
| 26 | |
| 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 . | |
| 28 </help> | |
| 29 <citations> | |
| 30 </citations> | |
| 31 </tool> |