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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
author | iuc |
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date | Tue, 18 Jul 2017 13:56:16 -0400 |
parents | 15197951a756 |
children | 6e9aea89e388 |
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<tool id="abricate" name="ABRicate" version="0.5"> <requirements> <requirement type="package" version="0.5">abricate</requirement> </requirements> <version_command>abricate --version</version_command> <command detect_errors="exit_code"><![CDATA[ abricate '$file_input' $adv.no_header #if $adv.min_dna_id --minid=$adv.min_dna_id #end if --db=$adv.db > '$report' ]]></command> <inputs> <param name="file_input" type="data" format="fasta,genbank,embl" label="Input file (Fasta, Genbank or EMBL file)" help="To screen for antibiotic resistant genes, can be a fasta file, a genbank file or an EMBL file." /> <section name="adv" title="Advanced options" expanded="False"> <param argument="--db" type="select" label="Database to use - default is 'resfinder'" help="Option to switch to other AMR/other database"> <option value="argannot">argannot</option> <option value="card">card</option> <option value="ncbibetalactamase">ncbi betalactamase</option> <option value="resfinder" selected="true">resfinder</option> <option value="plasmidfinder">plasmidfinder</option> <option value="vfdb">vfdb</option> </param> <param name="no_header" argument="--noheader" type="boolean" truevalue="--noheader" falsevalue="" label="Suppress header" help="Suppress output file's column headings" /> <param name="min_dna_id" argument="--minid" type="float" value="75" min="0" max="100" optional="true" label="Minimum DNA identity" /> </section> </inputs> <outputs> <data name="report" format="tabular" label="${tool.name} on ${on_string} report file" /> </outputs> <tests> <!-- Basic test 0 - will produce no results. --> <test> <param name="file_input" value="Acetobacter.fna"/> <output name="report" ftype="tabular" file="output_noresults.txt" /> </test> <!-- Basic test 1 - will produce results. --> <test> <param name="file_input" value="MRSA0252.fna"/> <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/> </test> <!-- Advanced test 2 - No header. --> <test> <param name="file_input" value="MRSA0252.fna"/> <param name="no_header" value="True"/> <output name="report" ftype="tabular" file="output_noheader.txt" compare="contains"/> </test> <!-- Advanced test 3 - Changed DB to card --> <test> <param name="file_input" value="MRSA0252.fna"/> <param name="db" value="card"/> <output name="report" ftype="tabular" file="output_db-card.txt" compare="contains"/> </test> <!-- Advanced test 4 - Min DNA ID 100 --> <test> <param name="file_input" value="MRSA0252.fna"/> <param name="min_dna_id" value="100"/> <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/> </test> <!-- Filetype test 5 - input a gbk --> <test> <param name="file_input" value="test.gbk"/> <output name="report" ftype="tabular" file="output_gbk.txt" compare="contains"/> </test> </tests> <help><![CDATA[ **What it does** Given a FASTA contig file or a genbank file, ABRicate will perform a mass screening of contigs and identify the presence of antibiotic resistance genes. The user can choose which database to search from a list of available AMR databases. **Output** ABRicate will produce a tab-seperated output file with the following outputs: +---------------+------------------------------------------------+ | Column | Description | +===============+================================================+ | FILE | The filename this hit came from | +---------------+------------------------------------------------+ | SEQUENCE | The sequence in the filename | +---------------+------------------------------------------------+ | START | Start coordinate in the sequence | +---------------+------------------------------------------------+ | END | End coordinate | +---------------+------------------------------------------------+ | GENE | ABR gene | +---------------+------------------------------------------------+ | COVERAGE | What proportion of the gene is in our sequence | +---------------+------------------------------------------------+ | COVERAGE_MAP | A visual represenation | +---------------+------------------------------------------------+ | GAPS | Was there any gaps in the | | | alignment - possible pseudogene? | +---------------+------------------------------------------------+ | %COVERAGE | Proportion of gene covered | +---------------+------------------------------------------------+ | %IDENTITY | Proportion of exact nucleotide matches | +---------------+------------------------------------------------+ | DATABASE | The database this sequence comes from | +---------------+------------------------------------------------+ | ACCESSION | The genomic source of the sequence | +---------------+------------------------------------------------+ **Example Output** :: #FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION 6159.fna NC_017338.1 39177 41186 mecA_15 1-2010/2010 =============== 0/0 100.00 100.000 resfinder AB505628 6159.fna NC_017338.1 727191 728356 norA_1 1-1166/1167 =============== 0/0 99.91 92.367 resfinder M97169 6159.fna NC_017339.1 10150 10995 blaZ_32 1-846/846 =============== 0/0 100.00 100.000 resfinder AP004832 ]]></help> <citations> <citation type="bibtex"> @UNPUBLISHED{Seemann2016, author = {Seemann, Torsten}, title = {ABRicate: mass screening of contigs for antiobiotic resistance genes}, year = {2016}, url = {https://github.com/tseemann/abricate}, } </citation> </citations> </tool>