Mercurial > repos > iuc > abricate
diff abricate.xml @ 2:2aa02d2a6af3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
author | iuc |
---|---|
date | Tue, 18 Jul 2017 13:56:16 -0400 |
parents | 15197951a756 |
children | 6e9aea89e388 |
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--- a/abricate.xml Fri Mar 03 14:56:09 2017 -0500 +++ b/abricate.xml Tue Jul 18 13:56:16 2017 -0400 @@ -1,39 +1,34 @@ -<tool id="abricate" name="ABRicate" version="0.3"> +<tool id="abricate" name="ABRicate" version="0.5"> <requirements> - <requirement type="package" version="0.3">abricate</requirement> + <requirement type="package" version="0.5">abricate</requirement> </requirements> <version_command>abricate --version</version_command> <command detect_errors="exit_code"><![CDATA[ - abricate '$fasta_input' - #if $settings.advanced == "advanced" - $settings.no_header - #if str($settings.min_dna_id) - --minid=$settings.min_dna_id - #end if - #if str($settings.cull_limit) - --cull=$settings.cull_limit - #end if + abricate '$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="fasta_input" type="data" format="fasta" label="FASTA file" help="To screen for antibiotic resistant genes" /> - <conditional name="settings"> - <param name="advanced" type="select" label="Specify advanced parameters"> - <option value="simple" selected="true">No, use program defaults.</option> - <option value="advanced">Yes, see full parameter list.</option> + <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> - <when value="simple"> - </when> - <when value="advanced"> - <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" /> - <param name="cull_limit" argument="--cull" type="integer" value="1" min="0" optional="true" label="Culling limit (encompassing hits)" /> - </when> - </conditional> + <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> @@ -41,49 +36,51 @@ </outputs> <tests> - <!-- Basic test - will produce no results. --> + <!-- Basic test 0 - will produce no results. --> <test> - <param name="fasta_input" value="Acetobacter.fna"/> - <param name="advanced" value="simple"/> + <param name="file_input" value="Acetobacter.fna"/> <output name="report" ftype="tabular" file="output_noresults.txt" /> </test> - <!-- Basic test - will produce results. --> + <!-- Basic test 1 - will produce results. --> <test> - <param name="fasta_input" value="MRSA0252.fna"/> - <param name="advanced" value="simple"/> + <param name="file_input" value="MRSA0252.fna"/> <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/> </test> - <!-- Advanced test - No header. --> + <!-- Advanced test 2 - No header. --> <test> - <param name="fasta_input" value="MRSA0252.fna"/> - <param name="advanced" value="advanced"/> + <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 - Cull limit 100 --> + <!-- Advanced test 3 - Changed DB to card --> <test> - <param name="fasta_input" value="MRSA0252.fna"/> - <param name="advanced" value="advanced"/> - <param name="cull_limit" value="100"/> - <output name="report" ftype="tabular" file="output_cull100.txt" compare="contains"/> + <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 - Min DNA ID 100 --> + <!-- Advanced test 4 - Min DNA ID 100 --> <test> - <param name="fasta_input" value="MRSA0252.fna"/> - <param name="advanced" value="advanced"/> + <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, ABRicate will perform a mass screening of contigs and identify the presence of antibiotic resistance genes. The database of these genes is built from ResFinder. +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** @@ -113,18 +110,20 @@ +---------------+------------------------------------------------+ | %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 - Processing: 6008.fna - Found 12 ABR genes in 6008.fna - Klebsiella.fna NC_021232.1 872545 872964 fosA 1-420/420 =============== 0 100.00 100.00 - Klebsiella.fna NC_021232.1 1381252 1382427 oqxA 1-1176/1176 =============== 0 100.00 99.32 - Klebsiella.fna NC_021232.1 2584899 2585759 blaSHV1 1-861/861 =============== 0 100.00 99.88 + #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>