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comparison abricate.xml @ 4:78c75f134c16 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
author iuc
date Mon, 19 Mar 2018 10:42:19 -0400
parents 6e9aea89e388
children f9bf6a8d8547
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3:6e9aea89e388 4:78c75f134c16
1 <tool id="abricate" name="ABRicate" version="0.7"> 1 <tool id="abricate" name="ABRicate" version="@VERSION@">
2 <requirements> 2 <description>
3 <requirement type="package" version="0.7">abricate</requirement> 3 Mass screening of contigs for antimicrobial and virulence genes
4 </requirements> 4 </description>
5 5 <macros>
6 <version_command>abricate --version</version_command> 6 <import>macros.xml</import>
7 </macros>
8 <expand macro="requirements" />
9 <expand macro="version_command" />
7 10
8 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
9 abricate '$file_input' 12 abricate '$file_input'
10 $adv.no_header 13 $adv.no_header
11 #if $adv.min_dna_id 14 #if $adv.min_dna_id
17 20
18 <inputs> 21 <inputs>
19 <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." /> 22 <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." />
20 <section name="adv" title="Advanced options" expanded="False"> 23 <section name="adv" title="Advanced options" expanded="False">
21 <param argument="--db" type="select" label="Database to use - default is 'resfinder'" help="Option to switch to other AMR/other database"> 24 <param argument="--db" type="select" label="Database to use - default is 'resfinder'" help="Option to switch to other AMR/other database">
22 <option value="argannot">argannot</option> 25 <option value="argannot">ARG-ANNOT</option>
23 <option value="card">card</option> 26 <option value="card">CARD</option>
24 <option value="ncbibetalactamase">ncbi betalactamase</option> 27 <option value="ecoh">EcOH</option>
25 <option value="resfinder" selected="true">resfinder</option> 28 <option value="ncbi">NCBI Bacterial Antimicrobial Resistance Reference Gene Database</option>
26 <option value="plasmidfinder">plasmidfinder</option> 29 <option value="resfinder" selected="true">Resfinder</option>
27 <option value="vfdb">vfdb</option> 30 <option value="plasmidfinder">PlasmidFinder</option>
31 <option value="vfdb">VFDB</option>
28 </param> 32 </param>
29 <param name="no_header" argument="--noheader" type="boolean" truevalue="--noheader" falsevalue="" label="Suppress header" help="Suppress output file's column headings" /> 33 <param name="no_header" argument="--noheader" type="boolean" truevalue="--noheader" falsevalue="" label="Suppress header" help="Suppress output file's column headings" />
30 <param name="min_dna_id" argument="--minid" type="float" value="75" min="0" max="100" optional="true" label="Minimum DNA identity" /> 34 <param name="min_dna_id" argument="--minid" type="float" value="75" min="0" max="100" optional="true" label="Minimum DNA identity" />
31 </section> 35 </section>
32 </inputs> 36 </inputs>
124 6159.fna NC_017338.1 39177 41186 mecA_15 1-2010/2010 =============== 0/0 100.00 100.000 resfinder AB505628 128 6159.fna NC_017338.1 39177 41186 mecA_15 1-2010/2010 =============== 0/0 100.00 100.000 resfinder AB505628
125 6159.fna NC_017338.1 727191 728356 norA_1 1-1166/1167 =============== 0/0 99.91 92.367 resfinder M97169 129 6159.fna NC_017338.1 727191 728356 norA_1 1-1166/1167 =============== 0/0 99.91 92.367 resfinder M97169
126 6159.fna NC_017339.1 10150 10995 blaZ_32 1-846/846 =============== 0/0 100.00 100.000 resfinder AP004832 130 6159.fna NC_017339.1 10150 10995 blaZ_32 1-846/846 =============== 0/0 100.00 100.000 resfinder AP004832
127 ]]></help> 131 ]]></help>
128 132
129 <citations> 133 <expand macro="citations"/>
130 <citation type="bibtex">
131 @UNPUBLISHED{Seemann2016,
132 author = {Seemann, Torsten},
133 title = {ABRicate: mass screening of contigs for antiobiotic resistance genes},
134 year = {2016},
135 url = {https://github.com/tseemann/abricate},
136 }
137 </citation>
138 </citations>
139 </tool> 134 </tool>