Mercurial > repos > iuc > abricate

comparison abricate.xml @ 2:2aa02d2a6af3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
1:15197951a756 2:2aa02d2a6af3
1 <tool id="abricate" name="ABRicate" version="0.3"> 1 <tool id="abricate" name="ABRicate" version="0.5">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.3">abricate</requirement> 3 <requirement type="package" version="0.5">abricate</requirement>
4 </requirements> 4 </requirements>
5 5
6 <version_command>abricate --version</version_command> 6 <version_command>abricate --version</version_command>
7 7
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 abricate '$fasta_input' 9 abricate '$file_input'
10 #if $settings.advanced == "advanced" 10 $adv.no_header
11 $settings.no_header 11 #if $adv.min_dna_id
12 #if str($settings.min_dna_id) 12 --minid=$adv.min_dna_id
13 --minid=$settings.min_dna_id
14 #end if
15 #if str($settings.cull_limit)
16 --cull=$settings.cull_limit
17 #end if
18 #end if 13 #end if
14 --db=$adv.db
19 > '$report' 15 > '$report'
20 ]]></command> 16 ]]></command>
21 17
22 <inputs> 18 <inputs>
23 <param name="fasta_input" type="data" format="fasta" label="FASTA file" help="To screen for antibiotic resistant genes" /> 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." />
24 <conditional name="settings"> 20 <section name="adv" title="Advanced options" expanded="False">
25 <param name="advanced" type="select" label="Specify advanced parameters"> 21 <param argument="--db" type="select" label="Database to use - default is 'resfinder'" help="Option to switch to other AMR/other database">
26 <option value="simple" selected="true">No, use program defaults.</option> 22 <option value="argannot">argannot</option>
27 <option value="advanced">Yes, see full parameter list.</option> 23 <option value="card">card</option>
24 <option value="ncbibetalactamase">ncbi betalactamase</option>
25 <option value="resfinder" selected="true">resfinder</option>
26 <option value="plasmidfinder">plasmidfinder</option>
27 <option value="vfdb">vfdb</option>
28 </param> 28 </param>
29 <when value="simple"> 29 <param name="no_header" argument="--noheader" type="boolean" truevalue="--noheader" falsevalue="" label="Suppress header" help="Suppress output file's column headings" />
30 </when> 30 <param name="min_dna_id" argument="--minid" type="float" value="75" min="0" max="100" optional="true" label="Minimum DNA identity" />
31 <when value="advanced"> 31 </section>
32 <param name="no_header" argument="--noheader" type="boolean" truevalue="--noheader" falsevalue="" label="Suppress header" help="Suppress output file's column headings" />
33 <param name="min_dna_id" argument="--minid" type="float" value="75" min="0" max="100" optional="true" label="Minimum DNA identity" />
34 <param name="cull_limit" argument="--cull" type="integer" value="1" min="0" optional="true" label="Culling limit (encompassing hits)" />
35 </when>
36 </conditional>
37 </inputs> 32 </inputs>
38 33
39 <outputs> 34 <outputs>
40 <data name="report" format="tabular" label="${tool.name} on ${on_string} report file" /> 35 <data name="report" format="tabular" label="${tool.name} on ${on_string} report file" />
41 </outputs> 36 </outputs>
42 37
43 <tests> 38 <tests>
44 <!-- Basic test - will produce no results. --> 39 <!-- Basic test 0 - will produce no results. -->
45 <test> 40 <test>
46 <param name="fasta_input" value="Acetobacter.fna"/> 41 <param name="file_input" value="Acetobacter.fna"/>
47 <param name="advanced" value="simple"/>
48 <output name="report" ftype="tabular" file="output_noresults.txt" /> 42 <output name="report" ftype="tabular" file="output_noresults.txt" />
49 </test> 43 </test>
50 44
51 <!-- Basic test - will produce results. --> 45 <!-- Basic test 1 - will produce results. -->
52 <test> 46 <test>
53 <param name="fasta_input" value="MRSA0252.fna"/> 47 <param name="file_input" value="MRSA0252.fna"/>
54 <param name="advanced" value="simple"/>
55 <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/> 48 <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
56 </test> 49 </test>
57 50
58 <!-- Advanced test - No header. --> 51 <!-- Advanced test 2 - No header. -->
59 <test> 52 <test>
60 <param name="fasta_input" value="MRSA0252.fna"/> 53 <param name="file_input" value="MRSA0252.fna"/>
61 <param name="advanced" value="advanced"/>
62 <param name="no_header" value="True"/> 54 <param name="no_header" value="True"/>
63 <output name="report" ftype="tabular" file="output_noheader.txt" compare="contains"/> 55 <output name="report" ftype="tabular" file="output_noheader.txt" compare="contains"/>
64 </test> 56 </test>
65 57
66 <!-- Advanced test - Cull limit 100 --> 58 <!-- Advanced test 3 - Changed DB to card -->
67 <test> 59 <test>
68 <param name="fasta_input" value="MRSA0252.fna"/> 60 <param name="file_input" value="MRSA0252.fna"/>
69 <param name="advanced" value="advanced"/> 61 <param name="db" value="card"/>
70 <param name="cull_limit" value="100"/> 62 <output name="report" ftype="tabular" file="output_db-card.txt" compare="contains"/>
71 <output name="report" ftype="tabular" file="output_cull100.txt" compare="contains"/>
72 </test> 63 </test>
73 64
74 <!-- Advanced test - Min DNA ID 100 --> 65 <!-- Advanced test 4 - Min DNA ID 100 -->
75 <test> 66 <test>
76 <param name="fasta_input" value="MRSA0252.fna"/> 67 <param name="file_input" value="MRSA0252.fna"/>
77 <param name="advanced" value="advanced"/>
78 <param name="min_dna_id" value="100"/> 68 <param name="min_dna_id" value="100"/>
79 <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/> 69 <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
80 </test> 70 </test>
71
72 <!-- Filetype test 5 - input a gbk -->
73 <test>
74 <param name="file_input" value="test.gbk"/>
75 <output name="report" ftype="tabular" file="output_gbk.txt" compare="contains"/>
76 </test>
77
81 </tests> 78 </tests>
82 79
83 <help><![CDATA[ 80 <help><![CDATA[
84 **What it does** 81 **What it does**
85 82
86 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. 83 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.
87 84
88 **Output** 85 **Output**
89 86
90 ABRicate will produce a tab-seperated output file with the following outputs: 87 ABRicate will produce a tab-seperated output file with the following outputs:
91 88
111 +---------------+------------------------------------------------+ 108 +---------------+------------------------------------------------+
112 | %COVERAGE | Proportion of gene covered | 109 | %COVERAGE | Proportion of gene covered |
113 +---------------+------------------------------------------------+ 110 +---------------+------------------------------------------------+
114 | %IDENTITY | Proportion of exact nucleotide matches | 111 | %IDENTITY | Proportion of exact nucleotide matches |
115 +---------------+------------------------------------------------+ 112 +---------------+------------------------------------------------+
113 | DATABASE | The database this sequence comes from |
114 +---------------+------------------------------------------------+
115 | ACCESSION | The genomic source of the sequence |
116 +---------------+------------------------------------------------+
116 117
117 118
118 **Example Output** 119 **Example Output**
119 120
120 :: 121 ::
121 122
122 #FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY 123 #FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION
123 Processing: 6008.fna 124 6159.fna NC_017338.1 39177 41186 mecA_15 1-2010/2010 =============== 0/0 100.00 100.000 resfinder AB505628
124 Found 12 ABR genes in 6008.fna 125 6159.fna NC_017338.1 727191 728356 norA_1 1-1166/1167 =============== 0/0 99.91 92.367 resfinder M97169
125 Klebsiella.fna NC_021232.1 872545 872964 fosA 1-420/420 =============== 0 100.00 100.00 126 6159.fna NC_017339.1 10150 10995 blaZ_32 1-846/846 =============== 0/0 100.00 100.000 resfinder AP004832
126 Klebsiella.fna NC_021232.1 1381252 1382427 oqxA 1-1176/1176 =============== 0 100.00 99.32
127 Klebsiella.fna NC_021232.1 2584899 2585759 blaSHV1 1-861/861 =============== 0 100.00 99.88
128 ]]></help> 127 ]]></help>
129 128
130 <citations> 129 <citations>
131 <citation type="bibtex"> 130 <citation type="bibtex">
132 @UNPUBLISHED{Seemann2016, 131 @UNPUBLISHED{Seemann2016,