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planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty
author iuc
date Tue, 29 Nov 2016 14:52:34 -0500
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1 <tool id="abricate" name="ABRicate" version="0.1.0">
2 <requirements>
3 <requirement type="package" version="0.3">abricate</requirement>
4 <requirement type="package" version="5.18.1">perl</requirement>
5 <requirement type="package" version="2.2.31">blast+</requirement>
6 </requirements>
7
8 <version_command>abricate --version</version_command>
9
10 <command detect_errors="exit_code"><![CDATA[
11 abricate "$fasta_input"
12 #if $settings.advanced == "advanced"
13 $settings.no_header
14 #if $settings.min_dna_id
15 --minid=$settings.min_dna_id
16 #end if
17 #if $settings.cull_limit
18 --cull=$settings.cull_limit
19 #end if
20 #end if
21 > "$report"
22 ]]></command>
23
24 <inputs>
25 <param name="fasta_input" type="data" format="fasta" label="Select fasta file" help="Specify fasta file to screen for antibiotic resistant genes"/>
26 <conditional name="settings">
27 <param name="advanced" type="select" label="Specify advanced parameters">
28 <option value="simple" selected="true">No, use program defaults.</option>
29 <option value="advanced">Yes, see full parameter list.</option>
30 </param>
31 <when value="simple">
32 </when>
33 <when value="advanced">
34 <param name="no_header" type="boolean" label="Suppress header" truevalue="--noheader" falsevalue=""
35 help="Suppress output file's column headings" optional="true" />
36 <param name="min_dna_id" type="integer" label="Minimum DNA identity" value="75" min="0" max="100" help="Minimum DNA identity (default 75, must be between 0-100)" optional="true" />
37 <param name="cull_limit" type="integer" label="Culling limit" value="1" min="0" help="Culling limit (encompassing hits) (default 1, must be a positive number)" optional="true">
38 <validator type="in_range" message="This value must be greater than or equal to 0" min="0" max="2147483647"/>
39 </param>
40 </when>
41 </conditional>
42 </inputs>
43
44 <outputs>
45 <data format="tabular" name="report" label="${tool.name} on ${on_string} report file"/>
46 </outputs>
47
48 <tests>
49 <!-- Basic test - will produce no results. -->
50 <test>
51 <param name="fasta_input" value="Acetobacter.fna"/>
52 <param name="advanced" value="simple"/>
53 <output name="report" ftype="tabular" file="output_noresults.txt" />
54 </test>
55
56 <!-- Basic test - will produce results. -->
57 <test>
58 <param name="fasta_input" value="MRSA0252.fna"/>
59 <param name="advanced" value="simple"/>
60 <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
61 </test>
62
63 <!-- Advanced test - No header. -->
64 <test>
65 <param name="fasta_input" value="MRSA0252.fna"/>
66 <param name="advanced" value="advanced"/>
67 <param name="no_header" value="True"/>
68 <output name="report" ftype="tabular" file="output_noheader.txt" compare="contains"/>
69 </test>
70
71 <!-- Advanced test - Cull limit 100 -->
72 <test>
73 <param name="fasta_input" value="MRSA0252.fna"/>
74 <param name="advanced" value="advanced"/>
75 <param name="cull_limit" value="100"/>
76 <output name="report" ftype="tabular" file="output_cull100.txt" compare="contains"/>
77 </test>
78
79 <!-- Advanced test - Min DNA ID 100 -->
80 <test>
81 <param name="fasta_input" value="MRSA0252.fna"/>
82 <param name="advanced" value="advanced"/>
83 <param name="min_dna_id" value="100"/>
84 <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
85 </test>
86 </tests>
87
88 <help><![CDATA[
89 **What it does**
90
91 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.
92
93 **Output**
94
95 ABRicate will produce a tab-seperated output file with the following outputs:
96
97 +---------------+------------------------------------------------+
98 | Column | Description |
99 +===============+================================================+
100 | FILE | The filename this hit came from |
101 +---------------+------------------------------------------------+
102 | SEQUENCE | The sequence in the filename |
103 +---------------+------------------------------------------------+
104 | START | Start coordinate in the sequence |
105 +---------------+------------------------------------------------+
106 | END | End coordinate |
107 +---------------+------------------------------------------------+
108 | GENE | ABR gene |
109 +---------------+------------------------------------------------+
110 | COVERAGE | What proportion of the gene is in our sequence |
111 +---------------+------------------------------------------------+
112 | COVERAGE_MAP | A visual represenation |
113 +---------------+------------------------------------------------+
114 | GAPS | Was there any gaps in the |
115 | | alignment - possible pseudogene? |
116 +---------------+------------------------------------------------+
117 | %COVERAGE | Proportion of gene covered |
118 +---------------+------------------------------------------------+
119 | %IDENTITY | Proportion of exact nucleotide matches |
120 +---------------+------------------------------------------------+
121
122
123 **Example Output**
124
125 ::
126
127 #FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY
128 Processing: 6008.fna
129 Found 12 ABR genes in 6008.fna
130 Klebsiella.fna NC_021232.1 872545 872964 fosA 1-420/420 =============== 0 100.00 100.00
131 Klebsiella.fna NC_021232.1 1381252 1382427 oqxA 1-1176/1176 =============== 0 100.00 99.32
132 Klebsiella.fna NC_021232.1 2584899 2585759 blaSHV1 1-861/861 =============== 0 100.00 99.88
133
134
135 ]]></help>
136
137 <citations>
138 <citation type="bibtex">
139 @UNPUBLISHED{Seemann2016,
140 author = "Seemann T",
141 title = "ABRicate: mass screening of contigs for antiobiotic resistance genes",
142 year = "2016",
143 note = "https://github.com/tseemann/abricate"}
144 </citation>
145 </citations>
146 </tool>