Mercurial > repos > iuc > abricate
comparison abricate.xml @ 1:15197951a756 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
author | iuc |
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date | Fri, 03 Mar 2017 14:56:09 -0500 |
parents | 862f5a86854d |
children | 2aa02d2a6af3 |
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0:862f5a86854d | 1:15197951a756 |
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1 <tool id="abricate" name="ABRicate" version="0.1.0"> | 1 <tool id="abricate" name="ABRicate" version="0.3"> |
2 <requirements> | 2 <requirements> |
3 <requirement type="package" version="0.3">abricate</requirement> | 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> | 4 </requirements> |
7 | 5 |
8 <version_command>abricate --version</version_command> | 6 <version_command>abricate --version</version_command> |
9 | 7 |
10 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
11 abricate "$fasta_input" | 9 abricate '$fasta_input' |
12 #if $settings.advanced == "advanced" | 10 #if $settings.advanced == "advanced" |
13 $settings.no_header | 11 $settings.no_header |
14 #if $settings.min_dna_id | 12 #if str($settings.min_dna_id) |
15 --minid=$settings.min_dna_id | 13 --minid=$settings.min_dna_id |
16 #end if | 14 #end if |
17 #if $settings.cull_limit | 15 #if str($settings.cull_limit) |
18 --cull=$settings.cull_limit | 16 --cull=$settings.cull_limit |
19 #end if | 17 #end if |
20 #end if | 18 #end if |
21 > "$report" | 19 > '$report' |
22 ]]></command> | 20 ]]></command> |
23 | 21 |
24 <inputs> | 22 <inputs> |
25 <param name="fasta_input" type="data" format="fasta" label="Select fasta file" help="Specify fasta file to screen for antibiotic resistant genes"/> | 23 <param name="fasta_input" type="data" format="fasta" label="FASTA file" help="To screen for antibiotic resistant genes" /> |
26 <conditional name="settings"> | 24 <conditional name="settings"> |
27 <param name="advanced" type="select" label="Specify advanced parameters"> | 25 <param name="advanced" type="select" label="Specify advanced parameters"> |
28 <option value="simple" selected="true">No, use program defaults.</option> | 26 <option value="simple" selected="true">No, use program defaults.</option> |
29 <option value="advanced">Yes, see full parameter list.</option> | 27 <option value="advanced">Yes, see full parameter list.</option> |
30 </param> | 28 </param> |
31 <when value="simple"> | 29 <when value="simple"> |
32 </when> | 30 </when> |
33 <when value="advanced"> | 31 <when value="advanced"> |
34 <param name="no_header" type="boolean" label="Suppress header" truevalue="--noheader" falsevalue="" | 32 <param name="no_header" argument="--noheader" type="boolean" truevalue="--noheader" falsevalue="" label="Suppress header" help="Suppress output file's column headings" /> |
35 help="Suppress output file's column headings" optional="true" /> | 33 <param name="min_dna_id" argument="--minid" type="float" value="75" min="0" max="100" optional="true" label="Minimum DNA identity" /> |
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" /> | 34 <param name="cull_limit" argument="--cull" type="integer" value="1" min="0" optional="true" label="Culling limit (encompassing hits)" /> |
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> | 35 </when> |
41 </conditional> | 36 </conditional> |
42 </inputs> | 37 </inputs> |
43 | 38 |
44 <outputs> | 39 <outputs> |
45 <data format="tabular" name="report" label="${tool.name} on ${on_string} report file"/> | 40 <data name="report" format="tabular" label="${tool.name} on ${on_string} report file" /> |
46 </outputs> | 41 </outputs> |
47 | 42 |
48 <tests> | 43 <tests> |
49 <!-- Basic test - will produce no results. --> | 44 <!-- Basic test - will produce no results. --> |
50 <test> | 45 <test> |
128 Processing: 6008.fna | 123 Processing: 6008.fna |
129 Found 12 ABR genes in 6008.fna | 124 Found 12 ABR genes in 6008.fna |
130 Klebsiella.fna NC_021232.1 872545 872964 fosA 1-420/420 =============== 0 100.00 100.00 | 125 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 | 126 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 | 127 Klebsiella.fna NC_021232.1 2584899 2585759 blaSHV1 1-861/861 =============== 0 100.00 99.88 |
133 | |
134 | |
135 ]]></help> | 128 ]]></help> |
136 | 129 |
137 <citations> | 130 <citations> |
138 <citation type="bibtex"> | 131 <citation type="bibtex"> |
139 @UNPUBLISHED{Seemann2016, | 132 @UNPUBLISHED{Seemann2016, |
140 author = "Seemann T", | 133 author = {Seemann, Torsten}, |
141 title = "ABRicate: mass screening of contigs for antiobiotic resistance genes", | 134 title = {ABRicate: mass screening of contigs for antiobiotic resistance genes}, |
142 year = "2016", | 135 year = {2016}, |
143 note = "https://github.com/tseemann/abricate"} | 136 url = {https://github.com/tseemann/abricate}, |
144 </citation> | 137 } |
138 </citation> | |
145 </citations> | 139 </citations> |
146 </tool> | 140 </tool> |