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comparison abricate.xml @ 1:15197951a756 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
author iuc
date Fri, 03 Mar 2017 14:56:09 -0500
parents 862f5a86854d
children 2aa02d2a6af3
comparison
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0:862f5a86854d 1:15197951a756
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>