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planemo upload commit 132092ff7fe1c4810d1221054419389180b81657
author nml
date Fri, 17 Nov 2017 11:49:10 -0500
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1 <tool id="getmlst" name="getmlst" version="0.1.4.1">
2 <description>Download MLST datasets by species from pubmlst.org</description>
3 <requirements>
4 <requirement type="package" version="0.1.4.6">srst2</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="2" level="fatal" description="Please be more specific."/>
8 <exit_code range="1" level="fatal" description="No species matched your query."/>
9 </stdio>
10 <command><![CDATA[
11 $__tool_directory__/getmlst.pl $mlst_db $mlst_defs '$species'
12 ]]></command>
13 <inputs>
14 <param name="species" type="text" label="The name of the genus, or genus and species that you want to download." help="Please note you will receive an error if multiple results are returned."/>
15 </inputs>
16 <outputs>
17 <data format="fasta" name="mlst_db" label="MLST Database"/>
18 <data format="tabular" name="mlst_defs" label="MLST Definitions"/>
19 </outputs>
20 <tests>
21 <test>
22 <param name="species" value="Listeria monocytogenes"/>
23 <output name="mlst_db" file="mlst_database_test.fasta" ftype="fasta"/>
24 <output name="mlst_defs" file="mlst_definitions_test.tabular" ftype="tabular"/>
25 </test>
26 </tests>
27 <help>
28
29 **GetMLST**
30
31 GetMLST_ downloads MLST datasets from pubmlst.org.
32
33 Data is downloaded for a species determined by the users
34
35 - profiles (maps STs to allele numbers)
36 - numbered sequences for each locus in the scheme
37
38 In addition, the alleles are concatenated together for use with SRST2.
39
40 .. _`GetMLST`: https://github.com/katholt/srst2
41
42 -----
43
44 **What it does**
45
46 Searches a database for a given organism and returns the MLST Database(fasta) and MLST Definitions(tabular).
47
48 **Usage**
49
50 Enter the genus and species of the organism to search and press Execute
51
52 **Tips**
53
54 1. To produce a list of all species avaialble for a specific genus, enter the genus name and press "Execute".
55
56 - *Helicobacter* will not generate MLST Database or MLST Definition files and an error will occur however the following output will be generated:
57
58 - *The following 3 species match your query, please be more specific:*
59 - Helicobacter cinaedi
60 - Helicobacter pylori
61 - Helicobacter suis
62
63 -
64
65 2. To return a list of all species available from a database leave the name blank and press "Execute".
66
67 - Leaving the text field blank will not generate MLST Database or MLST Definition files and an error will occur however the following output will be generated:
68
69 - *The following 114 species match your query, please be more specific:*
70 - Achromobacter spp.
71 - Acinetobacter baumannii#1
72 - Acinetobacter baumannii#2
73 - Aeromonas spp.
74 - Anaplasma phagocytophilum
75 - Arcobacter spp.
76 - Aspergillus fumigatus
77 - Bacillus cereus
78 - Bacillus licheniformis
79 - Bacillus subtilis
80 - Bifidobacterium
81 - Bordetella spp.
82 - Borrelia spp.
83 - Brachyspira hampsonii
84 - Brachyspira hyodysenteriae
85 - Brachyspira intermedia
86 - Brachyspira pilosicoli
87 - Brachyspira spp.
88 - Burkholderia cepacia complex
89 - Burkholderia pseudomallei
90 - Campylobacter concisus/curvus
91 - Campylobacter fetus
92 - Campylobacter helveticus
93 - Campylobacter hyointestinalis
94 - ...
95
96 </help>
97
98 <citations>
99 <citation type="doi">10.1186/s13073-014-0090-6</citation>
100 </citations>
101 </tool>