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author ulfschaefer
date Wed, 13 Jul 2016 05:50:48 -0400
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1 <tool id="fetch_mlst_data" name="Fetch MLST Data" version="0.0.1" tool_type="manage_data">
2 <description>fetching</description>
3 <requirements>
4 <requirement type="package" version="2.7.10">python</requirement>
5 </requirements>
6 <command interpreter="python">fetch_mlst_data.py --outfile "${out_file}" --species "$species" --reference $reference</command>
7 <inputs>
8 <param name="species" type="select" label="Select the organism">
9 <option value="Achromobacter spp.">Achromobacter spp.</option>
10 <option value="Acinetobacter baumannii">Acinetobacter baumannii</option>
11 <option value="Aeromonas spp.">Aeromonas spp.</option>
12 <option value="Anaplasma phagocytophilum">Anaplasma phagocytophilum</option>
13 <option value="Arcobacter spp.">Arcobacter spp.</option>
14 <option value="Aspergillus fumigatus">Aspergillus fumigatus</option>
15 <option value="Bacillus cereus">Bacillus cereus</option>
16 <option value="Bacillus licheniformis">Bacillus licheniformis</option>
17 <option value="Bacillus subtilis">Bacillus subtilis</option>
18 <option value="Bartonella henselae">Bartonella henselae</option>
19 <option value="Bordetella spp.">Bordetella spp.</option>
20 <option value="Borrelia spp.">Borrelia spp.</option>
21 <option value="Brachyspira hampsonii">Brachyspira hampsonii</option>
22 <option value="Brachyspira hyodysenteriae">Brachyspira hyodysenteriae</option>
23 <option value="Brachyspira intermedia">Brachyspira intermedia</option>
24 <option value="Brachyspira pilosicoli">Brachyspira pilosicoli</option>
25 <option value="Brachyspira spp.">Brachyspira spp.</option>
26 <option value="Burkholderia cepacia complex">Burkholderia cepacia complex</option>
27 <option value="Burkholderia pseudomallei">Burkholderia pseudomallei</option>
28 <option value="Campylobacter concisus/curvus">Campylobacter concisus/curvus</option>
29 <option value="Campylobacter fetus">Campylobacter fetus</option>
30 <option value="Campylobacter helveticus">Campylobacter helveticus</option>
31 <option value="Campylobacter hyointestinalis">Campylobacter hyointestinalis</option>
32 <option value="Campylobacter insulaenigrae">Campylobacter insulaenigrae</option>
33 <option value="Campylobacter jejuni">Campylobacter jejuni</option>
34 <option value="Campylobacter lanienae">Campylobacter lanienae</option>
35 <option value="Campylobacter lari">Campylobacter lari</option>
36 <option value="Campylobacter sputorum">Campylobacter sputorum</option>
37 <option value="Campylobacter upsaliensis">Campylobacter upsaliensis</option>
38 <option value="Candida albicans">Candida albicans</option>
39 <option value="Candida glabrata">Candida glabrata</option>
40 <option value="Candida krusei">Candida krusei</option>
41 <option value="Candida tropicalis">Candida tropicalis</option>
42 <option value="Carnobacterium maltaromaticum">Carnobacterium maltaromaticum</option>
43 <option value="Chlamydiales spp.">Chlamydiales spp.</option>
44 <option value="Citrobacter freundii">Citrobacter freundii</option>
45 <option value="Clonorchis sinensis">Clonorchis sinensis</option>
46 <option value="Clostridium botulinum">Clostridium botulinum</option>
47 <option value="Clostridium difficile">Clostridium difficile</option>
48 <option value="Clostridium septicum">Clostridium septicum</option>
49 <option value="Corynebacterium diphtheriae">Corynebacterium diphtheriae</option>
50 <option value="Cronobacter spp.">Cronobacter spp.</option>
51 <option value="Enterobacter cloacae">Enterobacter cloacae</option>
52 <option value="Enterococcus faecalis">Enterococcus faecalis</option>
53 <option value="Enterococcus faecium">Enterococcus faecium</option>
54 <option value="Escherichia coli">Escherichia coli</option>
55 <option value="Flavobacterium psychrophilum">Flavobacterium psychrophilum</option>
56 <option value="Haemophilus influenzae">Haemophilus influenzae</option>
57 <option value="Haemophilus parasuis">Haemophilus parasuis</option>
58 <option value="Helicobacter cinaedi">Helicobacter cinaedi</option>
59 <option value="Helicobacter pylori">Helicobacter pylori</option>
60 <option value="Helicobacter suis"> Helicobacter suis</option>
61 <option value="Kingella kingae">Kingella kingae</option>
62 <option value="Klebsiella oxytoca">Klebsiella oxytoca</option>
63 <option value="Klebsiella pneumoniae">Klebsiella pneumoniae</option>
64 <option value="Kudoa septempunctata">Kudoa septempunctata</option>
65 <option value="Lactobacillus salivarius">Lactobacillus salivarius</option>
66 <option value="Leptospira spp.">Leptospira spp.</option>
67 <option value="Listeria monocytogenes">Listeria monocytogenes</option>
68 <option value="Mannheimia haemolytica">Mannheimia haemolytica</option>
69 <option value="Melissococcus plutonius">Melissococcus plutonius</option>
70 <option value="Moraxella catarrhalis">Moraxella catarrhalis</option>
71 <option value="Mycobacterium abscessus">Mycobacterium abscessus</option>
72 <option value="Mycobacterium massiliense">Mycobacterium massiliense</option>
73 <option value="Mycoplasma agalactiae">Mycoplasma agalactiae</option>
74 <option value="Mycoplasma bovis">Mycoplasma bovis</option>
75 <option value="Mycoplasma hyorhinis">Mycoplasma hyorhinis</option>
76 <option value="Neisseria spp.">Neisseria spp.</option>
77 <option value="Orientia tsutsugamushi">Orientia tsutsugamushi</option>
78 <option value="Ornithobacterium rhinotracheale">Ornithobacterium rhinotracheale</option>
79 <option value="Paenibacillus larvae">Paenibacillus larvae</option>
80 <option value="Pasteurella multocida">Pasteurella multocida</option>
81 <option value="Pediococcus pentosaceus">Pediococcus pentosaceus</option>
82 <option value="Porphyromonas gingivalis">Porphyromonas gingivalis</option>
83 <option value="Propionibacterium acnes">Propionibacterium acnes</option>
84 <option value="Pseudomonas aeruginosa">Pseudomonas aeruginosa</option>
85 <option value="Pseudomonas fluorescens">Pseudomonas fluorescens</option>
86 <option value="Riemerella anatipestifer">Riemerella anatipestifer</option>
87 <option value="Salmonella enterica">Salmonella enterica</option>
88 <option value="Sinorhizobium spp.">Sinorhizobium spp.</option>
89 <option value="Staphylococcus aureus">Staphylococcus aureus</option>
90 <option value="Staphylococcus epidermidis">Staphylococcus epidermidis</option>
91 <option value="Staphylococcus haemolyticus">Staphylococcus haemolyticus</option>
92 <option value="Staphylococcus lugdunensis">Staphylococcus lugdunensis</option>
93 <option value="Staphylococcus pseudintermedius">Staphylococcus pseudintermedius</option>
94 <option value="Stapylococcus hominis">Stapylococcus hominis</option>
95 <option value="Stenotrophomonas maltophilia">Stenotrophomonas maltophilia</option>
96 <option value="Streptococcus agalactiae">Streptococcus agalactiae</option>
97 <option value="Streptococcus canis">Streptococcus canis</option>
98 <option value="Streptococcus dysgalactiae equisimilis">Streptococcus dysgalactiae equisimilis</option>
99 <option value="Streptococcus gallolyticus">Streptococcus gallolyticus</option>
100 <option value="Streptococcus oralis">Streptococcus oralis</option>
101 <option value="Streptococcus pneumoniae">Streptococcus pneumoniae</option>
102 <option value="Streptococcus pyogenes">Streptococcus pyogenes</option>
103 <option value="Streptococcus suis">Streptococcus suis</option>
104 <option value="Streptococcus thermophilus">Streptococcus thermophilus</option>
105 <option value="Streptococcus uberis">Streptococcus uberis</option>
106 <option value="Streptococcus zooepidemicus">Streptococcus zooepidemicus</option>
107 <option value="Streptomyces spp">Streptomyces spp</option>
108 <option value="Taylorella spp.">Taylorella spp.</option>
109 <option value="Tenacibaculum spp.">Tenacibaculum spp.</option>
110 <option value="Trichomonas vaginalis">Trichomonas vaginalis</option>
111 <option value="Vibrio cholerae">Vibrio cholerae</option>
112 <option value="Vibrio parahaemolyticus">Vibrio parahaemolyticus</option>
113 <option value="Vibrio spp.">Vibrio spp.</option>
114 <option value="Vibrio tapetis"> Vibrio tapetis</option>
115 <option value="Vibrio vulnificus">Vibrio vulnificus</option>
116 <option value="Wolbachia">Wolbachia</option>
117 <option value="Xylella fastidiosa">Xylella fastidiosa</option>
118 <option value="Yersinia pseudotuberculosis">Yersinia pseudotuberculosis</option>
119 <option value="Yersinia ruckeri">Yersinia ruckeri</option>
120 <option value="Yersinia spp.">Yersinia spp.</option>
121 </param>
122
123 <param name="reference" type="text" value="NC_xxxxxx" label="Please provide a NCBI accession number for the reference genome to use." help="A reference genome is used for extracting the flanking regions to tying genes. Please see help below." />
124
125 </inputs>
126 <outputs>
127 <data name="out_file" format="data_manager_json"/>
128 </outputs>
129
130 <help>
131 **What it does**
132
133 Fetches MLST loci and profiles for a given organism from pubmlst.org and populates the "mlst" data table.
134
135 A reference must be provided each time. Use an NBCI accession number (e.g. NC_003210) so it can be automatically downloaded.
136
137 Here are some valid accession number for the species we use most frequently:
138
139
140 ======================== =====================
141 Organism recommended accession
142 ======================== =====================
143 Campylobacter jejuni AL111168
144 Escherichia coli CP002797
145 Listeria monocytogenes NC_003210
146 Salmonella enterica NC_003197
147 Staphylococcus aureus NC_002952
148 Streptococcus pneumoniae NC_017769
149 Streptococcus pyogenes AE014074
150 ======================== =====================
151
152 ------
153
154 If your organism of choice is not on this list you need to look up the correct accession number for a valid reference genome on the NCBI website (http://www.ncbi.nlm.nih.gov/nuccore/).
155
156 </help>
157 </tool>