Mercurial > repos > ulfschaefer > data_manager_phemost
comparison data_manager/fetch_mlst_data.xml @ 0:c01ac945b067 draft
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| author | ulfschaefer |
|---|---|
| date | Mon, 11 Jul 2016 05:23:33 -0400 |
| parents | |
| children | d5b579102414 |
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| -1:000000000000 | 0:c01ac945b067 |
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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 <tests> | |
| 131 <test> | |
| 132 DON'T FORGET TO DEFINE SOME TOOL TESTS | |
| 133 </test> | |
| 134 </tests> | |
| 135 --> | |
| 136 <help> | |
| 137 **What it does** | |
| 138 | |
| 139 Fetches MLST loci and profiles for a given organism from pubmlst.org and populates the "mlst" data table. | |
| 140 | |
| 141 A reference must be provided each time. Use an NBCI accession number (e.g. NC_003210) so it can be automatically downloaded. | |
| 142 | |
| 143 Here are some valid accession number for the species we use most frequently: | |
| 144 | |
| 145 | |
| 146 ======================== ===================== | |
| 147 Organism recommended accession | |
| 148 ======================== ===================== | |
| 149 Campylobacter jejuni AL111168 | |
| 150 Escherichia coli CP002797 | |
| 151 Listeria monocytogenes NC_003210 | |
| 152 Salmonella enterica NC_003197 | |
| 153 Staphylococcus aureus NC_002952 | |
| 154 Streptococcus pneumoniae NC_017769 | |
| 155 Streptococcus pyogenes AE014074 | |
| 156 ======================== ===================== | |
| 157 | |
| 158 | |
| 159 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/). | |
| 160 | |
| 161 | |
| 162 ------ | |
| 163 | |
| 164 </help> | |
| 165 </tool> |