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