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1 <tool id="getmlst" name="getmlst" version="0.1.3">
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2 <description>Download MLST datasets by species from pubmlst.org</description>
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3 <command interpreter="perl">
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4 getmlst.pl \$BASE/getmlst.py $mlst_db $mlst_defs '$species'
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5 </command>
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6 <inputs>
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7 <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."/>
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8 </inputs>
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9 <stdio>
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10 <exit_code range="2" level="fatal" description="Please be more specific."/>
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11 <exit_code range="1" level="fatal" description="No species matched your query."/>
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12 </stdio>
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13 <outputs>
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14 <data format="fasta" name="mlst_db" label="MLST Database"/>
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15 <data format="tabular" name="mlst_defs" label="MLST Definitions"/>
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16 </outputs>
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17 <requirements>
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18 <requirement type="package" version="0.1.4.5">srst2</requirement>
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2
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19 <requirement type="package" version="2.7">python</requirement>
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0
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20 </requirements>
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21
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22 <tests>
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23 <test>
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24 <param name="species" value="Listeria monocytogenes"/>
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25 <output name="mlst_db" file="mlst_database_test.fasta" ftype="fasta"/>
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26 <output name="mlst_defs" file="mlst_definitions_test.tabular" ftype="tabular"/>
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27 </test>
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28 </tests>
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29 <help>
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30 **What it does**
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31
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32 Searches a database for a given organism and returns the MLST Database(fasta) and MLST Definitions(tabular).
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33
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34 **Usage**
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35
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36 Enter the genus and species of the organism to search and press Execute
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37
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38 **Tips**
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39
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40 1. To produce a list of all species avaialble for a specific genus, enter the genus name and press "Execute".
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41
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42 - *Helicobacter* will not generate MLST Database or MLST Definition files and an error will occur however the following output will be generated:
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43
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44 - *The following 3 species match your query, please be more specific:*
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45 - Helicobacter cinaedi
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46 - Helicobacter pylori
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47 - Helicobacter suis
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48
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49 -
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50
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51 2. To return a list of all species available from a database leave the name blank and press "Execute".
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52
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53 - 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:
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54
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55 - *The following 114 species match your query, please be more specific:*
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56 - Achromobacter spp.
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57 - Acinetobacter baumannii#1
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58 - Acinetobacter baumannii#2
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59 - Aeromonas spp.
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60 - Anaplasma phagocytophilum
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61 - Arcobacter spp.
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62 - Aspergillus fumigatus
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63 - Bacillus cereus
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64 - Bacillus licheniformis
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65 - Bacillus subtilis
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66 - Bifidobacterium
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67 - Bordetella spp.
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68 - Borrelia spp.
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69 - Brachyspira hampsonii
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70 - Brachyspira hyodysenteriae
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71 - Brachyspira intermedia
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72 - Brachyspira pilosicoli
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73 - Brachyspira spp.
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74 - Burkholderia cepacia complex
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75 - Burkholderia pseudomallei
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76 - Campylobacter concisus/curvus
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77 - Campylobacter fetus
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78 - Campylobacter helveticus
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79 - Campylobacter hyointestinalis
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80 - Campylobacter insulaenigrae
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81 - Campylobacter jejuni
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82 - Campylobacter lanienae
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83 - Campylobacter lari
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84 - Campylobacter sputorum
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85 - Campylobacter upsaliensis
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86 - Candida albicans
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87 - ...
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88
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89 </help>
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90 </tool>
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