<tool id="fetch_mlst_data" name="Fetch MLST Data" version="0.0.1" tool_type="manage_data">
    <description>fetching</description>
    <requirements>
         <requirement type="package" version="2.7.10">python</requirement>
    </requirements>
    <command interpreter="python">fetch_mlst_data.py --outfile "${out_file}" --species "$species" --reference $reference</command>
    <inputs>
      <param name="species" type="select" label="Select the organism">
        <option value="Achromobacter spp.">Achromobacter spp.</option>
        <option value="Acinetobacter baumannii">Acinetobacter baumannii</option>
        <option value="Aeromonas spp.">Aeromonas spp.</option>
        <option value="Anaplasma phagocytophilum">Anaplasma phagocytophilum</option>
        <option value="Arcobacter spp.">Arcobacter spp.</option>
        <option value="Aspergillus fumigatus">Aspergillus fumigatus</option>
        <option value="Bacillus cereus">Bacillus cereus</option>
        <option value="Bacillus licheniformis">Bacillus licheniformis</option>
        <option value="Bacillus subtilis">Bacillus subtilis</option>
        <option value="Bartonella henselae">Bartonella henselae</option>
        <option value="Bordetella spp.">Bordetella spp.</option>
        <option value="Borrelia spp.">Borrelia spp.</option>
        <option value="Brachyspira hampsonii">Brachyspira hampsonii</option>
        <option value="Brachyspira hyodysenteriae">Brachyspira hyodysenteriae</option>
        <option value="Brachyspira intermedia">Brachyspira intermedia</option>
        <option value="Brachyspira pilosicoli">Brachyspira pilosicoli</option>
        <option value="Brachyspira spp.">Brachyspira spp.</option>
        <option value="Burkholderia cepacia complex">Burkholderia cepacia complex</option>
        <option value="Burkholderia pseudomallei">Burkholderia pseudomallei</option>
        <option value="Campylobacter concisus/curvus">Campylobacter concisus/curvus</option>
        <option value="Campylobacter fetus">Campylobacter fetus</option>
        <option value="Campylobacter helveticus">Campylobacter helveticus</option>
        <option value="Campylobacter hyointestinalis">Campylobacter hyointestinalis</option>
        <option value="Campylobacter insulaenigrae">Campylobacter insulaenigrae</option>
        <option value="Campylobacter jejuni">Campylobacter jejuni</option>
        <option value="Campylobacter lanienae">Campylobacter lanienae</option>
        <option value="Campylobacter lari">Campylobacter lari</option>
        <option value="Campylobacter sputorum">Campylobacter sputorum</option>
        <option value="Campylobacter upsaliensis">Campylobacter upsaliensis</option>
        <option value="Candida albicans">Candida albicans</option>
        <option value="Candida glabrata">Candida glabrata</option>
        <option value="Candida krusei">Candida krusei</option>
        <option value="Candida tropicalis">Candida tropicalis</option>
        <option value="Carnobacterium maltaromaticum">Carnobacterium maltaromaticum</option>
        <option value="Chlamydiales spp.">Chlamydiales spp.</option>
        <option value="Citrobacter freundii">Citrobacter freundii</option>
        <option value="Clonorchis sinensis">Clonorchis sinensis</option>
        <option value="Clostridium botulinum">Clostridium botulinum</option>
        <option value="Clostridium difficile">Clostridium difficile</option>
        <option value="Clostridium septicum">Clostridium septicum</option>
        <option value="Corynebacterium diphtheriae">Corynebacterium diphtheriae</option>
        <option value="Cronobacter spp.">Cronobacter spp.</option>
        <option value="Enterobacter cloacae">Enterobacter cloacae</option>
        <option value="Enterococcus faecalis">Enterococcus faecalis</option>
        <option value="Enterococcus faecium">Enterococcus faecium</option>
        <option value="Escherichia coli">Escherichia coli</option>
        <option value="Flavobacterium psychrophilum">Flavobacterium psychrophilum</option>
        <option value="Haemophilus influenzae">Haemophilus influenzae</option>
        <option value="Haemophilus parasuis">Haemophilus parasuis</option>
        <option value="Helicobacter cinaedi">Helicobacter cinaedi</option>
        <option value="Helicobacter pylori">Helicobacter pylori</option>
        <option value="Helicobacter suis"> Helicobacter suis</option>
        <option value="Kingella kingae">Kingella kingae</option>
        <option value="Klebsiella oxytoca">Klebsiella oxytoca</option>
        <option value="Klebsiella pneumoniae">Klebsiella pneumoniae</option>
        <option value="Kudoa septempunctata">Kudoa septempunctata</option>
        <option value="Lactobacillus salivarius">Lactobacillus salivarius</option>
        <option value="Leptospira spp.">Leptospira spp.</option>
        <option value="Listeria monocytogenes">Listeria monocytogenes</option>
        <option value="Mannheimia haemolytica">Mannheimia haemolytica</option>
        <option value="Melissococcus plutonius">Melissococcus plutonius</option>
        <option value="Moraxella catarrhalis">Moraxella catarrhalis</option>
        <option value="Mycobacterium abscessus">Mycobacterium abscessus</option>
        <option value="Mycobacterium massiliense">Mycobacterium massiliense</option>
        <option value="Mycoplasma agalactiae">Mycoplasma agalactiae</option>
        <option value="Mycoplasma bovis">Mycoplasma bovis</option>
        <option value="Mycoplasma hyorhinis">Mycoplasma hyorhinis</option>
        <option value="Neisseria spp.">Neisseria spp.</option>
        <option value="Orientia tsutsugamushi">Orientia tsutsugamushi</option>
        <option value="Ornithobacterium rhinotracheale">Ornithobacterium rhinotracheale</option>
        <option value="Paenibacillus larvae">Paenibacillus larvae</option>
        <option value="Pasteurella multocida">Pasteurella multocida</option>
        <option value="Pediococcus pentosaceus">Pediococcus pentosaceus</option>
        <option value="Porphyromonas gingivalis">Porphyromonas gingivalis</option>
        <option value="Propionibacterium acnes">Propionibacterium acnes</option>
        <option value="Pseudomonas aeruginosa">Pseudomonas aeruginosa</option>
        <option value="Pseudomonas fluorescens">Pseudomonas fluorescens</option>
        <option value="Riemerella anatipestifer">Riemerella anatipestifer</option>
        <option value="Salmonella enterica">Salmonella enterica</option>
        <option value="Sinorhizobium spp.">Sinorhizobium spp.</option>
        <option value="Staphylococcus aureus">Staphylococcus aureus</option>
        <option value="Staphylococcus epidermidis">Staphylococcus epidermidis</option>
        <option value="Staphylococcus haemolyticus">Staphylococcus haemolyticus</option>
        <option value="Staphylococcus lugdunensis">Staphylococcus lugdunensis</option>
        <option value="Staphylococcus pseudintermedius">Staphylococcus pseudintermedius</option>
        <option value="Stapylococcus hominis">Stapylococcus hominis</option>
        <option value="Stenotrophomonas maltophilia">Stenotrophomonas maltophilia</option>
        <option value="Streptococcus agalactiae">Streptococcus agalactiae</option>
        <option value="Streptococcus canis">Streptococcus canis</option>
        <option value="Streptococcus dysgalactiae equisimilis">Streptococcus dysgalactiae equisimilis</option>
        <option value="Streptococcus gallolyticus">Streptococcus gallolyticus</option>
        <option value="Streptococcus oralis">Streptococcus oralis</option>
        <option value="Streptococcus pneumoniae">Streptococcus pneumoniae</option>
        <option value="Streptococcus pyogenes">Streptococcus pyogenes</option>
        <option value="Streptococcus suis">Streptococcus suis</option>
        <option value="Streptococcus thermophilus">Streptococcus thermophilus</option>
        <option value="Streptococcus uberis">Streptococcus uberis</option>
        <option value="Streptococcus zooepidemicus">Streptococcus zooepidemicus</option>
        <option value="Streptomyces spp">Streptomyces spp</option>
        <option value="Taylorella spp.">Taylorella spp.</option>
        <option value="Tenacibaculum spp.">Tenacibaculum spp.</option>
        <option value="Trichomonas vaginalis">Trichomonas vaginalis</option>
        <option value="Vibrio cholerae">Vibrio cholerae</option>
        <option value="Vibrio parahaemolyticus">Vibrio parahaemolyticus</option>
        <option value="Vibrio spp.">Vibrio spp.</option>
        <option value="Vibrio tapetis"> Vibrio tapetis</option>
        <option value="Vibrio vulnificus">Vibrio vulnificus</option>
        <option value="Wolbachia">Wolbachia</option>
        <option value="Xylella fastidiosa">Xylella fastidiosa</option>
        <option value="Yersinia pseudotuberculosis">Yersinia pseudotuberculosis</option>
        <option value="Yersinia ruckeri">Yersinia ruckeri</option>
        <option value="Yersinia spp.">Yersinia spp.</option>
	  </param>

    <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." />

    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>

    <help>
**What it does**

Fetches MLST loci and profiles for a given organism from pubmlst.org and populates the "mlst" data table.

A reference must be provided each time. Use an NBCI accession number (e.g. NC_003210) so it can be automatically downloaded.

Here are some valid accession number for the species we use most frequently:


========================  =====================
Organism                  recommended accession
========================  =====================
Campylobacter jejuni      AL111168
Escherichia coli          CP002797
Listeria monocytogenes    NC_003210
Salmonella enterica       NC_003197
Staphylococcus aureus     NC_002952
Streptococcus pneumoniae  NC_017769
Streptococcus pyogenes    AE014074
========================  =====================

------

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/).

    </help>
</tool>