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planemo upload commit 132092ff7fe1c4810d1221054419389180b81657

<tool id="getmlst" name="getmlst" version="0.1.4.1">
    <description>Download MLST datasets by species from pubmlst.org</description>
    <requirements>
        <requirement type="package" version="0.1.4.6">srst2</requirement>
    </requirements>
    <stdio>
        <exit_code range="2"  level="fatal"   description="Please be more specific."/>
        <exit_code range="1"  level="fatal"   description="No species matched your query."/>
    </stdio>
    <command><![CDATA[
        $__tool_directory__/getmlst.pl $mlst_db $mlst_defs '$species'
    ]]></command>
    <inputs>
        <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."/>
    </inputs>
    <outputs>
        <data format="fasta" name="mlst_db" label="MLST Database"/>
        <data format="tabular" name="mlst_defs" label="MLST Definitions"/>
    </outputs>
    <tests>
        <test>
            <param name="species" value="Listeria monocytogenes"/>
            <output name="mlst_db" file="mlst_database_test.fasta" ftype="fasta"/>
            <output name="mlst_defs" file="mlst_definitions_test.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help>

**GetMLST**

GetMLST_ downloads MLST datasets from pubmlst.org.

Data is downloaded for a species determined by the users

  - profiles (maps STs to allele numbers)
  - numbered sequences for each locus in the scheme

In addition, the alleles are concatenated together for use with SRST2.

.. _`GetMLST`: https://github.com/katholt/srst2

-----

**What it does**

Searches a database for a given organism and returns the MLST Database(fasta) and MLST Definitions(tabular).

**Usage**

Enter the genus and species of the organism to search and press Execute

**Tips**

1. To produce a list of all species avaialble for a specific genus, enter the genus name and press "Execute".

  - *Helicobacter* will not generate MLST Database or MLST Definition files and an error will occur however the following output will be generated:

  - *The following 3 species match your query, please be more specific:*
  - Helicobacter cinaedi
  - Helicobacter pylori
  - Helicobacter suis

  -

2. To return a list of all species available from a database leave the name blank and press "Execute".

  - 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:

  - *The following 114 species match your query, please be more specific:*
  - Achromobacter spp.
  - Acinetobacter baumannii#1
  - Acinetobacter baumannii#2
  - Aeromonas spp.
  - Anaplasma phagocytophilum
  - Arcobacter spp.
  - Aspergillus fumigatus
  - Bacillus cereus
  - Bacillus licheniformis
  - Bacillus subtilis
  - Bifidobacterium
  - Bordetella spp.
  - Borrelia spp.
  - Brachyspira hampsonii
  - Brachyspira hyodysenteriae
  - Brachyspira intermedia
  - Brachyspira pilosicoli
  - Brachyspira spp.
  - Burkholderia cepacia complex
  - Burkholderia pseudomallei
  - Campylobacter concisus/curvus
  - Campylobacter fetus
  - Campylobacter helveticus
  - Campylobacter hyointestinalis
  - ...

    </help>

    <citations>
        <citation type="doi">10.1186/s13073-014-0090-6</citation>
    </citations>
</tool>