view getmlst.xml @ 1:f1435033144b draft

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<tool id="getmlst" name="getmlst" version="0.1.3">
  <description>Download MLST datasets by species from pubmlst.org</description>
  <command interpreter="perl">
    getmlst.pl \$BASE/getmlst.py $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>
  <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>
  <outputs>
    <data format="fasta" name="mlst_db" label="MLST Database"/>
    <data format="tabular" name="mlst_defs" label="MLST Definitions"/>
  </outputs>
  <requirements>
    <requirement type="package" version="0.1.4.5">srst2</requirement>
  </requirements>

  <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>
**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
  - Campylobacter insulaenigrae
  - Campylobacter jejuni
  - Campylobacter lanienae
  - Campylobacter lari
  - Campylobacter sputorum
  - Campylobacter upsaliensis
  - Candida albicans
  - ...

  </help>
</tool>