<tool id="lissero" name="lissero" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
    <requirements>
        <requirement type="package">lissero</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        lissero 
        #if $settings.advanced=="advanced"
          --min_id $settings.min_id
          --min_cov $settings.min_cov
        #end if
        '$input1' > '$output1'
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="fasta" />
        <conditional name="settings">
            <param name="advanced" type="select" label="Specify advanced parameters">
                <option value="simple" selected="true">No, use program defaults.</option>
                <option value="advanced">Yes, see full parameter list.</option>
            </param>
            <when value="simple">
            </when>
            <when value="advanced">
                <param name="min_id" type="float" label="Minimum percent identity to accept a match" value="95.0" min="0" max="100" /> 
                <param name="min_cov" type="float" label="Minimum coverage of a gene to accept a match" value="95.0" min="0" max="100" /> 
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output1" format="txt" />
    </outputs>
    <help><![CDATA[
        Usage: lissero [OPTIONS] FASTA...

  In silico serogroup prediction for L. monocytogenes. Alleles: lmo1118,
  lmo0737, ORF2819, ORF2110, Prs

  References:

  Doumith et al. Differentiation of the major Listeria monocytogenes
  serovars by multiplex PCR. J Clin Microbiol, 2004; 42:8; 3819-22

Options:
  -h, --help              Show this message and exit.
  -s, --serotype_db TEXT  [default:
                          /home/user/miniconda3/lib/python3.9/site-
                          packages/lissero/db]
  --min_id FLOAT          Minimum percent identity to accept a match. [0-100][default=95.0]
  --min_cov FLOAT         Minimum coverage of the gene to accept a match. [0-100][default=95.0]
  --logfile TEXT          Save log to a file instead of printing to stderr
  --version               Show Version Information

    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githublissero,
  author = {LastTODO, FirstTODO},
  year = {TODO},
  title = {lissero},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/MDU-PHL/lissero},
}</citation>
    </citations>
</tool>