<tool id="shigatyper" name="ShigaTyper" version="1.0.5">
    <description>Shigella genoserotyping</description>
    <requirements>
        <requirement type="package" version="1.0.5">shigatyper</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        shigatyper -n "$input1.name" "$input1" "$input2" -vv > "$output1"
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="fastqsanger, fastqsanger.gz" />
        <param type="data" name="input2" format="fastqsanger, fastqsanger.gz" />
    </inputs>
    <outputs>
        <data name="output1" label="Shigella serotype prediction" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="CFSAN029786_S10_L001_R1_001.fastq.gz"/>
            <param name="input2" value="CFSAN029786_S10_L001_R2_001.fastq.gz"/>
            <output name="output1" file="output.tabular"/>
        </test>
    </tests>
    <help><![CDATA[
usage: shigatyper [-h] [-n SAMPLE_NAME] [--verbose] [--version] read1 read2

positional arguments:
  read1
  read2


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