jpayne@0: <tool id="shigatyper" name="ShigaTyper" version="1.0.5">
jpayne@0:     <description>Shigella genoserotyping</description>
jpayne@0:     <requirements>
jpayne@0:         <requirement type="package" version="1.0.5">shigatyper</requirement>
jpayne@0:     </requirements>
jpayne@0:     <command detect_errors="exit_code"><![CDATA[
jpayne@0:         shigatyper -n "$input1.name" "$input1" "$input2" -vv > "$output1"
jpayne@0:     ]]></command>
jpayne@0:     <inputs>
jpayne@0:         <param type="data" name="input1" format="fastqsanger, fastqsanger.gz" />
jpayne@0:         <param type="data" name="input2" format="fastqsanger, fastqsanger.gz" />
jpayne@0:     </inputs>
jpayne@0:     <outputs>
jpayne@0:         <data name="output1" label="Shigella serotype prediction" format="tabular" />
jpayne@0:     </outputs>
jpayne@0:     <tests>
jpayne@0:         <test>
jpayne@0:             <param name="input1" value="CFSAN029786_S10_L001_R1_001.fastq.gz"/>
jpayne@0:             <param name="input2" value="CFSAN029786_S10_L001_R2_001.fastq.gz"/>
jpayne@0:             <output name="output1" file="output.tabular"/>
jpayne@0:         </test>
jpayne@0:     </tests>
jpayne@0:     <help><![CDATA[
jpayne@0: usage: shigatyper [-h] [-n SAMPLE_NAME] [--verbose] [--version] read1 read2
jpayne@0: 
jpayne@0: positional arguments:
jpayne@0:   read1
jpayne@0:   read2
jpayne@0: 
jpayne@0: 
jpayne@0:     ]]></help>
jpayne@0:     <citations>
jpayne@0:         <citation type="bibtex">
jpayne@0: @misc{githubshigatyper,
jpayne@0:   author = {LastTODO, FirstTODO},
jpayne@0:   year = {TODO},
jpayne@0:   title = {shigatyper},
jpayne@0:   publisher = {GitHub},
jpayne@0:   journal = {GitHub repository},
jpayne@0:   url = {https://github.com/CFSAN-Biostatistics/shigatyper},
jpayne@0: }</citation>
jpayne@0:     </citations>
jpayne@0: </tool>