<tool id="spotyping" name="Spoligotype Prediction" version="0.1.1">
    <requirements>
        <requirement type="package" version="2.1">spotyping</requirement>
    </requirements>
    <command>
        SpoTyping.py 
        #if str( $data_input.data_selector ) == "paired"       
            $data_input.input1.forward $data_input.input1.reverse
        #end if
        #if str( $data_input.data_selector ) == "single"       
            $data_input.input2.element_identifier
        #end if
    </command>
    <inputs>
        <conditional name="data_input">
          <param name="data_selector" type="select" label="Single or Paired-end Data" help="Select between paired and single end data to add name to dataset">
            <option value="paired">Paired</option>
            <option value="single">Single</option>
          </param>
          <when value="paired">
            <param name="input1" format="data" type="data_collection" collection_type="paired" label="Select a paired collection" help="a paired data"/>
          </when>
          <when value="single">
            <param name="input2" format="data" type="data" label="input" help="Specify dataset with single reads"/>
          </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output1" label="spoligotyping results" format="data" from_work_dir="SpoTyping"/>
        <data name="output2" label="spoligotyping log" format="data" from_work_dir="SpoTyping.log"/>
        <data name="output3" label="query" format="data" from_work_dir="*.xls"/>
    </outputs>
    <help><![CDATA[
        Usage: python SpoTyping.py [options] FASTQ_1/FASTA FASTQ_2(optional) 
    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubSpoTyping,
  author = {Xia, Eryu},
  year = {2016},
  title = {SpoTyping},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/xiaeryu/SpoTyping},
}</citation>
    </citations>
</tool>