galaxy/test/functional/tools/for_workflows/mapper2.xml

<tool id="mapper2" name="mapper2" version="0.1.0">
    <command>
        cp $__tool_directory__/1.bam $out_file1
    </command>
    <inputs>
        <!-- Conditional input block loosely based on bwa-mem. -->
        <conditional name="fastq_input">
          <param name="fastq_input_selector" type="select" label="Single or Paired-end reads">
            <option value="paired">Paired</option>
            <option value="single">Single</option>
            <option value="paired_collection">Paired Collection</option>
            <option value="paired_iv">Paired Interleaved</option>
          </param>
          <when value="paired">
            <param name="fastq_input1" type="data" format="fastq" label="Select first set of reads" />
            <param name="fastq_input2" type="data" format="fastq" label="Select second set of reads" />
          </when>
          <when value="single">
            <param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset"/>
          </when>
          <when value="paired_collection">
            <param name="fastq_input1" format="fastq" type="data_collection" collection_type="paired" label="Select a paired collection" />
          </when>
          <when value="paired_iv">
            <param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset" />
          </when>
        </conditional>
        <param name="reference" type="data" format="fasta" label="Fasta Input"/>
    </inputs>
    <outputs>
        <data name="out_file1" format="bam" />
    </outputs>
</tool>