<tool id="micall-lite" name="micall-lite" version="@TOOL_VERSION@+galaxy0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">micall-lite</requirement>
    </requirements>
    <version_command>echo "@TOOL_VERSION@"</version_command>
    <command detect_errors="exit_code">
        <![CDATA[
          ln -s '${input_pair.forward}' '${input_pair.element_identifier}_R1.fastq.gz' &&
          ln -s '${input_pair.reverse}' '${input_pair.element_identifier}_R2.fastq.gz' &&
          mkdir 'outdir' &&
          micall
            '${input_pair.element_identifier}_R1.fastq.gz'
            '${input_pair.element_identifier}_R2.fastq.gz'
          --outdir 'outdir'
        ]]>
    </command>
    <inputs>
        <param format="fastqsanger,fastqsanger.gz" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />
    </inputs>
    <outputs>
        <collection type="list" name="outputs">
            <data name="align" format="tabular">
                <discover_datasets directory="outdir" pattern="*align\.csv" />
            </data>
            <data name="amino" format="tabular">
                <discover_datasets directory="outdir" pattern="*amino\.csv" />
            </data>
            <data name="conseq" format="tabular">
                <discover_datasets directory="outdir" pattern="*conseq\.csv" />
            </data>
            <data name="insert" format="tabular">
                <discover_datasets directory="outdir" pattern="*insert\.csv" />
            </data>
            <data name="nuc" format="tabular">
                <discover_datasets directory="outdir" pattern="*nuc\.csv" />
            </data>
        </collection>
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help><![CDATA[
    ]]></help>
    <expand macro="citations" />
</tool>