<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'
          --readlen ${readlen}
          --outdir 'outdir' &&
          mv outdir/*.align.csv ${align} &&
          mv outdir/*.amino.csv ${amino} &&
          mv outdir/*.conseq.csv ${conseq} &&
          mv outdir/*.insert.csv ${insert} &&
          mv outdir/*.nuc.csv ${nuc}
        ]]>
    </command>
    <inputs>
        <param format="fastqsanger,fastqsanger.gz" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />
        <param name="readlen" type="integer" min="1" value="251" max="600" label="Read Length" help="Read Length" />
    </inputs>
    <outputs>
        <data name="align" format="tabular" />
        <data name="amino" format="tabular" />
        <data name="conseq" format="tabular" />
        <data name="insert" format="tabular" />
        <data name="nuc" format="tabular" />
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help><![CDATA[
    ]]></help>
    <expand macro="citations" />
</tool>