annotate cnv_sim.xml @ 2:8216e150d1aa draft

initial CNV-Sim tool definition (0.9.0)

<tool id="cnv_sim" name="Simulate CNV" version="0.9.0">
    <description>in NGS short reads </description>
    <command interpreter="python" detect_errors="exit_code">
        #if $type.simulation_type=="whole_genome"
            cnv-sim.py genome $reference
        #else
            cnv-sim.py exome $reference $target
        #end if
    </command>
    <inputs>
        <conditional name="type">
            <param name="simulation_type" type="select" label="Simulation Type">
                <option value="whole_genome">CNV Simulation in Whole Genome</option>
                <option value="whole_exome">CNV Simulation in Exome Regions</option>
            </param>
            <when value="whole_genome">
                <param format="fasta" name="reference" type="data" label="Reference Genome"/>
            </when>
            <when value="whole_exome">
                <param format="fasta" name="reference" type="data" label="Reference Genome"/>
                <param format="bed" name="target" type="data" label="Target Regions"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="bed" name="cnv_list" from_work_dir="test/CNVList.bed"/>
    </outputs>
    <help>
        This tool generates artificial NGS short reads in FASTQ format afficted by Copy Number Variations.
    </help>
</tool>