view updio.xml @ 3:ea681f34ca41 draft default tip

planemo upload commit 6139391ea037a297a151c74a909f089c26ac77e6

<tool id="updio" name="UPDio" version="1.1.0+galaxy2" python_template_version="3.5" profile="21.05">
    <requirements>
        <requirement type="package" version="1.1.0">updio</requirement>
        <container type="docker">quay.io/biowdl/updio:1.1.0</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
       ln -s $multisample_vcf input.vcf.gz &&
        updio --multisample_vcf input.vcf.gz
        --childID $child_id
        --momID $mom_id
        --dadID $dad_id &&
        mv output_dir/${child_id}.table ${updio_table} &&
        mv output_dir/${child_id}.upd ${updio_verdict}
    ]]></command>
    <inputs>
        <param name="multisample_vcf" type="data" format="vcf_bgzip"
               label="multisample VCF file" />
        <param name="child_id" type="text"
               label="child sample ID in the VCF file" />
        <param name="mom_id" type="text"
               label="Mother sample ID in the VCF file" />
        <param name="dad_id" type="text"
               label="Father sample ID in the VCF file" />
    </inputs>
    <outputs>
        <data format="tsv" name="updio_table" label="${tool.name} on ${child_id}: table"/>
        <data format="tsv" name="updio_verdict" label="${tool.name} on ${child_id}: verdict"/>
    </outputs>
    <help><![CDATA[
        UPDio is designed to detect UPD events in probands from vcf trio data.
    ]]></help>
</tool>