comparison crossmap_region.xml @ 1:eb66d7a04bf8 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e10d34b547557b2bd4f0be69e31204bd5703e422"

0:8635b6b8a8f2

    <expand macro="version_command"/>
    <command><![CDATA[
CrossMap.py region
    '${chain_source.input_chain}'
    '${input}'
    --ratio $ratio
    '$output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="bed" label="BED file"
               help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>
        <expand macro="chain" />
        <param argument="--ratio" type="float" min="0" max="1" value="0.85" label="Minimum ratio of bases that must remap."/>
    </inputs>
    <outputs>
        <data name="output" format="bed"/>
    </outputs>
    <tests>

1:eb66d7a04bf8

    <expand macro="version_command"/>
    <command><![CDATA[
CrossMap.py region
    '${chain_source.input_chain}'
    '${input}'
    $output
    --chromid $chromid
    --ratio $ratio
    ]]></command>
    <inputs>
        <param name="input" type="data" format="bed" label="BED file"
               help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>
        <expand macro="chain" />
        <param argument="--ratio" type="float" min="0" max="1" value="0.85" label="Minimum ratio of bases that must remap."/>
        <param argument="--chromid" type="select" label="Chromid" help="The style of chromosome IDs">
            <option value="a" selected="true">Default (a)</option>
            <option value="s">Short style (s)</option>
            <option value="l">Long stype (l)</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="bed"/>
    </outputs>
    <tests>