comparison coverage.xml @ 5:9410f163f2e7 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb

4:9fd2e592743f

        <expand macro="reference_interface"/>
        <param argument="--count" type="boolean" checked="false" truevalue="--count" falsevalue="" label="Get read depths by counting read midpoints within each bin" help="" />
        <param argument="--min-mapq" optional="true" type="integer" label="Minimum mapping quality score to count a read for coverage depth" min="0" max="60" value="0" help="" />
    </inputs>
    <outputs>
        <data name="out_capture_target_coverage" format="tabular" label="${tool.name} on ${on_string}: Sample Target coverage" from_work_dir="sample.targetcoverage.cnn" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <conditional name="reference_source">
                <param name="ref_selector" value="history"/>

         when CNVkit finishes calculating the coverage of each sample (through either the
         batch or coverage commands)
         
         Target and antitarget bin-level coverages (.cnn) output file contains those columns
          chromosome, Start, end, gene, log2 and depth
    ]]></help>
    <expand macro="citations" />
</tool>

5:9410f163f2e7

        <expand macro="reference_interface"/>
        <param argument="--count" type="boolean" checked="false" truevalue="--count" falsevalue="" label="Get read depths by counting read midpoints within each bin" help="" />
        <param argument="--min-mapq" optional="true" type="integer" label="Minimum mapping quality score to count a read for coverage depth" min="0" max="60" value="0" help="" />
    </inputs>
    <outputs>
        <data name="out_capture_target_coverage" format="cnn" label="${tool.name} on ${on_string}: Sample Target coverage" from_work_dir="sample.targetcoverage.cnn" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <conditional name="reference_source">
                <param name="ref_selector" value="history"/>

         when CNVkit finishes calculating the coverage of each sample (through either the
         batch or coverage commands)
         
         Target and antitarget bin-level coverages (.cnn) output file contains those columns
          chromosome, Start, end, gene, log2 and depth

-----

**Target Coverage File (e.g., sample.targetcoverage.cnn):**

- **Columns:** chromosome, start, end, gene, reads (raw read count), depth (reads normalized by bin size).

- **Purpose:** Captures on-target sequencing depth.

    ]]></help>
    <expand macro="citations" />
</tool>