comparison varscan_somatic.xml @ 8:b79bb8b09822 draft

planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b

7:2657ab48e16a

<tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.3">
    <description>Call germline/somatic and LOH variants from tumor-normal sample pairs</description>
    <macros>
        <import>macros.xml</import>
        <macro name="test_mentions_contig">
            <assert_contents>

            <output name="output">
                <expand macro="test_mentions_contig" />
                <expand macro="test_mentions_filters" />
            </output>
        </test>
    </tests>

    <help>
@HELP_HEADER@

8:b79bb8b09822

<tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.4">
    <description>Call germline/somatic and LOH variants from tumor-normal sample pairs</description>
    <macros>
        <import>macros.xml</import>
        <macro name="test_mentions_contig">
            <assert_contents>

            <output name="output">
                <expand macro="test_mentions_contig" />
                <expand macro="test_mentions_filters" />
            </output>
        </test>
        <test expect_num_outputs="1">
            <!-- Test with an input bam with extremely high coverage at a
            variant site (high enough to trigger an AssertionError from
            pysam.libcalignedsegment.get_query_sequences) to see if the
            tool can handle this.
            Also test that the tool doesn't report SNVs against Ns in
            the reference genome (this would lead to more than one variant
            getting called). -->
            <conditional name="reference">
                <param name="source" value="history" />
                <param name="genome" value="hg19_chrM.fa" />
            </conditional>
            <param name="normal_bam" value="high_cov_chrM.bam" />
            <param name="tumor_bam" value="high_cov_chrM.bam" />
            <param name="split_output" value="false" />
            <conditional name="call_params">
                <param name="settings" value="varscan_defaults" />
            </conditional>
            <conditional name="filter_params">
                <param name="settings" value="varscan_defaults" />
            </conditional>
            <output name="output">
                <expand macro="test_mentions_contig" />
                <expand macro="test_mentions_filters" />
                <metadata name="data_lines" value="1" />
            </output>
        </test>
    </tests>

    <help>
@HELP_HEADER@