comparison varscan_somatic.xml @ 10:a57606054bd7 draft

"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 46018cbdd8b4ca124d5c6230862012b9081d56e4"

9:4e97191a1ff7

<tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.5">
    <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>

            <conditional name="filter_params">
                <param name="settings" value="varscan_defaults" />
            </conditional>
            <assert_stderr>
                <has_line_matching
                expression=" Min coverage:&#09;2x for Normal, 2x for Tumor" />
                <has_line_matching
                expression="Min reads2:&#09;1" />
                <has_line_matching
                expression="Min var freq:&#09;0.01" />
                <has_line_matching

10:a57606054bd7

<tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.6">
    <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>

            <conditional name="filter_params">
                <param name="settings" value="varscan_defaults" />
            </conditional>
            <assert_stderr>
                <has_line_matching
                expression=" *Min coverage:&#09;2x for Normal, 2x for Tumor" />
                <has_line_matching
                expression="Min reads2:&#09;1" />
                <has_line_matching
                expression="Min var freq:&#09;0.01" />
                <has_line_matching