comparison pangolin.xml @ 27:03ed9524dcd1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 533e4f638fe88be437066f2acb7aa2de710b8e2f

26:007ffbb11881

<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
    <description>Phylogenetic Assignment of Outbreak Lineages</description>
    <macros>
        <token name="@TOOL_VERSION@">4.1.3</token>
        <token name="@PANGOLIN_DATA_VERSION@">1.17</token>
        <token name="@CONSTELLATIONS_VERSION@">0.1.10</token>
        <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@">4</token>
        <!-- a regex describing the scorpio versions that this wrapper version
        is backwards-compatible with; can be used with the min_scorpio_version

    ]]></command>
    <inputs>
        <param type="data" name="input1" format="fasta,fasta.gz" label="Input FASTA File(s)" />
        <conditional name="engine">
            <param argument="--analysis-mode" type="select" label="Analysis mode"
            help="The analysis engine to use for lineage assignment. UShER is considered more accurate; pangoLEARN typically requires more memory, but might be faster in some cases.">
                <option value="usher">UShER</option>
                <option value="pangolearn">pangoLEARN</option>
            </param>
            <when value="usher">
                <expand macro="pangolin_data_sources">

27:03ed9524dcd1

<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
    <description>Phylogenetic Assignment of Outbreak Lineages</description>
    <macros>
        <token name="@TOOL_VERSION@">4.2</token>
        <token name="@PANGOLIN_DATA_VERSION@">1.17</token>
        <token name="@CONSTELLATIONS_VERSION@">0.1.10</token>
        <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@">4</token>
        <!-- a regex describing the scorpio versions that this wrapper version
        is backwards-compatible with; can be used with the min_scorpio_version

    ]]></command>
    <inputs>
        <param type="data" name="input1" format="fasta,fasta.gz" label="Input FASTA File(s)" />
        <conditional name="engine">
            <param argument="--analysis-mode" type="select" label="Analysis mode"
            help="The analysis engine to use for lineage assignment. Note: In this version, UShER mode is implemented through the usher-sampled algorithm of UShER. If you prefer to run the original usher algorithm, please use version 4.1.3 of the tool.">
                <option value="usher">UShER</option>
                <option value="pangolearn">pangoLEARN</option>
            </param>
            <when value="usher">
                <expand macro="pangolin_data_sources">