comparison pangolin.xml @ 29:2f1019071464 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit acc495bd77aa3defdda7ec8d8b84a37d6832f2ee

28:9d61d3fa046c

<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
    <description>Phylogenetic Assignment of Outbreak Lineages</description>
    <macros>
        <token name="@TOOL_VERSION@">4.3</token>
        <token name="@PANGOLIN_DATA_VERSION@">1.21</token>
        <token name="@CONSTELLATIONS_VERSION@">0.1.12</token>

        only compatible versions of that data. -->
        <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@"><![CDATA[^4$|^4\.3$]]></token>
        <!-- pangolin-data versions >=1.20 do not contain pangoLEARN models anymore.
        This version of pangolin still supports pangolearn analysis mode, but only when using
        older versions of pangolin-data. -->
        <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT_FOR_PANGOLEARN@">4></token>
        <!-- a regex describing the scorpio versions that this wrapper version
        is backwards-compatible with; can be used with the min_scorpio_version
        column of the pangolin_constellations data table to offer only compatible
        versions of constellations data. -->
        <token name="@COMPATIBLE_SCORPIO_DATA_FORMAT@"><![CDATA[(^0\.[1-3]$|^0\.[0-2]\.\d+$|^0\.3\.\d$|^0\.3\.1[0-7]$|^0$)]]></token>

        </xml>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
        <!-- Pin also the versions of all core dependencies - the ones
        reported with the all-versions option of pangolin plus ucsc-fatovcf,
        which the command is intended to report but currently cannot for
        technical reasons - to the versions you'd get installed in an unpinned
        conda install of pangolin at the time of release of this wrapper
        version! By turning these dependencies into explicit requirements the
        requirements section of the tool interface becomes the equivalent of
        the all-versions option as long as the user doesn't update the data
        dependencies.
        Wrapper updates are **explicitly encouraged** when new dependency
        versions become available. Also, please check for updated dependencies

29:2f1019071464

<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy1" profile="20.01">
    <description>Phylogenetic Assignment of Outbreak Lineages</description>
    <macros>
        <token name="@TOOL_VERSION@">4.3</token>
        <token name="@PANGOLIN_DATA_VERSION@">1.21</token>
        <token name="@CONSTELLATIONS_VERSION@">0.1.12</token>

        only compatible versions of that data. -->
        <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@"><![CDATA[^4$|^4\.3$]]></token>
        <!-- pangolin-data versions >=1.20 do not contain pangoLEARN models anymore.
        This version of pangolin still supports pangolearn analysis mode, but only when using
        older versions of pangolin-data. -->
        <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT_FOR_PANGOLEARN@">4</token>
        <!-- a regex describing the scorpio versions that this wrapper version
        is backwards-compatible with; can be used with the min_scorpio_version
        column of the pangolin_constellations data table to offer only compatible
        versions of constellations data. -->
        <token name="@COMPATIBLE_SCORPIO_DATA_FORMAT@"><![CDATA[(^0\.[1-3]$|^0\.[0-2]\.\d+$|^0\.3\.\d$|^0\.3\.1[0-7]$|^0$)]]></token>

        </xml>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
        <!-- Pin also the versions of all core dependencies - the ones
        reported with the all-versions option of pangolin and which have a
        direct impact on the lineage assignment process - to the versions
        you'd get installed in an unpinned conda install of pangolin at the
        time of release of this wrapper version!
        By turning these dependencies into explicit requirements the
        requirements section of the tool interface becomes the equivalent of
        the all-versions option as long as the user doesn't update the data
        dependencies.
        Wrapper updates are **explicitly encouraged** when new dependency
        versions become available. Also, please check for updated dependencies