comparison data_manager/checkv_datamanager.xml @ 2:88042a5ead89 draft

planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_checkv commit c78bd5eafa3d9450305cc8b32ba9cf8c64c42ba7

1:3756ac7a625b

<tool id="checkv_build_database" name="CheckV" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>database builder</description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.3</token>
        <token name="@VERSION_SUFFIX@">1</token>
        <token name="@PROFILE@">22.01</token>
    </macros>
    <requirements>
        <!-- DM only needs diamon (which comes with checkv) -->
        <requirement type="package" version="@TOOL_VERSION@">checkv</requirement>

        wget https://portal.nersc.gov/CheckV/checkv-db-v${version}.tar.gz &&
        tar -zxvf checkv-db-v${version}.tar.gz &&
        cd checkv-db-v${version}/genome_db/ &&
        diamond makedb --in checkv_reps.faa --db checkv_reps &&
        cd - &&
        mv checkv-db-v${version} checkv-db &&
        cp '$dmjson' '$out_file'
    ]]></command>
    <configfiles>
        <configfile name="dmjson"><![CDATA[
{

2:88042a5ead89

<tool id="checkv_build_database" name="CheckV" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>database builder</description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.3</token>
        <token name="@VERSION_SUFFIX@">2</token>
        <token name="@PROFILE@">22.01</token>
    </macros>
    <requirements>
        <!-- DM only needs diamon (which comes with checkv) -->
        <requirement type="package" version="@TOOL_VERSION@">checkv</requirement>

        wget https://portal.nersc.gov/CheckV/checkv-db-v${version}.tar.gz &&
        tar -zxvf checkv-db-v${version}.tar.gz &&
        cd checkv-db-v${version}/genome_db/ &&
        diamond makedb --in checkv_reps.faa --db checkv_reps &&
        cd - &&
        mkdir -p '$out_file.extra_files_path' &&
        mv checkv-db-v${version} '$out_file.extra_files_path'/checkv-db &&
        cp '$dmjson' '$out_file'
    ]]></command>
    <configfiles>
        <configfile name="dmjson"><![CDATA[
{