comparison data_manager/checkm2_datamanager.xml @ 3:6fd780865107 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit 2ae2ddbe15eb071a70355aa0738d753e8d2cdc2e

2:757826aa89c3

<tool id="checkm2_build_database" name="CheckM2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>database builder</description>
    <macros>
        <!-- on update run a local test setting `test` to something else than "true" -->
        <token name="@TOOL_VERSION@">1.0.2</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@PROFILE@">23.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">checkm2</requirement>
    </requirements>
    <version_command>checkm2 --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p '$out_file.extra_files_path' &&
        #if $test != "true"
            checkm2 database --download --path  '$out_file.extra_files_path'/ &&
            mv '$out_file.extra_files_path'/CheckM2_database/uniref100.KO.1.dmnd '$out_file.extra_files_path' &&
        #else
            touch '$out_file.extra_files_path'/uniref100.KO.1.dmnd &&
        #end if
        cp '$dmjson' '$out_file'

3:6fd780865107

<tool id="checkm2_build_database" name="CheckM2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>database builder</description>
    <macros>
        <!-- on update run a local test setting `test` to something else than "true" -->
        <token name="@TOOL_VERSION@">1.0.2</token>
        <token name="@VERSION_SUFFIX@">1</token>
        <token name="@PROFILE@">23.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">checkm2</requirement>
    </requirements>
    <version_command>checkm2 --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p '$out_file.extra_files_path' &&
        #if $test != "true"
            wget 'https://zenodo.org/records/5571251/files/checkm2_database.tar.gz' &&
            tar -xf 'checkm2_database.tar.gz' -C '$out_file.extra_files_path' &&
            mv '$out_file.extra_files_path'/CheckM2_database/uniref100.KO.1.dmnd '$out_file.extra_files_path' &&
        #else
            touch '$out_file.extra_files_path'/uniref100.KO.1.dmnd &&
        #end if
        cp '$dmjson' '$out_file'