view data_manager/gtdbtk_database_installer.xml @ 4:10232d2b5062 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be

<tool id="gtdbtk_database_installer" name="GTDB-Tk Database Installer" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description></description>
    <macros>
        <token name="@TOOL_VERSION@">202</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@PROFILE@">20.09</token>
    </macros>
    <requirements>
        <requirement type="package" version="3.10.2">python</requirement>
    </requirements>
    <command>
    <![CDATA[
        python '$__tool_directory__/gtdbtk_database_installer.py'
          --database_name '$database_name'
          --release '$release'
          --out_file '$out_file'
          $meta
          $test
    ]]>
    </command>
    <inputs>
	    <param name="database_name" type="text" value="" label="Database name or description" help="This value will be displayed in the GTDB-Tk Database select list"/>
        <param name="meta" type="boolean" truevalue="--meta" falsevalue="" checked="false" label="Only store GTDBTK metadata in a dedicated data table. " />
        <param name="test" type="hidden" value="" checked="false" label="Run a dry test run !" />
        <param name="release" type="select" multiple="false" label="GTDB Release">
            <option value="202">202</option>
            <option value="207">207</option>
            <option value="214">214</option>
            <option value="220">220</option>
        </param>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <!-- TODO -->
            <!-- Not actually installing a huge GTDB-Tk database -->
            <!-- but it will check if all urls exist -->
            <param name="release" value="202"/>
            <param name="database_name" value="GTDB-Tk database release 202"/>
            <param name="test" value="--test"/>
            <output name="out_file">
                <assert_contents>
                    <has_text text="GTDB-Tk database release 202"/>
                    <has_text text="release_202"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <!-- Test meta data download with tsv.gz-->
            <param name="release" value="220"/>
            <param name="database_name" value="GTDB-Tk database release 220 metadata"/>
            <param name="meta" value="true"/>
            <output name="out_file">
                <assert_contents>
                    <has_text text="GTDB-Tk database release 220 metadata"/>
                    <has_text text="release_220"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <!-- Test meta data download with tar.gz -->
            <param name="release" value="207"/>
            <param name="database_name" value="GTDB-Tk database release 207 metadata"/>
            <param name="meta" value="true"/>
            <output name="out_file">
                <assert_contents>
                    <has_text text="GTDB-Tk database release 207 metadata"/>
                    <has_text text="release_207"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
This data manager downloads the DB required for GTDB-Tk tools such as 
the `gtdbtk classify_wf`. The meta options allows downloading only the metadata for the 
corresponding DB, which is used by tools like `gtdb_to_taxdump`.
    </help>
    <citations>
        <citation type="doi">doi.org/10.1038/s41587-020-0501-8</citation>
        <citation type="doi">dx.doi.org/10.1038/nbt.4229</citation>
    </citations>
</tool>