view mapseq_db_fetcher.xml @ 4:19ef193d1316 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit abbc840d4383eee1f26abef04b1ce4df1e6e20a2

<tool id="mapseq_db_fetcher" name="Mapseq DB fetcher" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Fetches the DB required for mapseq</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version" />
    <command detect_errors="exit_code">
    <![CDATA[
        python '$__tool_directory__/data_manager_fetch_mapseq_db.py' 
        --out '${out_file}' 
        --version '${select_version.version}' 
        --database-type '${database_type}'
        $test_data_manager_v5
    ]]>
    </command>
    <inputs>
        <!-- <param name="test_data_manager" type="hidden" /> -->
        <param name="test_data_manager_v5" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry for v5." />
        <conditional name="select_version">
            <param argument="--version" type="select" label="Select MGnify version">
                <option value="5.0">v5.0</option>
                <option value="6.0">v6.0</option>
            </param>
            <when value="5.0">
                <param name="database_type" type="select" multiple="false" label="Database Type">
                    <option value="mgnify_v5_lsu">MGnify LSU (v5.0.7)</option>
                    <option value="mgnify_v5_ssu">MGnify SSU (v5.0.7)</option>
                    <option value="mgnify_v5_its_itsonedb">MGnify ITS ITSonedb (v5.0.7)</option>
                    <option value="mgnify_v5_its_unite">MGnify ITS UNITE (v5.0.7)</option>
                </param>
            </when>
            <when value="6.0">
                <param name="database_type" type="select" multiple="false" label="Database Type">
                    <option value="mgnify_v6_lsu">MGnify LSU (v6.0)</option>
                    <option value="mgnify_v6_ssu">MGnify SSU (v6.0)</option>
                    <option value="mgnify_v6_its_itsonedb">MGnify ITS ITSonedb (v6.0)</option>
                    <option value="mgnify_v6_its_unite">MGnify ITS UNITE (v6.0)</option>
                    <option value="mgnify_v6_pr2">MGnify PR2 (v6.0)</option>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="data_manager_json" name="out_file" />
    </outputs>
    <tests>
    <test expect_num_outputs="1">
        <param name="test_data_manager_v5" value="--test"/>
        <param name="version" value="5.0.7"/>
        <param name="database_type" value="mgnify_v5_lsu"/>
        <output name="out_file">
            <assert_contents>
                <has_text text="mgnify_v5_lsu"/>
                <has_text text="5.0.7"/>
            </assert_contents>
        </output>
    </test>
    </tests>
    <help>
    Downloads preformatted DBs form MGnify that can be used for mapseq. 
    The download paths were taken from: https://github.com/EBI-Metagenomics/pipeline-v5/
    </help>
    <expand macro="citations" />
    <expand macro="creator" />
</tool>