comparison data_manager/kraken2_build_database.xml @ 11:1e34d2e3d285 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545

10:13851aefa67a

<?xml version="1.0"?>
<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>database builder</description>
    <macros>
        <token name="@TOOL_VERSION@">2.1.3</token>
        <token name="@VERSION_SUFFIX@">1</token>
        <token name="@PROFILE@">22.01</token>
        <xml name="common_params">
            <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" />
            <param name="minimizer_len" type="integer" value="31" label="Minimizer length" />
            <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" />
            <param name="load_factor" type="float" value="0.7" min="0" max="1" label="Load factor" help="Proportion of the hash table to be populated" />
            <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" />
        </xml>
        <xml name="viral">
            <option value="viral">Viral (viral; ~50 GB)</option>
        </xml>
        <xml name="minusb">
            <option value="minusb">MinusB (archaea, viral, plasmid, human, UniVec_Core; ~8 GB)</option>
        </xml>
        <xml name="standard">

                <expand macro="common_params" />
            </when>
            <when value="standard_prebuilt">
                <conditional name="prebuild">
                    <param name="prebuilt_date" type="select" label="Select index build date">
                        <option value="2024-01-12">January 12, 2024</option>
                        <option value="2023-06-05">June 5, 2023</option>
                        <option value="2022-06-07">June 7, 2022</option>
                        <option value="2021-05-17">May 17, 2021</option>
                        <option value="2021-01-27">January 27, 2021</option>
                        <option value="2020-12-02">December 2, 2020</option>
                        <option value="2020-09-19">September 19, 2020</option>
                    </param>
                    <when value="2024-01-12">
                        <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
                            <expand macro="viral"/>
                            <expand macro="minusb"/>
                            <expand macro="standard"/>

                    <has_text text="Version"/>
                    <has_text text="Downloaded"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Build Kraken2 databases or download `prebuilt Kraken2 RefSeq indexes <https://benlangmead.github.io/aws-indexes/k2>`__
    ]]></help>
    <citations>

11:1e34d2e3d285

<?xml version="1.0"?>
<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>database builder</description>
    <macros>
        <token name="@TOOL_VERSION@">2.1.3</token>
        <token name="@VERSION_SUFFIX@">2</token>
        <token name="@PROFILE@">22.01</token>
        <xml name="common_params">
            <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" />
            <param name="minimizer_len" type="integer" value="31" label="Minimizer length" />
            <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" />
            <param name="load_factor" type="float" value="0.7" min="0" max="1" label="Load factor" help="Proportion of the hash table to be populated" />
            <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" />
        </xml>
        <xml name="viral">
            <option value="viral">Viral (viral; ~0.5 GB)</option>
        </xml>
        <xml name="minusb">
            <option value="minusb">MinusB (archaea, viral, plasmid, human, UniVec_Core; ~8 GB)</option>
        </xml>
        <xml name="standard">

                <expand macro="common_params" />
            </when>
            <when value="standard_prebuilt">
                <conditional name="prebuild">
                    <param name="prebuilt_date" type="select" label="Select index build date">
                        <option value="2024-06-05">June 5, 2024</option>
                        <option value="2024-01-12">January 12, 2024</option>
                        <option value="2023-06-05">June 5, 2023</option>
                        <option value="2022-06-07">June 7, 2022</option>
                        <option value="2021-05-17">May 17, 2021</option>
                        <option value="2021-01-27">January 27, 2021</option>
                        <option value="2020-12-02">December 2, 2020</option>
                        <option value="2020-09-19">September 19, 2020</option>
                    </param>
                    <when value="2024-06-05">
                        <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
                            <expand macro="viral"/>
                            <expand macro="minusb"/>
                            <expand macro="standard"/>
                            <expand macro="standard_08gb"/>
                            <expand macro="standard_16gb"/>
                            <expand macro="pluspf"/>
                            <expand macro="pluspf_08gb"/>
                            <expand macro="pluspf_16gb"/>
                            <expand macro="pluspfp"/>
                            <expand macro="pluspfp_08gb"/>
                            <expand macro="pluspfp_16gb"/>
                        </param>
                    </when>
                    <when value="2024-01-12">
                        <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
                            <expand macro="viral"/>
                            <expand macro="minusb"/>
                            <expand macro="standard"/>

                    <has_text text="Version"/>
                    <has_text text="Downloaded"/>
                </assert_contents>
            </output>
        </test>
        <!-- test with first 2024 version -->
        <test>
            <conditional name="database_type">
                <param name="database_type" value="standard_prebuilt" />
                <conditional name="prebuild">
                    <param name="prebuilt_date" value="2024-06-05"/>
                    <param name="prebuilt_db" value="viral"/>
                </conditional>
            </conditional>
            <output name="out_file">
                <assert_contents>
                    <has_text text="kraken2_databases"/>
                    <has_text text="path"/>
                    <has_text text="Viral"/>
                    <has_text text="_standard_prebuilt_viral_2024-06-05"/>
                    <has_text text="Version"/>
                    <has_text text="Downloaded"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Build Kraken2 databases or download `prebuilt Kraken2 RefSeq indexes <https://benlangmead.github.io/aws-indexes/k2>`__
    ]]></help>
    <citations>