comparison data_manager/kraken2_build_database.xml @ 13:e9ee4d074d5d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bb6d9b53b197610c5dbbb40c8ab590761755d91a

12:90b4d4f0a3a4

<?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@">3</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="7" label="Minimizer spaces" />

#else if $database_type.database_type == "standard_prebuilt"
    --prebuilt-db '$database_type.prebuild.prebuilt_db'
    --prebuilt-date '$database_type.prebuild.prebuilt_date'
#else if $database_type.database_type == "minikraken"
    --minikraken2-version '$database_type.minikraken2_version'
#else if $database_type.database_type == "special"
    --threads \${GALAXY_SLOTS:-1}
    --special-database-type '$database_type.special_database_type'
    --kmer-len $database_type.kmer_len
    --minimizer-len $database_type.minimizer_len

        <conditional name="database_type">
            <param name="database_type" type="select" multiple="false" label="Database Type">
                <option value="standard_local_build">Standard, Local Build</option>
                <option value="standard_prebuilt">Pre-Built Refseq indexes</option>
                <option value="minikraken">MiniKraken</option>
                <option value="special">Special</option>
                <option value="custom">Custom</option>
            </param>
            <when value="standard_local_build">
                <expand macro="common_params" />

                            <expand macro="pluspf_08gb"/>
                            <expand macro="pluspf_16gb"/>
                            <expand macro="pluspfp_08gb"/>
                            <expand macro="pluspfp_16gb"/>
                        </param>
                    </when>
                </conditional>
            </when>
            <when value="minikraken">
                <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download">

13:e9ee4d074d5d

<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@">4</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="7" label="Minimizer spaces" />

#else if $database_type.database_type == "standard_prebuilt"
    --prebuilt-db '$database_type.prebuild.prebuilt_db'
    --prebuilt-date '$database_type.prebuild.prebuilt_date'
#else if $database_type.database_type == "minikraken"
    --minikraken2-version '$database_type.minikraken2_version'
#else if $database_type.database_type == "special_prebuilt"
    --prebuilt-db '$database_type.special_prebuild.prebuilt_db'
    --prebuilt-date '$database_type.special_prebuild.prebuilt_date'
#else if $database_type.database_type == "special"
    --threads \${GALAXY_SLOTS:-1}
    --special-database-type '$database_type.special_database_type'
    --kmer-len $database_type.kmer_len
    --minimizer-len $database_type.minimizer_len

        <conditional name="database_type">
            <param name="database_type" type="select" multiple="false" label="Database Type">
                <option value="standard_local_build">Standard, Local Build</option>
                <option value="standard_prebuilt">Pre-Built Refseq indexes</option>
                <option value="minikraken">MiniKraken</option>
                <option value="special_prebuilt">Special Pre-Built indexes</option>
                <option value="special">Special</option>
                <option value="custom">Custom</option>
            </param>
            <when value="standard_local_build">
                <expand macro="common_params" />

                            <expand macro="pluspf_08gb"/>
                            <expand macro="pluspf_16gb"/>
                            <expand macro="pluspfp_08gb"/>
                            <expand macro="pluspfp_16gb"/>
                        </param>
                    </when>
                </conditional>
            </when>
            <when value="special_prebuilt">
                <conditional name="special_prebuild">
                    <param name="special_prebuilt_db" type="select" multiple="false" label="Select pre-built database to download">
                        <option value="eupathdb48_20230407">EuPathDB-46 (April 7, 2023)</option>
                        <option value="eupathdb48_20201113">EuPathDB-46 (November 13, 2020)</option>
                    </param>
                    <when value="eupathdb48_20230407">
                        <param name="prebuilt_db" type="hidden" value="eupathdb48"/>
                        <param name="prebuilt_date" type="hidden" value="2023-04-07"/>
                    </when>
                    <when value="eupathdb48_20201113">
                        <param name="prebuilt_db" type="hidden" value="eupathdb48"/>
                        <param name="prebuilt_date" type="hidden" value="2020-11-13"/>
                    </when>
                </conditional>
            </when>
            <when value="minikraken">
                <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download">