view data_manager/kraken2_build_database.xml @ 5:2f27f3b86827 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"

<?xml version="1.0"?>
<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@" profile="18.09">
    <macros>
        <token name="@TOOL_VERSION@">2.1.1</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>
    </macros>
    <description>database builder</description>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
        <requirement type="package" version="3.7">python</requirement>
    </requirements>
    <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
    <command detect_errors="exit_code">
    <![CDATA[
        python '$__tool_directory__/kraken2_build_database.py'
          '${out_file}'
          --database-type ${database_type.database_type}
          #if $database_type.database_type == "minikraken"
            --minikraken2-version ${database_type.minikraken2_version}
          #else if $database_type.database_type == "standard_prebuilt"
            --standard-prebuilt-size ${database_type.standard_prebuilt_size}
            #if $database_type.prebuilt_date_custom != ""
              --prebuilt-date ${database_type.prebuilt_date_custom}
            #else
              --prebuilt-date ${database_type.prebuilt_date}
            #end if
          #else if $database_type.database_type == "standard_local_build"
            --threads \${GALAXY_SLOTS:-1}
            --kmer-len ${database_type.kmer_len}
            --minimizer-len ${database_type.minimizer_len}
            --minimizer-spaces ${database_type.minimizer_spaces}
            --load-factor ${database_type.load_factor}
            ${database_type.clean}
          #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}
            --minimizer-spaces ${database_type.minimizer_spaces}
            --load-factor ${database_type.load_factor}
            ${database_type.clean}
          #else if $database_type.database_type == "custom"
            --threads \${GALAXY_SLOTS:-1}
            ${database_type.skip_maps}
            --custom-fasta ${database_type.custom_fasta}
            --custom-database-name ${database_type.custom_database_name}
            --kmer-len ${database_type.kmer_len}
            --minimizer-len ${database_type.minimizer_len}
            --minimizer-spaces ${database_type.minimizer_spaces}
            --load-factor ${database_type.load_factor}
            ${database_type.clean}
          #end if
    ]]>
    </command>
    <inputs>
        <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">Standard, Pre-Built</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" />
            </when>
            <when value="standard_prebuilt">
                <param name="standard_prebuilt_size" type="select" multiple="false" label="Select size of prebuilt database to download">
                    <option value="full">Standard-Full (~50 GB)</option>
                    <option value="16">Standard-16 (~16 GB)</option>
                    <option value="8">Standard-8 (~8 GB)</option>
                </param>
                <param name="prebuilt_date" type="select" multiple="false" optional="true" label="Select database build date">
                    <option value="2021-05-17">May 17, 2021</option>
                    <option value="2020-12-02">December 2, 2020</option>
                </param>
                <param name="prebuilt_date_custom" type="text" label="Custom date (YYYY-MM-DD)" help="Any text here will overwrite the selected date above." />
            </when>
            <when value="minikraken">
                <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download">
                    <option value="v2">Version 2</option>
                    <option value="v1">Version 1</option>
                </param>
            </when>
            <when value="special">
                <param name="special_database_type" type="select" multiple="false" label="Select database to build">
                    <option value="greengenes">Greengenes</option>
                    <option value="silva">Silva</option>
                    <option value="rdp">RDP</option>
                </param>
                <expand macro="common_params" />
            </when>
            <when value="custom">
                <param name="custom_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" />
                <param name="custom_database_name" type="text" label="Name for this database" />
                <param name="skip_maps" type="boolean" truevalue="--skip-maps" falsevalue="" label="Skip downloading accession number to taxid maps during taxonomy download." /> 
                <expand macro="common_params" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
        <test>
            <param name="database_type" value="custom" />
            <param name="custom_fasta" value="adapter.fa" />
            <param name="custom_database_name" value="database" />
            <param name="skip_maps" value="true" />
            <output name="out_file" value="kraken2_custom_data_manager.json" />
        </test>
    </tests>
    <help>
    </help>
    <citations>
        <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
    </citations>
</tool>