comparison data_manager/kraken2_build_database.xml @ 12:90b4d4f0a3a4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 9835da32741d05d129a1a44835f66e32713770ad

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="pluspfp_16gb">
            <option value="pluspfp_16gb">PlusPFP-16 (PlusPFP with DB capped at 16 GB; ~15 GB)</option>
        </xml>
    </macros>
    <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.clean
#else if $database_type.database_type == "custom"
    --threads \${GALAXY_SLOTS:-1}
    --custom-fasta '$database_type.custom_fasta'
    --custom-database-name '$database_type.custom_database_name'
    $database_type.skip_maps
    --kmer-len $database_type.kmer_len
    --minimizer-len $database_type.minimizer_len
    --minimizer-spaces $database_type.minimizer_spaces
    --load-factor $database_type.load_factor

                <expand macro="common_params" />
            </when>
            <when value="custom">
                <param name="custom_fasta" type="data" format="fasta" multiple="False" 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>

        <test expect_num_outputs="1">
            <conditional name="database_type">
                <param name="database_type" value="custom" />
                <param name="custom_fasta" value="adapter.fa" />
                <param name="custom_database_name" value="custom_database" />
                <param name="skip_maps" value="true" />
                <param name="kmer_len" value="35" />
                <param name="minimizer_spaces" value="6"/>
                <param name="load_factor" value="0.7" />
                <param name="clean" value="true"/>
            </conditional>
            <output name="out_file">
                <assert_contents>
                    <has_text text="kraken2_databases"/>
                    <has_text text="path"/>
                    <has_text text="custom_database"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <conditional name="database_type">

    </tests>
    <help><![CDATA[
Build Kraken2 databases or download `prebuilt Kraken2 RefSeq indexes <https://benlangmead.github.io/aws-indexes/k2>`__
    ]]></help>
    <citations>
        <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
    </citations>
</tool>

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" />
            <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="pluspfp_16gb">
            <option value="pluspfp_16gb">PlusPFP-16 (PlusPFP with DB capped at 16 GB; ~15 GB)</option>
        </xml>
    </macros>
    <xrefs>
        <xref type="bio.tools">kraken2</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
        <requirement type="package" version="3.13">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.clean
#else if $database_type.database_type == "custom"
    --threads \${GALAXY_SLOTS:-1}
    --custom-fasta '$database_type.custom_fasta'
    --custom-database-name '$database_type.custom_database_name'
    --custom-source-info '$database_type.custom_source_info'
    $database_type.skip_maps
    --kmer-len $database_type.kmer_len
    --minimizer-len $database_type.minimizer_len
    --minimizer-spaces $database_type.minimizer_spaces
    --load-factor $database_type.load_factor

                <expand macro="common_params" />
            </when>
            <when value="custom">
                <param name="custom_fasta" type="data" format="fasta" multiple="False" label="Select history item" />
                <param name="custom_database_name" type="text" label="Name for this database" />
                <param name="custom_source_info" type="text" label="Database source info" help="Concise description of how this build has been sourced. This description will be appended (in parentheses) to the user-facing name of the build. Example: https://doi.org/10.5281/zenodo.8339822, from v1 assembly_summary.txt sequences" />
                <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>

        <test expect_num_outputs="1">
            <conditional name="database_type">
                <param name="database_type" value="custom" />
                <param name="custom_fasta" value="adapter.fa" />
                <param name="custom_database_name" value="custom_database" />
                <param name="custom_source_info" value="from adapter.fa test data" />
                <param name="skip_maps" value="true" />
                <param name="kmer_len" value="35" />
                <param name="minimizer_spaces" value="6"/>
                <param name="load_factor" value="0.7" />
                <param name="clean" value="true"/>
            </conditional>
            <output name="out_file">
                <assert_contents>
                    <has_text text="kraken2_databases"/>
                    <has_text text="path"/>
                    <has_text text="custom_database (from adapter.fa test data, kmer-len=35, minimizer-len=31, minimizer-spaces=6, load-factor=0.7)"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <conditional name="database_type">

    </tests>
    <help><![CDATA[
Build Kraken2 databases or download `prebuilt Kraken2 RefSeq indexes <https://benlangmead.github.io/aws-indexes/k2>`__
    ]]></help>
    <citations>
        <citation type="doi">10.1186/s13059-019-1891-0</citation>
    </citations>
</tool>