comparison data_manager/kraken2_build_database.xml @ 4:0eebe086fd58 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"

3:19b6a2f0dbe2

<?xml version="1.0"?>
<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="2.0.8_beta+galaxy2" profile="18.09">
    <macros>
        <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="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" />
        </xml>
    </macros>
    <description>database builder</description>
    <requirements>
        <requirement type="package" version="2.0.8_beta">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[

          #else if $database_type.database_type == "standard"
            --threads \${GALAXY_SLOTS:-1}
            --kmer-len ${database_type.kmer_len}
            --minimizer-len ${database_type.minimizer_len}
            --minimizer-spaces ${database_type.minimizer_spaces}
            ${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}
            ${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}
            ${database_type.clean}
          #end if
    ]]>
    </command>
    <inputs>

4:0eebe086fd58

<?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[

          #else if $database_type.database_type == "standard"
            --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>