comparison data_manager/kraken2_build_database.xml @ 8:e4b4837f06f5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 09b56ef3e09ad6c5923c88616fea5cbd77d87616

7:ed1518ce2237

<?xml version="1.0"?>
<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <macros>
        <token name="@TOOL_VERSION@">2.1.2</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@PROFILE@">21.01</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" />

        </xml>
        <xml name="pluspfp_16gb">
            <option value="pluspfp_16gb">PlusPFP-16 (PlusPFP with DB capped at 16 GB; ~15 GB)</option>
        </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>

                <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" truevalue="--clean"/>
            </conditional>
            <output name="out_file">
                <assert_contents>
                    <has_text text="kraken2_databases"/>
                    <has_text text="path"/>

8:e4b4837f06f5

<?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@">2.1.2</token>
        <token name="@VERSION_SUFFIX@">1</token>
        <token name="@PROFILE@">21.01</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" />

        </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>

                <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"/>