comparison gtdbtk_classify_wf.xml @ 9:5c7ba3d85a01 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk commit 0f5d58e0011fcfc9c772ba9392deaed186e045eb

8:b907a3c0434f

    && cat output_dir/gtdbtk.warnings.log output_dir/gtdbtk.log > '$process_log'
#end if
    ]]></command>
    <inputs>
        <param name="input" type="data" format="fasta,fasta.gz" multiple="true" label="Fasta (Genome) files"/>
        <param name="gtdbtk_db" type="select" label="GTDB-Tk database" help="This version of GTDB-Tk required GTDB version R207_v2. Please contact your service administrator if this version is not available to select.">
            <options from_data_table="gtdbtk_database_versioned">
                <filter type="regexp" column="3" value="^2(07|14)$"/>
                <validator type="no_options" message="No locally cached GTDB-Tk database is available"/>
            </options>
        </param>
        <section name="advanced" title="Advanced options">
            <param argument="--min_perc_aa" type="integer" min="0" max="100" value="10" label="Exclude genomes that do not have at least this percentage of AA in the MSA" help="Inclusive bound"/>

9:5c7ba3d85a01

    && cat output_dir/gtdbtk.warnings.log output_dir/gtdbtk.log > '$process_log'
#end if
    ]]></command>
    <inputs>
        <param name="input" type="data" format="fasta,fasta.gz" multiple="true" label="Fasta (Genome) files"/>
        <param name="gtdbtk_db" type="select" label="GTDB-Tk database" help="This version of GTDB-Tk requires GTDB version 207 or 214. Please contact your service administrator if this version is not available to select.">
            <options from_data_table="gtdbtk_database_versioned">
                <filter type="regexp" column="version" value="^2(07|14)$"/>
                <validator type="no_options" message="No locally cached GTDB-Tk database is available"/>
            </options>
        </param>
        <section name="advanced" title="Advanced options">
            <param argument="--min_perc_aa" type="integer" min="0" max="100" value="10" label="Exclude genomes that do not have at least this percentage of AA in the MSA" help="Inclusive bound"/>