comparison gtdbtk_classify_wf.xml @ 1:dbf1798c0dcc draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk commit 1dddd355fe97cb9d6bb37f93b98f3402184b4320

0:c4db8c4de66f

--out_dir output_dir
--cpus \${GALAXY_SLOTS:-4}
--min_perc_aa $advanced.min_perc_aa
$advanced.force
--min_af $advanced.min_af
#if str($advanced.output_process_log) == 'yes':
    && 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">
            <options from_data_table="gtdbtk_database">
                <validator type="no_options" message="No locally cached GTDB-Tk database is available"/>
            </options>
        </param>
        <section name="advanced" title="Advanced options">

1:dbf1798c0dcc

--out_dir output_dir
--cpus \${GALAXY_SLOTS:-4}
--min_perc_aa $advanced.min_perc_aa
$advanced.force
--min_af $advanced.min_af

## Required unless mash_db is available:
--skip_ani_screen

#if str($advanced.output_process_log) == 'yes':
    && cat output_dir/gtdbtk.warnings.log output_dir/gtdbtk.log > '$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">
                <validator type="no_options" message="No locally cached GTDB-Tk database is available"/>
            </options>
        </param>
        <section name="advanced" title="Advanced options">