comparison gtdbtk_classify_wf.xml @ 6:a09c8c901603 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk commit 85683b4edaf9ec44550ff0de861023f794bf35f2

5:a68b985913ab

#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">
            <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"/>

        </test>
        -->
        <!-- GTDB-Tk databases are far too large to test currently -->
        <test expect_failure="true">
            <param name="input" value="genome_1.fna.gz" ftype="fasta.gz"/>
            <param name="gtdbtk_db" value="gtdbtk202"/>
            <assert_stderr>
                <has_text text="Fatal error: Exit code 1"/>
            </assert_stderr>
        </test>
    </tests>

6:a09c8c901603

#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="^v2(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"/>

        </test>
        -->
        <!-- GTDB-Tk databases are far too large to test currently -->
        <test expect_failure="true">
            <param name="input" value="genome_1.fna.gz" ftype="fasta.gz"/>
            <param name="gtdbtk_db" value="gtdbtk214"/>
            <assert_stderr>
                <has_text text="Fatal error: Exit code 1"/>
            </assert_stderr>
        </test>
    </tests>