comparison shovill.xml @ 2:f698c7604b3b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 686710a7d313b828f1daed20c4055479727f2d91

1:57d5928f456e

            #else if str($library.lib_type) == "collection"
                --R1 '$library.input1.forward'
                --R2 '$library.input1.reverse'
            #end if
            $trim
            --namefmt "$adv.namefmt"
            --depth '$adv.depth'
            #if $adv.gsize
                --gsize '$adv.gsize'
            #end if
            #if $adv.kmers

        <param name="trim" argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="Trim reads" help="Use Trimmomatic to remove common adaptors first (default: OFF)" />
        <param name="log" type="boolean" label="Output log file?" checked="true" help="Return the Shovill log file as part of the output. Default is on" />
        <section name="adv" title="Advanced options" expanded="False">
            <param name="namefmt" argument="--namefmt" type="text" value="contig%05d" label="Contig name format" help="Format of contig FASTA IDs in 'printf' style (default: 'contig%05d')" >
                <sanitizer>
                    <valid initial="string.printable" />
                </sanitizer>
            </param>
            <param name="depth" argument="--depth" type="integer" value="100" label="Depth" help="Sub-sample --R1/--R2 to this depth. Disable with --depth 0 (default: 100)" />
            <param name="gsize" argument="--gsize" type="text" value="" label="Estimated genome size" help="An estimate of the final genome size, it will autodetect if this is blank. (default: '')" />
            <param name="kmers" argument="--kmers" type="text" value="" label="List of kmer sizes to use" help="List of K-mer sizes to use in SPAdes. Blank is AUTO. default: ''" />

2:f698c7604b3b

            #else if str($library.lib_type) == "collection"
                --R1 '$library.input1.forward'
                --R2 '$library.input1.reverse'
            #end if
            $trim
            --namefmt '$adv.namefmt'
            --depth '$adv.depth'
            #if $adv.gsize
                --gsize '$adv.gsize'
            #end if
            #if $adv.kmers

        <param name="trim" argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="Trim reads" help="Use Trimmomatic to remove common adaptors first (default: OFF)" />
        <param name="log" type="boolean" label="Output log file?" checked="true" help="Return the Shovill log file as part of the output. Default is on" />
        <section name="adv" title="Advanced options" expanded="False">
            <param name="namefmt" argument="--namefmt" type="text" value="contig%05d" label="Contig name format" help="Format of contig FASTA IDs in 'printf' style (default: 'contig%05d')" >
                <sanitizer>
                    <valid initial="string.printable">
                        <remove value="&apos;" />
                    </valid>
                    <mapping initial="none">
                        <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
                    </mapping>
                </sanitizer>
            </param>
            <param name="depth" argument="--depth" type="integer" value="100" label="Depth" help="Sub-sample --R1/--R2 to this depth. Disable with --depth 0 (default: 100)" />
            <param name="gsize" argument="--gsize" type="text" value="" label="Estimated genome size" help="An estimate of the final genome size, it will autodetect if this is blank. (default: '')" />
            <param name="kmers" argument="--kmers" type="text" value="" label="List of kmer sizes to use" help="List of K-mer sizes to use in SPAdes. Blank is AUTO. default: ''" />