comparison macros.xml @ 9:f921014aba5a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3"

8:54f751e413f4

<macros>
    <token name="@VERSION@">2.0.8</token>

    <xml name="requirements">
        <requirements>
          <requirement type="package" version="@VERSION@">diamond</requirement>
        </requirements>
    </xml>

    <xml name="stdio">
        <stdio>

                    <option value="full_qqual">Query quality values</option>
                    <option value="qstrand">Query strand</option>
                    <option value="cigar">Cigar</option>
                    <yield/>
                </param>
            </when>
            <when value="100">
                <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/>
                <param argument="--sallseqid" type="boolean" truevalue="--sallseqid" falsevalue="" checked="true" label="Include all subject ids in DAA file?" help=""/>
            </when>

            </when>
        </conditional>
    </xml>

    <xml name="block_size_low_sens">
        <param name="block_size" argument="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time" help="" />
    </xml>

    <xml name="block_size_hi_sens">
        <param name="block_size" argument="--block-size" type="float" value="0.4" label="Block size in billions of sequence letters to be processed at a time" help="" />
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/nmeth.3176</citation>

            --outfmt '5'
            --out '$blast_xml'
        #else if $output.outfmt == "6"
            --outfmt '6' #echo ' '.join(str($output.fields).split(','))
            --out '$blast_tabular'
        #else if $output.outfmt == "100"
            --outfmt '100'
            --out output.daa
        #else if $output.outfmt == "101"
            --outfmt '101'
            --out '$sam_output'
        #else if $output.outfmt == "102"
            --outfmt '102'
            --out '$tax_output'
        #end if

9:f921014aba5a

<macros>
    <token name="@TOOL_VERSION@">2.0.8</token>

    <xml name="requirements">
        <requirements>
          <requirement type="package" version="@TOOL_VERSION@">diamond</requirement>
        </requirements>
    </xml>

    <xml name="stdio">
        <stdio>

                    <option value="full_qqual">Query quality values</option>
                    <option value="qstrand">Query strand</option>
                    <option value="cigar">Cigar</option>
                    <yield/>
                </param>
                <param argument="--unal" type="boolean" label="Report unaligned queries" truevalue="1" falsevalue="0" checked="false"/>
            </when>
            <when value="100">
                <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/>
                <param argument="--sallseqid" type="boolean" truevalue="--sallseqid" falsevalue="" checked="true" label="Include all subject ids in DAA file?" help=""/>
            </when>

            </when>
        </conditional>
    </xml>

    <xml name="block_size_low_sens">
        <param argument="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time" help="" />
    </xml>

    <xml name="block_size_hi_sens">
        <param argument="--block-size" type="float" value="0.4" label="Block size in billions of sequence letters to be processed at a time" help="" />
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/nmeth.3176</citation>

            --outfmt '5'
            --out '$blast_xml'
        #else if $output.outfmt == "6"
            --outfmt '6' #echo ' '.join(str($output.fields).split(','))
            --out '$blast_tabular'
            --unal $output.unal
        #else if $output.outfmt == "100"
            --outfmt '100'
            $output.salltitles
            $output.sallseqid
            --out output.daa
        #else if $output.outfmt == "101"
            --outfmt '101'
            $output.salltitles
            $output.sallseqid
            --out '$sam_output'
        #else if $output.outfmt == "102"
            --outfmt '102'
            --out '$tax_output'
        #end if