view macros.xml @ 1:220e2f7ff8bb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 2564b0ca982636c6c6f221d0c5072f52d39e6751

<macros>
    <token name="@CHEW_VERSION@">3.3.3</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@PROFILE@">22.05</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@CHEW_VERSION@">chewbbaca</requirement>
            <requirement type="package" version="2.15.0">blast</requirement>
            <requirement type="package" version="3.0">zip</requirement>
            <requirement type="package" version="2.1.11">fasttree</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1099/mgen.0.000166</citation>
        </citations>
    </xml>
    <xml name="species_id">
        <option value="1">Streptococcus pyogenes</option>
        <option value="2">Acinetobacter baumannii</option>
        <option value="3">Arcobacter butzleri</option>
        <option value="4">Campylobacter jejuni</option>
        <option value="5">Escherichia coli</option>
        <option value="6">Listeria monocytogenes</option>
        <option value="7">Yersinia enterocolitica</option>
        <option value="8">Salmonella enterica</option>
        <option value="9">Streptococcus agalactiae</option>
        <option value="10">Brucella melitensis</option>
        <option value="11">Brucella</option>
        <option value="12">Clostridium perfringens</option>
        <option value="13">Clostridium chauvoei</option>
        <option value="14">Bacillus anthracis</option>
        <option value="15">Klebsiella oxytoca</option>
        <option value="16">Clostridium neonatale</option>
    </xml>
    <token name="@COMMON_INPUT@">
        --bsr $blast_score_ratio
        --l $minimum_length
        --t $translation_table
        --st $size_threshold
    </token>
    <xml name="common_param">
        <param argument="--blast_score-ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" /> 
        <param argument="--translation-table" type="integer" min="0" value="11" label="Genetic code used to predict genes and to translate coding sequences"/>
        <param argument="--size-threshold" type="float" min="0" value="0.2" label="CDS size variation threshold"/>
    </xml>
</macros>