view rapidnj.xml @ 0:0c762bc76a1a draft default tip

Uploaded

<tool id="rapidnj" name="RapidNJ" version="2.3.0">
    <description>phylogeny reconstruction</description>
    <requirements>
        <requirement type="package" version="2.3.0">rapidnj</requirement>
    </requirements>
    <command>rapidnj
  #if int($bootstrap) > 0:
    --bootstrap $bootstrap
  #end if
    $neg_branch
    -t $aln_type
    -i fa
    -o t
    -x "${output}"
    -c \${GALAXY_SLOTS:-1}
    "${input}"
    </command>
    <inputs>
        <param format="fasta" help="Input isn't sanitised for alignment" label="Source FASTA Alignment" name="input" type="data" />
        <param label="Alignment Type" name="aln_type" type="select">
            <option value="d">DNA</option>
            <option value="p">Protein</option>
        </param>
        <param label="Number of bootstrap samples" min="0" name="bootstrap" type="integer" value="0" />
        <param checked="false" falsevalue="" label="Adjust for negative branch lengths" name="neg_branch" truevalue="-n" type="boolean" />
    </inputs>
    <outputs>
        <data format="nhx" name="output" type="data" />
    </outputs>
    <stdio>
        <regex match="ERROR"
               source="both"
               level="fatal"
               description="Unknown error, check tool output" />
    </stdio>
    <help>
RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining.
http://birc.au.dk/Software/RapidNJ/
  </help>
    <citations>
        <citation type="doi">10.1007/978-3-540-87361-7_10</citation>
    </citations>
</tool>