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1 <tool id="rapidnj" name="RapidNJ" version="2.3.0">
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2 <description>phylogeny reconstruction</description>
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3 <requirements>
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4 <requirement type="package" version="2.3.0">rapidnj</requirement>
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5 </requirements>
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6 <command>rapidnj
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7 #if int($bootstrap) > 0:
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8 --bootstrap $bootstrap
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9 #end if
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10 $neg_branch
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11 -t $aln_type
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12 -i fa
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13 -o t
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14 -x "${output}"
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15 -c \${GALAXY_SLOTS:-1}
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16 "${input}"
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17 </command>
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18 <inputs>
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19 <param format="fasta" help="Input isn't sanitised for alignment" label="Source FASTA Alignment" name="input" type="data" />
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20 <param label="Alignment Type" name="aln_type" type="select">
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21 <option value="d">DNA</option>
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22 <option value="p">Protein</option>
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23 </param>
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24 <param label="Number of bootstrap samples" min="0" name="bootstrap" type="integer" value="0" />
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25 <param checked="false" falsevalue="" label="Adjust for negative branch lengths" name="neg_branch" truevalue="-n" type="boolean" />
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26 </inputs>
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27 <outputs>
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28 <data format="nhx" name="output" type="data" />
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29 </outputs>
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30 <stdio>
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31 <regex match="ERROR"
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32 source="both"
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33 level="fatal"
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34 description="Unknown error, check tool output" />
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35 </stdio>
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36 <help>
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37 RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining.
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38 http://birc.au.dk/Software/RapidNJ/
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39 </help>
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40 <citations>
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41 <citation type="doi">10.1007/978-3-540-87361-7_10</citation>
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42 </citations>
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43 </tool>
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