Mercurial > repos > iuc > rapidnj

annotate rapidnj.xml @ 0:9f4a66e22580 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
author iuc
date Mon, 11 May 2020 17:03:25 -0400
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9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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1 <?xml version="1.0"?>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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2 <tool id="rapidnj" name="Join neighbors" version="@VERSION@">
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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3 <description>rapidly with RapidNJ</description>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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4 <macros>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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5 <token name="@VERSION@">2.3.2</token>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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6 </macros>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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7 <requirements>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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8 <requirement type="package" version="v@VERSION@">rapidnj</requirement>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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9 </requirements>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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10 <command detect_errors="exit_code"><![CDATA[
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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11 #if $alignments.is_of_type('fasta'):
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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12 #set $input_format = 'fa'
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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13 #else if $alignments.is_of_type('stockholm'):
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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14 #set $input_format = 'sth'
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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15 #else:
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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16 #set $input_format = 'pd'
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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17 #end if
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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18 ln -s '$alignments' input_file.$input_format &&
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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19 rapidnj '$alignments'
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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20 --input-format $input_format
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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21 --output-format $output_format
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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22 --evolution-model $evolution_model
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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23 --cores \${GALAXY_SLOTS:-1}
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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24 #if $bootstrap:
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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25 --bootstrap $bootstrap
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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26 #end if
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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27 --alignment-type $alignment_type
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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28 $no_negative_length
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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29 > '$distances'
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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30 ]]>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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31 </command>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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32 <inputs>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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33 <param name="alignments" type="data" format="phylip,fasta,stockholm" label="Input to construct or reconstruct trees" />
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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34 <param argument="--output-format" name="output_format" type="select" label="Output format">
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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35 <option value="t">Phylogenetic tree in newick format</option>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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36 <option value="m">Distance matrix</option>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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37 </param>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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38 <param argument="--evolution-model" name="evolution_model" type="select" label="Evolution model" help="Specifies which sequence evolution method to use when computing distance estimates from multiple alignments, using Kimura's model by default.">
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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39 <option value="kim">Kimura</option>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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40 <option value="jc">Jukes-Cantor</option>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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41 </param>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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42 <param argument="--bootstrap" type="integer" optional="true" label="Samples to use for computing bootstrap" help="The output tree will be annotated with bootstrap values" />
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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43 <param argument="--alignment-type" name="alignment_type" type="select" label="Input alignment type">
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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44 <option value="p">Protein</option>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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45 <option value="d">DNA</option>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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46 </param>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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47 <param argument="--no-negative-length" name="no_negative_length" type="boolean" truevalue="--no-negative-length" falsevalue="" label="Adjust for negative branch lengths." />
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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48 </inputs>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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49 <outputs>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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50 <data name="distances" format="nhx" label="${tool.name} on ${on_string}: Calculated distances">
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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51 <change_format>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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52 <when input="output_format" value="m" format="tabular" />
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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53 </change_format>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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54 </data>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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55 </outputs>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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56 <tests>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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57 <test>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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58 <param name="alignments" value="rapidnj-in1.fa" />
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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59 <param name="output_format" value="t" />
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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60 <output name="distances" ftype="nhx" value="rapidnj-out1.nhx" />
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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61 </test>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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62 <test>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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63 <param name="alignments" value="rapidnj-in2.fa" />
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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64 <param name="output_format" value="t" />
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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65 <output name="distances" ftype="nhx" value="rapidnj-out2.nhx" />
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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66 </test>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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67 </tests>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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68 <help><![CDATA[
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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69 ============
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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70 RapidNJ
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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71 ============
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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72
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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73 Especially useful for large datasets where maximum-likelihood based phylogenetic inference becomes intractable, RapidNJ reduces the computing time of canonical neighbour-joining for phylogenetic tree inference. RapidNJ accepts either matrices in phylip format or alignments in stockholm or FASTA format.
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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74 ]]>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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75 </help>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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76 <citations>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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77 <citation type="doi">doi:10.1007/978-3-540-87361-7_10</citation>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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78 </citations>
9f4a66e22580 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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79 </tool>