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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 08:18:43 +0000
parents 53c1f0899df0
children
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53c1f0899df0 "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"?>
53c1f0899df0 "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@">
53c1f0899df0 "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>
1
70e427b76f68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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4 <xrefs>
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5 <xref type="bio.tools">rapidnj</xref>
70e427b76f68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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6 </xrefs>
0
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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7 <macros>
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8 <token name="@VERSION@">2.3.2</token>
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9 </macros>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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10 <requirements>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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11 <requirement type="package" version="v@VERSION@">rapidnj</requirement>
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12 </requirements>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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13 <command detect_errors="exit_code"><![CDATA[
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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14 #if $alignments.is_of_type('fasta'):
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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15 #set $input_format = 'fa'
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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16 #else if $alignments.is_of_type('stockholm'):
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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17 #set $input_format = 'sth'
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18 #else:
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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19 #set $input_format = 'pd'
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20 #end if
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21 ln -s '$alignments' input_file.$input_format &&
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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22 rapidnj '$alignments'
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23 --input-format $input_format
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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24 --output-format $output_format
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25 --evolution-model $evolution_model
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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26 --cores \${GALAXY_SLOTS:-1}
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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27 #if $bootstrap:
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28 --bootstrap $bootstrap
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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29 #end if
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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30 --alignment-type $alignment_type
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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31 $no_negative_length
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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32 > '$distances'
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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33 ]]>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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34 </command>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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35 <inputs>
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36 <param name="alignments" type="data" format="phylip,fasta,stockholm" label="Input to construct or reconstruct trees" />
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37 <param argument="--output-format" name="output_format" type="select" label="Output format">
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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38 <option value="t">Phylogenetic tree in newick format</option>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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39 <option value="m">Distance matrix</option>
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40 </param>
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41 <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.">
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42 <option value="kim">Kimura</option>
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43 <option value="jc">Jukes-Cantor</option>
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44 </param>
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45 <param argument="--bootstrap" type="integer" optional="true" label="Samples to use for computing bootstrap" help="The output tree will be annotated with bootstrap values" />
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46 <param argument="--alignment-type" name="alignment_type" type="select" label="Input alignment type">
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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47 <option value="p">Protein</option>
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48 <option value="d">DNA</option>
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49 </param>
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50 <param argument="--no-negative-length" name="no_negative_length" type="boolean" truevalue="--no-negative-length" falsevalue="" label="Adjust for negative branch lengths." />
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51 </inputs>
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52 <outputs>
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53 <data name="distances" format="nhx" label="${tool.name} on ${on_string}: Calculated distances">
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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54 <change_format>
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55 <when input="output_format" value="m" format="tabular" />
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56 </change_format>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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57 </data>
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58 </outputs>
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59 <tests>
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60 <test>
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61 <param name="alignments" value="rapidnj-in1.fa" />
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62 <param name="output_format" value="t" />
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63 <output name="distances" ftype="nhx" value="rapidnj-out1.nhx" />
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64 </test>
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65 <test>
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66 <param name="alignments" value="rapidnj-in2.fa" />
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67 <param name="output_format" value="t" />
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68 <output name="distances" ftype="nhx" value="rapidnj-out2.nhx" />
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69 </test>
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70 </tests>
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71 <help><![CDATA[
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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72 ============
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73 RapidNJ
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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74 ============
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75
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
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76 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.
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77 ]]>
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78 </help>
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79 <citations>
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80 <citation type="doi">doi:10.1007/978-3-540-87361-7_10</citation>
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81 </citations>
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82 </tool>