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1 <?xml version="1.0" ?>
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2 <tool id="qiime_phylogeny_robinson-foulds" name="qiime phylogeny robinson-foulds"
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3 version="2020.8">
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4 <description>Calculate Robinson-Foulds distance between phylogenetic trees.</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime phylogeny robinson-foulds
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10
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11 --i-trees=$itrees
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12
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13 #if str($plabels):
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14 --p-labels=$plabels
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15 #end if
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16 #if str($pmissingtips) != 'None':
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17 --p-missing-tips=$pmissingtips
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18 #end if
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19
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20 --o-distance-matrix=odistancematrix
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21
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22 #if str($examples) != 'None':
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23 --examples=$examples
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24 #end if
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25
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26 ;
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27 cp odistancematrix.qza $odistancematrix
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28
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29 ]]></command>
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30 <inputs>
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31 <param format="qza,no_unzip.zip" label="--i-trees: ARTIFACTS... List[Phylogeny[Rooted | Unrooted]] Phylogenetic trees to compare with Robinson-Foulds. Rooting information and branch lengths are ignored by this metric. [required]" name="itrees" optional="False" type="data" />
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32 <param label="--p-labels: TEXT... Labels to use for the tree names in the distance List[Str] matrix. If ommited, labels will be \'tree_n\' where \'n\' ranges from 1..N. The number of labels must match the number of trees. [optional]" name="plabels" optional="False" type="text" />
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33 <param label="--p-missing-tips: " name="pmissingtips" optional="True" type="select">
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34 <option selected="True" value="None">Selection is Optional</option>
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35 <option value="error">error</option>
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36 <option value="intersect-all">intersect-all</option>
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37 </param>
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38 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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39
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40 </inputs>
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41
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42 <outputs>
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43 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
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44
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45 </outputs>
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46
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47 <help><![CDATA[
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48 Calculate Robinson-Foulds distance between phylogenetic trees.
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49 ###############################################################
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50
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51 Calculate the Robinson-Foulds symmetric difference metric between two or
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52 more phylogenetic trees.
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53
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54 Parameters
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55 ----------
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56 trees : List[Phylogeny[Rooted | Unrooted]]
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57 Phylogenetic trees to compare with Robinson-Foulds. Rooting information
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58 and branch lengths are ignored by this metric.
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59 labels : List[Str], optional
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60 Labels to use for the tree names in the distance matrix. If ommited,
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61 labels will be "tree_n" where "n" ranges from 1..N. The number of
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62 labels must match the number of trees.
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63 missing_tips : Str % Choices('error', 'intersect-all'), optional
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64 How to handle tips that are not shared between trees. "error" will
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65 raise an error if the set of tips is not identical between all input
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66 trees. "intersect-all" will remove tips that are not shared between all
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67 trees before computing distances beteen trees.
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68
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69 Returns
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70 -------
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71 distance_matrix : DistanceMatrix
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72 The distances between trees as a symmetric matrix.
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73 ]]></help>
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74 <macros>
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75 <import>qiime_citation.xml</import>
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76 </macros>
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77 <expand macro="qiime_citation"/>
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78 </tool> |
