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author q2d2
date Wed, 30 Oct 2024 19:53:54 +0000
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2024, QIIME 2 development team.
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
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6 -->
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7 <!--
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8 This tool was automatically generated by:
5
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9 q2galaxy (version: 2024.10.0)
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10 for:
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11 qiime2 (version: 2024.10.1)
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12 -->
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13 <tool name="qiime2 phylogeny robinson-foulds" id="qiime2__phylogeny__robinson_foulds" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Calculate Robinson-Foulds distance between phylogenetic trees.</description>
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15 <xrefs>
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16 <xref type="bio.tools">qiime2</xref>
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17 </xrefs>
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18 <requirements>
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19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
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20 </requirements>
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21 <version_command>q2galaxy version phylogeny</version_command>
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22 <command detect_errors="exit_code">q2galaxy run phylogeny robinson_foulds '$inputs'</command>
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23 <configfiles>
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24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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25 </configfiles>
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26 <inputs>
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27 <param name="trees" type="data" format="qza" label="trees: List[Phylogeny[Rooted | Unrooted]]" help="[required] Phylogenetic trees to compare with Robinson-Foulds. Rooting information and branch lengths are ignored by this metric." multiple="true">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="Phylogeny[Unrooted]"/>
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30 <filter type="add_value" value="Phylogeny[Rooted]"/>
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31 </options>
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32 </param>
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33 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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34 <repeat name="labels" help="[optional] Labels to use for the tree names in the distance matrix. If ommited, labels will be &quot;tree_n&quot; where &quot;n&quot; ranges from 1..N. The number of labels must match the number of trees." title="labels: List[Str]">
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35 <param name="element" type="text" label="element: Str" help="[required]">
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36 <sanitizer>
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37 <valid initial="string.printable"/>
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38 </sanitizer>
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39 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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40 </param>
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41 </repeat>
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42 <param name="missing_tips" type="select" label="missing_tips: Str % Choices('error', 'intersect-all')" display="radio">
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43 <option value="error" selected="true">error</option>
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44 <option value="intersect-all">intersect-all</option>
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45 </param>
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46 </section>
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47 </inputs>
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48 <outputs>
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49 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
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50 </outputs>
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51 <tests/>
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52 <help>
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53 QIIME 2: phylogeny robinson-foulds
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54 ==================================
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55 Calculate Robinson-Foulds distance between phylogenetic trees.
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56
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57
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58 Outputs:
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59 --------
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60 :distance_matrix.qza: The distances between trees as a symmetric matrix.
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61
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62 |
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63
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64 Description:
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65 ------------
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66 Calculate the Robinson-Foulds symmetric difference metric between two or more phylogenetic trees.
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67
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68
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69 |
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70
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71 </help>
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72 <citations>
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73 <citation type="bibtex">@article{cite1,
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74 author = {Robinson, David F and Foulds, Leslie R},
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75 journal = {Mathematical biosciences},
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76 number = {1-2},
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77 pages = {131--147},
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78 publisher = {Elsevier},
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79 title = {Comparison of phylogenetic trees},
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80 volume = {53},
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81 year = {1981}
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82 }
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83 </citation>
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84 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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85 </citations>
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86 </tool>