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comparison qiime2/qiime_phylogeny_robinson-foulds.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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28:c28331a63dfd 29:3ba9833030c1
1 <?xml version="1.0" ?>
2 <tool id="qiime_phylogeny_robinson-foulds" name="qiime phylogeny robinson-foulds"
3 version="2020.8">
4 <description>Calculate Robinson-Foulds distance between phylogenetic trees.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime phylogeny robinson-foulds
10
11 --i-trees=$itrees
12
13 #if str($plabels):
14 --p-labels=$plabels
15 #end if
16 #if str($pmissingtips) != 'None':
17 --p-missing-tips=$pmissingtips
18 #end if
19
20 --o-distance-matrix=odistancematrix
21
22 #if str($examples) != 'None':
23 --examples=$examples
24 #end if
25
26 ;
27 cp odistancematrix.qza $odistancematrix
28
29 ]]></command>
30 <inputs>
31 <param format="qza,no_unzip.zip" label="--i-trees: ARTIFACTS... List[Phylogeny[Rooted | Unrooted]] Phylogenetic trees to compare with Robinson-Foulds. Rooting information and branch lengths are ignored by this metric. [required]" name="itrees" optional="False" type="data" />
32 <param label="--p-labels: TEXT... Labels to use for the tree names in the distance List[Str] matrix. If ommited, labels will be \'tree_n\' where \'n\' ranges from 1..N. The number of labels must match the number of trees. [optional]" name="plabels" optional="False" type="text" />
33 <param label="--p-missing-tips: " name="pmissingtips" optional="True" type="select">
34 <option selected="True" value="None">Selection is Optional</option>
35 <option value="error">error</option>
36 <option value="intersect-all">intersect-all</option>
37 </param>
38 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
39
40 </inputs>
41
42 <outputs>
43 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
44
45 </outputs>
46
47 <help><![CDATA[
48 Calculate Robinson-Foulds distance between phylogenetic trees.
49 ###############################################################
50
51 Calculate the Robinson-Foulds symmetric difference metric between two or
52 more phylogenetic trees.
53
54 Parameters
55 ----------
56 trees : List[Phylogeny[Rooted | Unrooted]]
57 Phylogenetic trees to compare with Robinson-Foulds. Rooting information
58 and branch lengths are ignored by this metric.
59 labels : List[Str], optional
60 Labels to use for the tree names in the distance matrix. If ommited,
61 labels will be "tree_n" where "n" ranges from 1..N. The number of
62 labels must match the number of trees.
63 missing_tips : Str % Choices('error', 'intersect-all'), optional
64 How to handle tips that are not shared between trees. "error" will
65 raise an error if the set of tips is not identical between all input
66 trees. "intersect-all" will remove tips that are not shared between all
67 trees before computing distances beteen trees.
68
69 Returns
70 -------
71 distance_matrix : DistanceMatrix
72 The distances between trees as a symmetric matrix.
73 ]]></help>
74 <macros>
75 <import>qiime_citation.xml</import>
76 </macros>
77 <expand macro="qiime_citation"/>
78 </tool>