Mercurial > repos > florianbegusch > qiime2_suite_zmf
comparison qiime2-2020.8/qiime_phylogeny_robinson-foulds.xml @ 0:5c352d975ef7 draft
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author | florianbegusch |
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date | Thu, 03 Sep 2020 09:33:04 +0000 |
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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> |