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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
author iuc
date Mon, 11 May 2020 17:03:25 -0400
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-1:000000000000 0:9f4a66e22580
1 <?xml version="1.0"?>
2 <tool id="rapidnj" name="Join neighbors" version="@VERSION@">
3 <description>rapidly with RapidNJ</description>
4 <macros>
5 <token name="@VERSION@">2.3.2</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="v@VERSION@">rapidnj</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 #if $alignments.is_of_type('fasta'):
12 #set $input_format = 'fa'
13 #else if $alignments.is_of_type('stockholm'):
14 #set $input_format = 'sth'
15 #else:
16 #set $input_format = 'pd'
17 #end if
18 ln -s '$alignments' input_file.$input_format &&
19 rapidnj '$alignments'
20 --input-format $input_format
21 --output-format $output_format
22 --evolution-model $evolution_model
23 --cores \${GALAXY_SLOTS:-1}
24 #if $bootstrap:
25 --bootstrap $bootstrap
26 #end if
27 --alignment-type $alignment_type
28 $no_negative_length
29 > '$distances'
30 ]]>
31 </command>
32 <inputs>
33 <param name="alignments" type="data" format="phylip,fasta,stockholm" label="Input to construct or reconstruct trees" />
34 <param argument="--output-format" name="output_format" type="select" label="Output format">
35 <option value="t">Phylogenetic tree in newick format</option>
36 <option value="m">Distance matrix</option>
37 </param>
38 <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.">
39 <option value="kim">Kimura</option>
40 <option value="jc">Jukes-Cantor</option>
41 </param>
42 <param argument="--bootstrap" type="integer" optional="true" label="Samples to use for computing bootstrap" help="The output tree will be annotated with bootstrap values" />
43 <param argument="--alignment-type" name="alignment_type" type="select" label="Input alignment type">
44 <option value="p">Protein</option>
45 <option value="d">DNA</option>
46 </param>
47 <param argument="--no-negative-length" name="no_negative_length" type="boolean" truevalue="--no-negative-length" falsevalue="" label="Adjust for negative branch lengths." />
48 </inputs>
49 <outputs>
50 <data name="distances" format="nhx" label="${tool.name} on ${on_string}: Calculated distances">
51 <change_format>
52 <when input="output_format" value="m" format="tabular" />
53 </change_format>
54 </data>
55 </outputs>
56 <tests>
57 <test>
58 <param name="alignments" value="rapidnj-in1.fa" />
59 <param name="output_format" value="t" />
60 <output name="distances" ftype="nhx" value="rapidnj-out1.nhx" />
61 </test>
62 <test>
63 <param name="alignments" value="rapidnj-in2.fa" />
64 <param name="output_format" value="t" />
65 <output name="distances" ftype="nhx" value="rapidnj-out2.nhx" />
66 </test>
67 </tests>
68 <help><![CDATA[
69 ============
70 RapidNJ
71 ============
72
73 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.
74 ]]>
75 </help>
76 <citations>
77 <citation type="doi">doi:10.1007/978-3-540-87361-7_10</citation>
78 </citations>
79 </tool>