Mercurial > repos > iuc > rapidnj

annotate rapidnj.xml @ 0:53c1f0899df0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
author iuc
date Mon, 11 May 2020 20:59:46 +0000
parents
children 70e427b76f68
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
2 <tool id="rapidnj" name="Join neighbors" version="@VERSION@">
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
3 <description>rapidly with RapidNJ</description>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
4 <macros>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
5 <token name="@VERSION@">2.3.2</token>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
6 </macros>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
7 <requirements>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
8 <requirement type="package" version="v@VERSION@">rapidnj</requirement>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
9 </requirements>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
11 #if $alignments.is_of_type('fasta'):
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
12 #set $input_format = 'fa'
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
13 #else if $alignments.is_of_type('stockholm'):
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
14 #set $input_format = 'sth'
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
15 #else:
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
16 #set $input_format = 'pd'
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
17 #end if
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
18 ln -s '$alignments' input_file.$input_format &&
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
19 rapidnj '$alignments'
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
20 --input-format $input_format
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
21 --output-format $output_format
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
22 --evolution-model $evolution_model
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
23 --cores \${GALAXY_SLOTS:-1}
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
24 #if $bootstrap:
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
25 --bootstrap $bootstrap
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
26 #end if
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
27 --alignment-type $alignment_type
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
28 $no_negative_length
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
29 > '$distances'
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
30 ]]>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
31 </command>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
32 <inputs>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
33 <param name="alignments" type="data" format="phylip,fasta,stockholm" label="Input to construct or reconstruct trees" />
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
34 <param argument="--output-format" name="output_format" type="select" label="Output format">
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
35 <option value="t">Phylogenetic tree in newick format</option>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
36 <option value="m">Distance matrix</option>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
37 </param>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
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.">
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
39 <option value="kim">Kimura</option>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
40 <option value="jc">Jukes-Cantor</option>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
41 </param>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
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" />
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
43 <param argument="--alignment-type" name="alignment_type" type="select" label="Input alignment type">
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
44 <option value="p">Protein</option>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
45 <option value="d">DNA</option>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
46 </param>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
47 <param argument="--no-negative-length" name="no_negative_length" type="boolean" truevalue="--no-negative-length" falsevalue="" label="Adjust for negative branch lengths." />
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
48 </inputs>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
49 <outputs>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
50 <data name="distances" format="nhx" label="${tool.name} on ${on_string}: Calculated distances">
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
51 <change_format>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
52 <when input="output_format" value="m" format="tabular" />
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
53 </change_format>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
54 </data>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
55 </outputs>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
56 <tests>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
57 <test>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
58 <param name="alignments" value="rapidnj-in1.fa" />
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
59 <param name="output_format" value="t" />
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
60 <output name="distances" ftype="nhx" value="rapidnj-out1.nhx" />
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
61 </test>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
62 <test>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
63 <param name="alignments" value="rapidnj-in2.fa" />
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
64 <param name="output_format" value="t" />
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
65 <output name="distances" ftype="nhx" value="rapidnj-out2.nhx" />
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
66 </test>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
67 </tests>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
68 <help><![CDATA[
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
69 ============
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
70 RapidNJ
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
71 ============
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
72
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
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.
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
74 ]]>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
75 </help>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
76 <citations>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
77 <citation type="doi">doi:10.1007/978-3-540-87361-7_10</citation>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
78 </citations>
53c1f0899df0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
iuc
parents:
diff changeset
79 </tool>