annotate macros.xml @ 5:0cd45491b297 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 9fa2234b56facaf70fce12e5c60638d801997594"
author iuc
date Fri, 18 Jun 2021 15:28:51 +0000
parents a88848771d2d
children ec59f7a36a24
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
2 <macros>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
3 <xml name="inputs">
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
4 <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="If the input file type is NEXUS and it includes a valid newick tree, that tree will override an uploaded newick tree" />
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
5 <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
6 </xml>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
7 <xml name="substitution">
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
8 <param name="model" type="select" label="Substitution model">
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
9 <option value="GTR">GTR - General time reversible
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
10 model</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
11 <option value="LG">LG - Generalist empirical model from
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
12 Le and Gascuel (2008)</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
13 <option value="HIVBm">HIVBm - Specialist empirical model
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
14 for between-host HIV sequences</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
15 <option value="HIVWm">HIVWm - Specialist empirical model
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
16 for within-host HIV sequences</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
17 <option value="WAG">WAG - Generalist empirical model from
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
18 Whelan and Goldman (2001)</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
19 <option value="JTT">JTT - Generalist empirical model from
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
20 Jones, Taylor, and Thornton (1996)</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
21 <option value="JC69">JC69 - Generalist empirical model
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
22 from with equal exchangeability rates</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
23 <option value="mtMet">mtMet - Specialist empirical model
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
24 for metazoan mitochondrial genomes</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
25 <option value="mtVer">mtVer - Specialist empirical model
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
26 for vertebrate mitochondrial genomes</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
27 <option value="mtInv">mtInv - Specialist empirical model
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
28 for invertebrate mitochondrial genomes</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
29 <option value="gcpREV">gcpREV - Specialist empirical
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
30 model for green plant chloroplast genomes</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
31 </param>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
32 </xml>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
33
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
34 <xml name="conditional_posteriorEstimationMethod">
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
35 <conditional name="posteriorEstimationMethod">
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
36 <param argument="--method" type="select" label="Posterior estimation method">
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
37 <option value="Variational-Bayes">0-th order Variational Bayes approximation</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
38 <option value="Metropolis-Hastings">Full Metropolis-Hastings MCMC algorithm</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
39 <option value="Collapsed-Gibbs">Collapsed Gibbs sampler</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
40 </param>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
41 <when value="Variational-Bayes">
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
42 </when>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
43 <when value="Metropolis-Hastings">
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
44 <expand macro="mcmc_options" />
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
45 </when>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
46 <when value="Collapsed-Gibbs">
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
47 <expand macro="mcmc_options" />
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
48 </when>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
49 </conditional>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
50 </xml>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
51
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
52 <token name="@posteriorEstimationMethod_cmd@">
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
53 #if $posteriorEstimationMethod.method != "Variational-Bayes"
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
54 --chains '$posteriorEstimationMethod.chains'
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
55 --chain-length '$posteriorEstimationMethod.chain_length'
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
56 --burn-in '$posteriorEstimationMethod.samples'
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
57 --samples '$posteriorEstimationMethod.samples_per_chain'
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
58 #end if
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
59 </token>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
60
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
61 <xml name="mcmc_options">
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
62 <param argument="--chains" type="integer" value="5" min="2" max="20" label="Number of MCMC chains" />
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
63 <param argument="--chain-length" name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain" />
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
64 <param argument="--burn-in" name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in" />
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
65 <param argument="--samples" name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain" />
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
66 </xml>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
67
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
68 <xml name="gencode">
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
69 <param name="gencodeid" type="select" label="Genetic code">
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
70 <option value="Universal">Universal code</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
71 <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
72 code</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
73 <option value="Yeast-mtDNA">Yeast mitochondrial DNA
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
74 code</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
75 <option value="Mold-Protozoan-mtDNA">Mold, Protozoan and
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
76 Coelenterate mt; Mycloplasma/Spiroplasma</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
77 <option value="Invertebrate-mtDNA">Invertebrate mitochondrial
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
78 DNA code</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
79 <option value="Ciliate-Nuclear">Ciliate, Dasycladacean and
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
80 Hexamita Nuclear code</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
81 <option value="Echinoderm-mtDNA">Echinoderm mitochondrial DNA
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
82 code</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
83 <option value="Euplotid-Nuclear">Euplotid Nuclear
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
84 code</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
85 <option value="Alt-Yeast-Nuclear">Alternative Yeast Nuclear
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
86 code</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
87 <option value="Ascidian-mtDNA">Ascidian mitochondrial DNA
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
88 code</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
89 <option value="Flatworm-mtDNA">Flatworm mitochondrial DNA
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
90 code</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
91 <option value="Blepharisma-Nuclear">Blepharisma Nuclear
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
92 code</option>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
93 </param>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
94 </xml>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
95
2
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
96 <xml name="srv">
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
97 <conditional name="advanced" label="Advanced options">
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
98 <param name="srv_options" type="select" label="Set advanced parameters" help="If these parameters are not set, RELAX will calculate appropriate values at runtime">
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
99 <option value="defaults">Calculate</option>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
100 <option value="specify">Specify values</option>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
101 </param>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
102 <when value="defaults" />
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
103 <when value="specify">
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
104 <param argument="--grid-size" type="integer" value="250" label="Points in the initial distributional guess for likelihood fitting" />
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
105 <param argument="--starting-points" type="integer" value="1" label="Initial random guesses to seed rate values optimization" />
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
106 <param argument="--syn-rates" type="integer" min="1" max="10" value="3" label="Alpha rate classes to include in the model" />
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
107 <param argument="--rates" type="integer" min="2" max="10" value="3" label="Omega rate classes to include in the model" />
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
108 <param argument="--srv" type="boolean" truevalue="Yes" falsevalue="No" label="Include synonymous rate variation" />
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
109 <param name="save_alternative_model" type="boolean" label="Save alternative model fit" />
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
110 </when>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
111 </conditional>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
112 </xml>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
113
0
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
114 <xml name="branches">
2
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
115 <conditional name="branch_cond">
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
116 <param name="branch_sel" type="select" label="Set of branches to test">
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
117 <option value="All">All branches</option>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
118 <option value="Internal">Internal branches</option>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
119 <option value="Leaves">Leaf branches</option>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
120 <option value="'Unlabeled-branches'">Unlabeled branches</option>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
121 <option value="specify">Enter a branch label</option>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
122 </param>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
123 <when value="specify">
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
124 <param name="branch_label" type="text" value="Test" optional="false" label="Branch label">
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
125 <sanitizer invalid_char="">
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
126 <valid initial="default" />
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
127 </sanitizer>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
128 </param>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
129 </when>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
130 <when value="All" />
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
131 <when value="Internal" />
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
132 <when value="Leaves" />
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
133 <when value="'Unlabeled-branches'" />
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
134 </conditional>
0
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
135 </xml>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
136 <xml name="citations">
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
137 <citations>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
138 <citation type="doi">10.1093/molbev/msz197</citation>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
139 <yield/>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
140 </citations>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
141 </xml>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
142 <token name="@VERSION@">2.5.31</token>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
143 <xml name="requirements">
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
144 <requirements>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
145 <requirement type="package" version="@VERSION@">hyphy</requirement>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
146 <yield/>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
147 </requirements>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
148 </xml>
2
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
149 <xml name="alternative_model_output">
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
150 <data name="alternative_model" format="hyphy_results.json" from_work_dir="alternative_model.json">
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
151 <filter>advanced['save_alternative_model']</filter>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
152 </data>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
153 </xml>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
154 <token name="@INPUT_TREE@"><![CDATA[
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
155 #if $input_nhx:
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
156 --tree input.nhx
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
157 #end if
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
158 ]]>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
159 </token>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
160 <token name="@branch_options@"><![CDATA[
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
161 #if $branch_cond.branch_sel == 'specify':
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
162 --branches '$branch_cond.branch_label'
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
163 #else:
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
164 --branches $branch_cond.branch_sel
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
165 #end if
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
166 ]]>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
167 </token>
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
168 <token name="@advanced_options@"><![CDATA[
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
169 #if $advanced.srv_options == 'specify':
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
170 --grid-size $advanced.grid_size
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
171 --starting-points $advanced.starting_points
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
172 --syn-rates $advanced.syn_rates
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
173 --rates $advanced.rates
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
174 --srv $advanced.srv
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
175 #if $advanced.save_alternative_model:
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
176 --save-fit alternative_model.json
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
177 #end if
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
178 #end if
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
179 ]]></token>
0
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
180 <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token>
2
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
181 <token name="@ERRORS@"><![CDATA[
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
182 ; EC=\$? ; [[ -f errors.* ]] && cat errors.* >&2 ; exit \$EC
0
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
183 ]]></token>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
184 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
185 export HYPHY=`which hyphy` &&
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
186 export HYPHY_PATH=`dirname \$HYPHY` &&
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
187 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../share/hyphy` &&]]></token>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
188 <token name="@HYPHY_INVOCATION@"><![CDATA[
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
189 @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
190 ]]></token>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
191 <token name="@SYMLINK_FILES@"><![CDATA[
2
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
192 #if $input_nhx is not None:
0
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
193 ln -s '$input_nhx' input.nhx &&
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
194 #end if
2
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
195 ln -s '$input_file' input.$input_file.extension &&
a88848771d2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
196 #set $input_file = 'input.%s' % $input_file.extension
0
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
197 ]]></token>
df56795c3d89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
198 </macros>