Mercurial > repos > iuc > hyphy_busted
annotate macros.xml @ 16:98ee8ba908d6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80"
author | iuc |
---|---|
date | Fri, 18 Sep 2020 21:09:58 +0000 |
parents | cff70490dbec |
children | c92d5ec5d8d7 |
rev | line source |
---|---|
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
1 <?xml version="1.0"?> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
2 <macros> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
3 <xml name="inputs"> |
1
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
4 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
5 <param name="input_nhx" type="data" format="nhx" label="Input newick file"/> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
6 </xml> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
7 <xml name="substitution"> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
8 <param name="model" type="select" label="Substitution model"> |
6
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
9 <option value="GTR">GTR - General time reversible |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
10 model</option> |
1
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
11 <option value="LG">LG - Generalist empirical model from |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
12 Le and Gascuel (2008)</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
13 <option value="HIVBm">HIVBm - Specialist empirical model |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
14 for between-host HIV sequences</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
15 <option value="HIVWm">HIVWm - Specialist empirical model |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
16 for within-host HIV sequences</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
17 <option value="WAG">WAG - Generalist empirical model from |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
18 Whelan and Goldman (2001)</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
19 <option value="JTT">JTT - Generalist empirical model from |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
20 Jones, Taylor, and Thornton (1996)</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
21 <option value="JC69">JC69 - Generalist empirical model |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
22 from with equal exchangeability rates</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
23 <option value="mtMet">mtMet - Specialist empirical model |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
24 for metazoan mitochondrial genomes</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
25 <option value="mtVer">mtVer - Specialist empirical model |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
26 for vertebrate mitochondrial genomes</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
27 <option value="mtInv">mtInv - Specialist empirical model |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
28 for invertebrate mitochondrial genomes</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
29 <option value="gcpREV">gcpREV - Specialist empirical |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
30 model for green plant chloroplast genomes</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
31 </param> |
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
32 </xml> |
6
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
33 |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
34 <xml name="conditional_posteriorEstimationMethod"> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
35 <conditional name="posteriorEstimationMethod"> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
36 <param argument="--method" type="select" label="Posterior estimation method"> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
37 <option value="Variational-Bayes">0-th order Variational Bayes approximation</option> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
38 <option value="Metropolis-Hastings">Full Metropolis-Hastings MCMC algorithm</option> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
39 <option value="Collapsed-Gibbs">Collapsed Gibbs sampler</option> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
40 </param> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
41 <when value="Variational-Bayes"> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
42 </when> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
43 <when value="Metropolis-Hastings"> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
44 <expand macro="mcmc_options" /> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
45 </when> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
46 <when value="Collapsed-Gibbs"> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
47 <expand macro="mcmc_options" /> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
48 </when> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
49 </conditional> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
50 </xml> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
51 |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
52 <token name="@posteriorEstimationMethod_cmd@"> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
53 #if $posteriorEstimationMethod.method != "Variational-Bayes" |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
54 --chains '$posteriorEstimationMethod.chains' |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
55 --chain-length '$posteriorEstimationMethod.chain_length' |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
56 --burn-in '$posteriorEstimationMethod.samples' |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
57 --samples '$posteriorEstimationMethod.samples_per_chain' |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
58 #end if |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
59 </token> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
60 |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
61 <xml name="mcmc_options"> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
62 <param argument="--chains" type="integer" value="5" min="2" max="20" label="Number of MCMC chains" /> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
63 <param argument="--chain-length" name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain" /> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
64 <param argument="--burn-in" name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in" /> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
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" /> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
66 </xml> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
67 |
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
68 <xml name="gencode"> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
69 <param name="gencodeid" type="select" label="Genetic code"> |
1
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
70 <option value="Universal">Universal code</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
71 <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
72 code</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
73 <option value="Yeast-mtDNA">Yeast mitochondrial DNA |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
74 code</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
75 <option value="Mold-Protozoan-mtDNA">Mold, Protozoan and |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
76 Coelenterate mt; Mycloplasma/Spiroplasma</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
77 <option value="Invertebrate-mtDNA">Invertebrate mitochondrial |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
78 DNA code</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
79 <option value="Ciliate-Nuclear">Ciliate, Dasycladacean and |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
80 Hexamita Nuclear code</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
81 <option value="Echinoderm-mtDNA">Echinoderm mitochondrial DNA |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
82 code</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
83 <option value="Euplotid-Nuclear">Euplotid Nuclear |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
84 code</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
85 <option value="Alt-Yeast-Nuclear">Alternative Yeast Nuclear |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
86 code</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
87 <option value="Ascidian-mtDNA">Ascidian mitochondrial DNA |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
88 code</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
89 <option value="Flatworm-mtDNA">Flatworm mitochondrial DNA |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
90 code</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
91 <option value="Blepharisma-Nuclear">Blepharisma Nuclear |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
92 code</option> |
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
93 </param> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
94 </xml> |
13
686a8b41d09c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2413d0043c5d263ecfa75ec0f8614e322fb65f99"
iuc
parents:
12
diff
changeset
|
95 |
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
96 <xml name="branches"> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
97 <param name="branches" type="select" label="Set of branches to test"> |
1
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
98 <option value="All">All branches</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
99 <option value="Internal">Internal branches</option> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
100 <option value="Leaves">Leaf branches</option> |
6
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
101 <option value="'Unlabeled-branches'">Unlabeled branches</option> |
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
102 </param> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
103 </xml> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
104 <xml name="citations"> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
105 <citations> |
6
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
106 <citation type="doi">10.1093/molbev/msz197</citation> |
1
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
107 <yield/> |
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
108 </citations> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
109 </xml> |
15
cff70490dbec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit adf0f20535bd585663c291f8f15137a7ba947949"
iuc
parents:
14
diff
changeset
|
110 <token name="@VERSION@">2.5.17</token> |
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
111 <xml name="requirements"> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
112 <requirements> |
6
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
113 <requirement type="package" version="@VERSION@">hyphy</requirement> |
1
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
114 <yield/> |
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
115 </requirements> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
116 </xml> |
5
8c8640ca39d7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e31ca8967662206fc17d608efea398502569437a"
iuc
parents:
4
diff
changeset
|
117 <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token> |
9
6647e04e92a7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
iuc
parents:
8
diff
changeset
|
118 <token name="@CATCH_MPIERR@"><![CDATA[ |
6647e04e92a7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
iuc
parents:
8
diff
changeset
|
119 EC=\$? ; |
6647e04e92a7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
iuc
parents:
8
diff
changeset
|
120 if [ \$EC -ne 0 ] ; then |
6647e04e92a7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
iuc
parents:
8
diff
changeset
|
121 cat errors.log.mpinode0 >&2 ; |
6647e04e92a7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
iuc
parents:
8
diff
changeset
|
122 fi ; |
6647e04e92a7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
iuc
parents:
8
diff
changeset
|
123 exit \$EC |
6647e04e92a7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
iuc
parents:
8
diff
changeset
|
124 ]]></token> |
6
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
125 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[ |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
126 export HYPHY=`which hyphy` && |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
127 export HYPHY_PATH=`dirname \$HYPHY` && |
13
686a8b41d09c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2413d0043c5d263ecfa75ec0f8614e322fb65f99"
iuc
parents:
12
diff
changeset
|
128 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../share/hyphy` &&]]></token> |
6
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
129 <token name="@HYPHY_INVOCATION@"><![CDATA[ |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
130 @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
5
diff
changeset
|
131 ]]></token> |
1
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
132 </macros> |