Mercurial > repos > iuc > hyphy_annotate

comparison macros.xml @ 0:be1650bef38c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
author iuc
date Tue, 20 Apr 2021 10:17:07 +0000
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children 2219b0ceb19e
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-1:000000000000 0:be1650bef38c
1 <?xml version="1.0"?>
2 <macros>
3 <xml name="inputs">
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" />
5 <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/>
6 </xml>
7 <xml name="substitution">
8 <param name="model" type="select" label="Substitution model">
9 <option value="GTR">GTR - General time reversible
10 model</option>
11 <option value="LG">LG - Generalist empirical model from
12 Le and Gascuel (2008)</option>
13 <option value="HIVBm">HIVBm - Specialist empirical model
14 for between-host HIV sequences</option>
15 <option value="HIVWm">HIVWm - Specialist empirical model
16 for within-host HIV sequences</option>
17 <option value="WAG">WAG - Generalist empirical model from
18 Whelan and Goldman (2001)</option>
19 <option value="JTT">JTT - Generalist empirical model from
20 Jones, Taylor, and Thornton (1996)</option>
21 <option value="JC69">JC69 - Generalist empirical model
22 from with equal exchangeability rates</option>
23 <option value="mtMet">mtMet - Specialist empirical model
24 for metazoan mitochondrial genomes</option>
25 <option value="mtVer">mtVer - Specialist empirical model
26 for vertebrate mitochondrial genomes</option>
27 <option value="mtInv">mtInv - Specialist empirical model
28 for invertebrate mitochondrial genomes</option>
29 <option value="gcpREV">gcpREV - Specialist empirical
30 model for green plant chloroplast genomes</option>
31 </param>
32 </xml>
33
34 <xml name="conditional_posteriorEstimationMethod">
35 <conditional name="posteriorEstimationMethod">
36 <param argument="--method" type="select" label="Posterior estimation method">
37 <option value="Variational-Bayes">0-th order Variational Bayes approximation</option>
38 <option value="Metropolis-Hastings">Full Metropolis-Hastings MCMC algorithm</option>
39 <option value="Collapsed-Gibbs">Collapsed Gibbs sampler</option>
40 </param>
41 <when value="Variational-Bayes">
42 </when>
43 <when value="Metropolis-Hastings">
44 <expand macro="mcmc_options" />
45 </when>
46 <when value="Collapsed-Gibbs">
47 <expand macro="mcmc_options" />
48 </when>
49 </conditional>
50 </xml>
51
52 <token name="@posteriorEstimationMethod_cmd@">
53 #if $posteriorEstimationMethod.method != "Variational-Bayes"
54 --chains '$posteriorEstimationMethod.chains'
55 --chain-length '$posteriorEstimationMethod.chain_length'
56 --burn-in '$posteriorEstimationMethod.samples'
57 --samples '$posteriorEstimationMethod.samples_per_chain'
58 #end if
59 </token>
60
61 <xml name="mcmc_options">
62 <param argument="--chains" type="integer" value="5" min="2" max="20" label="Number of MCMC chains" />
63 <param argument="--chain-length" name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain" />
64 <param argument="--burn-in" name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in" />
65 <param argument="--samples" name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain" />
66 </xml>
67
68 <xml name="gencode">
69 <param name="gencodeid" type="select" label="Genetic code">
70 <option value="Universal">Universal code</option>
71 <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA
72 code</option>
73 <option value="Yeast-mtDNA">Yeast mitochondrial DNA
74 code</option>
75 <option value="Mold-Protozoan-mtDNA">Mold, Protozoan and
76 Coelenterate mt; Mycloplasma/Spiroplasma</option>
77 <option value="Invertebrate-mtDNA">Invertebrate mitochondrial
78 DNA code</option>
79 <option value="Ciliate-Nuclear">Ciliate, Dasycladacean and
80 Hexamita Nuclear code</option>
81 <option value="Echinoderm-mtDNA">Echinoderm mitochondrial DNA
82 code</option>
83 <option value="Euplotid-Nuclear">Euplotid Nuclear
84 code</option>
85 <option value="Alt-Yeast-Nuclear">Alternative Yeast Nuclear
86 code</option>
87 <option value="Ascidian-mtDNA">Ascidian mitochondrial DNA
88 code</option>
89 <option value="Flatworm-mtDNA">Flatworm mitochondrial DNA
90 code</option>
91 <option value="Blepharisma-Nuclear">Blepharisma Nuclear
92 code</option>
93 </param>
94 </xml>
95
96 <xml name="branches">
97 <param name="branches" type="select" label="Set of branches to test">
98 <option value="All">All branches</option>
99 <option value="Internal">Internal branches</option>
100 <option value="Leaves">Leaf branches</option>
101 <option value="'Unlabeled-branches'">Unlabeled branches</option>
102 </param>
103 </xml>
104 <xml name="citations">
105 <citations>
106 <citation type="doi">10.1093/molbev/msz197</citation>
107 <yield/>
108 </citations>
109 </xml>
110 <token name="@VERSION@">2.5.31</token>
111 <xml name="requirements">
112 <requirements>
113 <requirement type="package" version="@VERSION@">hyphy</requirement>
114 <yield/>
115 </requirements>
116 </xml>
117 <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token>
118 <token name="@CATCH_ERROR@"><![CDATA[
119 EC=\$? ;
120 if [ \$EC -ne 0 ] ; then
121 if [ -f errors.log.mpinode0 ] ; then
122 cat errors.log.mpinode0 >&2 ;
123 else
124 cat errors.log >&2 ;
125 fi ;
126 fi ;
127 exit \$EC
128 ]]></token>
129 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[
130 export HYPHY=`which hyphy` &&
131 export HYPHY_PATH=`dirname \$HYPHY` &&
132 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../share/hyphy` &&]]></token>
133 <token name="@HYPHY_INVOCATION@"><![CDATA[
134 @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB
135 ]]></token>
136 <token name="@SYMLINK_FILES@"><![CDATA[
137 ln -s '$input_file' input.$input_file.extension &&
138 ln -s '$@operation@_output' input.${input_file.extension}.@OPERATION@.json &&
139 #set $input_file = 'input.%s' % $input_file.extension
140 #if $input_nhx:
141 ln -s '$input_nhx' input.nhx &&
142 #end if
143 ]]></token>
144 </macros>