Mercurial > repos > iuc > hyphy_meme

comparison macros.xml @ 0:7b3f9c78cf6d 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/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
author iuc
date Wed, 21 Aug 2019 12:26:38 -0400
parents
children d02c8e6f7f2a
comparison
equal deleted inserted replaced
-1:000000000000 0:7b3f9c78cf6d
1 <?xml version="1.0"?>
2 <macros>
3 <xml name="inputs">
4 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
5 <param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
6 </xml>
7 <xml name="substitution">
8 <param name="model" type="select" label="Substitution model">
9 <option value="LG">LG - Generalist empirical model from
10 Le and Gascuel (2008)</option>
11 <option value="HIVBm">HIVBm - Specialist empirical model
12 for between-host HIV sequences</option>
13 <option value="HIVWm">HIVWm - Specialist empirical model
14 for within-host HIV sequences</option>
15 <option value="WAG">WAG - Generalist empirical model from
16 Whelan and Goldman (2001)</option>
17 <option value="JTT">JTT - Generalist empirical model from
18 Jones, Taylor, and Thornton (1996)</option>
19 <option value="JC69">JC69 - Generalist empirical model
20 from with equal exchangeability rates</option>
21 <option value="mtMet">mtMet - Specialist empirical model
22 for metazoan mitochondrial genomes</option>
23 <option value="mtVer">mtVer - Specialist empirical model
24 for vertebrate mitochondrial genomes</option>
25 <option value="mtInv">mtInv - Specialist empirical model
26 for invertebrate mitochondrial genomes</option>
27 <option value="gcpREV">gcpREV - Specialist empirical
28 model for green plant chloroplast genomes</option>
29 <option value="GTR">GTR - General time reversible
30 model</option>
31 </param>
32 </xml>
33 <xml name="gencode">
34 <param name="gencodeid" type="select" label="Genetic code">
35 <option value="Universal">Universal code</option>
36 <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA
37 code</option>
38 <option value="Yeast-mtDNA">Yeast mitochondrial DNA
39 code</option>
40 <option value="Mold-Protozoan-mtDNA">Mold, Protozoan and
41 Coelenterate mt; Mycloplasma/Spiroplasma</option>
42 <option value="Invertebrate-mtDNA">Invertebrate mitochondrial
43 DNA code</option>
44 <option value="Ciliate-Nuclear">Ciliate, Dasycladacean and
45 Hexamita Nuclear code</option>
46 <option value="Echinoderm-mtDNA">Echinoderm mitochondrial DNA
47 code</option>
48 <option value="Euplotid-Nuclear">Euplotid Nuclear
49 code</option>
50 <option value="Alt-Yeast-Nuclear">Alternative Yeast Nuclear
51 code</option>
52 <option value="Ascidian-mtDNA">Ascidian mitochondrial DNA
53 code</option>
54 <option value="Flatworm-mtDNA">Flatworm mitochondrial DNA
55 code</option>
56 <option value="Blepharisma-Nuclear">Blepharisma Nuclear
57 code</option>
58 </param>
59 </xml>
60 <xml name="branches">
61 <param name="branches" type="select" label="Set of branches to test">
62 <option value="All">All branches</option>
63 <option value="Internal">Internal branches</option>
64 <option value="Leaves">Leaf branches</option>
65 <option value="'Unlabeled-branches'">Unlabeled
66 branches</option>
67 </param>
68 </xml>
69 <xml name="citations">
70 <citations>
71 <citation type="doi">10.1093/bioinformatics/bti079</citation>
72 <yield/>
73 </citations>
74 </xml>
75 <token name="@VERSION@">2.5.0</token>
76 <xml name="requirements">
77 <requirements>
78 <requirement type="package" version="@VERSION@">
79 hyphy</requirement>
80 <yield/>
81 </requirements>
82 </xml>
83 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which hyphy` &&
84 export HYPHY_PATH=`dirname \$HYPHY` &&
85 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token>
86 <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB ]]></token>
87 </macros>