Mercurial > repos > iuc > hyphy_slac

comparison macros.xml @ 1:c2bed8cc8fc1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
author iuc
date Wed, 21 Aug 2019 12:27:21 -0400
parents 9da003917dcb
children a603e2f909e5
comparison
equal deleted inserted replaced
0:9da003917dcb 1:c2bed8cc8fc1
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <xml name="inputs"> 3 <xml name="inputs">
4 <param name="input_file" type="data" format="fasta" label="Input FASTA file" /> 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" /> 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>
6 </xml> 32 </xml>
7 <xml name="gencode"> 33 <xml name="gencode">
8 <param name="gencodeid" type="select" label="Genetic code"> 34 <param name="gencodeid" type="select" label="Genetic code">
9 <option value="1">Universal code</option> 35 <option value="Universal">Universal code</option>
10 <option value="2">Vertebrate mitochondrial DNA code</option> 36 <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA
11 <option value="3">Yeast mitochondrial DNA code</option> 37 code</option>
12 <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option> 38 <option value="Yeast-mtDNA">Yeast mitochondrial DNA
13 <option value="5">Invertebrate mitochondrial DNA code</option> 39 code</option>
14 <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option> 40 <option value="Mold-Protozoan-mtDNA">Mold, Protozoan and
15 <option value="7">Echinoderm mitochondrial DNA code</option> 41 Coelenterate mt; Mycloplasma/Spiroplasma</option>
16 <option value="8">Euplotid Nuclear code</option> 42 <option value="Invertebrate-mtDNA">Invertebrate mitochondrial
17 <option value="9">Alternative Yeast Nuclear code</option> 43 DNA code</option>
18 <option value="10">Ascidian mitochondrial DNA code</option> 44 <option value="Ciliate-Nuclear">Ciliate, Dasycladacean and
19 <option value="11">Flatworm mitochondrial DNA code</option> 45 Hexamita Nuclear code</option>
20 <option value="12">Blepharisma 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>
21 </param> 58 </param>
22 </xml> 59 </xml>
23 <xml name="branches"> 60 <xml name="branches">
24 <param name="branches" type="select" label="Set of branches to test"> 61 <param name="branches" type="select" label="Set of branches to test">
25 <option value="1">All branches</option> 62 <option value="All">All branches</option>
26 <option value="2">Internal branches</option> 63 <option value="Internal">Internal branches</option>
27 <option value="3">Leaf branches</option> 64 <option value="Leaves">Leaf branches</option>
28 <option value="4">Unlabeled branches</option> 65 <option value="'Unlabeled-branches'">Unlabeled
66 branches</option>
29 </param> 67 </param>
30 </xml>
31 <xml name="version_command">
32 <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
33 </xml> 68 </xml>
34 <xml name="citations"> 69 <xml name="citations">
35 <citations> 70 <citations>
36 <citation type="doi">10.1093/bioinformatics/bti079</citation> 71 <citation type="doi">10.1093/bioinformatics/bti079</citation>
37 <yield /> 72 <yield/>
38 </citations> 73 </citations>
39 </xml> 74 </xml>
40 <token name="@VERSION@">2.3.14</token> 75 <token name="@VERSION@">2.5.0</token>
41 <xml name="requirements"> 76 <xml name="requirements">
42 <requirements> 77 <requirements>
43 <requirement type="package" version="@VERSION@">hyphy</requirement> 78 <requirement type="package" version="@VERSION@">
44 <yield /> 79 hyphy</requirement>
80 <yield/>
45 </requirements> 81 </requirements>
46 </xml> 82 </xml>
47 <token name="@HYPHY_INVOCATION@"><![CDATA[export HYPHY=`which HYPHYMP` && 83 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which hyphy` &&
48 export HYPHY_PATH=`dirname \$HYPHY` && 84 export HYPHY_PATH=`dirname \$HYPHY` &&
49 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` && 85 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token>
50 cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]> 86 <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB ]]></token>
51 </token>
52 <token name="@HYPHYMPI_INVOCATION@"><![CDATA[export HYPHY=`which HYPHYMP` &&
53 export HYPHY_PATH=`dirname \$HYPHY` &&
54 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&
55 cat tool_params | mpirun -np \${GALAXY_SLOTS:-1} HYPHYMPI LIBPATH=\$HYPHY_LIB ]]>
56 </token>
57 </macros> 87 </macros>